Slide 1

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 2

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 3

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 4

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 5

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 6

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 7

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 8

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 9

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 10

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 11

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 12

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 13

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 14

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 15

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 16

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 17

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 18

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 19

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 20

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 21

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 22

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 23

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 24

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 25

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 26

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 27

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 28

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 29

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 30

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 31

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 32

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 33

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 34

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 35

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 36

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 37

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 38

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 39

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 40

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 41

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 42

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 43

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 44

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 45

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 46

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 47

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 48

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 49

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 50

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 51

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 52

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 53

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 54

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 55

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 56

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 57

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 58

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 59

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 60

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 61

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 62

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 63

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 64

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 65

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 66

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 67

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 68

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 69

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 70

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 71

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 72

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 73

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 74

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 75

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 76

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 77

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 78

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 79

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 80

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 81

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 82

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 83

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 84

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 85

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 86

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 87

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 88

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 89

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 90

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 91

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 92

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93


Slide 93

BIO 168

CHEMICAL LEVEL OF
ORGANIZATION
CHAPTER 2

created by Dr. C. Morgan

1

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

2

Introduction Objectives

Discuss the composition of matter.

Learn why you need to understand some basic
chemistry.
Learn about the relationship between chemical
reactions and living systems.

3

Introduction
For all practical purposes, we may say that
everything is composed of chemicals—atoms
and molecules.
Therefore, to understand living systems, you must
understand some basic chemistry.

The structure and function of living systems is a
constant interplay of finely tuned chemical
reactions.
You will learn about the nature of chemicals, how they
react, and their role in the structure and function of
living things.
4

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

5

Atoms and Molecules Objectives
Define matter and know its three states
Learn the structure of an atom

Distinguish between atomic number, atomic weight,
and molecular weight
Define isotope

Understand that electrons have energy and are in
motion
Learn the importance of electrons in chemical
reactions
Understand the formation of chemical bonds
6

Atoms and Molecules
Matter
By definition, matter is anything that occupies a space
and has mass (on earth mass = weight).
Matter exists in 3 states, gas, liquid, or solid.
Matter is made up of materials that are known as
elements which cannot be further broken down by
ordinary means.
Appendix II shows the Periodic Chart of the
Elements (many should be familiar to you).

TABLE 1 in your text lists the main elements in your
body along with their abbreviation and significance.
O, C, H, N, Ca are the 5 body elements in greatest %.
7

Atoms and Molecules (cont)
Atomic Structure
Nucleus

Protons &
neutrons
have
mass

Protons +
Neutrons

+

+
+
Electrons
In motion
electron cloud
Fig. 2 b

Electrons
have almost
zero mass
8

Atoms and Molecules (cont)

The atomic number of an atom = its number of protons.
The mass number = number of protons + neutrons.
The atomic weight = average number of protons +
neutrons in atoms of an element including isotopes.
An isotope is an element that has atoms with a different
number of neutrons from the most commonly occurring
type of that atom under consideration.

For example: carbon (C) usually has 6 neutrons but some
isotopes of carbon have 7 or 8 neutrons making the
atomic weight of carbon 12.01.

9

Atoms and Molecules (cont)
Electrons and electron shells
Remember forever, only electrons enter into chemical
reactions.
Atoms are electrically neutral because they have the
same number of protons (+) and electrons (–).
Electrons have energy and are in motion in specific
orbitals or electron shells around the nucleus.

Atoms” try” to become stable but can do so only if they
have a full outermost electron shell.
It is the outermost shell electrons that react and
determine the chemical properties of an atom.
10

Atoms and Molecules (cont)
Electrons and electron shells (cont)

Fig. 2
11

Atoms and Molecules (cont)
Electrons and electron shells (cont)
The first shell holds 2 electrons, the second 8, and the
outermost shell holds 8.

Atoms with full outer shells are inert (do not react).
Atoms lose, gain, or share electrons in order to become
stable with a full outermost electron shell.
This process of atoms losing, gaining, or sharing
electrons causes chemical reactions.
When atoms lose or gain electrons, their electrical
charge balance is upset causing an atom to have
more positive or negative charge.
12

Atoms and Molecules (cont)
Electrons and electron shells (cont)

+

Is this atom stable?
+
13

Atoms and Molecules (cont)

Electrons and electron shells (cont)

Is this atom stable?
Fig. 2 d
14

Atoms and Molecules (cont)
Chemical bonding
The energy and electrical charges associated with
electrons that participate in chemical reactions
produces relationships between atoms known as
chemical bonds.
Chemical bonds contain energy.

A molecule consists of of a chemical structure
containing more than one atom.
Its molecular weight = its atomic weight of all atoms
expressed in grams.
A compound consists of a molecule with more than
one kind of atom and new properties (i.e., water).
15

Atoms and Molecules (cont)
Ionic chemical bonds
Atoms that have a net positive or negative charge are
called ions which are highly reactive.
Cations have a net positive charge.
Anions have a net negative charge.
Ions present in body fluids are very important in cell
function and water balance.
Atoms (or molecules) with positive and negative
charges are attracted to each other and will stay
together to form an ionic bond which is strong.
For example: table salt is sodium chloride formed by
ionic bonds between adjacent sodium and chloride
atoms (ions).

16

Atoms and Molecules (cont)

Ionic chemical bonds (cont)

? To become
stable, Na
must ____
one electron.

? To become
NaCl

stable, Cl must
____ one
electron.

Fig. 3 a
17

Atoms and Molecules (cont)
Ionic chemical bonds (cont)

NaCl

Fig. 3 b
18

Atoms and Molecules (cont)

Chemical covalent bonds
Sharing electrons is another option for atoms to
complete their outermost electron shell.
At any moment in time, each atom may “claim” the
electron(s) belonging to the other atom because
shared electrons spend time orbiting around both
nuclei.
If sharing is equal, this forms a nonpolar covalent
bond between participating atoms.

If only one electron pair is shared between two atoms, it
is a single covalent bond; two pairs shared = double
covalent bond; three pairs shared = triple bond.
Covalent bonds are strong bonds.

19

Atoms and Molecules (cont)
Covalent bonds (cont)

Fig. 4

free radical

free radicals
are highly
reactive
20

Atoms and Molecules (cont)
Polar covalent bonds
Sometimes shared electrons spend more time around
one atom’s nucleus than around the other one(s)
nucleus (unequal sharing).
This causes a slight charge to be established on the
atoms participating in the covalent bonds.
The atom where shared electrons spend relatively
more time becomes slightly negative; the atom(s)
deprived of their electrons for relatively more time
become slightly positive.
This produces a polar covalent bond.
There are positive and negative poles on the “polar”
molecule.

21

Atoms and Molecules (cont)
Polar covalent bonds (cont)

WATER
the most
famous
polar
molecule
Fig. 5
22

Atoms and Molecules (cont)
Hydrogen bonds
There are several weaker chemical bonds that help
hold adjacent molecules together.
Hydrogen bonds are the most important weak bonds.
To test the strength of hydrogen bonds, you may see a
needle float horizontally on the surface of water.
However, the needle tip may easily pierce the surface.
The unique properties of water are associated with the
hydrogen bonds between adjacent water molecules.
Water is the most abundant molecule in the body.
23

Atoms and Molecules (cont)
Hydrogen bonds (cont)

surface tension
needle

Try this!
Fig. 6
24

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

25

Chemical Notation Objectives

Learn the rules pertaining to chemical notation
Learn how to write formulae in chemical notation
Recognize a balanced chemical equation

Distinguish between reactants and products of a
chemical reaction written in chemical notation
Recognize ionic forms of atoms written in chemical
notation

26

Chemical Notation

TABLE 2 (focus) gives the rules of chemical notation.
1. Abbreviations: H = one atom of hydrogen
2. 2 H = two individual atoms of hydrogen

3. H2 = a molecule of hydrogen (H–H)
4. Reactants 2H + O  H2O Products
Atoms on the left = atoms on the right
A Balanced Chemical Equation
5. Na+ = sodium ion that lost one electron
Cl– = chlorine ion that gained one electron
Ca2+ = calcium ion that lost two electrons
27

TOPICS
Introduction
Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions
Inorganic Compounds

Organic Compounds
Chemicals and Living Cells

28

Chemical Reactions Objectives
Relate chemical reactions with metabolism
Define work and define energy

Distinguish between kinetic and potential energy
Recognize the types of chemical reactions
Distinguish between catabolism and anabolism

Learn the importance of reversible reactions
Discuss the role of enzymes in metabolic reactions
Distinguish between acids and bases

Define pH; learn the pH scale and normal blood pH
Learn about the role of buffers in maintaining pH
29

Chemical Reactions

Every living cell has thousands of chemical reactions
occurring simultaneously at all times.

Some reactions are breaking molecules while others
are building molecules.
In chemical reactions, atoms are rearranged.

The sum of all chemical reactions that sustain life is
called metabolism.
Because energy is associated with electrons which form
chemical bonds, metabolism involves releasing,
storing, and using energy.

30

Chemical Reactions (cont)
Energy concepts

Work is movement or events that cause a change in the
physical structure of matter.
Energy is the capacity to do work.

Kinetic energy is the energy associated with motion.
Potential energy is stored (i.e., water behind a dam).
Energy may be changed from potential to kinetic as
when chemical energy is used to contract muscle fibers.
Conversions are not 100% efficient so some energy is
lost as heat.
31

Chemical Reactions (cont)
Types of Chemical Reactions
Decomposition reactions: AB  A + B

Catabolic reactions are metabolic reactions that
breakdown molecules to harvest the potential energy in
their chemical bonds.
Synthesis reactions: A + B  AB
Anabolic reactions are metabolic reactions that make
new complex molecules from small molecular units such
as assembling hair protein from individual amino acids.

Exchange reactions: AB + CD  AD + BC
Exergonic reactions release energy; endergonic reactions
require an input of energy to make them happen.
32

Chemical Reactions (cont)
Types of Chemical Reactions (cont)
Reversible reactions: A + B  AB
Notice that both decomposition and synthesis occur.
Usually these reactions occur at rates that represent
an equilibrium or balance.
However, if the product is continuously used up by a
cell, in which direction will the reaction proceed?
Many important reactions in the body are reversible
such as hemoglobin loading oxygen in the lungs and
then giving it up for cellular use.
33

Chemical Reactions (cont)
Enzymes and Chemical Reactions
Atoms and molecules are in constant motion in a liquid.

In order to react, atoms or molecules must make contact.
In living systems, without the help of special proteins
called enzymes, reactions would proceed too slowly to
sustain life.
An enzyme decreases the amount of energy (= activation
energy) that is needed to get a reaction to occur.
Enzymes cause reactions to proceed faster.
Metabolic pathways utilize a specific enzyme for each
step (chemical reaction) in the pathway.
A

enzyme 1

B

enzyme 2

C

enzyme 3

D
34

Chemical Reactions (cont)

Enzymes and Chemical Reactions (cont)

activation energy
decreases in presence
of enzyme

enzyme

A+B

AB

Fig. 7
35

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

36

Inorganic Compounds Objectives

Distinguish between inorganic and organic compounds.
Describe nutrients and metabolites
List the three most important inorganic compounds in the
body.
Learn why water is important in the human body.
Define a solution and the ionization process.

Discuss pH, the pH scale, and buffering.
Learn some inorganic acids found in the body.
Define a salt and an electrolyte; learn about importance
of electrolytes in body fluids.
37

Inorganic Compounds

Nutrients are the essential chemical materials that you
normally obtain from your diet.
Metabolites include all molecules synthesized or broken
down during the chemical reactions in your body.
Nutrients and metabolites fall into two broad categories,
inorganic and organic compounds.

The minerals your body needs are inorganic
compounds.
The energy sources and vitamins your body needs are
organic compounds.
38

Inorganic Compounds (cont)

Inorganic compounds are small molecules that do not
contain C and H atoms as the main ones with one
exception, carbon dioxide (CO2) which is considered to
be inorganic.
CO2 is plentiful in the body because it is a waste
product of cellular respiration, a process that makes a
widely utilizable form of energy for cellular work.
You get rid of CO2 when you exhale air from your
lungs.
The most plentiful inorganic substances in the body
besides CO2 are oxygen, water, some acids and
bases, and some salts.
39

Inorganic Compounds (cont)

In contrast to inorganic compounds, organic
compounds have carbon as their main atom, often
occurring as chains of carbon atoms.
Organic compounds are usually larger and more
complex than inorganic compounds.
Carbon dioxide and oxygen are inorganic substances
that exist as gases in the body.

What kind of chemical bonds hold the atoms of these
molecules together?

40

Inorganic Compounds (cont)
Water
Water, the most important inorganic substance in your
body, makes up about 2/3 of your weight and its
balance is critically important.
The polar covalent bond of water makes each molecule
have a slight negative charge on the oxygen side and
a slight positive charge on the hydrogen side.
Water is a polar molecule and will react with other
molecules that are polar or charged.

Ionic compounds often break apart when placed in
water, a process called ionization because ions are
formed (like dissolving table salt in water).
41

Inorganic Compounds (cont)
Water (cont)
Table salt releases Na+ and Cl– which represent the
largest number of ion types in body fluids bathing cells.
Also, when ionized, salts will conduct an electrical
current so they are called electrolytes.
Every heart beat, every nerve impulse, and every muscle
contraction in your body depends on the presence of
certain electrolytes, especially K+ and Na+.
TABLE 3 lists the most important electrolytes in the body.

42

Inorganic Compounds (cont)
Water (cont)
Many organic substances have polar covalent bonds so
they will also dissolve in water.
Substances that readily react with water are hydrophilic.
Substances that do not react with water are hydrophobic.
Oil and water do not mix because oil is hydrophobic.
Oils and fats are nonpolar (lack polar covalent bonds)
so hydration spheres do not form to dissolve them.
Several more characteristics of water are due to its
polarity and hydrogen bonding.
43

Inorganic Compounds (cont)
Water (cont)
(1) Water is an excellent solvent because it dissolves
many kinds of inorganic and organic substances.
Hydration

Many substances release
ions when they dissolve.
Ions form bonds with
water molecules.

Fig. 8

44

Inorganic Compounds (cont)

Water (cont)
(2) Metabolic reactions occur in water as water is
added during catabolic reactions (hydrolysis) and
is removed during dehydration synthesis.
(3) Water also resists changes in temperature or in
other words, it has a high heat capacity.
Body temperature may be maintained at minimal
energy costs and chemical reactions will occur at
predictable rates in the cells and body fluids.
(4) Water is a good lubricant.

45

Inorganic Compounds (cont)
Water (cont)
A solution consists of a solvent (such as water) and
solute(s) which are molecules or atoms of
substances that are dissolved in the solvent.
Solute concentrations of important electrolytes are
closely followed in ill patients.
Concentrations are usually reported in moles per liter (m /
l) or millimoles per liter (mm / l) of solution.
Other concentration expressions are also used.
A mole is a sample that has the weight in grams equal to
the elements atomic or molecular weight of a substance.
g/l, g/dl, mg/l, mg/dl are used to express concentration.
46

Inorganic Compounds (cont)
Water (cont)
Body fluids are mostly water.
Fluids in tissues, blood, lymph, and within cells contain
large amounts of protein or other large molecules.
This solution is called a colloid.
Liquid gelatin is a colloid.

A suspension consists of particles large enough to
settle out due to gravity.
Blood is a suspension because red blood cells will
settle out of the plasma (liquid portion) if the clotting
factors are removed.
47

Inorganic Compounds (cont)
Hydrogen ions and pH
Because H+ are so reactive and we have many of
them in our body fluids, their concentration is of
special concern and must be regulated.
The concentration of H+ is measured in pH units, each
a 10X difference in concentration.
The pH values range from 0 to14 with 0 being the
most acidic and 14 the least acidic (most basic).
pH 7 is considered neutral (blood is about 7.4)

pHs above 7 are basic and those below are acidic.
If the pH of body fluids is not maintained within a
narrow range, cells will not function properly and will
die which may eventually lead to organismic death.

48

Inorganic Compounds (cont)

pH scale

acidic
Fig. 9

basic or
alkaline
4949

Inorganic Compounds (cont)
Buffers and pH control
The body maintains pH by the use of buffers which are
substances that may donate or remove H+ from fluids.
All body fluids contains some buffers.
Most body buffers participate in reversible reactions.
They may take up or supply H+ to solution.
You may take an antacid tablet or liquid to settle an
overly acidic stomach to relieve “heartburn”.
The antacids remove excess H+ from stomach fluid
so they are acting as a buffer.
50

Inorganic Compounds (cont)
Acids, Bases, and Salts

A substance that releases hydrogen ions (H+) into a
solution is an acid.
Ex. HCl  H+ + Cl–
A substance that removes hydrogen ions from solution
is a base.
Substances that supply OH– (hydroxide ions) are good
bases because the hydroxide ions quickly combine
with H+ thereby removing them from solution.

Ex. H+ + OH–  H2O
Your stomach contains HCl, a strong acid.
Strong acids dissociate completely.
51

Inorganic Compounds (cont)
Acids, Bases, and Salts (cont)

Besides HCl in the stomach, there are other important
inorganic acids and bases in the body, especially
carbonic acid which is part of a buffer system.
Carbonic acid is a weak acid which means that is does
not dissociate completely into CO2 and H2O.
H2CO3

CO2 + H2O

Bases in your body are all weak meaning there are
always some undissociated molecules present.
Salts are inorganic compounds that release cations
and anions when they are dissolved but the cations
are not H+ and the anions are not OH–.
52

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

53

Organic Compounds Objectives
Learn the chemical characteristics of the four main
classes of organic compounds: carbohydrates, lipids,
proteins, and nucleic acids.
Understand the importance of each class of organic
compound in the human body.

Distinguish between dehydration synthesis and
hydrolysis.
Understand the role of enzymes in chemical reactions.

Learn the structure and use of ATP, a high-energy
compound.
54

Organic Compounds
General considerations
Most organic compounds are built around a carbon
skeleton with the carbon atoms covalently bonded to
each other in a linear or ring fashion.
H and O
usually
present
Carbon shares
4 electrons
(atomic # =6)

Fig. 10

55

Organic Compounds
General considerations
Functional groups: certain atomic groupings are common
as part of organic molecules and they confer particular
properties on those molecules.
Carboxyl group – COOH (acts as an acid by releasing H+
Amino group – NH2 (acts as a acid or a base by releasing
or accepting an H+ depending on the pH)
Hydroxyl group – OH (may combine with H+ to form H2O;
participates in dehydration synthesis)
Phosphate group – PO4 (links molecules to form
macromolecules (DNA, RNA); high energy molecules)
TABLE 4 shows the important functional groups.
56

Organic Compounds (cont)
Carbohydrates

Know shape
of glucose

C:H:O
1:2:1

Glucose =
C6H12O6

Fig. 10

linear

ring
57

Organic Compounds (cont)
Carbohydrates (cont)
A monosaccharide is a small carbohydrate with 3 to 7
carbons (i.e., glucose, fructose; energy sources).
A disaccharide is two monosaccharides joined
(i.e., sucrose or table sugar, lactose; energy sources).
A polysaccharide is a chain of monosaccharides joined
to form a large molecule.

Glycogen is a polysaccharide of glucose (energy
source) and some polysaccharides are structural
molecules.
Starch is the storage form of glucose in plants.
TABLE 5 concerns carbohydrates.
58

Organic Compounds (cont)
Building molecules—dehydration synthesis

Fig. 11 a

Multiple unit molecules are made by dehydration
synthesis, the removal water.
New covalent bonds form between adjacent units.
The resulting disaccharide above is a new molecule
with different properties from either monosaccharide.
59

Organic Compounds (cont)
Breaking molecules—hydrolysis
Large molecules are broken into their component units
by adding water back in, a process called hydrolysis.
New covalent bonds form to yield small units, each with
its own chemical characteristics.
Hydrolysis is the reverse of dehydration synthesis and
vice-versa.

Fig. 11 b

60

Organic Compounds (cont)
Glycogen

Which process
builds glycogen?

Fig. 12

A branched polysaccharide of glucose
61

Organic Compounds (cont)
Lipids
carboxyl group

Energy
source
Protection
Linear
fatty acid

Fig. 15

Triglyceride (fat) has 3 fatty acids

62

Organic Compounds (cont)
Lipids (cont)

C=C

Dehydration
synthesis of a
triglyceride
or fat

Fig. 15
63

Lipids (cont)
Lipids include oils, waxes, and fats.
Lipids are not soluble in water.
Lipids are carried in the blood attached to proteins which
then makes them temporarily water soluble.
Fats are important energy storage molecules since when
broken down, a gram of fat yields 2X the amount of
energy as a gram of carbohydrate or protein.

Triglycerides also provide insulation and protection of
internal organs.
TABLE 6 concerns lipids.
64

Organic Compounds (cont)
Lipids (cont)

Lipids may also be ring
shaped molecules—
these are steroids.

Fig. 16

65

Organic Compounds (cont)
Lipids (cont)
Eicosanoids are essential fatty acids which must be
derived from your diet.

Prostaglandins and leukotrienes are two types of
eicosanoids.
These act as local hormones which coordinate responses
and events in cells, a tissue region, or an organ.
Prostaglandins also have a ring structure.

Fig. 14

66

Organic Compounds (cont)
Lipids (cont)
Fatty acid chains may be combined with other
chemical groups to form different types of molecules.
H2O
soluble
end

Insoluble
end

Fig. 17 a

Phospholipid
Cell
membranes
are made of
double layered
phospholipids

67

Organic Compounds (cont)
Lipids (cont)

Phospholipid heads will orient toward water while tails
will orient away from water.
Micelles will move into the intestinal cells.

carbohydrate

Fig. 17 c

68

Organic Compounds (cont)
Proteins—functions
You have more types of proteins (100,000+) than any
other kind of molecule in your body.
They have structural and functional roles.
Structural proteins examples:
* hair and nails,
* connective tissue fibers that form the substance of
spongy tissues (liver, spleen)
* connective tissue fibers that form muscle fibers,
tendons, ligaments, and bone.
69

Organic Compounds (cont)
Proteins—functions (cont)
Functional protein examples:

* transport proteins such as hemoglobin that carries
oxygen to cells
* cell membrane channels that transport substances into
and out of cells
* buffers that help maintain pH
* enzymes that control chemical reactions
* hormones that control expression of genetic information
* blood clotting enzymes and proteins
* immune system components and cell markers.

70

Organic Compounds (cont)
Proteins—structure
Amino acid unit structure

Buffering
Amino gp
may
accept an
H+

Fig. 18

Buffering

H

20 amino acids differ in R group only

H may be
donated
as H+ to
solution

71

Organic Compounds (cont)
Proteins—structure (cont)
Peptides are chains of amino acids each linked to
the next by a peptide bond (covalent).

Av.=1,000
a.a.s


Fig. 19





72

Organic Compounds (cont)
Proteins—structure (cont)
Proteins have four levels of structural complexity.

The primary structure of a protein is the sequence
of amino acids in the polypeptide chain.
Fig. 20 a
73

Organic Compounds (cont)
Proteins—structure (cont)
Folds and helices established by weak bonds
between repeating sequences along the
polypeptide chain forms the secondary structure.

Fig. 20 b

The alpha helix and pleated sheet are common
secondary structures.
74

Organic Compounds (cont)
Proteins—structure (cont)

Tertiary structure

3D shape

Fig. 20 c

Bonds between side groups cause complex folding of
the peptide chain (note embedded secondary helix).
75

Organic Compounds (cont)
Proteins—structure (cont)
functional
protein

structural
protein
hair

nails
skin
tendons
ligaments

Fig. 20 d

Quaternary structure: more than 1 polypeptide chain

76

Organic Compounds (cont)
Proteins—structure (cont)
Shape is the key to protein function.
Complex shape is maintained by weak bonds including
hydrogen bonds and S–S (disulfide) bonds.
Weak bonds are broken by increasing temperature or
altering the chemical environment (pH).
A protein that has lost its shape is no longer functional
and is said to be denatured.
Body temperature and pH must be maintained so
functional proteins are not denatured.
77

Organic Compounds (cont)
Proteins—enzymes
Enzymes are proteins that speed up chemical reactions
in cells.
Many different synthetic and hydrolytic enzymes exist.
Without enzymes, reactions in cells would be too slow
to sustain life.
Again, it is the three dimensional shape of each
enzyme that is the key to its function.
An enzyme lowers the activation energy for a reaction.
Enzymes make it easier to for a reaction to begin.

Enzymes are needed for all types of metabolic reactions.
78

Organic Compounds (cont)
How enzymes work—
Specific enzyme for each reaction

Enzyme does not enter reaction

Enzyme may be reused
Fig. 21

Some require cofactors

79

Organic Compounds (cont)
Proteins—enzymes (cont)
Basic characteristics of enzymes:
Specificity: specific enzyme for each reaction

Saturation limits: depends on number of enzyme
molecules present; limits speed of a reaction
Regulation: enzyme reactions may be controlled by
the presence of inorganic cofactors such as ions
(Ca2+ and Mg2+) or organic coenzymes.
Binding of these factors changes the shape of the
enzyme to make it functional.

Vitamins function as coenzymes.
TABLE 7 concerns proteins.

80

Organic Compounds (cont)
Nucleic acids—functions
DNA stores genetic information for making
proteins and duplicating the cell’s genes.

Genetic information is contained in the sequence of
bases along the length of the nucleic acid molecule.
Bases

TABLE 8

RNA
DNA

Fig. 23
81

Organic Compounds (cont)

Nucleic acids--structure

The bases are nitrogen
containing rings.
Purine bases have a
double ring structure.
Pyrimidine bases have a
single ring structure.
Thymine is unique to DNA.
Uracil is unique to RNA.
Fig. 22
8282

Organic Compounds (cont)
Nucleic acids--structure

DNA
Sugar-phosphate chains
with bases attached.
Forms a double helix
Complementary bases
held together by
hydrogen bonds in DNA.

G pairs with C
A pairs with T
RNA helps make protein.
Fig. 23b

8383

Organic Compounds (cont)
ATP (adenosine triphosphate)
Note the nucleotide
structure—what
does it resemble?
Terminal phosphate bond
is easily broken and
yields much energy for all
types of cellular work.

Fig. 24

84

Organic Compounds (cont)

ATP (cont)
When the terminal phosphate bond is broken to
provide energy for cellular work, ADP remains.
ADP is recharged by adding back a terminal
phosphate to again make ATP.
ATP  ADP + phosphate group + energy

ATP
energy in from
nutrients + P

energy out
ADP

for work
85

TOPICS
Introduction

Atoms, Molecules, and Bonds
Chemical Notation
Chemical Reactions

Inorganic Compounds
Organic Compounds
Chemicals and Living Cells

86

Chemicals and Living Cells Objectives

By analogy, compare a cell with a factory
Discuss the importance of compartmentation

Review the role of various organic compounds
Discuss metabolic turnover.
Reinforce why you need to understand basic
chemical principles in order to understand
anatomy and physiology.

87

Chemicals and Living Cells

Each living cell has all the working components to
sustain its life as if it were a single cell organism.
Cells have compartments which allows for various
cellular activities to be occurring simultaneously.
A cell is a bit like a factory with various rooms,
assembly lines, and one or more products
produced.
Some products are used within the room or factory
while others are delivered for use elsewhere outside
the factory.
88

Chemicals and Living Cells (cont)

The cellular factory must be supplied with raw
materials, energy, and must have a stable
environment.
Energy is supplied primarily by ATP made within the
cell from nutrients (glucose).
Phospholipids form the walls and partitions of the
factory to create compartments or rooms.
Proteins form the hardware (machines), internal
structure, and supply the enzymes (workers) to help
carry out the chemical reactions.
Nucleic acids contain the computer code that directs
all the activities within the cellular factory.
89

Chemicals and Living Cells (cont)

The chemical composition of a cell is constantly
changing as materials are taken in or removed during
the metabolic processes.
Organic molecules are replaced as needed.

The turnover rate is the time between cellular
synthesis and recycling of the molecule.
The turnover rate varies with the kind of molecule and
metabolic activity of the tissue.
Liver protein is 5-6 days; triglycerides are 20 days,
phospholipids last 200 days.
TABLE 10 lists some turnover rates.
90

Chemicals and Living Cells (cont)

The activities that occur within the cell are all
chemical in nature.

Likewise, the activities that occur in tissues, organs,
systems, and the organism are chemical in nature.
Therefore, to understand physiology, one must know
some elements of basic chemistry.

That is why you must work hard to understand the
materials presented in this chapter.
Since anatomy and physiology are linked, the basis
for understand both is
CHEMISTRY

CHEMISTRY

CHEMISTRY
91

Chemicals and Living Cells (cont)

92

TOPICS

Introduction
Atoms, Molecules, and Bonds
Chemical Notation

Chemical Reactions
Inorganic Compounds
Organic Compounds

Chemicals and Living Cells

93