Transcript Chapter 2: Chemistry Raw materials and fuel for our bodies 117 confirmed elements as of 10/16/06 (element 118 has been synthesized). Nearly 1.5 miles.

Chapter 2: Chemistry
Raw materials and fuel for our bodies
117 confirmed elements as of 10/16/06
(element 118 has been synthesized).
Nearly 1.5 miles beneath Earth's surface, scientists have discovered pockets of the oldest
water on the planet that have remained in isolation for 1 to 2.6 billion years. The water could
be teeming with microscopic life.
-- By Deborah Netburn. May 16, 2013, LAT
Learning Objectives
• Relate major principles of chemistry to the study of biology
• Understand atomic structure
• Compare and contrast the major chemical bonds involved in
important molecules and compounds
• Understand water’s features that help it support all life.
• Understand the concept of pH and buffer.
-- Relate the above to Lab #2 (pH and Water)
• Identify the major macromolecules that make up living
organisms
• Explain the importance of the function of each of the four
major macromolecules
• Describe the different types of carbohydrates and their uses
• Compare and contrast different types of lipids and their
structures
• Understand the importance of shape in the protein function
2.1–2.3 Atoms form molecules through
bonding.
2.1 Everything is made of atoms.
• An element is a substance that cannot be
broken down chemically into any other
substances.
• An atom is a bit of matter
that cannot be subdivided
any further without losing
its essential properties.
Atomic Structure:
The nucleus, protons, and neutrons
This diagram is not to scale
Interesting concept: the
distance between an electron
and proton in the nucleus is
about 100,000 times the size of
a proton – so even an atom is
mostly “empty space.” So even
a solid block of iron is mostly
empty spaces.
Atomic Numbers
Insert new figure 2.3
Know these symbols
for common elements
found in living things.
Radioactive Atoms
• A few atomic nuclei are not stable and break down spontaneously.
• These atoms are radioactive.
• They release, at a constant rate, a tiny, high-speed particle carrying
a lot of energy.
25 Elements Found in Your Body and the Big 4
Take-home message 2.1
• Everything around us,
living or not, is made from
atoms, the smallest unit into
which material can be divided.
• Atoms all have the same
general structure.
• They are made up of
protons and neutrons in the
nucleus and electrons,
which circle far around the
nucleus.
2.2 An atom’s electrons determine how (and
whether) the atom will bond with other atoms.
The Versatility of Carbon
Insert fig 2-7
Ions
Take-home message 2.2
Insert new fig 2-8
• The chemical
characteristics of an
atom depend upon
number of electrons
in their outermost
shells.
• Atoms are most
stable and least
likely to bond with
other atoms when
their outermost
electron shell is
full.
2.3 Atoms can bond together to form Molecules
or compounds.
Molecules are products
of bonding!
There are three major
types of bonds:
Covalent, ionic, and
hydrogen bonds.
Ions and Ionic Bonds
Hydrogen Bonds
Take-home message 2.3
• Atoms can be bound together in
three different ways.
• Covalent bonds, in which atoms
share electrons, are the
strongest.
 In ionic bonds, one atom
transfers its electrons to another
and the two oppositely charged
ions are attracted to each other,
forming a compound.
 Hydrogen bonds, which are
weaker than covalent and ionic
bonds, involve the attraction
between a hydrogen atom and a
polar molecule.
2.4–2.6 Water has features that enable it to support all life.
2.4 Hydrogen bonds make water cohesive.
Insert fig 2-13
Take-home message 2.4
 Water
molecules easily form hydrogen bonds,
giving water great cohesiveness.
2.5 Water has unusual properties that make
it critical to life.
 Cohesion
 Large
heat
capacity
 Low
density as a
solid
 Good
solvent
WATER’S LIFE-SUPPORTING PROPERTIES
Heat Capacity
Why do coastal areas have milder,
less variable climates than
Low Density as a Solid
inland areas?
Malibu vs. the Valley
Why don’t oceans freeze as
easily as fresh water lakes?
Take home message 2.5

The hydrogen bonds between water molecules give water several
of its most important characteristics:
• cohesiveness
• reduced density as a solid
• the ability to resist temperature changes
• broad effectiveness as a solvent for ionic and polar substances
The distribution of life in water
>70% planet’s surface
97% is sea water. Of the remaining
fresh water, 75% is ice trapped at
the poles. Only 1% of total water is
drinkable - but mostly deep
underground. Thus only 0.05% of
water is biologically available.
California Drought Emergency
Declared By Governor Brown
Obama turns attention to
California drought, Fresno
President announces millions
in drought aid. 2/14/14
2.6 Living systems are highly sensitive to
acidic and basic conditions.
Hydrogen Ions and Hydroxide Ions
OH -
H2O
O
O
H
Ionized Hydroxide
Molecule
H
H
Non-Ionized Water
Molecule
pH Scale
The amount of H+ in a solution is a
measure of its acidity and is called pH.
 Acids: pH < 7
 Bases: pH > 7
H+ Ions and Acids
 H+ very reactive
 Acids can donate H+ to other
chemicals
 Stomach juice: extremely acidic
Bases
 Low H+; High OH
 Antacids
 Baking soda, seltzer, milk of
magnesia
Buffers
• can quickly absorb excess H+
ions to keep a solution from
becoming too acidic
• can quickly release H+ ions to
counteract any increases in OH
concentration
Blood pH
Take-home message 2.6
 The
pH of a fluid is a measure of how acidic or
basic a solution is and depends on the
concentration of dissolved H+ ions present.
 The lower the pH, the more acidic the solution
 Acids, such as vinegar, can donate protons to
other chemicals while bases, including baking
soda, bind with free protons.
2·7 THIS IS HOW WE DO IT
Do anti-acid drugs impair digestion and increase the
risk of food allergies?
How does the stomach’s acidic environment aid in
digestion?
Does reducing stomach acidity have health
consequences?
How could we evaluate whether acidity-reducing
medications increase the potential for food allergy?
Two Experimental Strategies
First they evaluated the effectiveness of proteindigesting enzymes at several different levels of
acidity.
Results?
• At typical stomach pH of 2:
– the proteins in milk are completely digested within 1 minute.
• At less acidic pH values of 3 and 5:
– the milk proteins were largely undigested, even after 1 hour.
From these results, what could the researchers conclude
about the role of stomach acidity in digesting proteins?
• In their second experimental strategy, the researchers
observed 152 people who were seeking treatment for an ulcer,
before and after a three-month anti-acid treatment.
• They evaluated each participant for signs of allergic reactions
to a variety of proteins.
Results?
• Before the three-month anti-acid treatment:
– 10% of the subjects exhibited signs of having had an immune response to at
least 1 of the 19 dietary proteins the researchers tested.
• After three months of anti-acid treatment:
– 26% of the subjects exhibited signs of having had an immune response to at
least 1 of the 19 tested dietary proteins.
• From these results, what could the research team conclude about the
role of anti-acid medications in causing normal dietary proteins to
stimulate an allergic response?
Take-home message 2.7
• Dietary proteins are not digested by the stomach when the
stomach’s pH is increased as a result of medications taken to
treat ulcers, heartburn, and other digestive problems.
• This can put people who take anti-acid medications at risk for
developing allergic responses to common foods.
2·8–2·11 Carbohydrates are fuel for living machines.
Four Types of Macromolecules
 Carbohydrates
 Lipids
(9)
 Proteins
(4)
 Nucleic
acids
(4 Cal per gram)
2.8 Carbohydrates include macromolecules that
function as fuel.
Health topics of the year
 Low-carb diet?
 Hi-carb diet?
 “Carbo-loading”?
 Fiber intake?
What are carbohydrates?
C, H, and O
 Primary fuel for
organisms
 Cell structure

Energy is in the chemical bonds!
Take-home message 2-8






Carbohydrates are the primary fuel for running all cellular machinery and also
form much of the structure of cells in all life forms.
Carbohydrates contain carbon, hydrogen, and oxygen, and generally have the same
number of carbon atoms as they do H2O units.
The C-H bonds of carbohydrates store a great deal of energy and are easily broken
by organisms.
The simplest carbohydrates, including glucose, are monosaccharides or simple
sugars.
They contain from three to six carbon atoms.
As the chemical bonds of carbohydrates are broken down and other more stable
bonds are formed, a great deal of energy is released that can be used by organisms.
2.9 Glucose provides energy for the body’s
cells.
Glucose



Fuel for cellular activity
Stored temporarily as
glycogen
Converted to fat
Most carbohydrates—
ultimately converted
into glucose
 Blood sugar
 Glucose is a
monosaccharide
What is “carbo-loading”?
Take home message 2.9


Glucose is the most important carbohydrate to living organisms.
Glucose in the bloodstream can be used as an energy source, can
be stored as glycogen in the muscles and liver for later use, or
can be converted to fat.
2.10 Many complex carbohydrates are timereleased packets of energy.

More than 1 sugar
(monosaccharide) unit

Disaccharides
• Sucrose: glucose + fructose
• lactose

Polysaccharides
• Starch
> 100’s of glucose molecules joined
together
Barley, wheat, rye, corn, and rice
•
•
Cellulose: cell wall
Glycogen—“animal
starch”
Complex Carbohydrates: “Time-release” fuel pellets
Take-home message 2.10
Multiple simple carbohydrates sometimes link together
into more complex carbohydrates.
 Types of complex carbohydrates include starch, the
primary form of energy storage in plants, and glycogen,
a primary form of energy storage in animals.

2.11 Not all carbohydrates
are digestible.
 Chitin
 Cellulose
 Can cows
digest
cellulose?
Fiber



“Roughage”
Colon cancer
prevention/reduction
Termites ecological role
See narrative
Take-home message 2.11
 Some complex carbohydrates, including chitin and
cellulose, cannot be digested by most animals.
 Such indigestible carbohydrates in the diet, called fiber,
aid in digestion and have numerous health benefits.
2.12–2.14 Lipids store energy for a rainy day
2.12 Lipids are macromolecules with several functions,
including energy storage.
Why does a salad dressing made
with vinegar and oil separate into
two layers shortly after you shake
it?
 Hydrophobic
 Hydrophilic
In making a homemade salad dressing you mix olive oil,
vinegar, and water together. You notice when you add the
vinegar to the water it mixes immediately. When you add the
olive oil it floats on top of the solution. The vinegar is
____________ and the oil is ____________.
1.
2.
3.
4.
hydrophobic; hydrophilic
acidic; basic
hydrophilic; hydrophobic
basic; acidic
Take-home
message 2.12
Lipids are non-soluble in water and greasy to the
touch.
 They are valuable to organisms in long-term energy
storage and insulation, membrane formation, and as
hormones.

2.13 Fats are tasty molecules too plentiful
in our diets.
 Glycerol:
“head”
region
 Fatty
acid “tails”
 Triglycerides
 Relate
this to the
Enzymes lab.
Saturated and Unsaturated Fats

Fat molecules
contain much
more stored
energy than
carbohydrate
molecules.

# of bonds in the hydrocarbon chain in a fatty
acid
Health considerations
Which answer below is solid at room temperature?
1.
2.
3.
4.
Saturated fat (like animal fat)
Unsaturated fat (like canola oil)
Trans fat (like margarine)
Both 1 and 3 are correct.
Chocolate chip cookie recipes call for some lipids.
 How will the “chewy-ness” of the cookies differ
depending on whether you use butter or vegetable oil as
the lipid?
 Which cookies will be healthier?

Many snack foods contain “partially hydrogenated”
vegetable oils.
 Why might it be desirable to add hydrogen atoms to a
vegetable oil?
What are trans fats?

is a recently developed “fake fat” chemical
that gives foods the taste of fat, without adding the
calories of fats.
 What chemical structure might make this possible?
 Olestra
If you analyze the nutrition label of some commercially available
chocolate chip cookies you will find that they say they have zero trans
fats. Many times this is false because when you look in the list of
ingredients you find… 1. Butter
2.
3.
4.
5.
Canola oil
Partially hydrogenated canola oil
Lard
Palm oil
Take-home message 2.13



Fats, including the triglycerides common in the food we eat, are
one type of lipid.
Characterized by long hydrocarbon tails, fats effectively store
energy in the many carbon-hydrogen and carbon-carbon bonds.
Their caloric density is responsible for humans’ preferring fats to
other macromolecules in the diet, and is also responsible for their
association with obesity and illness in the modern world.
2.14 Cholesterol and phospholipids are used to build
sex hormones and membranes.
Not all lipids are fats
The sterols
Cholesterol
Important component of most
cell membranes.
 Can attach to blood vessel walls
and cause them to thicken.
 Cells in our liver produce
almost 90% of the circulating
cholesterol.
Steroid Hormones
 Estrogen
 Progesterone
 Testosterone

•synthetic variants of testosterone
 Cortisol
Phospholipids and Waxes
 Phospholipids
are the major
component of
the cell
membrane.
 Waxes
are
strongly
hydrophobic.
Take-home message 2.14
 Cholesterol
and phospholipids are lipids that
are not fats.
 Both are important components in cell
membranes.
 Cholesterol also serves as a precursor to
steroid hormones, important regulators of
growth and development.
2.15–2.18 Proteins are versatile macromolecules that serve as
building blocks.
Hair and feathers are built from proteins.
2.15 Proteins are bodybuilding
macromolecules. They are also
workers inside our cells.
Amino Acids
 Twenty
different
amino
acids
 Strung
together to
make
proteins
Take-home message 2.15
Unique combinations of 20 amino acids give rise to
proteins, the chief building blocks of physical
structures that make up all organisms.
 Proteins perform myriad functions, from assisting
chemical reactions to causing blood clotting to
building bones to fighting microorganisms.

2.16 Proteins are an essential dietary
component.
Growth
 Repair
 Replacement

 Food
labels indicate an item’s protein content.
 Why
is this insufficient for you to determine
whether you are protein deficient, even if your
protein intake exceeds your recommended
daily amount?
Complete Proteins
 Have
all essential amino acids
 Incomplete proteins
 Complementary proteins
Insert new fig 2-38
Which answer below will provide all of the essential amino
acids in a meal?
1. Hamburger
2. Corn and a legume (complementary)
3. Apple
4. Both 1 and 2 are correct.
Take-home message 2.16
 Twenty
amino acids make up all the proteins
necessary for growth, repair, and replacement
of tissue in living organisms.
 Of these amino acids, about half are essential
for humans: they cannot be synthesized by the
body so must be consumed in the diet.
 Complete proteins contain all essential amino
acids, while incomplete proteins do not.
2.17 A protein’s function is influenced by
its three-dimensional shape.
 Peptide
bonds
Primary Structure
Secondary Structure
The sequence of amino acids
Hydrogen
bonding between amino acids
The two most common patterns:
 twist in a corkscrew-like shape
 zig-zag folding
Tertiary Structure


Folding and bending of the secondary structure
Due to bonds such as hydrogen bonds or
covalent sulfur-sulfur bonds.
Quaternary Structure


When two or more polypeptide chains
are held together by bonds between the
amino acids on the different chains.
Hemoglobin
Egg whites contain much protein.
 Why does beating them change their texture,
making them stiff?

Why do some people have
curly hair and others have
straight hair?
Why is wet hair easier to style than dry hair?
Getting hair straightened at a hair salon involves…
1. Changing the tertiary structure of the
hair proteins.
2. Reforming hydrogen bonds that have
been broken.
3. Changing the primary structure of the
hair proteins.
4. 1 and 2.
Take-home message 2.17
A protein’s particular amino acid sequence determines
how it folds into a particular three-dimensional shape.
 This shape determines many of the protein's features,
such as which molecules it will interact with.
 When a protein's shape is deformed, the protein usually
loses its ability to function.

2.18 Enzymes are proteins that initiate and
speed up chemical reactions.
Activation Energy
Chemical
reactions occurring in organisms can either release energy or
consume energy.
In either case, the reaction needs a little “push” in order to initiate the
reaction―called activation energy.
Enzymes act as catalyst by lowering the activation energy.
An enzyme can reduce the activation energy in a
variety of ways.
1.
2.
3.
4.
By stressing, bending, or stretching critical chemical bonds
By directly participating in the reaction
By creating a microhabitat that is conducive to the reaction
By simply orienting or holding substrate molecules in place so that
they can be modified.
Why can’t we digest cellulose?
The polysaccharides amylose and cellulose are both made of
glucose. Why can’t the enzyme salivary amylase breakdown both?
1. The orientation of the covalent bonds are different.
2. The active site of the enzyme cannot bind to glucose.
3. The enzyme cannot digest cellulose at normal body temperatures
(32oC).
4. The covalent bonds in cellulose are stronger than in amylose.
Take-home message 2.18
 Enzymes
are proteins that help initiate and
speed up chemical reactions.
 They aren’t permanently altered in the process
but rather can be used again and again.
2-19 Enzymes regulate reactions in several ways
(but malformed enzymes can cause problems).
The rate at which an enzyme catalyzes a reaction is
influenced by several chemical and physical factors.
“Misspelled” Proteins
 Incorrect
amino acid sequence
 Active site disruptions
 Phenylketonuria
Why do some adults get sick when
they drink milk?
Lactase cannot function properly in
this example because the….
1. shape is incorrect.
2. amino acid sequence is
incorrect.
3. color is incorrect.
4. 1 and 2
When lactase is functioning correctly it…
1. lowers the activation energy required to
digest lactose.
2. increases the activation energy required to
digest lactose.
3. acts as an inhibitor to decrease the activity
of enzymes that breakdown lactose.
4. acts as an activator to increase the activity of
enzymes that breakdown lactose.
Take-home message 2.19
Enzyme activity is influenced by physical factors such as
temperature and pH, as well as chemical factors, including
enzyme and substrate concentrations.
 Inhibitors and activators are chemicals that bind to enzymes,
and by blocking the active site or altering the shape or
structure of the enzyme can change the rate at which the
enzyme catalyzes reactions.

2.20–2.22 Nucleic acids store information on how to build and run a body.
2.19 Nucleic acids are macromolecules that store information.
Two Types of Nucleic Acids
Deoxyribonucleic acid
(DNA)
 Ribonucleic acid (RNA)
 Both play central roles in
directing the production
of proteins.

Information Storage
 The
information in a molecule of DNA is
determined by its sequence of bases.
 Adenine, guanine, cytosine, and thymine
• CGATTACCCGAT
Take-home message 2.20
 The
nucleic acids DNA and RNA are
macromolecules that store information in their
unique sequences of bases contained in
nucleotides, their building-block molecules.
 Both nucleic acids play central roles in
directing protein production in organisms.
2.21 DNA holds the genetic information to build an organism.
Base-Pairing
A&T
G&C

What is the complimentary strand
to this strand:
CCCCTTAGGAACC?
 ___________________
What is the complimentary strand to
this strand: CCCCTTAGGAACC?
1. CCCCTTAGGAACC
2. GGGGTTAGGAACC
3. GGGGAATCCTTGG
4. GGTTCCTAAGGCC
2.22 RNA is a universal translator, reading DNA and
directing protein production.
RNA differs from DNA in
three important ways.



The sugar molecule of the
sugar-phosphate backbone
Single-stranded
Uracil (U) replaces thymine (T)
Which sequence below is the RNA
synthesized from the DNA sequence
below:
CCCCTTAGGAACC
1. GGGGAATCCTTGG
2. CCCCTTAGGAACC
3. GGUUCCUAAGGGG
4. GGGGAAUACCUUGG
Take-home message 2.21
DNA is shaped like a ladder in which the long vertical
sides of the ladder are made from a sequence of sugarphosphate-sugar-phosphate molecules and the rungs are
pairs of nucleotide bases.
 The sequence of nucleotide bases contains the
information about how to produce a particular protein.

Take-home message 2.22
 RNA
acts as a middleman molecule—taking
the instructions for protein production from
DNA to another part of the cell where, in
accordance with the RNA instructions, amino
acids are pieced together into proteins.