Chapter 2 Lecture Outline

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2-1

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The Chemistry of Life

• • • •

Atoms, Ions and Molecules Water and Mixtures Energy and Chemical Reactions Organic compounds 2-2

Atoms, Ions and Molecules

• • • • •

The chemical elements Atomic structure Isotopes and radioactivity Ions, electrolytes and free radicals Molecules and chemical bonds 2-3

The Chemical Elements

• •

Element = simplest form of matter with unique chemical properties Atomic number = # of protons in nucleus

–

periodic table

•

elements arranged by atomic number

–

24 elements have biological role

• •

6 elements = 98.5% of body weight trace elements in minute amounts 2-4

2-5

2-6

Minerals

• •

Inorganic elements absorbed from soil by plants Equals 40% of body weight

–

structure (teeth, bones, etc)

–

enzymes 2-7

Structure of an Atom

• •

Nucleus = center of atom

–

protons: single + charge, mass = 1 amu

–

neutrons: no charge, mass = 1 amu Electron shells surround the nucleus

–

electrons: single negative charge, little mass

–

valence electrons in the outermost shell

•

interact with other atoms

•

determine chemical behavior 2-8

Planetary Models of Elements

p + represents protons, n o represents neutrons

2-9

Isotopes and Radioactivity

• •

Isotopes

–

differ in # of neutrons

–

extra neutrons increase atomic weight

–

isotopes of an element are chemically similar

•

have same valence electrons Atomic weight

–

average atomic mass of the isotopes 2-10

Radioisotopes and Radioactivity

• • •

Isotopes

– –

same chemical behavior, differ in physical behavior breakdown gives off radiation Radioisotopes

– –

unstable isotopes every element has at least one radioisotope Radioactivity

–

radioisotopes decay to stable isotopes releasing radiation

–

we are all mildly radioactive 2-11

Marie Curie

• • •

First woman in world to receive a Ph.D.

First woman to receive Nobel Prize (1903)

–

discovered radioactivity of radium

–

trained physicians in use of X rays and radiation therapy as cancer treatment Died of radiation poisoning at 67 2-12

Ionizing Radiation

• • • • •

Radiation ejects electrons forming ions Destroys molecules and produces free radicals

–

sources include:

•

UV light, X rays, nuclear decay (



,



,



)



particle (dangerous if inside the body)

 –

2 protons + 2 neutrons can’t penetrate skin particle (dangerous if inside the body)

–

free electron - penetrates skin a few millimeters



particle (emitted from uranium and plutonium)

–

penetrating; very dangerous gamma rays 2-13

Ionizing Radiation 2

• • •

Physical half-life of radioisotopes

– –

time needed for 50% to decay nuclear power plants create radioisotopes Biological half-life of radioisotopes

– –

time for 50% to disappear from the body decay and physiological clearance Radiation exposure in sieverts (Sv) – biological effect of radiation

–

background radiation = radon gas and cosmic rays

–

sources = X rays and radiation therapy 2-14

Ions and Ionization

•

Ions - carry a charge due to an unequal number of protons and electrons

•

Ionization = transfer of electrons from one atom to another (



stability of valence shell) 2-15

• • •

Anions and Cations

Anion

–

atom that gained electrons (net negative charge) Cation

–

atom that lost an electron (net positive charge) Ions with opposite charges are attracted to each other 2-16

Electrolytes

•

Salts that ionize in water to form body fluids

–

capable of conducting electricity

•

Electrolyte importance

–

chemical reactivity

–

osmotic effects (influence water movement)

–

electrical effects on nerve and muscle tissue

•

Imbalances cause muscle cramps, brittle bones, coma and death 2-17

2-18

Free Radicals

• • •

Particle with an odd number of electrons Produced by

–

normal metabolic reactions, radiation, chemicals Causes tissue damage

–

reactions that destroy molecules

–

causes cancer, death of heart tissue and aging

•

Antioxidants

–

neutralize free radicals

–

in diet (vitamin E, carotenoids, vitamin C) 2-19

Molecules and Chemical Bonds

• • • •

Molecules

–

two or more atoms covalently bonded Compounds

–

two or more atoms of different elements covalently bonded Molecular formula

–

elements and how many atoms of each Structural formula

–

location of each atom

–

structural isomers revealed 2-20

Structural Formula of Isomers

•

Molecular formulae are identical, but structural formulas differ for grain alcohol and ether 2-21

Molecular Weight

• •

MW of compound = sum of atomic weights of atoms expressed in atomic mass unit (amu) Calculate: MW of glucose (C 6 H 12 O 6 ) 6 C atoms x 12 amu each = 72 amu 12 H atoms x 1 amu each = 12 amu 6 O atoms x 16 amu each = 96 amu Molecular weight (MW) = 180 amu 2-22

Chemical Bonds

• • • •

Ionic bonds Covalent bonds Hydrogen bonds Van der Waals force 2-23

Ionic Bonds

• • •

Attraction of oppositely charged ions No sharing of electrons Weak bond (easily dissociates in water) 2-24

Covalent Bonds

• •

Formed by sharing of valence electrons Types of covalent bonds

–

single = sharing of single pair electrons

–

double = sharing of 2 pairs

–

nonpolar

• •

shared electrons (equal time around each nucleus) strongest of all bonds

–

polar

•

negative charge where electrons spend most time 2-25

Single Covalent Bond

•

One pair of electrons are shared 2-26

Double covalent bonds:

Two pairs of electrons are shared each C=O bond 2-27

Nonpolar /Polar Covalent Bonds

electrons shared equally electrons shared unequally 2-28

Hydrogen Bonds

• • •

Weakest bond = no sharing of electrons Attraction between polar molecules

–

positive hydrogen atoms to negative oxygen atoms in a 2 nd molecule Physiological importance

–

properties of water created by shapes of large complex molecules

–

determined by folding due to hydrogen bonds 2-29

Hydrogen Bonding in Water

2-30

Van der Waals Forces

• • •

Weak attractions between neutral atoms Fluctuations in electron density create polarity Only 1% as strong as a covalent bond

–

folding of large molecules

–

significant when 2 large surfaces meet 2-31

Mixtures and Water

• • •

Substances physically but not chemically combined Mixtures in our bodies contain water Water 50-75% of body weight

–

depends on age, sex, percentage body fat, etc.

2-32

Solvency

•

Solvency - ability to dissolve other chemicals

–

Hydrophilic (charged substances) dissolve easily in water

–

Hydrophobic (neutral substances) do not easily dissolve in water

•

Water = universal solvent

–

metabolic reactions and transport of substances 2-33

Water as a Solvent

•

Polar water molecules overpower the ionic bond in Na + Cl -

– –

forming hydration spheres around each ion water molecules: negative pole faces Na + , positive pole faces Cl 2-34

Adhesion and Cohesion

• •

Adhesion – tendency of one substance to cling to another Cohesion – tendency of like molecules to cling to each other

–

water is very cohesive due to its hydrogen bonds

–

surface film on water formed by surface tension 2-35

Chemical Reactivity of Water

•

Participation in chemical reactions

–

water ionizes into H + and OH -

–

water ionizes other chemicals (acids and salts)

–

water involved in hydrolysis and dehydration synthesis reactions 2-36

Thermal Stability of Water

•

Water stabilizes internal temperature

–

has high heat capacity

•

hydrogen bonds inhibit temperature increases by inhibiting molecular motion

–

water absorbs heat without changing temperature

–

effective coolant

•

1 ml of perspiration removes 500 calories

–

calorie: amount of heat required to raise temperature of 1g of water by 1 °C 2-37

Solutions

• • • •

Mixture of a solute into a solvent Small solute particles

–

pass through cell membranes Solution transparent Remains mixed 2-38

Colloids

• • • •

Mixture of protein and water

–

change from liquid to gel state within and between cells Particles too large to pass through cell membranes Cloudy Remains mixed 2-39

Suspensions and Emulsions

• •

Suspension

–

particles suspended in a solvent

–

particles exceed 100nm

•

too large to pass through a cell membrane

–

cloudy or opaque appearance

–

separates on standing Emulsion

–

suspension of one liquid in another

–

fat in breast milk 2-40

2-41

Measures of Concentration

• • •

Weight per Volume

–

weight of solute in given volume of solution

•

IV saline: 8.5 grams NaCl/liter of solution Percentages

–

Weight/volume of solute in solution

•

IV D 5 W (5% w/v dextrose in distilled water)

–

5 grams of dextrose and fill to 100 ml water Molarity

–

moles of solute/liter in solution

–

physiologic effects based on number of molecules in solution not on weight 2-42

Molarity

• •

Molecular weight in grams = 1 mole of molecules 1 mole = Avogadro’s number of molecules

•

Molarity is the number of moles of solute/ liter of solution

–

MW of glucose is 180

–

one-molar (1.0M) glucose solution contains 180g/L 2-43

Percentage vs. Molar Concentrations

• •

Percentage

–

# of molecules unequal

–

weight of solute equal Molar

–

# of molecules equal

–

weight of solute unequal 2-44

Electrolyte Concentrations

• •

Effect the body chemically, physically and electrically

–

depends on charge and concentration Measured in equivalents

–

1 Eq will electrically neutralize 1 mole of H + or OH ions

– – –

multiply molar concentration x valence of the ion 1 M Na + = 1 Eq/L 1 M Ca 2+ = 2 Eq/L 2-45

Acids, Bases and pH

• • •

An acid is proton donor (releases H + ions) A base is proton acceptor (accepts H + pH = the concentration of H + ions in solution

–

a pH of less than 7 is acidic solution

– –

a pH of greater than 7 is basic solution a pH of 7.0 is neutral pH ions) 2-46

pH

•

pH = measurement of molarity of H + [H+] on a logarithmic scale

–

pH = -log [H + ] thus pH = - log [10 -3 ] = 3

–

a change of one number on the pH scale represents a 10 fold change in H + concentration

•

a solution with pH of 4.0 is 10 times as acidic as one with pH of 5.0

•

Our body uses buffers to prevent change

–

pH of blood ranges from 7.35 to 7.45

–

tremors, paralysis or even death 2-47

pH Scale

2-48

Work and Energy

• •

Energy - capacity to do work Kinetic energy - energy of motion

–

heat is kinetic energy of molecular motion

•

Potential energy- energy due to object’s position (ions on one side only of cell membrane)

–

chemical energy - potential energy stored in the molecular bonds 2-49

Chemical Reaction

•

Process that forms or breaks an ionic or covalent bond

•

Symbolized by chemical equation

–

reactants



products

• • •

Classes of reactions Decomposition reactions Synthesis reactions Exchange reactions 2-50

Decomposition Reactions

• •

Large molecules broken down into smaller ones AB



A + B 2-51

Synthesis Reactions

• •

Two or more small molecules combine to form a larger one A + B



AB 2-52

• •

Exchange Reactions

Two molecules collide and exchange atoms or group of atoms AB+CD



ABCD



AC + BD Stomach acid (HCl) and sodium bicarbonate (NaHCO3) from the pancreas combine to form NaCl and H2CO3.

2-53

Reversible Reactions

• • •

Go in either direction (symbolized with double-headed arrow) CO 2

–

+ H 2 O H 2 CO 3 HCO 3 + H + most common equation discussed in this book Law of mass action determines direction

–

side of equation with greater quantity of reactants dominates 2-54

Reaction Rates

• •

Basis for reactions is molecular motion and collisions

–

reactions occur when molecules collide with enough force and the correct orientation Reaction Rates affected by:

–

concentration

•

more concentrated, more collisions, faster rate

–

temperature

•

higher temperature, greater collision force, faster rate

–

Catalysts (enzymes)

• •

speed up reactions without permanent change to itself holds reactant molecules in correct orientation 2-55

Metabolism

• • •

All the chemical reactions of the body Catabolism

–

energy releasing (exergonic) decomposition reactions

•

breaks covalent bonds, produces smaller molecules, releases useful energy Anabolism

–

energy storing (endergonic) synthesis reactions

•

requires energy input 2-56

• • •

Oxidation-Reduction Reactions

Oxidation

–

molecule gives up electrons and releases energy

–

accepting molecule is the oxidizing agent

•

oxygen is often the electron acceptor Reduction

– –

molecule gains electrons and energy donating molecule is the reducing agent Oxidation-reduction (redox) reactions

–

Electrons are often transferred as hydrogen atoms 2-57

2-58

Organic Chemistry

• •

Study of compounds containing carbon 4 categories of carbon compounds

–

carbohydrates

–

lipids

–

proteins

–

nucleotides and nucleic acids 2-59

Organic Molecules and Carbon

•

Only 4 valence electrons

–

bonds readily to gain more valence electrons

•

Forms long chains, branched molecules and rings

–

serve as the backbone for organic molecules

•

Carries a variety of functional groups 2-60

Functional Groups

• •

Atoms attached to carbon backbone Determines chemical properties 2-61

Monomers and Polymers

• •

Macromolecules = very large molecules Polymers = macromolecules formed from monomers bonded together

•

Monomers = an identical or similar subunit 2-62

Polymerization

• •

Bonding of monomers together to form a polymer Formed by dehydration synthesis

–

starch molecules are a polymer of 3000 glucose monomers

–

protein molecules are a polymer of amino acids 2-63

Dehydration Synthesis

•

Monomers covalently bond together to form a polymer with the removal of a water molecule

–

A hydroxyl group is removed from one monomer and a hydrogen from the next 2-64

Hydrolysis

• •

Splitting a polymer (lysis) by the addition of a water molecule (hydro)

–

a covalent bond is broken All digestion reactions consists of hydrolysis reactions 2-65

Organic Molecules: Carbohydrates

• • •

Hydrophilic organic molecule General formula

–

(CH 2 O) n

– –

n = number of carbon atoms for glucose, n = 6, so formula is C 2:1 ratio of hydrogen to oxygen 6 H 12 O 6 Names of carbohydrates

–

word root sacchar- or the suffix -ose often used

•

monosaccharide or glucose 2-66

Monosaccharides

• •

Simple sugars General formula is C 6 H 12 O 6

–

structural isomers

• Major monosaccharides

– glucose, galactose and fructose – produced by digestion of complex carbohydrates • glucose is blood sugar

2-67

Disaccharides

• •

Sugar molecule composed of 2 monosaccharides Major disaccharides

–

sucrose = table sugar

•

glucose + fructose

–

Lactose = sugar in milk

•

glucose + galactose

–

Maltose = grain products

•

glucose + glucose 2-68

Polysaccharides

• •

Chains of glucose subunits Starch: energy storage in plants

–

digestible by humans for energy

•

Cellulose: structural molecule of plant cell walls

–

fiber in our diet

•

Glycogen: energy storage in animals

–

liver synthesizes after a meal and breaks down between meals 2-69

Carbohydrate Functions

• •

All digested carbohydrates converted to glucose and oxidized to make ATP Conjugated carbohydrate = bound to lipid or protein

–

glycolipids

•

external surface of cell membrane

–

glycoproteins

• •

external surface of cell membrane mucus of respiratory and digestive tracts

–

proteoglycans

• • •

gels that hold cells and tissues together joint lubrication rubbery texture of cartilage 2-70

2-71

•

Organic Molecules: Lipids

•

Hydrophobic organic molecule

–

composed of carbon, hydrogen and oxygen

•

Less oxidized and thus has more calories/gram Five primary types in humans

–

fatty acids

–

triglycerides

–

phospholipids

–

eicosanoids

–

steroids 2-72

Fatty Acids

• •

Chain of 4 to 24 carbon atoms

–

carboxyl (acid) group on one end, methyl group on the other and hydrogen bonded along the sides Classified

–

saturated - carbon atoms saturated with hydrogen

–

unsaturated - contains C=C bonds without hydrogen 2-73

Triglycerides (Neutral Fats)

• • •

3 fatty acids bonded to glycerol molecule (dehydration synthesis) At room temperature

–

when liquid called oils

•

often polyunsaturated fats from plants

–

when solid called fat

•

saturated fats from animals Function - energy storage, insulation and shock absorption 2-74

Phospholipids

• •

Triglyceride with one fatty acid replaced by a phosphate group Amphiphilic character

–

fatty acid “tails” are hydrophobic

–

Phosphate “head” is hydrophilic 2-75

Eicosanoids

• • •

Derived from arachidonic acid (a fatty acid) Hormone-like chemical signals between cells Includes prostaglandins – produced in all tissues

–

role in inflammation, blood clotting, hormone action, labor contractions, blood vessel diameter 2-76

Steroids and Cholesterol

•

Steroid = lipid with carbon atoms in four rings

–

all steroids are derived from cholesterol

•

cortisol, progesterone, estrogens, testosterone and bile acids

•

Cholesterol

–

important component of cell membranes

–

produced only in animal liver cells

•

naturally produced by our body 2-77

2-78

Organic Molecules: Proteins

• •

Protein = polymer of amino acids Combination determines structure and function

•

Amino acid = carbon with 3 attachments

–

Amino (NH2), carboxy (COOH) and radical group (R group)

•

20 unique amino acids

–

-R groups differ

–

properties determined by -R group 2-79

Naming of Peptides

• •

Peptide = polymer of 2 or more amino acids Named for the number of amino acids

– – – –

dipeptides have 2, tripeptides have 3 oligopeptides have fewer than 10 to 15 polypeptides have more than 15 proteins have more than 100 2-80

Dipeptide Synthesis

•

Dehydration synthesis creates a peptide bond that joins amino acids 2-81

Protein Structure and Shape

• • • •

Primary structure

–

amino acid sequence Secondary structure

– –

coiled or folded shape hydrogen bonds between negative C=O and positive N-H groups Tertiary structure

–

further folding and bending into globular and fibrous shapes Quaternary structure

–

associations of two or more separate polypeptide chains 2-82

2-83

Conjugated Proteins

• •

Contain a non-amino acid moiety Hemoglobin contains complex iron containing ring called a heme moiety 2-84

Protein Conformation and Denaturation

•

Conformation – unique 3-D shape crucial to function

–

ability to reversibly change their conformation

•

opening and closing of cell membrane pores

•

Denaturation

–

conformational change that destroys function

•

extreme heat or pH 2-85

Protein Functions

• • • •

Structure

–

collagen, keratin Communication

–

some hormones, cell receptors Membrane Transport

–

channels, carriers Catalysis

–

enzymes 2-86

Protein Functions 2

• • •

Recognition and protection

–

antigens, antibodies and clotting proteins Movement

–

molecular motor = molecules that can change shape repeatedly Cell adhesion

–

proteins bind cells together 2-87

Enzymes

• • • •

Proteins as biological catalysts

–

promote rapid reaction rates Substrate - substance an enzyme acts upon Naming Convention

–

named for substrate with -ase as the suffix

•

amylase enzyme digests starch (amylose) Lowers activation energy = energy needed to get reaction started

–

enzymes facilitate molecular interaction 2-88

Enzymes and Activation Energy

2-89

Steps of an Enzyme Reaction

• • • • •

Substrate approaches enzyme molecule Substrate binds to active site forming enzyme-substrate complex

–

highly specific Enzyme breaks bonds in substrate Reaction products released Enzyme repeats process over and over 2-90

Enzymatic Reaction Steps

2-91

Enzymatic Action

• • •

Reusability of enzymes

–

enzymes are unchanged by the reactions Astonishing speed

–

millions of molecules per minute Temperature and pH

–

change shape of enzyme and alter its ability to bind

–

enzymes vary in optimum pH

•

salivary amylase works best at pH 7.0

•

pepsin works best at pH 2.0

–

temperature optimum for human enzymes = body temperature 2-92

Cofactors and Coenzymes

•

Cofactors

–

nonprotein partners (iron, copper, zinc, magnesium or calcium ions)

–

bind to enzyme and change its shape

–

essential to function

•

Coenzymes

–

organic cofactors derived from water-soluble vitamins (niacin, riboflavin)

–

transfer electrons between enzymes 2-93

Coenzyme NAD

+

•

NAD + transports electrons from one metabolic pathway to another 2-94

Metabolic Pathways

• • • •

Chain of reactions, each catalyzed by an enzyme

 

A



B



C

 

D A is initial reactant, B+C are intermediates and D is the end product Regulation of metabolic pathways

– –

activation or deactivation of the enzymes cells can turn on or off pathways 2-95

•

Organic Molecules: Nucleotides

3 components

–

nitrogenous base

–

sugar (monosaccharide)

–

one or more phosphate groups

•

Physiological important nucleotides

–

ATP = energy carrying molecule

–

cAMP = activates metabolic pathways

–

DNA = carries genetic code

–

RNA = assists with protein synthesis 2-96

ATP (Adenosine Triphosphate)

ATP contains adenine, ribose and 3 phosphate groups 2-97

• • •

ATP

Holds energy in covalent bonds

–

2nd and 3rd phosphate groups have high energy bonds ~ ATPases hydrolyze the 3 rd phosphate bond high energy

–

separates into ADP + P i + energy Phosphorylation

–

addition of free phosphate group to another molecule 2-98

Overview of ATP Production

• •

ATP consumed within 60 seconds Continually replenished 2-99

Other Nucleotides

•

Cyclic adenosine monophosphate (cAMP)

–

formed by removal of both high energy P i ’s from ATP

–

formation triggered by hormone binding to cell surface

–

cAMP becomes “second messenger” within cell

–

activates effects inside cell 2-100

Nucleic Acids

• •

DNA (deoxyribonucleic acid)

–

100 million to 1 billion nucleotides long

–

contains genetic code

•

cell division, sexual reproduction, protein synthesis RNA (ribonucleic acid) – 3 types

–

transfer RNA, messenger RNA, ribosomal RNA

–

70 to 10,000 nucleotides long

–

involved in protein synthesis coded for by DNA 2-101