Chapter 2:

Chemistry of Life

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The Chemical Elements

2-2

Atomic Structure
Nucleuscenter of atom
Protons
Neutrons
Atomic mass is approximately equal to total number of
protons and neutrons
Electronsin concentric clouds surrounding nucleus
Valence electrons orbit in the outermost shell and
determine chemical bonding properties of an atom
An atom is electrically neutral, as number of electrons equals
number of protons
2-3

Bohr Planetary Models of Elements

Figure 2.1
2-4

Isotopes and Radioactivity

Isotopesvarieties of an element that differ only
in the number of neutrons
Extra neutrons increase atomic weight
Isotopes of an element are chemically similar because
they have the same number of valence electrons

Radioisotopes
Unstable isotopes that decay and give off radiation
Medical imaging

2-5

Ions and Electrolytes

Anionparticle that gains electron(s) (net negative charge)
Cationparticle that loses electron(s) (net positive charge)
Ions with opposite charges are attracted to each other
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11 protons
12 neutrons
10 electrons

Sodium
ion (Na+)

17 protons
18 neutrons
18 electrons

Chloride
ion (Cl)

Figure 2.4 (2)

Sodium chloride
2

The charged sodium ion (Na+) and chloride ion (Cl) that result

2-6

Ions and Electrolytes

2-7

Molecules and Chemical Bonds

Molecule
Compound
Isomers

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Structural
formulae

Ethanol

H
Ethyl ether

C
H

OH

Condensed
structural
formulae

Molecular
formulae

CH3CH2OH

C2H6O

CH3CH2OH

C2H6O

H
O

Figure 2.5

2-8

Molecules and Chemical Bonds

The molecular weight (MW) of a compound is
the sum of the atomic weights of its atoms.
Calculate: MW of glucose (C6H12O6)
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

2-9

Molecules and Chemical Bonds

Types of Chemical Bonds

Chemical bondshold atoms together within a

molecule or attract one molecule to another
TABLE 2.3

Ionic bonds
Covalent
Double, single, triple
Polar vs nonpolar

Hydrogen

2-10

Molecules and Chemical Bonds

Nonpolar bond:
electrons shared
Nonpolar covalent
equally
C C bond
(strongest bond)

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(a)

Polar covalent
O H bond

O
_

(b)

Polar bond:
electrons shared
unequally (spend
more time near
oxygen)

Figure 2.7
2-11

Molecules and Chemical Bonds

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+
H

o
H
+

+
H

H +

Covalent bond
H +
Hydrogen bond

o
+
H

Water molecule

2-12

Figure 2.8

Water and Mixtures

Mixturesphysically blended but not chemically
combined
Body fluids are complex mixtures of chemicals
Water is 50% to 75% of body weight
Depends on age, sex, fat content, etc.

Properties of Water
Solvency, cohesion, adhesion, reactivity, stability

2-13

Solutions, Colloids, and Suspensions

2-14

Solutions, Colloids, and Suspensions

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Figure 2.10
Solution

Colloid

Suspension

2-15

Measures of Concentration
Weight per volume
Weight of solute in a given volume of solution
IV saline: 8.5 g NaCl per liter of solution
Common biology units: milligrams per deciliter (mg/dL)
Example: serum cholesterol may be 200 mg/dL

Percentages
Might be weight of solute (solid) per volume
Example: 5% dextrose solution

Might be volume of solute (liquid) per volume of solution

Example: 70% ethanol

Molarity (M)moles of solute/liter of solution

Allows knowledge of number of solute molecules present
Example: glucose weighs 180 amu; A 1M solution of glucose contains
180 g of glucose in 1 L of solution

Body fluids are often in millimolar (mM)

2-16

Measures of Concentration
Electrolytes are crucial for heart, nerve,
muscle
Measured in equivalents (Eq)
1 Eq is the amount of electrolyte that will neutralize
1 mole of H+ or OH- ions
Often expressed as milliequivalents (mEq/L)
Multiply molar concentration x valence of the ion
1 mM Na+ = 1 mEq/L
1 mM Ca2+ = 2 mEq/L

2-17

Acids, Bases, and pH

An acid is a proton donor
A base is a proton acceptor
pH is a measure derived from the molarity of H+
a pH of 7.0 is neutral pH
(H + = OH-)
a pH of less than 7 is acidic solution (H + > OH-)
a pH of greater than 7 is basic solution (OH - > H+ )

Bufferschemical solutions that resist changes in pH

Maintaining normal (slightly basic) pH of blood is crucial
for physiological functions
2-18

Acids, Bases, and pH

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Wine,
vinegar
(2.43.5)

Gastric juice
(0.93.0) Lemon
1M
hydrochloric
acid(0)

Bananas,
tomatoes
(4.7)

Milk, Pure water

Egg white
saliva
(7.0)
(8.0)
(6.36.6)

Bread,
black
coffee
(5.0)

Household
bleach
(9.5)

Household
ammonia
(10.511.0)
Oven cleaner, lye
(13.4)
1 M sodium
hydroxide
(14)

juice
(2.3)

3
2
1

Neutral

Figure 2.12

10

11
12
13

14

2-19

Classes of Chemical Reactions

Chemical reactiona process in which a
covalent or ionic bond is formed or broken
Classes
Decomposition reactions
Synthesis reactions
Exchange reactions

2-20

Reaction Rates
Reaction rates increase when
the reactants are more concentrated
the temperature rises
a catalyst is present
Enzyme catalysts bind to reactants and hold them in orientations
that facilitate the reaction
Catalysts are not changed by the reaction and can repeat the
process frequently

2-21

Metabolism, Oxidation, and Reduction

Metabolismall chemical reactions of the body
Catabolism
Energy-releasing decomposition reactions
Anabolism
Energy-storing synthesis reactions

Catabolism and anabolism are inseparably linked

Anabolism is driven by energy released by catabolism

2-22

Metabolism, Oxidation, and Reduction

Oxidation
A chemical reaction in which a molecule gives up
electrons and releases energy
Electron acceptor molecule is the oxidizing agent
Oxygen is often involved as the electron acceptor

Reduction
Any chemical reaction in which a molecule gains electrons
and energy
Molecule that donates electrons is the reducing agent
2-23

Carbon Compounds and

Functional Groups
Organic chemistrythe study of compounds
containing carbon
Four categories of carbon compounds

Carbohydrates
Lipids
Proteins
Nucleic acids

2-24

Carbon Compounds and

Functional Groups
Carbon has four valence electrons
Binds with other atoms that can provide it with four more
electrons to fill its valence shell

Carbon atoms bind readily with each other to form

carbon backbones
Form long chains, branched molecules, and rings
Form covalent bonds with hydrogen, oxygen, nitrogen,
sulfur, and other elements

Carbon backbones carry a variety of functional groups

2-25

Carbon Compounds and

Functional Groups
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Name and
Symbol

Functional groupssmall
clusters of atoms attached
to carbon backbone

Hydroxyl
(OH)

Examples: hydroxyl, methyl,

carboxyl, amino, phosphate

Occurs in

Sugars, alcohols

Fats, oils,
steroids,
amino acids

H
Methyl
(CH3)

Determine many of the

properties of organic
molecules

Structure

C
H

O
Carboxyl
(COOH)

Amino acids,
sugars, proteins

C
O
H

Amino
(NH2)

Amino acids,
proteins

N
H

H
O
Phosphate
(H2PO4)

Nucleic acids, ATP

O
H

Figure 2.14

2-26

Monomers and Polymers

Dehydration synthesismonomers covalently
bind together to form a polymer with the removal
of a water molecule
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Dimer
Monomer 1

Monomer 2
O

OH HO
H+ + OH

H2O

(a) Dehydration synthesis

Figure 2.15a
2-27

Monomers and Polymers

Hydrolysissplitting a polymer by the addition of a
water molecule
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Dimer
Monomer 1

Monomer 2
OH HO

O
H2O

H+ + OH

(b) Hydrolysis

Figure 2.15b

2-28

Carbohydrates
Hydrophilic organic
molecule
Examples: sugars and
starches

General formula
(CH2O)n, n = number
of carbon atoms
Glucose, n = 6, so
formula is C6H12O6
2:1 ratio of hydrogen
to oxygen
2-29

Lipids
Lipids are hydrophobic organic molecules with a high
ratio of hydrogen to oxygen
Have more calories per gram than carbohydrates
Five primary types in humans

Fatty acids
Triglycerides
Phospholipids
Eicosanoids
Steroids
2-30

Lipids

Fatty acids

Chains of 4-24 carbon atoms with carboxyl group on

one end and methyl group on the other
Saturated fatty acids have a lot of hydrogen
Unsaturated fatty acids contain some double bonds
between carbons in chain
Polyunsaturated fatty acids have multiple double bonds
between carbons in chain
Essential fatty acids must be obtained from food
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O
HO

Palmitic acid (saturated)

CH3(CH2)14COOH

Figure 2.19

2-31

Lipids
Triglycerides (Neutral Fats)
Three fatty acids linked to glycerol
Each bond formed by dehydration synthesis
Broken down by hydrolysis

Triglycerides at room temperature

When liquid, called oils
Often polyunsaturated fats from plants

When solid, called fat

Saturated fats from animals

Primary function: energy storage

Also help with insulation and shock absorption (adipose
tissue)
2-32

Trans Fats and Cardiovascular Health

Trans-fatty acids

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Two covalent single C-C bonds

angle in opposites (trans, across
from each other) on each side of
the C=C double bond
Resist enzymatic breakdown in the
human body, remain in circulation
longer, deposits in the arteries;
thus, raises the risk of heart
disease

O
OH
(a) A trans-fatty acid (elaidic acid)

Cis-fatty acids
Two covalent single C-C bonds
angle in the same direction
adjacent to the C=C double bond

O
(b) A cis-fatty acid (oleic acid)

Figure 2.20

OH

2-33

Lipids
Phospholipidssimilar
to neutral fats except one
fatty acid is replaced by a
phosphate group

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CH3
CH3 N+ CH3
CH2
CH2
O

Nitrogencontaining
group
(choline)

Hydrophilic region (head)

Phosphate
group

Structural foundation
of cell membrane

CH CH2

CH3

Glycerol

(CH2)5 (CH2)12
CH

Amphipathic
Fatty acid tails are
hydrophobic
Phosphate head is
hydrophilic

CH2

Fatty acid
tails

CH
Hydrophobic region (tails)

(CH2)5
CH3
(a)

(b)

Figure 2.21a,b
2-34

Lipids
Eicosanoids
Hormone-like chemical signals between cells
Includes prostaglandins
Role in inflammation, blood clotting, hormone action, labor
contractions, blood vessel diameter

Figure 2.22

2-35

Lipids
Steroida lipid with 17 carbon atoms in four rings
Cholesterolthe parent steroid from which the
other steroids are synthesized
Important for nervous system function and structural
integrity of all cell membranes
15% of our cholesterol comes from diet
85% is internally synthesized (mostly in liver)

Other steroids: cortisol, progesterone, estrogens,

testosterone, and bile acids

2-36

Cholesterol

Figure 2.23

2-37

Good and Bad Cholesterol

Refers to droplets of lipoprotein in the blood
Complexes of cholesterol, fat, phospholipid, and protein

HDL (high-density lipoprotein): good cholesterol

Lower ratio of lipid to protein
May help to prevent cardiovascular disease

LDL (low-density lipoprotein): bad cholesterol

High ratio of lipid to protein
Contributes to cardiovascular disease
2-38

Lipids and Functions

2-39

Proteins
Proteina polymer of amino acids
Amino acidcentral carbon with three attachments
Amino group (NH2), carboxyl group (COOH), and radical
group (R group)

20 amino acids used to make the proteins are

identical except for the radical (R) group
Properties of amino acid determined by R group

Peptideany molecule composed of two or more

amino acids joined by peptide bonds
2-40

Proteins
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Some nonpolar amino acids

Some polar amino acids

Methionine
H

Cysteine
H

CH2

CH2

CH3

OH

Tyrosine
H

(a)

OH

H
N

CH2

OH

C
O

Amino acids
differ only in
the R group

Arginine

N
H

SH

C
O

CH2

NH2+
(CH2)3

C
NH2

C
OH

NH

OH

Figure 2.24a
2-41

Protein Structure
Conformationunique, three-dimensional shape of
protein crucial to function
Proteins can reversibly change conformation and thus
function
Important examples seen in muscle contraction, enzyme catalysis,
membrane channel opening

Denaturation
Extreme conformational change that destroys function
Extreme heat or pH
Example: when you cook an egg
2-42

Protein Structure
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Amino acids
Primary structure
Peptide
bonds

Alpha
helix

N
O
H
C

Beta
sheet

H
N

N
H

O
C

Folding and coiling

due to interactions
among R groups
and between R
groups and
surrounding water

O
C

C= O

HN

C
O= C
NH

Tertiary structure

Sequence of amino
acids joined by
peptide bonds

H
N

C=O

NH

O=C
C
HN

C=O
HN
C
C
NH
O=C
O=C
NH
C
C
C=O HN
HN
C=O
C
C

Chain 1

Secondary structure
Alpha helix or beta
sheet formed by
hydrogen bonding

Beta chain

Alpha
chain

Heme
groups

Chain 2

Alpha
chain

Beta
chain

Quaternary structure
Association of two
or more polypeptide
chains with each
other

Figure 2.25
2-43

Protein Structure
Conjugated proteins contain a nonamino acid moiety
called a prosthetic group
Hemoglobin contains four complex iron-containing rings
called a heme moiety
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Beta chain

Alpha
chain

Association of two or
more polypeptide chains
with each other

Heme
groups
Alpha
chain

Quaternary structure

Beta
chain

Figure 2.25 (4)

2-44

Protein Functions
Structure
Communication
Membrane transport
Catalysis
Recognition and protection
Movement
Cell adhesion

2-45

Enzymes and Metabolism

Enzymesproteins that function as biological
catalysts
Substratesubstance enzyme acts upon
Enzymes lower activation energy

2-46

Enzymes and Metabolism

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Free energy content

Activation
energy

Activation
energy

Net
energy
released
by
reaction

Energy level
of reactants

Net
energy
released
by
reaction

Energy level
of products
Time
(a) Reaction occurring without a catalyst

Time
(b) Reaction occurring with a catalyst

Figure 2.27a, b

2-47

Enzyme Structure and Action

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Sucrose (substrate)

Enzyme action example

of sucrose hydrolysis
Sucrose approaches
sucrases active site
Molecules bind together
forming enzyme
substrate complex
Sucrase breaks bonds
between sugar subunits
and adds H+ and OH Enzyme unchanged and
can repeat process

1 Enzyme and
substrate

O
Active site

Sucrase (enzyme)

2 Enzymesubstrate
complex
O

Figure 2.28
Glucose

Fructose

3 Enzyme
and reaction
products

2-48

Enzyme Structure and Action

Reusability of enzymes
Enzymes are not consumed by the reactions

Astonishing speed
One enzyme molecule can consume millions of substrate
molecules per minute

Temperature, pH and other factors can change

enzyme shape and function
Can alter ability of enzyme to bind to substrate
Enzymes vary in optimum pH
Salivary amylase works best at pH 7.0
Pepsin in stomach works best at pH 2.0

Temperature optimum for human enzymesnear body

temperature (37C)
2-49

Cofactors
Cofactors
About two-thirds of human enzymes require a
nonprotein cofactor
Some bind to enzyme and induce a change in its
shape, which activates the active site
Essential to function
Inorganic cofactors
Divalent cations

Coenzymesorganic cofactors derived from watersoluble vitamins (niacin, riboflavin)

Accept electrons from an enzyme in one metabolic pathway
and transfer them to an enzyme in another
For example, NAD+
2-50

Nucleic Acids
Three components of nucleotides
Nitrogenous base (single or double carbon
nitrogen ring)
Sugar (monosaccharide)
One or more phosphate groups

ATPbest-known nucleotide
Adenine (nitrogenous base)
Ribose (sugar)
Phosphate groups (3)
2-51

Adenosine Triphosphate
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Adenine
NH2

Adenine
NH2

C
N

CH

Figure 2.30a, b

HC

CH
HC

Adenosine

Ribose

Ribose

Triphosphate

P O

P O

Monophosphate

CH2

HO
H H
OH

(a) Adenosine triphosphate (ATP)

O
P

CH2
O

H H
OH

H H
O

H H
OH

(b) Cyclic adenosine monophosphate (cAMP)

ATP contains adenine, ribose, and three phosphate groups

2-52

Adenosine Triphosphate
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Glucose + 6 O2

ATP is bodys most important

energy-transfer molecule

6 CO2 + 6 H2O

which releases
energy
which is used for

Stores energy in covalent bonds

Second and third phosphate groups
have high energy bonds (~)
Most energy transfers to and from
ATP involve adding or removing the
third phosphate

are converted to

Releases it within seconds for

physiological work

ADP + Pi

ATP
which is then available for

Figure 2.31

Muscle contraction
Ciliary beating
Active transport
Synthesis reactions
etc.

2-53

ATP Production

Stages of
glucose
oxidation
and ATP
synthesis

Glycolysis: splitting
glucose into two
pyruvates
If ATP demand
outpaces oxygen
supply pyruvic acid
anaerobically
ferments to lactic
acid.
If enough oxygen
present aerobic
respiration occurs in
mitochondria

Figure 2.32
2-54

Other Nucleotides
Guanosine triphosphate (GTP)
Another nucleotide involved in energy transfer

Cyclic adenosine monophosphate (cAMP)

Formed by removal of second and third phosphate
groups from ATP
Formation triggered by hormone binding to cell surface
cAMP becomes second messenger within cell

2-55

Nucleic Acids
Polymers of nucleotides
DNA (deoxyribonucleic acid)
Contains millions of nucleotides
Constitutes genes
Instructions for synthesizing proteins

RNA (ribonucleic acid)three types

Messenger RNA, ribosomal RNA, transfer RNA

70 to 10,000 nucleotides long
Carries out genetic instruction for synthesizing proteins
Assembles amino acids in right order to produce proteins
2-56