PowerLecture:
Chapter 2
Molecules of Life
Learning Objectives
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Understand how protons, electrons, and
neutrons are arranged into atoms and ions.
Explain how the distribution of electrons in
an atom or ion determines the number and
kinds of chemical bonds that can be formed.
Know the various types of chemical bonds,
the circumstances under which each forms,
and the relative strengths of each type.
Learning Objectives (cont’d)
 Understand
the essential chemistry of water
and of some common substances dissolved
in it.
 Understand how small organic molecules can
be assembled into large macromolecules by
condensation. Understand how large
macromolecules can be broken apart into
their basic subunits by hydrolysis.
Learning Objectives (cont’d)
 Memorize
the functional groups presented
and know the properties they confer when
attached to other molecules.
 Know the general structure of a
monosaccharide with six carbon atoms,
glycerol, a fatty acid, an amino acid, and a
nucleotide.
 Know the macromolecules into which these
essential building blocks can be assembled
by condensation.
Learning Objectives (cont’d)
 Know
where these carbon compounds tend
to be located in cells or organelles and the
activities in which they participate.
Impacts/Issues
It’s Elemental
It’s Elemental
Life depends on chemical reactions.
An element is a fundamental form of matter
that has mass and takes up space.
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Organisms consist mostly of carbon, oxygen,
hydrogen, and nitrogen.
Trace elements are needed only in small
quantities.
Elements in the Human Body
vs. Earth’s Crust
Human Body
Oxygen
Carbon
Hydrogen
Nitrogen
Calcium
Phosphorus
Potassium
Sulfur
Sodium
Chlorine
Magnesium
Iron
65%
18
10
3
2
1.1
0.35
0.25
0.15
0.15
0.05
0.004
Earth’s Crust
Oxygen
Silicon
Aluminum
Iron
Calcium
Sodium
Potassium
Magnesium
46.6%
27.7
8.1
5.0
3.6
2.8
2.1
1.5
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 Many
communities add fluoride to drinking
water supplies. Do you want it in yours?


a. Yes, screening lets people make informed
reproductive decisions about the risk to their
children.
b. No, therapies and medications
for CF continue to improve; a
person with CF can live a full life.
Section 1
Atoms, the Starting Point
Atoms, the Starting Point
Atoms are composed of smaller particles.
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An atom is the smallest unit of matter that is
unique to a particular element.
Atoms are composed of three particles:
•
•
•
Protons (p+) are part of the atomic nucleus and have
a positive charge. Their quantity is called the atomic
number (unique for each element).
Electrons (e-) have a negative charge. Their
quantity is equal to that of the protons. They move
around the nucleus.
Neutrons are also a part of the nucleus; they are
neutral. Protons plus neutrons = atomic mass
number.
Fig. 2.1, p. 16
Atoms, the Starting Point

Electron activity is the basis for organization of
materials and the flow of energy in living things.
Isotopes are varying forms of atoms.
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
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Atoms with the same number of protons (e.g.,
carbon has six) but a different number of
neutrons (carbon can have six, seven, or eight)
are called isotopes (12C, 13C, 14C).
Some radioactive isotopes are unstable and
tend to decay into more stable atoms.
•
•
They can be used to date rocks and fossils.
Some can be used as tracers to follow the path of an
atom in a series of reactions or to diagnose disease.
Section 2
Medical Uses for
Radioisotopes
Medical Uses for Radioisotopes
Radioisotopes have many important uses in
medicine.
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Tracers are substances containing
radioisotopes that can be injected into patients
to study tissues or tissue function.
Radiation therapy uses the radiation from
isotopes to destroy or impair the activity of cells
that do not work properly, such as cancer cells.
For safety, clinicians usually use isotopes
with short half-lives (the time it takes the
isotope to decay to a more stable isotope).
Example of Radioactive Iodine
Figure 2.2
Section 3
What Is a Chemical
Bond?
What Is a Chemical Bond?
Interacting atoms: Electrons rule!
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In chemical reactions, an atom can share
electrons with another atom, accept extra
electrons, or donate electrons.
Electrons are attracted to protons, but are
repelled by other electrons.
Orbitals can be thought of as occupying shells
around the nucleus, representing different
energy levels.
Electron Arrangements
Figure 2.4
What Is a Chemical Bond?
Chemical bonds join atoms.
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
A chemical bond is a union between the
electron structures of atoms.
Having a filled outer shell is the most stable
state for atoms.
•
•
•
The shell closest to the nucleus has one orbital
holding a maximum of two electrons.
The next shell can have four orbitals with two
electrons each for a total of eight electrons.
Atoms with “unfilled” orbitals in their outermost shell
tend to be reactive with other atoms—they want to
“fill” their outer shell with the maximal eight electrons
allowed.
Shell Model
Figure 2.5
What Is a Chemical Bond?
Atoms can combine into molecules.
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Molecules may contain more than one atom of
the same element; N2 for example.
Compounds consist of two or more elements
in strict proportions.
A mixture is an intermingling of molecules in
varying proportions.
Section 4
Important Bonds in
Biological Molecules
Important Bonds in Biological Molecules
An ionic bond joins atoms that have
opposite charges.
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When an atom loses or gains one or more
electrons, it becomes positively or negatively
charged—an ion.
In an ionic bond, (+) and (–) ions are linked by
mutual attraction of opposite charges, for
example, NaCl.
Example of an Ionic Bond
Figure 2.7a
Important Bonds in Biological Molecules
Electrons are shared in a covalent bond.
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A covalent bond holds together two atoms that
share one or more pairs of electrons.
In a nonpolar covalent bond, atoms share
electrons equally; H2 is an example.
In a polar covalent bond, because atoms share
the electron unequally, there is a slight difference in charge (electronegativity) between the
two atoms participating in the bond; water is an
example.
Examples of Covalent Bonds
Figure 2.7b
Important Bonds in Biological Molecules
A hydrogen bond is a weak bond between
polar molecules.
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In a hydrogen bond, a slightly negative atom
of a polar molecule interacts weakly with a
hydrogen atom already taking part in a polar
covalent bond.
These bonds impart structure to liquid water
and stabilize nucleic acids and other large
molecules.
Example of a Hydrogen Bond
Figure 2.7c
Section 5
Antioxidants
Antioxidants
Free radicals are formed by the process of
oxidation.
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Oxidation is the process whereby an atom or
molecule loses one or more electrons.
Oxidation can produce free radicals that may
“steal” electrons from other molecules.
In large numbers, free radicals can damage
other molecules in a cell, such as DNA.
Antioxidants
 Antioxidants
are chemicals that can give up
an electron to a free radical before it does
damage to a DNA molecule.
Figure 2.8
Section 6
Life Depends on Water
Figure 2.9c
Life Depends on Water
Hydrogen bonding makes water liquid.
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Water is a polar molecule
because of a slightly negative
charge at the oxygen end and
a slightly positive charge at
the hydrogen end.
Water molecules can form
hydrogen bonds with each
other.
Figure 2.9a-b
Life Depends on Water

Polar substances are
hydrophilic (water loving);
nonpolar ones are
hydrophobic (water
dreading) and are repelled
by water.
Life Depends on Water
Water can absorb and hold heat.
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

Water tends to stabilize temperature because it
has a high heat capacity—the ability to absorb
considerable heat before its temperature
changes.
This is an important property in evaporative and
freezing processes.
Life Depends on Water
Water is a biological solvent.
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The solvent properties of water
are greatest with respect to
polar molecules because
“spheres of hydration” are
formed around the solute
(dissolved) molecules.
For example, the Na+ of salt
attracts the negative end of water molecules,
while the Cl- attracts the positive end.
Figure 2.10
Section 7
Acids, Bases, and
Buffers: Body Fluids
in Flux
Acids, Bases, and Buffers
The pH scale indicates the concentration of
hydrogen ions.
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
pH is a measure of the H+ concentration in a
solution; the greater the H+ the lower the value
on the pH scale.
The scale extends from 0 (acidic) to 7 (neutral)
to 14 (basic).
The pH Scale
Figure 2.11
Acids, Bases, and Buffers
Acids give up H+ and bases accept H+.
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A substance that releases hydrogen ions (H+) in
solution is an acid—for example, HCl.
Substances that release ions such as (OH-) that
can combine with hydrogen ions are called
bases (example: baking soda).
High concentrations of
strong acids or bases
can disrupt living
systems both internal
and external to the body.
Figure 2.12
Acids, Bases, and Buffers
Buffers protect against shifts in pH.
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
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Buffer molecules combine with, or release, H+
to prevent drastic changes in pH.
Bicarbonate is one of the body’s major buffers.
Acids, Bases, and Buffers
A salt releases other kinds of ions.
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

A salt is an ionic compound formed when an
acid reacts with a base; example: HCl + NaOH
 NaCl + H2O.
Many salts dissolve into ions that have key
functions in the body; for example, Na, K, and
Ca in nerve and muscles.
Section 8
Molecules of Life
Molecules of Life
Biological molecules contain carbon.
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Only living cells synthesize the molecules
characteristic of life—carbohydrates, lipids,
proteins, and nucleic acids.
These molecules are organic compounds,
meaning they consist of atoms of carbon and
one or more other elements, held together by
covalent bonds.
Molecules of Life
Carbon’s key feature: versatile bonding.
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Living organisms are mostly oxygen, hydrogen,
and carbon.
Much of the hydrogen and oxygen are linked as
water.
Carbon can form four covalent bonds with other
atoms to form organic molecules of several
configurations.
Molecules of Life
Functional groups affect the chemical
behavior of organic compounds.
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

By definition a hydrocarbon has only hydrogen
atoms attached to a carbon backbone.
Functional groups—atoms or groups of atoms
covalently bonded to a carbon backbone—
convey distinct properties, such as solubility, to
the complete molecule.
Examples of
Functional Groups
Figure 2.13
Molecules of Life
Cells have chemical tools to assemble and
break apart biological molecules.



Enzymes speed up specific metabolic
reactions.
In condensation reactions, one molecule is
stripped of its H+; another is stripped of its OH-.
•
•
The two molecule fragments join to form a new
compound; the H+ and OH- form water (dehydration
synthesis).
Cells use series of condensation reactions to build
polymers out of smaller monomers.
Examples of Condensation Reactions
Figure 2.14a
Molecules of Life

In hydrolysis reactions, the reverse happens:
one molecule is split by the addition of H+ and
OH- (from water) to yield the individual
components.
Figure 2.14b
Section 9
Carbohydrates: Plentiful
and Varied
Carbohydrates: Plentiful and Varied
A carbohydrate can be a simple sugar or a
larger molecule composed of sugar units.
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

Carbohydrates are the most abundant
biological molecules.
Carbohydrates serve as energy sources or
have structural roles.
Carbohydrates: Plentiful and Varied
Simple sugars—the simplest carbohydrates.
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A monosaccharide—one sugar unit—is the
simplest carbohydrate.
Sugars are soluble in water and may be sweettasting.
Ribose and deoxyribose (five-carbon
backbones) are building blocks for nucleic
acids.
Glucose (six-carbon backbone) is a primary
energy source and precursor of many organic
molecules.
Carbohydrates: Plentiful and Varied
Oligosaccharides are short chains of sugar
units.
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An oligosaccharide is a short chain resulting
from the covalent bonding of two or three
monosaccharides.
Lactose (milk sugar) is glucose plus galactose;
sucrose (table sugar) is glucose plus fructose.
Oligosaccharides are used to modify protein
structure and have a role in the body’s defense
against disease.
Formation of a
Sucrose
Molecule
Figure 2.15
Carbohydrates: Plentiful and Varied
Polysaccharides are sugar chains that store
energy.
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A polysaccharide consists of many sugar units
(same or different) covalently linked.
Glycogen is a storage form of glucose found in
animal tissues.
Starch (energy storage in plants) and cellulose
(structure of plant cell walls) are made of
glucose units but in different bonding
arrangements.
Examples of Polysaccharides
Figure 2.16
Section 10
Lipids: Fats and Their
Chemical Kin
Lipids: Fats and Their Chemical Kin
Lipids are composed mostly of nonpolar
hydrocarbon and are hydrophobic.
Fats are energy-storing lipids.
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Fats are lipids that have one, two, or three fatty
acids attached to glycerol.
A fatty acid is a long, unbranched hydrocarbon
with a carboxyl group (—COOH) at one end.
•
Saturated fatty acids have only single C—C bonds
in their tails, are solids at room temperature, and are
derived from animal sources.
Lipids: Fats and Their Chemical Kin
•
Unsaturated fatty acids have one or more double
bonds between the carbons that form “kinks” in the
tails; they tend to come from plants and are liquid at
room temperature.
Figure 2.17
Lipids: Fats and Their Chemical Kin

Triglycerides have three fatty acids attached to
one glycerol.
•
•

They are the body’s most abundant lipids.
On a per-weight basis, these molecules yield twice
as much energy as carbohydrates.
Trans fatty acids are partially saturated
(hydrogenated) lipids implicated in some types
of heart disease.
Formation of a Triglyceride
Figure 2.18
Lipids: Fats and Their Chemical Kin
Phospholipids are key building blocks of cell
membranes.
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
A phospholipid has a
glycerol backbone, two
fatty acids, a phosphate
group, and a small
hydrophilic group.
They are important
components of cell
membranes.
Figure 2.19a-c
Lipids: Fats and Their Chemical Kin
Sterols are building blocks of cholesterol
and steroids.
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Steroids have a backbone of four carbon rings,
but no fatty acids.
Cholesterol is an
essential component
of cell membranes in
animals and can be
modified to form sex
hormones.
Figure 2.19d-e
Section 11
Proteins: Biological
Molecules with
Many Roles
Proteins

Because they are the most diverse of the
large biological molecules, proteins function
as enzymes, in cell movements, as storage
and transport agents, as hormones, as
antidisease agents, and as structural
material throughout the body.
Figure 2.20
Proteins
Proteins are built from amino acids.
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
Amino acids are small organic molecules with
an amino group, an acid group, a hydrogen
atom, and one of 20 varying “R” groups.
They form large polymers called proteins.
Figures 2.20 and 2.21
Proteins
The sequence of amino acids is a protein’s
primary structure.
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Primary structure is defined as the chain
(polypeptide) of amino acids.
The amino acids are linked together in a
definite sequence by peptide bonds between an
amino group of one and an acid group of
another.
The final shape and function of any given
protein is determined by its primary structure.
Formation of
Peptide Bonds
in Proteins
Figure 2.22
Section 12
A Protein’s Function
Depends on Its Shape
A Protein’s Function
Depends on Its Shape

Primary structure determines the shape and
function of proteins by positioning different
amino acids so that hydrogen bonds can
form between them and by putting R groups
in positions that force them to interact.
Figure 2.23a
A Protein’s Function
Depends on Its Shape
Many proteins fold two or three times.
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
Secondary structure is the helical coil or
sheetlike array that will result from hydrogen
bonding of side groups on the amino acid
chains.
Tertiary structure is caused by interactions
among R groups, resulting in a complex threedimensional shape.
Figure 2.23b-c
one
peptide
group
a
primary
structure
b
secondary
structure
coil, helix
sheet
c
tertiary
structure
Stepped Art
coiled coils
Fig. 2.23, p. 34
A Protein’s Function
Depends on Its Shape
Proteins can have more than one
polypeptide chain.
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
Hemoglobin, the oxygen-carrying protein in the
blood, is an example of a protein with
quaternary structure—the complexing of two
or more polypeptide chains to form globular or
fibrous proteins.
Hemoglobin has four polypeptide chains
(globins), each coiled and folded with a heme
group at the center.
Figure 2.24
A Protein’s Function
Depends on Its Shape
Glycoproteins have sugars attached;
lipoproteins have lipids.
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
Certain proteins combine with triglycerides,
cholesterol, and phospholipids to form
lipoproteins for transport in the body.
Glycoproteins form when oligosaccharides are
added to proteins.
A Protein’s Function
Depends on Its Shape
Disrupting a protein’s shape denatures it.
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

High temperatures or chemicals can cause the
three-dimensional shape to be disrupted.
Normal functioning is lost upon denaturation,
which is often irreversible.
Figure 2.25
Section 13
Nucleotides and
Nucleic Acids
Nucleotides and Nucleic Acids
Nucleotides: energy carriers and other
roles.
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
Each nucleotide has a five-carbon sugar
(ribose or deoxyribose), a nitrogen-containing
base, and a phosphate group.
ATP molecules link cellular reactions that
transfer energy.
Other nucleotides include the coenzymes,
which accept and transfer hydrogen atoms and
electrons during cellular reactions, and
chemical messengers
Figure 2.26
Nucleotides and Nucleic Acids
Nucleic acids include DNA and RNA.
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
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
In nucleic acids, nucleotides are bonded
together to form large single- or doublestranded molecules.
DNA (deoxyribonucleic acid) is doublestranded; genetic messages are encoded in its
base sequences.
RNA (ribonucleic acid) is single-stranded; it
functions in the assembly of proteins.
Figure 2.27
Section 14
Food Production and a
Chemical Arms Race
Food Production and
a Chemical Arms Race
Nearly half of the food grown each year
around the world is lost to disease or
insects.
Natural plant defenses have been
augmented by the development of synthetic
toxins designed to kill pests and increase
crop yields.

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Herbicides kill unwanted plants (weeds).
Insecticides kill insects.
Fungicides kill or inhibit the growth of harmful
mold or fungi.
Food Production and
a Chemical Arms Race

Synthetic chemicals are not without
dangers; some kill “good” insects and plants
while others harm humans through
exposure.