22.
Chemistry of Living Things
It has been said that if biology is the study of live
things, then physical science is the study of dead things.
There was a time when a great chasm in our under-
standing separated living things from nonliving, but
bridges across that gulf have begun to appear in recent
decades. We now know that the atoms of living things
are indistinguishable from the atoms of nonliving
things. They obey the same laws and principles. In the
last several decades science has made great progress in
understanding the physical basis for life. We have
begun to understand how living cells keep blueprints for
the production of identical new cells, and we have also
begun to understand how these blueprints are read and
translated into reality. It is clear that the understanding
of the genetic code and the chemical basis of life will
significantly affect a variety of human endeavors. It is
also clear that this understanding will allow manipula-
tion of the genetic code in ways that will raise profound
ethical and moral questions.
This chapter lays a foundation for the chapter that
follows. In doing so, it introduces much new terminol-
ogy. The chapter also includes a large number of dia-
grams of molecules, some of which are quite compli-
cated. At this point, do not try to memorize the diagrams
or the names of the more complex molecules. Instead,
try to form a conceptual picture of an answer to the
question: How does life work?
Table 22.1. The chemical makeup of a human and alfalfa contrasted (in percent of dry weight).
Encyclopedia Britannica.)
Element Adult Human
C 48.43
O 23.70
N 12.85
H 6.60
Ca 3.45
S 1.60
P 1.58
Na 0.65
K 0.55
Cl 0.45
Mg 0.10
TOTAL 99.96
201
The chemistry of life is intimately connected with
the carbon atom and its ability to hold together the large,
complicated molecules of living things. But this chap-
ter will show how these complicated molecules are built
up from rather simple pieces. The shapes of the pieces
(which govern how they fit together) are determined by
the shapes of the orbitals of the valence electrons of the
atoms. In turn, the shapes of the orbitals spring from the
basic wave-particle duality of matter. Life is thus
grounded in the most fundamental physical laws of the
universe. This, then, is this chapter’s basic message.
Carbon Chains
To most people it comes as a startling realization
that living things are remarkably alike in their chemical
composition. Things as different as a human and an
alfalfa plant are made of basically the same elements
and in essentially the same proportions. Table 22.1 con-
trasts the chemical makeup of a human and an alfalfa
plant.
The number of valence electrons of carbon (which
can be read from its column in the Periodic Table) is
four. To fill its outermost shell, carbon requires an addi-
tional four electrons, which it can easily obtain by enter-
ing covalent bonds with hydrogen. The resulting com-
(From the
Alfalfa
45.37
41.04
3.30
5.54
2.31
0.44
0.28
0.16
0.91
0.28
0.33
99.96
pound is methane and has the chemical formula CH4.
Although the chemical formula tells us something about
the compound, the structural formula
gives us the additional information about which atom is
bonded to which. Methane is the simplest of hydro-
carbons, the class of chemical compounds made up of
hydrogen and carbon. Molecules containing carbon are
the building blocks of life and are called organic mole-
cules.
However, the structural formula of methane still
does not communicate an important piece of informa-
tion about the molecule. The valence electrons of car-
bon can be found in orbitals which protrude from the
carbon atom as shown in Figure 22.1. Hydrogen atoms
bond to carbon through these orbitals. The resulting
molecule has the shape of a regular tetrahedron (a pyra-
mid with triangular base and equilateral sides).
a single covalent bond. If the tetrahedral methane mol-
ecules are thought of as single links from which chains
can be built, then ethane is a two-link chain. Similarly,
propane, butane, pentane, hexane, heptane, and octane
are, respectively, three-, four-, five-, six-, seven-, and
eight-carbon chains. The C-C bond is particularly strong
and lends stability to the “backbone” of the molecule.
The need for structural formulas becomes evident
when we examine butane C4H10. Figure 22.2 shows two
forms of butane that have the same formula, C4H10, but
differ in chemical and physical properties because of
their distinct molecular structures. Structures that share
the same chemical formula are called isomers. Even
then the structural formulas do not show the complicat-
ed three-dimensional structure of these molecules.

Figure 22.2. Isomers of C4H10. Upper: normal butane.

H C Lower: isobutane.

Sometimes the carbon atoms in a chain share four

H electrons rather than the two as they do in an ordinary
H single bond. An example is ethene (usually called eth-
ylene):
Figure 22.1. Protruding orbitals of carbon and the
resulting tetrahedral shape of the methane molecule.

Another saturated hydrocarbon is the molecule

ethane, C2H6. Its structural formula is

As before, the prefix eth is chemist’s shorthand for two

carbon atoms, and ene is shorthand for the double bond
between carbon atoms.
In longer chains, double bonds may occur instead
The prefix eth is a chemist’s shorthand to indicate that
of some single bonds. These double bonds are sensitive
there are two carbon atoms rather than one (meth). The
to “attack” by some chemicals. Consider the reaction of
molecule has been formed from two methane building
ethene with an initiator molecule RO• having an
blocks. A hydrogen atom has been removed from each,
unpaired electron (Fig. 22.3). The RO• reacts with an
and the two carbon atoms bond directly to each other in

202
Figure 22.3. Polymerization of ethene in a chain reaction. The dot represents an unpaired electron that is eager to pair
with another electron to form a normal, two-electron bond.
ethene molecule and converts the double bond to a sin-
gle bond, but the unpaired electron is now on a carbon
atom. This carbon atom now plays the role of initiator
in a reaction with a second ethene molecule. Another
pair of carbon atoms has been added to the chain, but
this has not solved the problem of the unpaired electron
so the process occurs again and again, forming what is
called a polymer. Chains containing millions of carbon
atoms can be formed this way. The chains become tan-
gled as they form and result in flexible solids. In this
case, the polymer is the substance called polyethylene.
Carbon clearly is the “chain maker.” However, a
molecule that historically did not seem to fit this pattern
of chains was C6H6, perhaps because it had so few
hydrogens for its number of carbons. The German
chemist Friederich August Kekule von Stradonitz
(1829-1896) had a dream one evening in which he saw
snakes. One of the snakes caught his attention because
it reached around to grab its own tail. Awaking from his
dream, Kekule realized that benzene (C6H6) might do
the same thing. The resulting “benzene ring” is an
important chemical structure:
Functional Groups
With a carbon chain or ring as a sturdy “backbone,”
we can begin to build some of the molecules important
203
to life. Many of these are formed by substituting vari-
ous functional groups in place of hydrogen on a carbon
chain or ring. A functional group is a group of atoms
bonded together which exists in a molecule as a subunit.
The presence of the group defines a class of molecules
sharing common chemical behavior. Four functional
groups (hydroxyl, carbonyl, carboxyl, and amino) are of
interest here.
The hydroxyl group
is the functional group associated with alcohols (Fig.
22.4). The prefixes meth and eth carry the same mean-
ing as before, and the presence of the O-H group makes
the molecule an alcohol (indicated by the ol in
methanol). At one time methanol was prepared by heat-
ing wood in the absence of air. The complicated mole-
cules in the wood would break down into smaller units,
one of which was methanol, sometimes for this reason
called “wood alcohol.” Ethanol, on the other hand, is
commonly produced by microscopic living cells from
sugar (fermentation) and is the intoxicating compound
in alcoholic beverages.
Figure 22.4. Upper: methanol or methyl alcohol.
Lower: ethanol or ethyl alcohol.
 The structure of water, H-O-H, can be viewed as an
H atom attached to an OH group. If a carbon chain or
ring contains an H and an OH on nearly every C, the
compound is a carbohydrate (which means literally car-
bon-water). Carbohydrates usually (but not always)
have the formula Cn(H2O)n, or CnH2nOn.
The carbonyl group
six-carbon sugars and the ring forms of two five-carbon
sugars, ribose and deoxyribose. The prefix deoxy draws
attention to the absence of an oxygen atom as compared
to ribose.
Sugars that have a single ring are called “monosac-
charides.” Monosaccharides can chain together by
eliminating a water molecule:
C O H H O C

In such a case, sugars are said to condense. For exam-

is a functional group associated with the simplest car-
bohydrates, sugars, which taste sweet. The sugar mol-
ecule is a carbohydrate chain with a carbonyl group near
the end. In some instances the molecule will double
back on itself and the double bond of the oxygen in the
carbonyl group will open up and splice the molecule
into a ring. Figure 22.5 shows the linear forms of two
ple, when glucose and fructose condense a two-sugar
chain is formed called sucrose. Sucrose is the sugar of
cane or beets. Organisms often store energy in such
condensed sugars. However, the human body cannot
use such polysaccharides directly and must break them
back down into monosaccharides. Moreover, glucose is
the only sugar that the body uses directly as a source of

Figure 22.5. Upper left: glucose (C6H12O6). Upper right: fructose (C6H12O6). Lower left: ribose (C5H10O5). Lower
right: deoxyribose (C5H10O4). In the lower drawings, the oxygen in the carbonyl group (the oxygen in the rear center)
forms a bridge to create a ring structure. Which pair of molecules are isomers?

204
energy. The process is in reality a complex series of considerably longer.
chemical reactions that can be summarized A base is a molecule which has an affinity for a
hydrogen ion, especially when dissolved in water. A
base is somewhat the opposite of an acid: an acid mole-
C6H12O6 ! 6O2 → 6CO2 ! 6H2O ! energy.
cule easily loses a hydrogen ion; a base accepts a hydro-
gen ion. Organic bases contain nitrogen, and they are
The carboxyl group
viewed as being related to ammonia, NH3. The ammo-
nia molecule NH3 has four pairs of electrons in orbitals
that point to the corners of a tetrahedron, like CH4 (Fig.
contains both a carbonyl group and a hydroxyl group. 22.7). However, NH3 has one pair of electrons that is
The carboxyl group was named by combining carbonyl not shared with an H; it is called a lone pair. The lone
with hydroxyl. pair enables NH3 to accept an H+ and form NH4+, the
Compounds that easily lose a hydrogen ion (espe- ammonium ion.
cially when dissolved in water) are called acids. The
easier it loses the hydrogen ion, the stronger the acid.
The hydrogen on the carboxyl group can be lost, but H! ! :NH3! → H:NH3! or NH4!
with some difficulty, so any molecule containing this
group is a weak acid. Molecules that contain the car-
boxyl group are classed as carboxylic acids.
Two common carboxylic acids (Fig. 22.6) are
methanoic acid (also called formic acid) and ethanoic
acid (also called acetic acid). Formic acid is the sting-
ing substance of nettles and red ants, whereas acetic
acid gives the sour taste to vinegar. The word acid, in
fact, means sour, and sour taste is a distinguishing char- H N
acteristic of acids.

H
H
Figure 22.7. The tripod structure of ammonia NH3.
Note the lone pair of electrons.

Ammonia is a base (it accepts a hydrogen ion)

because it has a lone electron pair. If one, two, or even
all three hydrogens of NH3 are replaced by carbon
atoms, the molecule still has a lone pair and is still a
base. Three simple examples are shown in Figure 22.8,
and five complex examples are shown in Figure 22.9.

Figure 22.6. Upper: methanoic or formic acid. Lower:

ethanoic or acetic acid.

As the molecular chains grow longer and more

complex, the carboxylic acids are known as fatty acids.
Such molecules are the components of the fatty and oily
tissues found in plants and animals. Butyric acid, a
component of rancid butter, is a relatively short chain,
whereas cerotic acid C25H51COOH (found in beeswax) is

H H H O

H C C C C O H
Figure 22.8. Three simple bases. Upper: methylamine.
Middle: dimethlyamine. Lower: trimethylamine.
H H H

205
Figure 22.9. Five complex bases. Upper left: guanine (G). Upper middle: cytosine (C). Lower left: adenine (A).
Lower middle: thymine (T). Lower right: uracil (U).

The symbol [R] stands for a variety of possible groups

The NH2 group shown above in methylamine (Fig. of atoms. Examples of the amino acids are glycine and
22.8) is the amino group. alanine (Fig. 22.10).

H
N
H

Of special importance to living things are the amino

acids, molecules that contain both an amino group and
a carboxyl group attached to the same carbon atom.

H O
H
N C C O H
H
R
Figure 22.10. Upper: glycine. Lower: alanine.

206
 Figure 22.11. Joining of amino acids. What molecule is produced besides the linked amino acids?
The two end groups of amino acids have an impor-
tant characteristic property—they can easily join (Fig.
22.11). The resulting molecule has been linked togeth-
er by eliminating a water molecule between two amino
acids. But the most important observation is that the
chains can grow longer because the same functional
groups for forming additional linkages are at each end.
Proteins
Many amino acids are possible, but only 20 are
important to living organisms. Chains of amino acids
(incorporating any or all of the 20) are called proteins.
The chains may have hundreds of amino acid links. The
number of atoms in protein molecules ranges from sev-
eral hundred, as in insulin, to several million, as in the
protein of the tobacco mosaic virus.
The variations in protein molecules are almost end-
less. Yet not all combinations are useful. A one-celled
organism may use “only” 5000 distinct proteins. But
when new proteins are constructed for growth of an
organism, the new molecules must be exactly the right
combination of amino acids, both in number and order
of linkage.
Some protein molecules are long and straight and
intertwine with others to form a fibrous material—ideal
for making skin, hair, and wool, which they do. Others
are all wrapped up like a snarled ball of twine. These
“globular proteins” are designed for mobility. They
form the jellylike substance of cells and perform vari-
ous functions.
207
Insulin is a 51-amino-acid chain (actually two par-
allel chains cross-linked with sulfur atoms) that regu-
lates the human body’s use of sugars and other carbo-
hydrates. Insulin insures that the blood sugar level does
not get too high. (An inadequate supply of insulin leads
to the condition called diabetes.) Glucagon, on the
other hand, is a 29-amino-acid chain that keeps the
blood sugar level from falling too low. Between the
two, the blood sugar is kept in balance.
The insulin molecules of a pig, ox, or sheep are
almost identical—but not quite. In one section there is
a difference of three amino acids for each species. Each
species must produce its own special brand of insulin.
Even among individuals of the same species, the organ-
ism must construct unique proteins for growth. The
proteins that make up skin, for example, differ from
individual to individual, and this “uniqueness” causes
the immune reaction that interferes with skin grafts
from one individual to another.
Enzymes are a specific kind of protein, sometimes
called an “organic catalyst.” A catalyst is a molecule
that plays a part in a chemical reaction but itself remains
unchanged in the process, which seems almost paradox-
ical. Enzymes are often present in an organism to help
assemble molecules needed by the organism. How,
then, can a molecule “know” how to construct another
molecule to meet certain specifications? Here it seems
that the three-dimensional shapes of molecules play an
important role. For example, we have pointed out that
the methane molecule is tetrahedral in shape, the ammo-
nia molecule is a tripod, and the carbon chains have
complicated shapes. Some enzymes seem to have sites
that accommodate molecules of only a certain shape. If
the enzyme has such adjacent sites, it is possible that
“building blocks” will be lined up in just the right way
to hook together in the molecular structure of the
desired new molecule. The molecule thus produced
then slips away and the enzyme is available to produce
yet another identical molecule without the enzyme itself
being consumed (see Fig. 22.12).
Figure 22.12. A simple model of molecular assembly
by enzymes. Upper: An enzyme molecule with two
special sites is surrounded by various kinds of smaller
molecules: spheres, cubes, pyramids. Upper middle: A
sphere and a pyramid settle into the sites on the enzyme
where they fit. There is no appropriate site for cubes, so
these molecules do not settle on the enzyme molecule.
Lower middle: The finished product separates away
from the enzyme molecule. The sites are left open
again. Lower: Another sphere and pyramid settle into
the open sites, and the reaction repeats itself. (After
Nason and Goldstein, 1969)
Figure 22.13. A short piece of a chain of nucleotides.
208
The pieces could, of course, randomly collide and
sometimes hook together without the enzyme.
However, to interact they must be at the same place at
the same time, and the shapes of the molecules must be
properly oriented in the collision if they are to bond
together. The enzyme speeds this process by catching
one piece, fixing it in a particular orientation, and then
allowing the second piece to settle into position in just
the proper orientation for bonding.
Whereas some enzymes can put molecules together,
others can take molecules apart. For example, some
enzymes play an important role in catalyzing digestion
where proteins and carbohydrates must be broken down
into simpler pieces that can be used by an organism either
for growth or for energy. Enzymes also control other
chemical reactions of the cells of an organism. In all,
they are remarkable “machines” with awesome powers.
Nucleic Acids
Organic acids are also found in living cells, but in
small amounts compared to proteins. Nucleic acids are
organic acids found primarily in the nucleus of the cell.
Nucleic acids are chains that are much longer than pro-
tein chains. The “links” in the nucleic acid chain are
called nucleotides.
Each nucleotide is composed of three portions—a
hydrogen phosphate group (from phosphoric acid,
H3PO4), a five-carbon sugar, and a base—joined togeth-
er into a single unit. The sugar of one nucleotide is
joined to the hydrogen phosphate of the next one to
form a sugar-phosphate backbone. The hydrogen phos-
phates are the acidic groups of nucleic acids. The bases
stick out from the sugars like tails (see Fig. 22.13). The
sugars are identical in any given chain, but there are two
possible kinds of chains depending on whether the
sugar is ribose (C5H10O5) or deoxyribose (C5H10O4).
The corresponding nucleic acids are then either ribonu-
cleic acid (RNA) or deoxyribonucleic acid (DNA).
There are only five possible bases used in DNA and
RNA: guanine (G), cytosine (C), adenine (A), thymine
(T), and uracil (U). These are shown in Figure 22.9.
The simpler of the two nucleic acids is RNA, a sin-
gle-strand structure containing the bases G, C, A, and U
(but not T) in a variety of orders. Figure 22.13 is a sim-
ple model of RNA. The DNA molecule contains the
bases G, C, A, and T (but not U), and its structure is
 Figure 22.14. The guanine-cytosine and adenine-thymine base pairs in DNA.
more complicated. In fact, DNA is two chains bonded
together at each step by the bonds illustrated in Figure
22.14 and shown schematically in Figure 22.15.
Guanine and cytosine are so shaped (and the shape must
be exact) that they bond at three points if brought into
proximity. Adenine and thymine bond at two points.
Because of the differences in structure, it is never pos-
sible for adenine or thymine to bond to guanine or cyto-
sine, nor is it possible for identical bases to bond to one
another. The DNA molecule consists of two parallel
matched chains linked together to form a ladder in
which the rungs are A-T or C-G. The ladder is actually
twisted to form a double helix (Fig. 22.16).
In living cells, DNA molecules may be of enor-
mous lengths. They can contain as many as several
hundred million pairs of nucleotides in a row. When
found in a cell, the spiral is all coiled up in a snarled
ball. Unfolded, the total length of the spiral ladder
209
would be about an eighth of an inch in bacteria cells and
as long as several feet in human cells! Such “macro-
molecules” exist in each of the trillions of cells in the
human body. The DNA molecules in each cell of the
human body contain both the information to direct the
reproduction of that cell and the blueprints of the entire
multicellular organism. In both bacterium and human,
the DNA molecules, together with protein, form struc-
tures called chromosomes. A gene is a subsection of a
chromosome.
Before James Watson and Francis Crick received the
Nobel Prize for discovering the structure of DNA, it was
still an unresolved question whether the hereditary infor-
mation was carried in the protein or in the DNA of the
chromosomes. Watson had just received his Ph.D. and
Crick was still working on his Ph.D. when they began
collaborating on a solution to the puzzle of heredity. It
was a scientific quest of utmost significance and one
 Figure 22.15. A short section of DNA, flattened for clarity.
Figure 22.16. The double helix of DNA.
surely destined to bring a Nobel Prize to the victor. A
number of workers were engaged in painstakingly slow
and methodical studies that surely would have yielded the
answer in the end. But Watson and Crick, novices though
they were, soon found themselves in a race with Linus
Pauling (himself the winner of two Nobel Prizes) to find
a shortcut to the answer. Watson relates the fascinating
story in his book The Double Helix.
Summary
In the beginning of our quest for understanding of
the nature of matter, we investigated the nature of light.
We found that light has a dual wave-particle character
and that electrons have the same duality. To satisfy this
duality in nature, we described the Wave Model of the
atom. The resulting orbitals have peculiar shapes that
210
are reflected in the shapes of molecules, shapes com-
pletely foreign to the “planetary model” of the atom.
Shapes have considerable importance in understanding
how molecules are formed and reproduced.
The molecules of life are based on the chemistry of
carbon. Of particular importance is the carbon-carbon
bond which forms the backbones of organic molecules.
Carbon atoms can form linear chains, rings, and branch-
ing structures. Functional groups may be appended to
the molecules to give a class of characteristics to the
molecules that are somewhat independent of the mole-
cule’s remaining structure. The hydroxyl and carbonyl
groups are important components in carbohydrates, the
carboxyl group is important in fats, and the amino group
is important in proteins.
Acids are molecules which are hydrogen ion donors.
Bases are molecules which are hydrogen ion acceptors.
The carboxyl group loses a hydrogen ion and is an acid.
On the other hand, the ammonia molecule has a lone pair
of electrons, readily accepts a hydrogen ion, and is a base.
Guanine, cytosine, adenine, thymine, and uracil are bases
which play an important role in the chapter to follow.
Proteins are chains of amino acids. Much of the tis-
sue of living organisms is protein. Enzymes are a spe-
cific kind of protein that catalyze certain chemical reac-
tions. Some enzymes construct molecules from simpler
substructures; other enzymes take molecules apart and
reduce them to simpler structures.
Nucleotides are molecular complexes which con-
sist of a phosphate group, a five-carbon sugar and one
of the five organic bases: guanine, cytosine, adenine,
thymine, or uracil. Nucleic acids are chains of
nucleotides. Single strand chains (RNA) incorporate
guanine, cytosine, adenine, or uracil and the sugar,
ribose. Double strand chains (DNA) incorporate gua-
nine, cytosine, adenine, or thymine and the sugar,
deoxyribose. The genetic instructions for building
organisms are encoded in nucleic acids.
Historical Perspectives
Paracelsus (actually Philippus Aureolus
Theophrastus Bombast von Hohenheim, ca. 1493-
1541) was an alchemist whom we have already encoun-
tered in Chapter 18 as one of the founders of chemistry.
Paracelsus held the view that God created the primor-
dial matter with numerous seeds scattered through it.
Within each seed was a vital or spiritual essence or force
that guided the development of living things as they
organized inorganic matter into living creatures.
This idea of a living essence in matter (vitalism)
has always been a strong current in the flow of ideas
about the nature of life. Through most of history it has
been the dominating view. The idea is akin to, or some-
times identical with, the religious idea of “spirit.” For
example, kinetic energy was first known (ca. 1700) as
vis viva, which means “living force.” Brownian motion,
before it became understood as evidence for the exis-
tence of molecules, was taken by some as evidence for
a living force in matter.
With René Descartes (1597-1650) and Isaac
Newton (1642-1727), a new idea began to form. This
idea took the tough-minded view that life could be
understood purely as matter and motion (mecha-
nism)—without a vital force. There developed a
schism from about this time forward between vitalism
and mechanism with the German philosophers (Baron
Gottfried Wilhelm von Leibniz [1646-1716], Johann
Wolfgang von Goethe [1749-1832], and others) gener-
ally taking a vitalist position and the French and English
followers of Newton and Descartes defending the
mechanistic viewpoint. In the vitalist view, the intro-
duction of life introduces a principle to the world, one
which is nonmechanical, nonmaterial (perhaps), and
nonchemical. In the mechanistic view biology merely
becomes an extension of physics and chemistry.
Indeed, even if plants and animals are really
machines, it is difficult to see how they might have
formed from matter and random, purposeless motion.
There is a kind of common sense that says there is more
to life. There is also a strong emotional appeal that may
flow from religious conviction. Moreover, physics and
chemistry do not yet hold the detailed answers to the
almost overwhelming complexity of life. One aspect of
life that is hard for the mechanists to explain is the orga-
nized, purposeful behavior of living things. Even an
amoeba will move toward food and away from injurious
substance. When the mechanists explain the motion of
a falling ball, it is in terms of preexisting causes, not in
terms of a future goal or purpose of the ball. So is there
not a fundamental difference between living and non-
living things?
This chapter and the next take a mechanistic view
211
by limiting the definition of life to growth and repro-
duction. In the absence of the identification of a “vital
force” that can be subjected to controlled experiment
and the scientific method, the vitalistic view remains
outside (or at least on the periphery) of the realm of sci-
ence. The almost inexorable march of science since the
16th century has been toward mechanistic explanations.
The more precise and quantitative science has become,
the more it has become mechanistic. Modern biology is
rapidly marching down the path already taken by
physics and chemistry. Conservation of mass, conser-
vation of energy, the laws of thermodynamics, and the
laws governing atoms and molecules are all seen to be
applicable to understanding life.
But the question remains: Can one account for the
vital, purposeful, organized activities of life by reducing
these activities to the motion of atoms?
STUDY GUIDE
Chapter 22: Chemistry of Living Things
A. FUNDAMENTAL PRINCIPLES
1. The Electromagnetic Interaction: See Chapter 4.
2. The Wave-Particle Duality of Matter and
Electromagnetic Radiation: See Chapters 14 and
16.
B. MODELS, IDEAS, QUESTIONS, OR APPLICA-
TIONS
1. How does the Wave Model of the atom lead to
atoms and molecules with specialized shapes?
2. How are covalent bonds important in forming the
molecules of life?
3. What is the relationship between carbon chains and
the molecules of life?
4. What is a functional group?
5. What important compounds include the hydroxyl
group in their structure?
6. What important compounds include the carbonyl
group in their structure?
7. What important compounds include the carboxyl
group in their structure?
8. What functional groups identify an amino acid?
9. What is a protein and what are its subunits?
10. What is an enzyme and how does it participate in
building or breaking up a molecule?
11. What is a nucleotide?
12. What is “CATGU?”
13. What is nucleic acid and what are its subunits?
C. GLOSSARY
1. Acid: A molecule which releases hydrogen ions
(protons) into water solution.
2. Alcohol: A carbon chain with the hydroxyl group
as a functional group at the end of the chain.
3. Amino Acid: A particular structure characterized
 by a carbon atom serving as a link between an
amino group and a carboxyl group. The carbon
atom completes the requirements of the octet rule
by a single bond to a hydrogen and a single bond to
some other structure.
4. Amino Group: The functional group consisting of
a nitrogen atom single-bonded to each of two
hydrogens and single-bonded to the structure in
which it is a functional group to satisfy the octet
rule.
5. Base: A molecule which accepts (attaches to)
hydrogen ions (protons).
6. Carbohydrate: Literally, “carbon-water.” Carbon
chains that (usually) have the formula Cn(H2O)n.
7. Carbon Chain: A sequence of carbon atoms cova-
lently bonded together in chainlike fashion.
Carbon chains are common structures in the mole-
cules that characterize living things.
8. Carbonyl Group: The functional group in which
a carbon is double-bonded to oxygen, single-bond-
ed to a carbon chain, and single-bonded to some-
thing else, usually to hydrogen, to satisfy the octet
rule.
9. Carboxyl Group: The functional group which is a
combination of the carbonyl and hydroxyl groups
and which gives acid properties to molecules con-
taining it.
10. Deoxyribonucleic Acid (DNA): A double-strand,
helical nucleic acid molecule in which the
nucleotides incorporate deoxyribose instead of
ribose as the sugar. Thymine occurs in DNA but
uracil does not.
11. Deoxyribose: A five-carbon sugar, closely related
to ribose, that plays an important role in the mole-
cules that control growth and reproduction in living
things.
12. Ethane: C2H6. The next simplest hydrocarbon
with two carbons with a single covalent bond to
each other and with single covalent bonds to hydro-
gen to satisfy the octet rule for each carbon.
13. Fatty Acid: Long carbon chains having a carboxyl
group at the end which gives the molecule acid
properties.
14. Functional Group: A group of atoms bonded
together which exists in a molecule as a subunit and
which defines a class of molecules sharing com-
mon chemical behavior.
15. Hydrocarbon: The class of chemical compounds
made up of hydrogen and carbon.
16. Hydroxyl Group: The functional group -O-H.
17. Mechanism: In the context of the explanation of
the origin of life, that school of thought which
endeavors to explain life as a consequence of the
physical laws of matter and motion only.
18. Methane: The simplest hydrocarbon, CH4. The
lone carbon is covalently bonded to each of four
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hydrogens by a single covalent bond.
19. Nucleic Acid: A class of chainlike molecules in
which the links are formed from nucleotides.
20. Nucleotides: A structure formed from three sub-
units: a sugar (ribose or deoxyribose), a phosphate
group, and one of five possible organic bases
(thymine, uracil, guanine, cytosine, or adenine).
21. Protein: A chainlike molecule in which the links
are formed from amino acids. Proteins are the
basic structural materials for living forms.
22. Ribonucleic Acid (RNA): A single-strand, nucle-
ic acid molecule in which the nucleotides incorpo-
rate ribose instead of deoxyribose as the sugar.
Uracil occurs in RNA but not thymine.
23. Ribose: A five-carbon sugar that plays an impor-
tant role in the molecules that control growth and
reproduction in living things.
24. Structural Formula: A diagram of a molecule
which explicitly shows the individual atoms and
the covalent bonds that connect them.
25. Sugar: The class of carbohydrates containing the
carbonyl group as a functional group.
26. Vitalism: In the context of the explanation of the
origin of life, that school of thought which endeav-
ors to explain life as a consequence of a living
essence or “force” in matter that goes beyond the
laws of matter and motion alone.
D. FOCUS QUESTIONS
1. The important molecules of life include fats (fatty
acids), carbohydrates (sugars), and proteins (amino
acids). Use structural formulas to describe and
illustrate how all of these are made up of carbon
chains with appropriate functional groups.
2. Describe what an enzyme is and what it does. Use
the mechanical analogy and diagram of Figure
22.12 to help you explain how it functions.
E. EXERCISES
22.1. The shapes of molecules can be related to
fundamental principles of physical law. Methane, CH4,
is said to have a tetrahedral shape. Just what is it about
a methane molecule that has shape? What fundamental
principle leads to the existence of the shapes of orbitals?
What is an orbital?
22.2. Seemingly different living things are remark-
ably alike in many regards at the molecular level. The
most abundant elements in a cow (in percent of dry
weight) are (in decreasing order) carbon, oxygen, nitro-
gen, hydrogen, and calcium. What is the second most
abundant element in an oak tree?
(a) carbon
(b) oxygen
(c) nitrogen
(d) hydrogen
 (e) calcium While it is not important for our purposes to be able
to make accurate structural drawings of the functional
One declared objective of this chapter is to show groups, it is important to know some of the important
that the complex molecules are made up of simpler general features of the four groups: hydroxyl, carbonyl,
pieces. Although it is not important for our purposes to carboxyl, amino.
be able to make complicated technical drawings, it is
important to know what the building blocks are at each 22.10. Which functional group is associated with
level. The following questions will help to define the acid properties?
degree to which terminology must be mastered. (a) carbonyl group
While it is not important for our purposes to know (b) carboxyl group
the chemical characteristics of things like propane and (c) hydroxyl group
isobutane, it is important to know that hydrocarbon (d) amino group
chains of ever increasing length and complexity can be
built up from simpler structures in a systematic way. 22.11. Which functional group contains nitrogen?
The following questions illustrate these issues. (a) carbonyl group
(b) carboxyl group
22.3. Structural formulas for methane and ethane (c) hydroxyl group
are shown in the text. Draw propane. (d) amino group

22.4. Structural formulas for methanol and ethanol 22.12. All amino acids contain which two simpler
are shown in the text. Draw propanol. structures?
(a) amino group and carbonyl group
22.5. Structural formulas for methanoic acid and (b) amino group and carboxyl group
ethanoic acid are shown in the text. Draw propanoic (c) amino group and hydroxyl group
acid.
While it is not important for our purposes to know
22.6. DNA is composed of which of the following that glucose is a monosaccharide and sucrose isn’t, it is
simpler structure(s)? important to know that sugars can chain together into
(a) nucleotides polysaccharides and that amino acids can chain togeth-
(b) enzymes er into proteins.
(c) catalysts
(d) chlorophyll 22.13. When two sugar molecules chain together
(e) insulin (or two amino acids), what simple molecule is produced
besides the longer chain?
22.7. A nucleotide is composed of which of the fol- (a) carbon dioxide (CO2)
lowing simpler structures? (b) methane (CH4)
(a) phosphate group (c) water (H2O)
(b) ribose or deoxyribose sugar (d) hydrogen sulfide (H2S)
(c) organic bases (e) ammonia (NH3)
(d) all of the above
22.14. When two amino acids chain together,
22.8. Which simpler structure(s) are not to be
which two functional groups are involved at the point of
found in a sugar?
the splice?
(a) hydroxyl group
(a) hydroxyl group
(b) carbon-oxygen covalent bonds
(b) carbonyl group
(c) carbon-hydrogen covalent bonds
(c) carboxyl group
(d) carbon-carbon covalent bonds
(d) amino group
(e) carboxyl group
For our purposes it is not important to know the
22.9. Proteins are composed of which simpler
names or formulas of the amino acids or nucleotide
structures?
bases which are important in living organisms, but it is
(a) chlorophyll
important to understand that the number is very limited
(b) nucleotides
and that the same amino acids and nucleotide bases are
(c) sugars
used by all living systems.
(d) amino acids
(e) nucleic acids

213
 22.15. Approximately how many different kinds of enzyme might catalyze the building of a molecule.
amino acids are important to living organisms? 22.22 Which of the following is false?
(a) 2 (a) Carbohydrates contain hydroxyl groups.
(b) 20 (b) Amino acids chain to form proteins.
(c) 2000 (c) RNA and DNA are proteins.
(d) 2,000,000 (d) Nucleotides chain to form nucleic acids.
(e) More than 2 billion (e) Nucleotides contain organic bases.

22.16. Approximately how many different kinds of 22.23. Which of the following is false?
organic bases are incorporated in DNA? (a) RNA is usually double stranded.
(a) 4 (b) RNA and DNA contain different sugars.
(b) 40 (c) RNA and DNA share three common bases.
(c) 4000 (d) DNA contains equal amounts of bases A and T.
(d) 4,000,000 (e) DNA contains equal amounts of bases C and G.
(e) More than 4 billion

There are five bases used in DNA and RNA. You

do not need to know the technical names, but you
should at least know the letters C, A, T, G, U (remem-
ber “cat goo”), which stand for them, and which bases
bond to which bases in DNA.

22.17. When Watson and Crick (who won the

Nobel Prize for the discovery of the structure of DNA)
were still trying to decipher the structure of DNA, they
became aware of the piece of experimental evidence
(from other workers) that in DNA guanine (G) and cyto-
sine (C) always occur in equal amounts. For some time
they ignored this information because they doubted its
experimental reliability. It turned out to be an important
clue. What is its significance?

22.18. If a DNA molecule were analyzed, there

would be equal amounts of which two bases?
(a) A and G
(b) A and T
(c) A and C
(d) G and T
(e) C and T

22.19. If a DNA molecule were divided along its

length and on one half, in order, were found the bases
ACGT, what would be the bases on the other half, in
corresponding order?
(a) ACGT
(b) ACGU
(c) CATG
(d) GTAC
(e) TGCA

22.20. In what ways are DNA and RNA similar?

In what ways are DNA and RNA different?

The following are some miscellaneous questions:

22.21. With a simple drawing show how an

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