Download Chapter 22: Chemistry of Living Things

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 understanding 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 manipulation 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 terminology. The chapter also includes a large number of diagrams of molecules, some of which are quite complicated. 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?
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 chapter 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 contrasts 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 additional four electrons, which it can easily obtain by entering covalent bonds with hydrogen. The resulting com-
Table 22.1. The chemical makeup of a human and alfalfa contrasted (in percent of dry weight).
Encyclopedia Britannica.)
Element
C
O
N
H
Ca
S
P
Na
K
Cl
Mg
Adult Human
48.43
23.70
12.85
6.60
3.45
1.60
1.58
0.65
0.55
0.45
0.10
Alfalfa
45.37
41.04
3.30
5.54
2.31
0.44
0.28
0.16
0.91
0.28
0.33
TOTAL
99.96
99.96
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(From the
pound is methane and has the chemical formula CH4.
Although the chemical formula tells us something about
the compound, the structural formula
a single covalent bond. If the tetrahedral methane molecules 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 complicated three-dimensional structure of these molecules.
gives us the additional information about which atom is
bonded to which. Methane is the simplest of hydrocarbons, the class of chemical compounds made up of
hydrogen and carbon. Molecules containing carbon are
the building blocks of life and are called organic molecules.
However, the structural formula of methane still
does not communicate an important piece of information about the molecule. The valence electrons of carbon 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 pyramid with triangular base and equilateral sides).
H
Figure 22.2. Isomers of C4H10. Upper: normal butane.
Lower: isobutane.
C
H
H
Sometimes the carbon atoms in a chain share four
electrons rather than the two as they do in an ordinary
single bond. An example is ethene (usually called ethylene):
H
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
of some single bonds. These double bonds are sensitive
to “attack” by some chemicals. Consider the reaction of
ethene with an initiator molecule RO• having an
unpaired electron (Fig. 22.3). The RO• reacts with an
The prefix eth is a chemist’s shorthand to indicate that
there are two carbon atoms rather than one (meth). The
molecule has been formed from two methane building
blocks. A hydrogen atom has been removed from each,
and the two carbon atoms bond directly to each other in
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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 single 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 tangled 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:
to life. Many of these are formed by substituting various 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 meaning 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 heating wood in the absence of air. The complicated molecules 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.
Functional Groups
With a carbon chain or ring as a sturdy “backbone,”
we can begin to build some of the molecules important
Figure 22.4. Upper: methanol or methyl alcohol.
Lower: ethanol or ethyl alcohol.
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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 carbon-water). Carbohydrates usually (but not always)
have the formula Cn(H2O)n, or CnH2nOn.
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 “monosaccharides.” Monosaccharides can chain together by
eliminating a water molecule:
The carbonyl group
C
O H
H
O C
In such a case, sugars are said to condense. For example, 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
is a functional group associated with the simplest carbohydrates, sugars, which taste sweet. The sugar molecule 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
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?
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energy. The process is in reality a complex series of
chemical reactions that can be summarized
considerably longer.
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 molecule easily loses a hydrogen ion; a base accepts a hydrogen ion. Organic bases contain nitrogen, and they are
viewed as being related to ammonia, NH3. The ammonia molecule NH3 has four pairs of electrons in orbitals
that point to the corners of a tetrahedron, like CH4 (Fig.
22.7). However, NH3 has one pair of electrons that is
not shared with an H; it is called a lone pair. The lone
pair enables NH3 to accept an H+ and form NH4+, the
ammonium ion.
C6H12O6 ! 6O2 → 6CO2 ! 6H2O ! energy.
The carboxyl group
contains both a carbonyl group and a hydroxyl group.
The carboxyl group was named by combining carbonyl
with hydroxyl.
Compounds that easily lose a hydrogen ion (especially 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
with some difficulty, so any molecule containing this
group is a weak acid. Molecules that contain the carboxyl 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 stinging 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 characteristic of acids.
H! ! :NH3! → H:NH3! or NH4!
N
H
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
H
O
C
C
C
C
H
H
H
O
H
Figure 22.8. Three simple bases. Upper: methylamine.
Middle: dimethlyamine. Lower: trimethylamine.
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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
of atoms. Examples of the amino acids are glycine and
alanine (Fig. 22.10).
The NH2 group shown above in methylamine (Fig.
22.8) is the amino group.
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
H
H O
N C C
O H
R
Figure 22.10. Upper: glycine. Lower: alanine.
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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 important characteristic property—they can easily join (Fig.
22.11). The resulting molecule has been linked together 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.
Insulin is a 51-amino-acid chain (actually two parallel chains cross-linked with sulfur atoms) that regulates the human body’s use of sugars and other carbohydrates. 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 organism 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 paradoxical. 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 ammonia 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
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 several hundred, as in insulin, to several million, as in the
protein of the tobacco mosaic virus.
The variations in protein molecules are almost endless. 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 various functions.
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“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).
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 protein 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 together 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 phosphates 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 ribonucleic 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 single-strand structure containing the bases G, C, A, and U
(but not T) in a variety of orders. Figure 22.13 is a simple model of RNA. The DNA molecule contains the
bases G, C, A, and T (but not U), and its structure is
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.
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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 possible for adenine or thymine to bond to guanine or cytosine, 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 enormous 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
would be about an eighth of an inch in bacteria cells and
as long as several feet in human cells! Such “macromolecules” 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 structures 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 information 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
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Figure 22.15. A short section of DNA, flattened for clarity.
are reflected in the shapes of molecules, shapes completely 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 branching structures. Functional groups may be appended to
the molecules to give a class of characteristics to the
molecules that are somewhat independent of the molecule’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 tissue of living organisms is protein. Enzymes are a specific kind of protein that catalyze certain chemical reactions. Some enzymes construct molecules from simpler
substructures; other enzymes take molecules apart and
reduce them to simpler structures.
Nucleotides are molecular complexes which consist 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 guanine, cytosine, adenine, or thymine and the sugar,
deoxyribose. The genetic instructions for building
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
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organisms are encoded in nucleic acids.
by limiting the definition of life to growth and reproduction. 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 science. 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, conservation 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?
Historical Perspectives
Paracelsus
(actually
Philippus
Aureolus
Theophrastus Bombast von Hohenheim, ca. 14931541) was an alchemist whom we have already encountered in Chapter 18 as one of the founders of chemistry.
Paracelsus held the view that God created the primordial 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 sometimes 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 existence 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 (mechanism)—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) generally taking a vitalist position and the French and English
followers of Newton and Descartes defending the
mechanistic viewpoint. In the vitalist view, the introduction 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 organized, 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 nonliving things?
This chapter and the next take a mechanistic view
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 APPLICATIONS
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
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4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
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.
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.
Base: A molecule which accepts (attaches to)
hydrogen ions (protons).
Carbohydrate: Literally, “carbon-water.” Carbon
chains that (usually) have the formula Cn(H2O)n.
Carbon Chain: A sequence of carbon atoms covalently bonded together in chainlike fashion.
Carbon chains are common structures in the molecules that characterize living things.
Carbonyl Group: The functional group in which
a carbon is double-bonded to oxygen, single-bonded to a carbon chain, and single-bonded to something else, usually to hydrogen, to satisfy the octet
rule.
Carboxyl Group: The functional group which is a
combination of the carbonyl and hydroxyl groups
and which gives acid properties to molecules containing it.
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.
Deoxyribose: A five-carbon sugar, closely related
to ribose, that plays an important role in the molecules that control growth and reproduction in living
things.
Ethane: C2H6. The next simplest hydrocarbon
with two carbons with a single covalent bond to
each other and with single covalent bonds to hydrogen to satisfy the octet rule for each carbon.
Fatty Acid: Long carbon chains having a carboxyl
group at the end which gives the molecule acid
properties.
Functional Group: A group of atoms bonded
together which exists in a molecule as a subunit and
which defines a class of molecules sharing common chemical behavior.
Hydrocarbon: The class of chemical compounds
made up of hydrogen and carbon.
Hydroxyl Group: The functional group -O-H.
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.
Methane: The simplest hydrocarbon, CH4. The
lone carbon is covalently bonded to each of four
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 subunits: 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, nucleic acid molecule in which the nucleotides incorporate ribose instead of deoxyribose as the sugar.
Uracil occurs in RNA but not thymine.
23. Ribose: A five-carbon sugar that plays an important 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 endeavors 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 remarkably 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, nitrogen, hydrogen, and calcium. What is the second most
abundant element in an oak tree?
(a) carbon
(b) oxygen
(c) nitrogen
(d) hydrogen
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(e) calcium
While it is not important for our purposes to be able
to make accurate structural drawings of the functional
groups, it is important to know some of the important
general features of the four groups: hydroxyl, carbonyl,
carboxyl, amino.
One declared objective of this chapter is to show
that the complex molecules are made up of simpler
pieces. Although it is not important for our purposes to
be able to make complicated technical drawings, it is
important to know what the building blocks are at each
level. The following questions will help to define the
degree to which terminology must be mastered.
While it is not important for our purposes to know
the chemical characteristics of things like propane and
isobutane, it is important to know that hydrocarbon
chains of ever increasing length and complexity can be
built up from simpler structures in a systematic way.
The following questions illustrate these issues.
22.10. Which functional group is associated with
acid properties?
(a) carbonyl group
(b) carboxyl group
(c) hydroxyl group
(d) amino group
22.11. Which functional group contains nitrogen?
(a) carbonyl group
(b) carboxyl group
(c) hydroxyl group
(d) amino group
22.3. Structural formulas for methane and ethane
are shown in the text. Draw propane.
22.4. Structural formulas for methanol and ethanol
are shown in the text. Draw propanol.
22.12. All amino acids contain which two simpler
structures?
(a) amino group and carbonyl group
(b) amino group and carboxyl group
(c) amino group and hydroxyl group
22.5. Structural formulas for methanoic acid and
ethanoic acid are shown in the text. Draw propanoic
acid.
While it is not important for our purposes to know
that glucose is a monosaccharide and sucrose isn’t, it is
important to know that sugars can chain together into
polysaccharides and that amino acids can chain together into proteins.
22.6. DNA is composed of which of the following
simpler structure(s)?
(a) nucleotides
(b) enzymes
(c) catalysts
(d) chlorophyll
(e) insulin
22.13. When two sugar molecules chain together
(or two amino acids), what simple molecule is produced
besides the longer chain?
(a) carbon dioxide (CO2)
(b) methane (CH4)
(c) water (H2O)
(d) hydrogen sulfide (H2S)
(e) ammonia (NH3)
22.7. A nucleotide is composed of which of the following simpler structures?
(a) phosphate group
(b) ribose or deoxyribose sugar
(c) organic bases
(d) all of the above
22.14. When two amino acids chain together,
which two functional groups are involved at the point of
the splice?
(a) hydroxyl group
(b) carbonyl group
(c) carboxyl group
(d) amino group
22.8. Which simpler structure(s) are not to be
found in a sugar?
(a) hydroxyl group
(b) carbon-oxygen covalent bonds
(c) carbon-hydrogen covalent bonds
(d) carbon-carbon covalent bonds
(e) carboxyl group
For our purposes it is not important to know the
names or formulas of the amino acids or nucleotide
bases which are important in living organisms, but it is
important to understand that the number is very limited
and that the same amino acids and nucleotide bases are
used by all living systems.
22.9. Proteins are composed of which simpler
structures?
(a) chlorophyll
(b) nucleotides
(c) sugars
(d) amino acids
(e) nucleic acids
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22.15. Approximately how many different kinds of
amino acids are important to living organisms?
(a) 2
(b) 20
(c) 2000
(d) 2,000,000
(e) More than 2 billion
enzyme might catalyze the building of a molecule.
22.22 Which of the following is false?
(a) Carbohydrates contain hydroxyl groups.
(b) Amino acids chain to form proteins.
(c) RNA and DNA are proteins.
(d) Nucleotides chain to form nucleic acids.
(e) Nucleotides contain organic bases.
22.23. Which of the following is false?
(a) RNA is usually double stranded.
(b) RNA and DNA contain different sugars.
(c) RNA and DNA share three common bases.
(d) DNA contains equal amounts of bases A and T.
(e) DNA contains equal amounts of bases C and G.
22.16. Approximately how many different kinds of
organic bases are incorporated in DNA?
(a) 4
(b) 40
(c) 4000
(d) 4,000,000
(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 (remember “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 cytosine (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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