CHAPTER 4 CARBON AND THE MOLECULAR DIVERSITY OF LIFE

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CHAPTER 4CARBON AND THE MOLECULAR DIVERSITY OF
LIFE
-THE IMPORTANCE OF CARBON
-FUNCTIONAL GROUPS
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Although water  is the universal medium for life
on Earth, most of the chemicals that make up
living organisms are based on the element carbon.
Of all chemical elements, carbon is unparalleled
in its ability to form molecules that are large,
complex, and diverse, and this molecular
diversity has made possible the diversity of
organisms that have evolved on Earth. The protein
shown in the computer graphic image above is an
example of a large, complex molecule based on
carbon (the green atoms). Proteins are a major
topic of Chapter 5. In this chapter, we focus on
smaller molecules, using them to illustrate a few
concepts of molecular architecture that highlight
carbons importance to life and the theme that
emergent properties arise from the organization
of the matter of living organisms.
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THE IMPORTANCE OF CARBON
Although a cell is composed of 70-95 water, the
rest consists mostly of carbon-based compounds.
Proteins, DNA, carbohydrates, and other molecules
that distinguish living matter from inanimate
material are all composed of carbon atoms bonded
to one another and to atoms of other elements.
Hydrogen (H), oxygen (O), nitrogen (N), sulfur
(S), and phosphorus (P) are other common
ingredients of these compounds, but it is carbon
(C) that accounts for the large diversity of
biological molecules.
Carbon
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Organic chemistry is the study of carbon
compounds
Compounds containing carbon are said to be
organic, and the branch of chemistry that
specializes in the study of carbon compounds is
called organic chemistry. Once thought to come
only from living things, organic compounds range
from simple molecules, such as carbon dioxide
(CO2) and methane (CH4), to colossal ones, such
as proteins, with thousands of atoms and
molecular weights in excess of 100,000 daltons.
Most organic compounds contain hydrogen atoms.
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The overall percentages of the major elements of
life--C, H, O, N, S, and P--are quite uniform
from one organism to another. Because of carbons
versatility, however, this limited assortment of
atomic building blocks, taken in roughly the same
proportions, can be used to build an
inexhaustible variety of organic molecules.
Different species of organisms, and different
individuals within a species, are distinguished
by variations in their organic molecules.
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Since the dawn of human history, people have used
other organisms as sources of valued
substances--from foods to medicines and fabrics.
The science of organic chemistry originated in
attempts to purify and improve the yield of such
products. By the early 19th century, chemists had
learned to make many simple compounds in the
laboratory by combining elements under the right
conditions. Artificial synthesis of the complex
molecules extracted from living matter seemed
impossible, however. It was at that time that the
Swedish chemist Jöns Jakob Berzelius first made
the distinction between organic compounds, those
that seemingly could arise only within living
organisms, and inorganic compounds, those that
were found in the nonliving world. The new
discipline of organic chemistry was first built
on a foundation of vitalism, the belief in a life
force outside the jurisdiction of physical and
chemical laws.
Jöns Jakob Berzelius
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Chemists began to chip away at the foundation of
vitalism when they learned to synthesize organic
compounds in their laboratories. In 1828,
Friedrich Wöhler, a German chemist who had
studied with Berzelius, attempted to make an
inorganic salt, ammonium cyanate, by mixing
solutions of ammonium (NH4) and cyanate (CNO-)
ions. Wöhler was astonished to find that instead
of the expected product, he had made urea, an
organic compound present in the urine of animals.
Wöhler challenged the vitalists when he wrote, "I
must tell you that I can prepare urea without
requiring a kidney or an animal, either man or
dog." However, one of the ingredients used in the
synthesis, the cyanate, had been extracted from
animal blood, and the vitalists were not swayed
by Wöhlers discovery. However, a few years
later, Hermann Kolbe, a student of Wöhlers, made
the organic compound acetic acid from inorganic
substances that could themselves be prepared
directly from pure elements
Hermann Kolbe
Friedrich Wöhler
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The foundation of vitalism finally crumbled after
several more decades of laboratory synthesis of
increasingly complex organic compounds. In 1953,
Stanley Miller, then a graduate student at the
University of Chicago, helped bring this abiotic
(nonliving) synthesis of organic compounds into
the context of evolution. Miller used a
laboratory simulation of chemical conditions on
the primitive Earth to demonstrate that the
spontaneous synthesis of organic compounds could
have been an early stage in the origin of life.
Abiotic synthesis of organic compounds under
"early Earth" conditions. Here Stanley Miller
re-creates his 1953 experiment, a laboratory
simulation demonstrating that environmental
conditions on the lifeless, primordial Earth
allowed the spontaneous synthesis of some organic
molecules. Miller used electrical discharges
(simulated lightning) to trigger reactions in a
primitive "atmosphere" of H2O, H2, NH3 (ammonia),
and CH4 (methane)--some of the gases released by
volcanoes. From these ingredients, Millers
apparatus made a variety of organic compounds
that play key roles in living cells. Similar
chemical reactions may have set the stage for the
origin of life on Earth, a hypothesis we will
explore in more detail in Chapter 26.
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The pioneers of organic chemistry helped shift
the mainstream of biological thought from
vitalism to mechanism, the belief that all
natural phenomena, including the processes of
life, are governed by physical and chemical laws.
Organic chemistry was redefined as the study of
carbon compounds, regardless of their origin.
Most naturally occurring organic compounds are
produced by organisms, and these molecules
represent a diversity and range of complexity
unrivaled by inorganic compounds. However, the
same rules of chemistry apply to inorganic and
organic molecules alike. The foundation of
organic chemistry is not some intangible life
force, but the unique chemical versatility of the
element carbon.
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Carbon atoms are the most versatile building
blocks of molecules
The key to the chemical characteristics of an
atom, as you learned in Chapter 2, is in its
configuration of electrons, because electron
configuration determines the kinds and number of
bonds an atom will form with other atoms. Carbon
has a total of 6 electrons, with 2 in the first
electron shell and 4 in the second shell. Having
4 valence electrons in a shell that holds 8,
carbon has little tendency to gain or lose
electrons and form ionic bonds it would have to
donate or accept 4 electrons to do so. Instead, a
carbon atom usually completes its valence shell
by sharing electrons with other atoms in four
covalent bonds. Each carbon atom thus acts as an
intersection point from which a molecule can
branch off in up to four directions. This
tetravalence is one facet of carbons versatility
that makes large, complex molecules possible.
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In Chapter 2, you also learned that when a carbon
atom forms single covalent bonds, the arrangement
of its four hybrid orbitals causes the bonds to
angle toward the corners of an imaginary
tetrahedron (see FIGURE 2.15c). The bond angles
in methane (CH4) are 109 (FIGURE a), and they
are approximately the same in any group of atoms
where carbon has four single bonds. For example,
ethane (C2H6) is shaped like two tetrahedrons
joined at their apexes (FIGURE b). In molecules
with still more carbons, every grouping of a
carbon bonded to four other atoms has a
tetrahedral shape. But when two carbon atoms are
joined by a double bond, all bonds around those
carbons are in the same plane. For example,
ethene is a flat molecule its atoms all lie in
the same plane (FIGURE c). It is convenient to
write all structural formulas as though the
molecules represented were flat, but it is
important to remember that molecules are
three-dimensional and that the shape of a
molecule often determines its function.
The shapes of three simple organic molecules.
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The electron configuration of carbon gives it
covalent compatibility with many different
elements. The figure below reviews the valences
of the four major atomic components of organic
molecules carbon and its most frequent
partners--oxygen, hydrogen, and nitrogen. We can
think of these valences as the rules of covalent
bonding in organic chemistry--the building code
that governs the architecture of organic
molecules.
Valences for the major elements of organic
molecules. Valence is the number of covalent
bonds an atom will usually form. It is generally
equal to the number of electrons required to
complete the atoms outermost (valence) electron
shell.
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A couple of additional examples will show how the
rules of covalent bonding apply to carbon atoms
with partners other than hydrogen. In the carbon
dioxide molecule (CO2), a single carbon atom is
joined to two atoms of oxygen by double covalent
bonds. The structural formula for CO2 is OCO.
Each line (bond) in a structural formula
represents a pair of shared electrons. Notice
that the carbon atom in CO2 is involved in four
covalent bonds, two with each oxygen atom. The
arrangement completes the valence shells of all
atoms in the molecule. Because carbon dioxide is
a very simple molecule and lacks hydrogen, it is
often considered inorganic, even though it
contains carbon. Whether we call CO2 organic or
inorganic is an arbitrary distinction, but there
is no ambiguity about its importance to the
living world. Taken from the air by plants and
incorporated into sugar and other foods during
photosynthesis, CO2 is the source of carbon for
all the organic molecules found in organisms.
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Another relatively simple molecule is urea,
CO(NH2)2. This is the organic compound found in
urine that Wöhler learned to synthesize in the
early 19th century. The structural formula for
urea is shown on the following page.          
Again, each atom has the
required number of covalent bonds. In this case,
one carbon atom is involved in both single and
double bonds.
Both urea and carbon dioxide are molecules with
only one carbon atom. But as the figure above
shows, a carbon atom can also use one or more of
its valence electrons to form covalent bonds to
other carbon atoms, making it possible to link
the atoms into chains of seemingly infinite
variety.
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Variation in carbon skeletons contributes to the
diversity of organic molecules
Carbon chains form the skeletons of most organic
molecules. The skeletons vary in length and may
be straight, branched, or arranged in closed
rings. Some carbon skeletons have double bonds,
which vary in number and location. Such variation
in carbon skeletons is one important source of
the molecular complexity and diversity that
characterize living matter. In addition, atoms of
other elements can be bonded to the skeletons at
available sites.
Variations in carbon skeletons. Hydrocarbons,
organic molecules consisting only of carbon and
hydrogen, illustrate the diversity of the carbon
skeletons of organic molecules.
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All the molecules shown in the figure below are
hydrocarbons, organic molecules consisting only
of carbon and hydrogen. Atoms of hydrogen are
attached to the carbon skeleton wherever
electrons are available for covalent bonding.
Hydrocarbons are the major components of
petroleum, which is called a fossil fuel because
it consists of the partially decomposed remains
of organisms that lived millions of years ago.
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Although hydrocarbons are not prevalent in living
organisms, many of a cells organic molecules
have regions consisting of only carbon and
hydrogen. For example, the molecules known as
fats have long hydrocarbon tails attached to a
nonhydrocarbon component. Neither petroleum nor
fat mixes with water both are hydrophobic
compounds because the bonds between the carbon
and hydrogen atoms are nonpolar. Another
characteristic of hydrocarbons is that they store
a relatively large amount of energy. The gasoline
that fuels a car consists of hydrocarbons, and
the hydrocarbon tails of fat molecules serve as
stored fuel for animal bodies.
The role of hydrocarbons in fats. (a) A fat
molecule consists of a headpiece and three
hydrocarbon tails. The tails store energy and
account for the hydrophobic behavior of fats.
(Black carbon gray hydrogen red oxygen)
(b) Mammalian adipose cells stockpile fat
molecules as a fuel reserve. Each adipose cell in
this micrograph is almost filled by a large fat
droplet, which stockpiles a huge number of fat
molecules.
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Isomers
Variation in the architecture of organic
molecules can be seen in isomers, compounds that
have the same molecular formula but different
structures and hence different properties.
Compare, for example, the two butanes in FIGURE
a. Both have the molecular formula C4H10, but
they differ in the covalent arrangement of their
carbon skeletons. The skeleton is straight in
butane, but branched in isobutane. We will
examine three types of isomers structural
isomers, geometric isomers, and enantiomers.
Butane
Isobutane
Structural isomers differ in the covalent
arrangements of their atoms. The number of
possible isomers increases tremendously as carbon
skeletons increase in size. There are only two
butanes, but there are 18 variations of C8H18 and
366,319 possible structural isomers of C20H42.
Structural isomers may also differ in the
location of double bonds.
Geometric isomers have the same covalent
partnerships, but they differ in their spatial
arrangements. Geometric isomers arise from the
inflexibility of double bonds, which, unlike
single bonds, will not allow the atoms they join
to rotate freely about the bond axis. The subtle
difference in shape between geometric isomers can
dramatically affect the biological activities of
organic molecules. For example, the biochemistry
of vision involves a light-induced change of
rhodopsin, a chemical compound in the eye, from
one geometric isomer to another.
Enantiomers are molecules that are mirror images
of each other. In the ball-and-stick models shown
in FIGURE 4.6c, the middle carbon is called an
asymmetric carbon because it is attached to four
different atoms or groups of atoms. The four
groups can be arranged in space about the
asymmetric carbon in two different ways that are
mirror images. They are, in a way, left-handed
and right-handed versions of the molecule. A cell
can distinguish these isomers based on their
different shapes. Usually, one isomer is
biologically active and the other is inactive.
Three types of isomers. Compounds with the same
molecular formula but different structures,
isomers are a source of diversity in organic
molecules.
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The concept of enantiomers is important in the
pharmaceutical industry because the two
enantiomers of a drug may not be equally
effective. In some cases, one of the isomers may
even produce harmful effects. This was the case
with thalidomide, a drug prescribed for thousands
of pregnant women in the late 1950s and early
1960s. The drug was a mixture of two enantiomers.
One enantiomer reduced morning sickness, the
desired effect, but the other caused severe birth
defects. (And unfortunately, even if the "good"
thalidomide enantiomer is used in purified form,
some of it soon converts to the "bad" enantiomer
in the patients body.) The differing effects of
enantiomers in the body demonstrate that
organisms are sensitive to even the most subtle
variations in molecular architecture. Once again,
we see that molecules have emergent properties
that depend on the specific arrangement of their
atoms.
The pharmacological importance of enantiomers.
L-Dopa is a drug used to treat Parkinsons
disease, a disorder of the central nervous
system. The drugs enantiomer, the mirror-image
molecule designated D-Dopa, has no effect on
patients.
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FUNCTIONAL GROUPS
The distinctive properties of an organic molecule
depend not only on the arrangement of its carbon
skeleton, but also on the molecular components
attached to that skeleton. We will now examine
certain groups of atoms that are frequently
attached to the skeletons of organic molecules.
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Functional groups contribute to the molecular
diversity of life
The components of organic molecules that are most
commonly involved in chemical reactions are known
as functional groups. If we think of hydrocarbons
as the simplest organic molecules, we can view
functional groups as attachments that replace one
or more of the hydrogens bonded to the carbon
skeleton of the hydrocarbon. (However, some
functional groups include atoms of the carbon
skeleton, as we will see.)
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Each functional group behaves consistently from
one organic molecule to another, and the number
and arrangement of the groups help give each
molecule its unique properties. Consider the
differences between testosterone and estradiol (a
type of estrogen). These compounds are male and
female sex hormones, respectively, in humans and
other vertebrates (FIGURE 4.8). Both are
steroids, organic molecules with a common carbon
skeleton in the form of four fused rings. These
sex hormones differ mainly in the functional
groups attached to the rings. The different
actions of these two molecules on many targets
throughout the body help produce the contrasting
features of females and males. Thus, even our
sexuality has its biological basis in variations
of molecular architecture.
A comparison of functional groups of female
(estradiol) and male (testosterone) sex hormones.
The two molecules differ mainly in the
attachment of functional groups to a common
carbon skeleton of four fused rings. (The carbon
skeleton has been simplified here by omitting the
carbons in the rings, as well as their
hydrogens.) These subtle variations in molecular
architecture influence the development of the
anatomical and physiological differences between
female and male vertebrates.
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The six functional groups most important in the
chemistry of life are the hydroxyl, carbonyl,
carboxyl, amino, sulfhydryl, and phosphate groups
(TABLE). All are hydrophilic and thus increase
the solubility of organic compounds in water.
The ionized forms of the carboxyl and amino
groups prevail in cells. However, acetic acid
and glycine are represented here in their
non-ionized forms.
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The Hydroxyl Group
In a hydroxyl group, a hydrogen atom is bonded to
an oxygen atom, which in turn is bonded to the
carbon skeleton of the organic molecule. Organic
compounds containing hydroxyl groups are called
alcohols, and their specific names usually end in
-ol, as in ethanol, the drug present in alcoholic
beverages. In a structural formula, the hydroxyl
group is usually abbreviated by omission of the
covalent bond between the oxygen and hydrogen and
is written as--OH or HO--. (Do not confuse this
functional group with the hydroxide ion, OH-,
formed by the dissociation of bases such as
sodium hydroxide.) The hydroxyl group is polar as
a result of the electronegative oxygen atom
drawing electrons toward itself. Consequently,
water molecules are attracted to the hydroxyl
group, and this helps dissolve organic compounds
containing such groups. Sugars, for example, owe
their solubility in water to the presence of
multiple hydroxyl groups (see FIGURE 5.3).
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The Carbonyl Group
The carbonyl group (      ) consists of a carbon
atom joined to an oxygen atom by a double bond.
If the carbonyl group is on the end of a carbon
skeleton, the organic compound is called an
aldehyde otherwise the compound is called a
ketone. The simplest ketone is acetone, which is
three carbons long. Acetone has different
properties from propanal, a three-carbon
aldehyde. (Acetone and propanal are structural
isomers.) Thus, variation in locations of
functional groups along carbon skeletons is a
major source of molecular diversity.
Propanal (aldehyde)
Acetone (ketone)
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The Carboxyl Group
When an oxygen atom is double-bonded to a carbon
atom that is also bonded to a hydroxyl group, the
entire assembly of atoms is called a carboxyl
group (--COOH). Compounds containing carboxyl
groups are known as carboxylic acids, or organic
acids. The simplest is the one-carbon compound
called formic acid (HCOOH), the substance some
ants inject when they sting. Acetic acid, which
has two carbons, gives vinegar its sour taste.
(In general, acids taste sour.)
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Why does a carboxyl group have acidic properties?
A carboxyl group is a source of hydrogen ions.
The covalent bond between the oxygen and the
hydrogen is so polar that the hydrogen tends to
dissociate reversibly from the molecule as an ion
(H). In the case of acetic acid, we have
                                
Dissociation occurs as a result of the two
electronegative oxygen atoms of the carboxyl
group pulling shared electrons away from
hydrogen. If the double-bonded oxygen and the
hydroxyl group were attached to separate carbon
atoms, there would be less tendency for the --OH
group to dissociate because the second oxygen
would be farther away. Here is another example of
how emergent properties result from a specific
arrangement of building components.
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The Amino Group
The amino group (--NH2) consists of a nitrogen
atom bonded to two hydrogen atoms and to the
carbon skeleton. Organic compounds with this
functional group are called amines. An example is
glycine, illustrated in TABLE 4.1. Because
glycine also has a carboxyl group, it is both an
amine and a carboxylic acid. Most of the cells
organic compounds have two or more different
functional groups. Glycine and similar compounds
having both amino and carboxyl groups are called
amino acids these are the molecular building
blocks of proteins.
Glycine
The amino group acts as a base. You learned in
Chapter 3 that ammonia (NH3) can pick up a proton
from the surrounding solution. Amino groups of
organic compounds can do the same
                    
This process gives the amino group a charge of
1, its most common state within the cell.
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The Sulfhydryl Group
Sulfur is directly below oxygen in the periodic
table both have 6 valence electrons and form two
covalent bonds. The organic functional group
known as the sulfhydryl group (--SH), which
consists of a sulfur atom bonded to an atom of
hydrogen, resembles a hydroxyl group in shape
(see TABLE 4.1). Organic compounds containing
sulfhydryls are called thiols. In Chapter 5, you
will learn how sulfhydryl groups can interact to
help stabilize the intricate structure of a
protein.
stabilizing protein structure
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The Phosphate Group
Phosphate is an anion formed by dissociation of
an inorganic acid called phosphoric acid (H3PO4).
The loss of hydrogen ions by dissociation leaves
the phosphate with two negative charges. Organic
compounds containing a phosphate group (
        ) have a phosphate ion covalently
attached by one of its oxygen atoms to the carbon
skeleton (see TABLE 4.1). One function of
phosphate groups is the transfer of energy
between organic molecules. In Chapter 6, you will
learn how cells harness the transfer of phosphate
groups to perform work, such as the contraction
of muscle cells.
ATP
DNA
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The chemical elements of life a review
Living matter, as you have learned, consists
mainly of carbon, oxygen, hydrogen, and nitrogen,
with smaller amounts of sulfur and phosphorus.
These elements share the characteristic of
forming strong covalent bonds, a quality that is
essential in the architecture of complex organic
molecules. Of all these elements, carbon is the
virtuoso of the covalent bond. The chemical
behavior of carbon makes it exceptionally
versatile as a building block in molecular
architecture It can form four covalent bonds,
link together into intricate molecular skeletons,
and join with several other elements. The
versatility of carbon makes possible the great
diversity of organic molecules, each with special
properties that emerge from the unique
arrangement of its carbon skeleton and the
functional groups appended to that skeleton. At
the foundation of all biological diversity lies
this variation at the molecular level.
Now that we have examined the basic architectural
principles of organic compounds, we can move on
to the next chapter, where we will explore the
specific structures and functions of the large
and complex molecules made by living cells
carbohydrates, lipids, proteins, and nucleic
acids.