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AP Biology
Chapter 4
Carbon and the Molecular
Diversity of Life
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The Importance of Carbon
Organic Chemistry is the Study of Carbon Compounds
Most cells comprise 70% to 95% water with the remaining portions
consisting of carbon based compounds.
Biological molecules consist mainly of Hydrogen, Oxygen, Nitrogen,
Sulfur, and Phosphorus.
Organic Chemistry is mainly the study of carbon based compounds.
Jons Jakob Berzelius made the distinction between organic
compounds and inorganic compounds in living organisms.
Wohler made Urea from Ammonium Cyanate.
Kolbe made Acetic Acid from inorganic substances.
During the early study of organic chemistry the mechanism for
biological life were controlled or governed by chemical laws.
Carbon Atoms are the most versatile Building Blocks of
Molecules
The key to the characteristics of atoms is the configuration of
the electrons.
Classification normally starts with the hydrocarbons:
compounds which contain only carbon and hydrogen.
Other elements, present themselves in atomic configurations
called functional groups which have decisive influence on
the chemical and physical characteristics of the compound;
thus those containing the same atomic formations have
similar characteristics, which may be miscibility with water,
acidity/ alkalinity, chemical reactivity, oxidation resistance, or
others.
Some functional groups are also radicals, similar to those in
inorganic chemistry, defined as atomic configurations which
pass during chemical reactions from one chemical
compound into another without change.
Some of the elements of the functional groups (O, S, N,
halogens) may stand alone and the group name is not
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strictly appropriate, but because of their decisive effect on
the way they modify the characteristics of the hydrocarbons
in which they are present they are classed with the functional
groups, and their specific effect on the properties lends
excellent means for characterisation and classification.
Names of Some Organic Compounds
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Variation in Carbon Skeletons Constitutes a Diversity of Organic
Molecules
Organic compounds are generally covalently bonded. This allows
for unique structures such as long carbon chains and rings. The
reason carbon is excellent at forming unique structures and that
there are so many carbon compounds is that carbon atoms form
very stable covalent bonds with one another (catenation).
In contrast to inorganic materials, organic compounds typically
melt, boil, sublimate, or decompose below 300°C. Neutral organic
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compounds tend to be less soluble in water compared to many
inorganic salts, with the exception of certain compounds such as
ionic organic compounds and low molecular weight alcohols and
carboxylic acids where hydrogen bonding occurs.
Organic compounds tend rather to dissolve in organic solvents
which are either pure substances like ether or ethyl alcohol, or
mixtures, such as the paraffinic solvents such as the various
petroleum ethers and white spirits, or the range of pure or mixed
aromatic solvents obtained from petroleum or tar fractions by
physical separation or by chemical conversion. Solubility in the
different solvents depends upon the solvent type and on the
functional groups if present. Solutions are studied by the science of
Physical Chemistry.
Like inorganic salts, organic compounds may also form crystals.
Unique property of carbon in organic compounds is that its valency
does not always have to be taken up by atoms of other elements,
and when it is not, a condition termed unsaturation results. In such
cases we talk about carbon carbon double bonds or triple bonds.
Double bonds alternating with single in a chain are called
conjugated double bonds.
An aromatic structure is a special case in which the conjugated
chain is a closed ring.
Compounds that for the most part are hydrophobic are nonpolar.
Isomers
isomers are compounds with the same molecular formula but
different structural formulae[1] Isomers do not necessarily share
similar properties unless they also have the same functional
groups. This should not be confused with a nuclear isomer, which
involves a nucleus at different states of excitement. There are many
different classes of isomers, like stereoisomers, enantiomers,
geometrical isomers, et cetera (see graph below).
A simple example of isomerism is given by propanol: it has the
formula C3H8O (or C3H7OH) and occurs as two isomers: propan-1ol (n-propyl alcohol; I) and propan-2-ol (isopropyl alcohol; II)
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Note that the position of the oxygen atom differs between the two: it
is attached to an end carbon in the first isomer, and to the center
carbon in the second.
There is, however, another isomer of C3H8O which has significantly
different properties: methoxyethane (methyl-ethyl-ether; III). Unlike
the isomers of propanol, methoxyethane has an oxygen atom that
is connected to two carbons rather than to one carbon and one
hydrogen. This makes it an ether, not an alcohol, as it lacks a
hydroxyl group, and has chemical properties more similar to other
ethers than to either of the above alcohol isomers.
There are two main forms of isomerism: structural isomerism and
stereoisomerism.
In structural isomers, the atoms and functional groups are joined
together in different ways, as in the example of propyl alcohol
above. This group includes chain isomerism whereby hydrocarbon
chains have variable amounts of branching; position isomerism
which deals with the position of a functional group on a chain; and
functional group isomerism in which one functional group is split up
into different ones.
In stereoisomers the bond structure is the same, but the
geometrical positioning of atoms and functional groups in space
differs. This class includes enantiomers where different isomers are
non-superimposable mirror-images of each other, and
diastereomers when they are not. Diastereomerism is again
subdivided into conformational isomerism (conformers) when
isomers can interconvert by chemical bond rotations and cis-trans
isomerism when this is not possible. Note that although conformers
can be referred to as having a diastereomeric relationship, the
isomers over all are not diastereomers, since bonds in conformers
can be rotated to make them mirror images.
In skeletal isomers the main carbon chain is different between the
two isomers. This type of isomerism is most identifiable in
secondary and tertiary alcohol isomers.
Tautomers are structural isomers of the same chemical substance
that spontaneously interconvert with each other, even when pure.
They have different chemical properties, and consequently, distinct
reactions characteristic to each form are observed.
If the interconversion reaction is fast enough, tautomers cannot be
isolated from each other. An example is when they differ by the
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position of a proton, such as in keto/enol tautomerism, where the
proton is alternately on the carbon or oxygen.
In food chemistry, medicinal chemistry and biochemistry, cis-trans
isomerism is always considered. In medicinal chemistry and
biochemistry, enantiomers are of particular interest since most
changes in these types of isomers are now known to be meaningful
in living organisms.
Pharmaceuti
cal and
academic
researchers
have found
chromatogra
phical
methods to
reliably
separate
these from
each other.
On an
industrial
scale,
however,
these methods are rather costly and are mostly used to filter out the
potentially harmful or biologically inactive enantiomer.
While structural isomers typically have different chemical
properties, stereoisomers behave identically in most chemical
reactions, except in their reaction with other stereoisomers.
Enzymes however can distinguish between different enantiomers of
a compound, and organisms often prefer one isomer over the other.
Some stereoisomers also differ in the way they rotate polarized
light.
Other types of isomerism exist outside this scope. Topological
isomers called topoisomers are generally large molecules that wind
about and form different shaped knots or loops. Molecules with
topoisomers include catenanes and DNA. Topoisomerase enzymes
can knot DNA and thus change its topology. There are also
isotopomers or isotopic isomers that have the same numbers of
each type of isotopic substitution but in chemically different
positions. In nuclear physics, nuclear isomers are excited states of
atomic nuclei. Spin isomers have differing distributions of spin
among their constituent atoms.
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Enantiomers
Enantiomers are non-superimposable mirror images of one
another. Not being able to superimpose one molecule on top of the
other simply means that the two molecules are not equivalent or
identical. For a compound to form an enantiomeric pair, it must
have chiral molecules. Chiral molecules must not have an internal
plane of symmetry, and they must have a stereocenter.
Each enantiomer exhibits what is called optical activity. Each
isomer of the pair is capable of rotating plane polarized light. One
isomer rotates this light to the right "x" number of degrees, and the
other isomer of the pair rotates this light to the left for the same
number of degrees. In fact, this is the only difference in the two
isomers, their ability to rotate plane polarized light in opposite
directions. All other physical properties are exactly the same. This
makes it extremely difficult to separate the two isomers should they
be mixed as often they are. If the enantiomers are crystalline salts
like Pasteur's Tartrate salts, then the enantiomers will have a
different appearance when observed under magnification and one
can pick them out to separate them, but most enantiomeric pairs
are not salts and therefore look the same. There is a way that we
can separate such a mixture of enantiomers which is referred to as
resolution to be disscussed in a later lesson.
Another characteristic that Enantiomers exhibit is configuration.
Configuration is the spacial way that non-equivalent groups arrange
themselves around a stereocenter carbon. One enantiomer will be
configured right handedly (R) and the other will be configured left
handedly (S).
Enantiomers are usually dipicted on a planar surface either as a 3dimensional structural formula, or we can show the structure as a
Fisher Projection. A Fisher projection is a 2-dimensional projection
of a 3-dimensional chiral molecule. A Fisher projection consists of a
long vertical line representing the longest contineous chain of the
molecule with a series of horizontal line intersecting this vertical line
along its length. At the point where the horizontal lines intersect the
vertical line there will be a carbon atom. At the ends of the
horizontal lines will be atoms or groups of atoms.
In a Fisher projection atoms or groups that are projected in front of
the plane where the vertical line extends will be at the ends of the
horizontal lines.Those atoms along the vertical line will be projected
behind the plane. For example 2-Bromobutane is a chiral molecule,
and therefore, will be one of an enantiomeric pair with its mirror
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image. We can show this molecule in 3-D formula as is usually the
case using solid wedges to show atoms in front of the plane and
dotted wedges for atoms behind the plane with any atoms within
the plane to be connected to a solid line(See Fig 1-a). Its mirror
image could be projected as in Fig 1-b.
On the other hand we can dipict the same chiral molecule and
its mirror image using a Fisher Projection (See Fig 2).
One has to be very careful about using Fisher Projections when
you go and try to manipulate the projections by rotation out of
plane. In fact, one cannot rotate Fisher projections of acyclic
molecules out of plane without leading to incorrect conclusions
concerning whether or not the mirror images are nonsuperimposable. That is because when you rotate out of plane (flip
over) then you still have atoms that were at the end of horizontal
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lines, and therefore projected forward in front of the plane at the
end of horizontal lines after flipping. However the use of simple
molecular models will show that when you flip a molecule out of
plane 180 degrees you will project the groups that were in front to
the back of the plane. This is not indicated within a Fisher
projection. Suffice to say that when dealing with Fisher projections,
it is best not to manipulate out of plane. Any manipulations using
Fisher Projections should be done within the plane either
translation or rotation within the plane.
Functional Groups
Functional Groups Contribute to Molecular Diversity of Life
A distinctive property of an organic molecule can depend on the
arrangement of the carbon skeleton structure.
The Hydroxyl Group represents alcohols. The ending name is “ol”.
This group is soluble in water implicating easy distribution to the
cells.
The Carboxyl Group consists of a double carbon oxygen bond. If
this group is at the end of the carbon skeleton then the organic
compounds represents aldehydes otherwise the compound will be
a ketone. The simplest being Acetone.
The Carboxyl Group consists of a double bonded oxygen atom off a
carbon atom that is attached to an hydroxyl group. These
compounds form organic acids or carboxylic acids. Formic Acid or
Acetic Acid are example compounds.
The Amino Group consist of a nitrogen aton bonded with 2
hydrogen atoms. These compounds are also the amines. All these
compounds are the opposite of the carboxyl acids and form bases.
The Sulfhydryl Group has a sulfur atom bonded to an hydrogen
atom. These compounds also called “thiols” help to stabilize
protein complexes.
The Phosphate Group forms from the dissociation of Phosphoric
Acid to give: OPO32 . This ion is then attached to a carbon
skeleton.
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Organic Functional Groups
Name
General Structure
Example
Carboxylic acid
acetic acid (vinegar is aqueous
soln.)
Anhydride
acetic anhydride
Ester
isoamyl acetate (banana oil)
Amide
propanamide
Aldehyde
benzaldehyde (almond smell)
Ketone
acetone (solvent)
Alcohol
ROH, R is not H
CH3CH2OH
ethanol, ethyl alcohol (grain
alcohol)
Thiol
(Mercaptan)
RSH, R is not H
(CH3)3CSH
tert-butyl mercaptan (natural gas
odorant)
Amine
RNH2, R2NH, R3N
(CH3)2NH dimethylamine
Ether
ROR, R is not H
CH3CH2OCH2CH3 diethyl ether
(solvent)
Sulfide
RSR, R is not H
CH3CH2SCH3 ethyl methyl sulfide
Aromatic
toluene (in model airplane glue)
Alkyne
ethyne (fuel for welding torch)
Alkene
CH3CH2CH=CH2 1-butene
Haloalkane
R—Cl, R—Br, R—I,
R—F
CHCl3 chloroform
(trichloromethane)
Alkane
R—H
CH3CH2CH3 propane (fuel)
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

R = hydrocarbon group such as methyl (CH3), ethyl (CH3CH2). Can sometimes be H or
aromatic. Where two R groups are shown in a single structure, they do not have to be the
same, but they can be.
Ph refers to "phenyl," the substituent name for benzene and is the same as "C 6H5"; Ar
refers to a general aromatic group.
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