Bioorganic Chemistry
3
nature. An understanding of these prin-
ciples will allow a deeper understanding
of all of biochemistry. The principles will
be divided into two subareas: covalent and
noncovalent. The covalent section will ex-
plore some of the fundamental organic
reactions that one sees in much of bio-
chemistry. The noncovalent section will
examine the forces that govern the associ-
ation of molecules.
2
General Principles
2.1
Covalent
There are literally hundreds of speciFc
chemical reactions that are found in biolog-
ical systems, and a study of the breadth of
theseisobviouslyoutsidethescopeofthis
review. This huge number of reactions can
be ordered by a variety of reaction types.
One of the most prevalently observed reac-
tions in biochemistry is hydrolysis and its
reverse reaction, which is considered a type
of condensation. These two general classes
of reaction account for such processes as
DNA/RNA polymerization and degrada-
tion, protein synthesis and degradation,
muscle action, regulation via phosphory-
lation, and so on. Despite the variety of
the reactants and products in these exam-
ples, they all have features that make them
chemically similar.
To deFne terms, let us examine the
hydrolysis of ethyl acetate, which is the
ethanolic ester of acetic acid (±ig. 1). In
the reaction, the electropositive carbonyl
carbon is attacked by a water molecule.
A tetrahedral intermediate is formed that
can either revert to the starting materials
or form products, that is, acetic acid and
ethanol. In this reaction, ethanol is the
leaving group and water is the attacking
group or nucleophile. The reverse reaction,
in which ethanol and acetic acid form ethyl
acetate, is called a
condensation
because in
the process of reaction, a molecule of water
is released.
Ethyl acetate is an ester, a subclass of
the compounds known as acyl derivatives,
that is, compounds that are formed when
carboxylic acids condense with another
species.
±igure 2
shows
some
of
the
variety of acyl derivatives found in nature
and in the laboratory. The amide is the
condensation product of an amine with
a carboxylic acid, in the same way that
an ester is the condensation product of
an alcohol with a carboxylic acid. The
thioester is the product of condensation
of the thioether coenzyme A with butyric
acid. Acetyl chloride is the condensation
product of acetic acid and hydrochloric
acid. As with the ester ethyl acetate,
each of these compounds can undergo
hydrolysis to form the free acid and
another product. The ease with which this
reaction can occur depends crucially on
the species that has condensed with the
carboxylic acid. ±or example, in aqueous
solution at pH 7, it will take weeks for an
amide to show signs of decomposition by
hydrolysis, whereas an acid chloride will
O
O
H
O
H
O
HO
OH
OH
HO
O
+
Fig. 1
Hydrolysis of ethyl acetate.
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