Enzymes - Bioprocess Engineering: Kinetics, Biosystems, Sustainability and Reactor Design - page 330

The differences in rates between intramolecular catalysis and the corresponding inter-
molecular catalysis can be employed to define an apparent concentration of reactant at
the reaction site in intramolecular catalysis. In intermolecular catalysis, reactants A and
B may react at a rate which is first order in both A and B, the overall rate can be expressed
as k 2 [A][B], where k 2 is a second-order rate constant (1 mol 1

$ s 1 ). In the case of intramo-
lecular catalysis, both A and B are present in the same compound, and the rate will now be
k 1 [A e B], with k l (s l ) being a first-order rate constant. Thus, the ratio k 1 /k 2 , which has units
of molarity, represents the effective concentration of reactant A which would need to be
present at the catalytic site to cause a smaller concentration of B to react at a pseudo-
first-order rate equivalent to that of the intramolecularly catalyzed rate. Hence k 1 /k 2 can
then be thought of as an “effective” concentration of catalyst A at the reaction site. Such
concentrations can be extremely high. When the effective molarities exceed attainable
values, then other factors influencing catalysis, in addition to approximation, must be
important.
In enzyme-catalyzed reactions, this enhanced local concentration effect can account for
some of the rate enhancement but is generally not sufficiently large. It does provide a lower
limit to the rate acceleration that might be expected however. We must turn to other mecha-
nisms to provide an explanation for the catalytic abilities of enzymes.
Covalent Catalysis: Electrophilic and Nucleophilic Catalysis is another main route an
enzyme may employ to enhance the reaction rate. An enzyme can form a covalent bond
with one or more reactants and so alter the reaction path from that observed in the unca-
talyzed case. The discovery that enzymes may indeed form covalent intermediates relied
on early kinetic observations, including “burst” kinetics and the observation of constant
rates of product release from substrates with varying substituents. Today, the crystallo-
graphic structures of many enzymes and their substrate-containing intermediates are
well-known, providing further evidence for the formation of such covalent intermediate
compounds.
Covalent catalysis is divided into two types: electrophilic and nucleophilic catalysis. In
nucleophilic catalysis, the nucleophilic groups on the enzyme are more electron donating
than the normal attacking groups, and a reactive intermediate is formed which breaks
down rapidly to form the products. Electrophilic catalysis on the other hand involves cata-
lysts that withdraw electrons from the reaction center of the intermediate. We will first
consider nucleophilic catalysis.
The most common nucleophiles in enzymes are the serine hydroxyl (found in serine prote-
ases, esterases, lipases, and phosphatases), the cysteine thiol (thiol proteases), the carboxylic
group of aspartic acid, the amino group of lysine (aldolase, transaldolase, DNA ligase), the
-OH of tyrosine (in topoisomerases), and possibly the imidazole (in conjunction with phos-
phoryl groups in phosphate transfer, otherwise it functions by general base catalysis).
A simple example of nucleophilic catalysis by the serine hydroxyl is afforded by acetylcho-
line esterase. Acetylcholine is found in the nervous tissue and motor nerve tracts; it is an
active neurotransmitter. When a nerve impulse travels along the nerve axon to the synapse,
acetylcholine is released and diffuses from the nerve ending to the postsynaptic receptor for
acetylcholine on the muscle cell membrane. Acetylcholine esterase functions by breaking
down acetylcholine, thus ensuring that the nerve signal is of a short, finite duration. If the