Enzyme Mechanisms

Introduction
All enzymatic reactions go through a transition state (unstable intermediate form with a
structure between that of reactant and product).
Reactants must collide precisely to form transition state.
Must have correct orientation.
Must collide with enough energy = activation energy = G
Enzymes work by lowering G
Substrates are correctly oriented. All increase probability of reaction.
Transition states are stabilized.
Chemical Catalysis
Active site of most enzymes is lined with hydrophobic amino acids.
There are a few polar a.a. which make up the catalytic center of the active site and can be
ionized.
Histidine (basic a.a.) is common.
Aspartate and glutamate - negatively charged
Lysine and arginine - positively charged; electrostatic binding can occur
There are several types of chemical catalysis:
1) acid-base catalysis
Enzymes that use this have a.a. side chains that can donate or accept
electrons to substrate.
Can accelerate a chemical reaction by a factor of 10-100.
2) covalent catalysis
Substrate forms a covalent bond with enzymes, then part of substrate is
transferred to a second substrate in a 2 step process.
A-X + E X-E + A
X-E + B B-X + E
3) proximity effect
Collection of substrate molecules in the active site increases the
concentration over those molecules found freely in solution.
Result is that there is a more frequent formation of transition states.
4) transition state stabilization
2
Increase binding of transition states to enzymes compared to substrate or
product alone binding.
Binding forces are charge-charge interactions, hydrogen bonds, hydrophobic
interactions, van der Waals forces.
Often seen in side chains of aspartate, glutamate, histidine, lysine, and
arginine.
pH affects enzymatic rates:
Inflection points approximate pKa of ionizable residues important in active site.
e.g. papain