Transcript A. General Acid-Base Catalysis

Modes of Enzymatic Catalysis
1. Chemical modes
A. General Acid-Base Catalysis
B. Covalent Catalysis
2. Binding modes
A. Proximity Effects
B. Transition State Stabilization
1. Chemical Modes of Catalysis
A. General Acid-Base Catalysis
• Reaction acceleration is achieved by catalytic transfer of a proton
• A general base (B:) can act as a proton acceptor
• Can remove a proton from water and thereby generate the
equivalent of OH- in neutral solution
• Can produce a stronger nucleophilic reactant (X:-)
• A general acid (BH+) can donate protons
• A covalent bond may break more easily if one of its atoms is
protonated (below)
B. Covalent Catalysis
• All or part of a substrate is bound covalently to the enzyme to form
a reactive intermediate
• Can be used for group transfer
A-X + E
X-E + A
X-E + B
B-X + E
Example: Sucrose phosphorylase
Step one: a glucosyl residue is transferred to enzyme
*Sucrose + Enz
Glucosyl-Enz + Fructose
Step two: Glucose is donated to phosphate
Glucosyl-Enz + Pi
Glucose 1-phosphate + Enz
*(Sucrose is composed of a glucose and a fructose)
2. Binding Modes of Enzymatic Catalysis
Binding forces utilized for catalysis – binding energy is a major
source of energy for catalysis
1.
2.
3.
4.
Charge-charge interactions
Hydrogen bonds
Hydrophobic interactions
Van der Waals forces
A. The Proximity Effect - collecting and positioning
substrate molecules in the active site
(1) Reduces their degrees of freedom
(2) Results in a large loss of entropy
(3) The relative enhanced concentration of substrates (“effective
molarity”) predicts the rate acceleration expected due to this effect
B. Transition-State (TS) Stabilization transition states bind more
tightly than substrates
• The enzyme distorts the substrate, forcing it toward TS
• An enzyme must be complementary to the TS
• Enzymes may bind their transition states 1010 to 1015 times more
tightly than their substrates
Transition-state (TS) analogs
• Stable compounds whose structures resemble unstable transition
states
• 2-Phosphoglycolate, a TS analog for the enzyme triose phosphate
isomerase
• Can be used medically as enzyme inhibitors
Diffusion-Controlled Reactions
• Enzyme rates can approach the physical limit of the rate of diffusion
of two molecules in solution
• Under physiological conditions the encounter frequency is about 10 8
to 109 M-1s-1
• A few enzymes have rate-determining steps that are roughly as fast
as the binding of substrates to the enzymes
Triose Phosphate Isomerase (TPI)
Properties of Serine Proteases
• Includes Trypsin, Chymotrypsin,Elastase
• Many digestive proteases similar in 1o,2o and 3o structure
• Chymotrypsin, trypsin and elastase - similar backbone structure
• Active site substrate specificities differ due to relatively small
differences in specificity pockets
Serine Proteases Use Chemical and Binding Modes of Catalysis
Catalytic Triad (3 amino acids) - Ser
His
Asp