Biochemistry I
Lecture 15
February 18, 2013
Lecture 15: Introduction to Enzymes
Horton 6.2, 6.5, 6.7.
Cox and Nelson Chapter 6-1, 6-2.
Key Terms:


Active site, catalytic groups
Transition state theory
A. Enzyme Kinetics:
For the simple enzyme-catalyzed reaction:




Enzyme
S 
 P
The enzyme forms a complex with the substrate (S),
often undergoing some degree of conformational
change.
The interaction between the enzyme and the
substrate are similar to protein-ligand interactions.
Catalytic groups on the enzyme perform some
chemical reaction/transformation of the bound
substrate.
The resultant product (P) is released.
B. Important Features of Enzyme Catalysis.
1. Enzymes increase the rate of reactions, in both
directions
2. Enzymes do not change the equilibrium point of
reactions.
3. Enzymes are not changed by the overall reaction.
(Although they may be modified during the reaction)
4. Catalysis occurs at the "active site", which is specific
for certain substrates. The active site has the
following with respect to its substrate:
 Geometric complementarity;
 Energetic complementarity.
5. Enzymatic reactions are usually regulated by allosteric activators and inhibitors.
C. Transition State Theory – Accounting for Rate Enhancements: rate  [Transition State]
The transition state is a high energy intermediate in the reaction, a distorted substrate on its way to becoming
product. Most enzymes enhance reactions by lowering the energy of the transition state, thus increasing its
concentration and thus the overall rate of the reaction.
Example: In the hydrolysis of a peptide bond by hydroxide ion, the transition state is the unstable tetrahedral
oxyanion.
O
O
N
N
H
H
O
H
O
N
O
H
H
O
H
1
Biochemistry I
Lecture 16
February 18, 2013
The transition state of the enzyme substrate complex is stabilized in many ways:
1. The enzyme may provide a number of functional groups to aid in catalysis. Since these groups are
positioned in well defined locations, the entropy of bringing these groups into the catalytic site is
substantially less than having these functional groups freely diffuse in solution. This entropy change
contributes to G‡ via the relationship Go = -TSo.
In this example, the three amino acids (Asp, His, and Ser) are involved in cleaving a peptide bond,
converting the substrate (a peptide) to product via the transition state “X”
Non-enzyme Reaction
(same mechanism)
Enzyme Catalysed Reaction
Ser
His
S
Asp
His
Ser
X
Asp
His
Ser
S
Asp
His
Ser
X
Asp
Don't underestimate the effect of Entropy:
O
O
H3C
H3C
C
O
H3C
Br
+
O
C
H3C
O
O
H2
C C
H2
C C
O
Br
C
O
O
O
C
O
O
Br
O
H2
C C
H2
C C
O
O
O
+
Br
O
O
2. The enzyme transition-state complex is stabilized by direct interactions between the enzyme
and the transition state. This reduces the free energy of the transition state due to Ho
(enthalphy).
O
O
N
N
H
H
O
N
O
H
H
ES
2
O
EX
H
H
EP
O
Biochemistry I
Lecture 16
February 18, 2013
3. The enzyme may provide a different mechanism to catalyze the reaction, e.g. transport proteins that
facilitate the movement of polar molecules across the non-polar lipid bilayer.
D. Quantitative Measure of Rate
Enhancement by Stabilization of the
Transition State:
 The rate or velocity (v) of the reaction is
directly proportional to the concentration
of the transition state:

The substrates (and products) are in
equilibrium with the transition state.
Uncatalyzed Reaction
Enzyme Catalyzed reaction
v  [X  ]
ve  [ EX  ]
S  X
ES  EX 
[ EX  ]
[ ES ]
[X  ]
[S ]
v  K EQ [ S ]
e
ve  K EQ
[ ES ]
G    RT ln K EQ
e
Ge   RT ln K EQ

K EQ  e G / RT

e
K EQ
 e  Ge / RT

v  e G / RT [ S ]

ve  e  Ge / RT [ ES ]
K EQ 
e
K EQ


ve e Ge / RT [ ES ] ( G  Ge ) / RT
( G  ) / RT


e

e

v
e G / RT [ S ]

3