6| Enzymes

© 2017 W. H. Freeman and Company

 Catalytic Mechanisms
Enzymes may use one or a combination of the
following:
– acid-base catalysis: give and take protons
– covalent catalysis: change reaction paths
– metal ion catalysis: use redox cofactors
 Catalytic Mechanisms
Enzymes may use one or a combination of the
following:

covalent catalysis: change reaction paths

- Many enzymes especially digestive enzymes
- Active sites contain catalytic residues that can
form temporary Covalent bonds with substrate
 Covalent Catalysis
• A transient covalent bond between the enzyme and the
substrate
• Changes the reaction pathway
– uncatalyzed:
H2O
A—B AB
– catalyzed (X = catalyst):
H2O
A — B  X : A — X  B  A  X : B
• Requires a nucleophile on the enzyme
– can be a reactive serine, thiolate, amine, or carboxylate
 Catalytic Mechanisms
Enzymes may use one or a combination of the
following:
acid-base catalysis: give and take protons
- Activate nucleophiles required in catalysis
- Stabilize charged groups
- Increase electrostatic interaction that may
stabilize transition state
 Amino Acids in
General Acid-Base Catalysis
 Catalytic Mechanisms
Enzymes may use one or a combination of the
following:
• Metal Ion catalysis
- Involves a metal ion bound to the enzyme
- Interacts with substrate to facilitate binding
- stabilizes negative charges
- Participates in oxidation reactions
Active Site of Chymotrypsin with Substrate
 Chymotrypsin
• During digestion, dietary proteins must be broken down into
small peptides by proteases.
• Chymotrypsin is one of several proteases that cuts peptides
at specific locations on the peptide backbone.
• This protease is able to cleave the peptide bond adjacent to
aromatic amino acids.
Chymotrypsin cuts this bond.
Chymotrypsin Uses Most of
the Enzymatic Mechanisms
Structure of chymotrypsin. The polypeptide backbone
as a ribbon structure. Disulfide bonds are yellow; the three
chains are colored as in part (a).
example Example of enzymatic
Reactions
Structure of chymotrypsin. A
representation of primary
structure, showing disulfide bonds
and the amino acid residues crucial
to catalysis.
The protein consists of three
polypeptide chains linked by
disulfide bonds.
The active-site amino acid residues
are grouped together in the three-
dimensional structure.
 Hydrolytic cleavage of a peptide bond by
chymotrypsin. The reaction has two phases.
In the acylation phase (steps 1 to 3), formation of
a covalent acyl-enzyme intermediate is coupled to
cleavage of the peptide bond.
In the deacylation phase (steps 4 to 7),
deacylation regenerates the free enzyme
Chymotrypsin Mechanism
Step 1: Substrate Binding
Chymotrypsin Mechanism
Step 2: Nucleophilic Attack
Chymotrypsin Mechanism
Step 3: Substrate Cleavage
Chymotrypsin Mechanism
Step 4: Water Comes In
Chymotrypsin Mechanism
Step 5: Water Attacks
Chymotrypsin Mechanism
Step 6: Break-off from the Enzyme
Chymotrypsin Mechanism
Step 7: Product Dissociates
 Chapter 6: Summary

In this chapter, we learned:

• why nature needs enzyme catalysis
• how enzymes can accelerate chemical reactions
• how chymotrypsin breaks down peptide bonds
• how to perform and analyze kinetic studies
• how to characterize enzyme inhibitors