Download CHMI 2227E Biochemistry I

CHMI 2227E
Biochemistry I
Enzymes:
-
catalysis
CHMI 2227 - E.R. Gauthier, Ph.D.
1
Enzyme catalysis

Upon binding to the
enzyme’s active site,
the substrate is
surrounded by
several side chains
that:
 Hold
the substrate in
place;
 Participate in the
reaction.
CHMI 2227 - E.R. Gauthier, Ph.D.
2
Enzyme catalysis
Basic reaction mechanisms


Three main types of catalysis are found:
General acid/base
catalysis:

Involves the transfer of
protons between side
chains of the enzyme
and the substrate;

The most common form
of enzyme catalysis

Metal ion catalysis:

Several enzymes use
metal ions for catalysis
(Mg+2, Mn+2, Zn+2, Fe+2,
Cu+2);

The metal ion can act is
different ways:
Stabilises the transition
state;

Helps to orientate the
substrate vs the enzyme;

Participates in the transfer
of electrons/protons
between the enzyme and
CHMI 2227 - the
E.R.substrate;
Gauthier, Ph.D.


Covalent catalysis:

Involves the formation
of a transient
covalent bond
between the enzyme
and substrate;

This covalent bond
activates the
substrate for further
reaction ;
3
Enzyme catalysis
General acid/base catalysis
O
R
H
+
OH
HOR
Chymotrypsin
CHMI 2227 - E.R. Gauthier, Ph.D.
4
Enzyme catalysis
Metal ion catalysis
H+
CHMI 2227 - E.R. Gauthier, Ph.D.
5
Enzyme catalysis
Covalent catalysis
Nucleophile
CHMI 2227 - E.R. Gauthier, Ph.D.
6
Enzyme catalysis
Refresher – nucleophiles and electrophiles
CHMI 2227 - E.R. Gauthier, Ph.D.
7
Enzyme catalysis
- Enzymes often combine two catalytic strategies
General Acid/
base catalysis
Covalent catalysis
CHMI 2227 - E.R. Gauthier, Ph.D.
8
Example of enzyme catalysis
1. Chymotrypsin

Protease:


Serine protease:


Cuts peptide bonds C-ter of Tyr/Phe/Trp
Ser195 actively participates in the catalysis
Catalytic triad:

His57, Asp102, Ser195
CHMI 2227 - E.R. Gauthier, Ph.D.
9
Example of enzyme catalysis
1. Chymotrypsin
CHMI 2227 - E.R. Gauthier, Ph.D.
10
Example of enzyme catalysis
Importance of the catalytic triad

The determine the
importance of the
catalytic triad in
catalysis, each amino
acid of the triad of the
protease subtilisin were
changed to alanines;

Note: the Y axis is a Log
scale.
CHMI 2227 - E.R. Gauthier, Ph.D.
11
Example of enzyme catalysis
1. Chymotrypsin - specificity
CHMI 2227 - E.R. Gauthier, Ph.D.
12
Example of enzyme catalysis
1. Chymotrypsin - specificity
Ser195
CHMI 2227 - E.R. Gauthier, Ph.D.
Ser195
13
Example of enzyme catalysis
1. Chymotrypsin - catalysis
Covalent intermediate
Catalytic triad
Substrate
Peptide bond cleavage
C-ter part
of the protein
Enzyme regeneration
N-ter part
of the protein
CHMI 2227 - E.R. Gauthier, Ph.D.
14
Example of enzyme catalysis
1. Chymotrypsin - catalysis

The oxyanion hole is
formed by Ser195 and
Gly193;

The formation of Hbonds between the
peptide bond NH group
of these amino acids
and the O- stabilizes the
reaction intermediate
CHMI 2227 - E.R. Gauthier, Ph.D.
15
Example of enzyme catalysis
Similarities between different proteases
CHMI 2227 - E.R. Gauthier, Ph.D.
16
Example of enzyme catalysis
Similarities between different proteases
CHMI 2227 - E.R. Gauthier, Ph.D.
17
Example of enzyme catalysis
2. Enolase

Enolase catalyses one of the multiple enzymatic
reactions of glycolysis (the degradation of
glucose into pyruvate);
CHMI 2227 - E.R. Gauthier, Ph.D.
18
Example of enzyme catalysis
2. Enolase
CHMI 2227 - E.R. Gauthier, Ph.D.
19
Example of enzyme catalysis
2. Enolase
CHMI 2227 - E.R. Gauthier, Ph.D.
20
Example of enzyme catalysis
3. Lysozyme

Lysozyme is present in
tears and egg white;

It degrades sugars found
on the bacterial cell wall
(peptidoglycan);
CHMI 2227 - E.R. Gauthier, Ph.D.
21
Example of enzyme catalysis
3. Lysozyme
Sugar portion
of peptidoglycan
CHMI 2227 - E.R. Gauthier, Ph.D.
22
Example of enzyme catalysis
3. Lysozyme
CHMI 2227 - E.R. Gauthier, Ph.D.
23
Example of enzyme catalysis
3. Lysozyme
HO
2
2
CHMI 2227 - E.R. Gauthier, Ph.D.
24