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Review Chapter 1
Read Chapter 6
5e Chapter 1: p20-27
6e Chapter 1: p21-25
1
Examples of enzymes
Why enzymes?
2) Thermodynamics a
review
) Mechanisms of catalysis
4) Enzyme kinetics
5) Chymotrypsin
E(Enzyme) + S(Substrate)
3
Substrate
Activesite
H
-
+
NH3
OOC
+
NH3
No binding
+
NH3
OOC
H
OOC
H
-
OH
OH
HO
H
H
OH
H
NH
CH3
Binding but no
reaction
Why biocatalysis?
In other words, why enzymes?
Co-Enzymes
Enzyme structure
A complete enzyme
(functional) =
holoenzyme
Alcohol
dehydrogenase:
Needs Zn (prosthetic
group, also a cofactor): a holoenzyme
with Zn2+ atom
Enzyme classification
and nomenclature (1)
Usually enzyme names end with a ase suffix
Usually ase is attached to a name that designates the
substrate or the activity
Example 1: urease catalyses hydrolysis of urea
Example 2: DNA polymerase catalyses
polymerization of DNA.
But it is not always the case: example pepsin
and trypsin there is a systematic classification
11
S
+S
12
G positive
reaction
favours
SUBSTRATE
S
G negative
reaction
favours
PRODUCTS
14
16
Properties of enzymatic
reactions
G
+G
HOW FAST?
17
S
19
G
+G
Metabolism
Photosynthesis
20
21
G = +H (T(-S)) = +ve
+H
- S
+S
-H
G = -H (T(+S))= -ve
Chemical energy of glucose oxidation is coupled in the
respiratory chain to drive +G reactions like making
ATP
22
Glucose + Pi
Glucose 6-phosphate
ATP
ATP + Pi
Glucose + ATP
23
24
S
25
G
+G
26
The enzyme-substrate
complex
-G , k1
No enzyme S
P
+G , k-1
-G = -G
+G = +G
cat
-G cat , kcat1
E+S
ES
+G
EP
cat
, kcat-1
cat
E + P k >>>k
cat1
1
kcat-1 >>>k-1
Enzymes accelerate
reaction
rates
Enzymes (and catalysts in general) lower the
activation barrier compared to the uncatalyzed reaction
28
30
35
Chemical example:
The rate of anhydride formation
from esters and carboxylates
shows a strong dependence on
proximity of two reactive groups
36
37
38
39
40
CH3
H3C
H2O
slow
O
O
H3C
2 H
CH3
H3C
fast
+
N
CH3
..
N
..
..
N
H3C
H3C
+
N
OH
H
CH3
H3C
H2O
H2O
A
A-X+ B
+ B
+ X: + B
Covalent Catalysis: In
Enzymes
Proteases and peptidases
chymotrypsin, elastase, subtilisin
reactive serine nucleophile
Some aldehyde dehydrogenase
glyceraldehyde-3phosphate dehydrogenase
reactive thiolate nucleophile
Aldolases and decarboxylases
amine nucleophile
Dehalogenases and some glycosidases
carboxylate nucleophile
NH2
HO
O
S
44
45
46
47
EnzymeSubstrate EnzymeSubstrate
complex
ES
V
EnzymeProduct
complex
Enzyme Product
EP
= reaction rate
= has units of (moles of Product)/s
48
k
k-1
S1 + S2
k-1
Equilibrium constant
Keq = [P]
[S]
Reaction equation
V = k[S]
Second-order reaction
[P]
Keq =
[S1][S2]
V = k[S1][S2]
First-order reaction
49
50
Initial time
of
reaction;
rates are
nearlinear
51
52
53
k1
k-1
ES
k2 = (kcat)
E + PSlower, rate-limiting
[ES] is going to determine overall rate
k-2
Steady-state Kinetics
Studies the initial rate, V0
At this stage, [S] can be assumed to be nearly constant
[P] is very small
ES breakdown to E + P is rate limiting step;
Enzyme-Substrate complex is nearly constant
Overall rate proportional to [ES]
E+S
k1
k-1
ES
k2
E+P
k-2 is negligible in
early reaction
because there is
little P! 55
E S
ES
EP
56
Vmax [ S ]
Vvo
Km S
57
58
Double-Reciprocal Plot
(Lineweaver-Burke plot)
59
Double-Reciprocal Plot
60
Competitive inhibition
ES
EI
(Inhibitor)
61
Uncompetitive
inhibition
ES
+
(inhibitor)
ESI
62
Types of enzyme
inhibitors
Competitive
Non-competitive
63
Chapter 6: Summary
Assigned Reading:
Suggested problems
Worked example 6-1 and 6-2 (page 199-200 5e, page 206 6e)
Problems (page 229-233): #1, 3, 6, 7-13
64