the chemical nature of enzyme catalysis polar non- polar tyr*his gly acidicneutralbasic asp glu gln...
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The Chemical Nature of Enzyme Catalysis
PO
LAR
NO
N-
PO
LAR
Tyr* His
Gly
Acidic Neutral Basic
Asp
Glu GlnCys
Asn Ser*
Thr* Lys
Arg
AlaVal
IleLeu Met
Phe TrpPro
*OH
Amino acids
• Acid-Base Catalysis• Covalent catalysis: Nucleophilic
catalysis• Metal ion catalysis• Electrostatic catalysis• Transition state binding• Proximity-Orientation effect
Enzyme Catalysis
Acid-Base Catalysis
• An acid is a "proton donor" and a base is a "proton acceptor”
• In acid catalysis and base catalysis a chemical reaction is catalyzed by an acid or a base.
HO
H
Acid-Base Catalysis
CO=
NH
HCH
NH
+
C- OOH
OH
-d
+d
HO
H
CO=
NH
HCH
CO=
NH
HCH
CO=
NH
HCH
Acid-baseCatalysis Acid
catalysis
Basecatalysis
Both
NH
+
C- OO
HO
H
Keto enol
Slow Fast Fast Very Fast
Acid-Base Catalysis
• Hydrolases: Hydrolysis of esters, peptides, phosphate
• Isomerases: Tautomesism (keto enol; amino:imino)
Side chains of Asp/Glu/ His/Cys/Tyr/Lys act as general acid/base
Covalent catalysis: Nucleophilic catalysis
Decarboxylation of acetoacetate in to acetone
Covalent catalysis: Nucleophilic catalysis
1. The enzyme forms a covalent bond to the substrate at some point during reaction
2. Lysine in the active site forms a Schiff base with the acetoacetate. (amine nucleophilically attack carboxyl group)
3. The positive charge of the Schiff base then facilitates decarboxylation (new electrophilic group withdraw electron from reaction centre)
Covalent catalysis: Nucleophilic catalysis
Covalent catalysis: Nucleophilic catalysis
N
H
H
:B
O+
H-A
N
H
CH
HOH N
H
C + OH-
Schiff base (w PLP)
N+
HCN+
H
Lys
CH3
2-O3PO
H
O-
H2CO
CH2 CO
O-
CO2
H2C
O-
CH2
H+
H2CO
CH3
acetoacetate Enolate Acetone
RNH2
OH-
N+R H
H2C CH2 CO
O-
CO2
H2C
N
CH2
H+
H2C
N+
CH3
OH-
RNH2
R HR H
Schiff base (imine)
Activity Regulation: Metal ion catalysis
Metal ion catalysis
1. Bind to substrate for proper orientation2. Mediate oxidation reduction reaction3. Metal-Electrostatic catalysis
Metal-Electrostatic catalysis1. Charge stablization (similar to or better
than Proton (pH not altered & >1charge2. Promote nucleophilic cartalysis3. Promote reaction through charge shielding
Metal ion catalysis: Charge stablization
Metal ion catalysis: nucleophilic cartalysis
OH- is a weak nucleophilic agent but in presence of Zn it becomes a good nucleophilic
Nucleophilic cartalysis: carboxypeptidase
Activity Regulation: Electrostatic catalysis
Electrostatic catalysis: serine protease
Ser195
His 57
Asp 102
H–O–CH2
O
C–O -
=
Active Ser
H–N N
C C
C
H
H
CH2
Ser195
His 57
Asp 102
- O–CH2
OC–O–H
=
N N–H
C C
C
H
H
CH2
Substrate
If enzyme just binds substrate then there will be no further reaction
Transition state Product
Enzyme not only recognizes substrate, but also induces the formation of transition state
X
Activity Regulation: transition state binding
Activity Regulation: transition state binding
Preferred binding of the transition state complexTransition state analogues are competitive inhibitors
N
CCOO-
H
H
N
C-
H
COO-
N
CH
COO-
H
L-proline
proline racemase
planar TSD-proline
H+ H+
NCOO-
H
pyrrole-2-carboxylate
N+COO-
H
D-1-pyrroline-2-carboxylate
competitive inhibitors
Activity Regulation: Proximity-Orientation effect