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How is TS Stabilization
Achieved?
acid-base catalysis: give and take protons
covalent catalysis: change reaction paths
metal ion catalysis: use redox cofactors, pKashifters
electrostatic catalysis: preferential interactions with TS
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Acid-base Catalysis:
Chemical Example
Consider ester hydrolysis:
R
O CH3
O
R
OCH
3
O
OH H+
R
O
OH+ H - +
+ C H3O
Water is a poor nucleophile, and methanol is a
poor leaving group
Aqueous hydrolysis can be catalyzed eitherby
acids or by bases
Enzymes can do acid and base catalysis simultaneously
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General Acid-Base Catalysis
Example: amide hydrolysis
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Amino Acids
in General Acid-Base catalysis
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The anhydride hydrolysis
reaction is catalyzed by
pyridine, a better
nucleophilethan water
(pKa=5.5).
Hydrolysis is accelerated
because of charge loss in
the transition state
makes pyridine a good
leaving group.
Covalent Catalysis: Chemical Example
CH3
O
O
CH3
O
CH3
O
O
CH3
O
O
H+
- -+H2O
slow + 2
CH3
O
O
CH3
O
N
CH3
O
O
N CH3
O
OH H
N CH3
O
OH
N
CH3
O
O
H+
..
fast-
+
+
..
+
-
-+
..
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Covalent Catalysis: In Enzymes
Proteases and peptidases chymotrypsin, elastase, subtilisin
reactive serinenucleophile
Some aldehyde dehydrogenase
glyceraldehyde-3phosphate dehydrogenase reactive
thiolatenucleophile
Aldolases and decarboxylases
aminenucleophile
Dehalogenases carboxylatenucleophile
OH S
NH2
O
O-
-
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Chymotrypsin MechanismStep 1: Substrate Binding
Endo-peptidase specificity
P3 - P2 - P1-|-P1- P2- P3
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Chymotrypsin MechanismStep 2: Nucleophilic Attack
Serine protease catalytic triad activates
serine hydroxyl
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Chymotrypsin
Mechanism
Step 3: SubstrateCleavage
N-terminal peptide released
Covalent acyl intermediate
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Chymotrypsin
MechanismStep 4:Water attack
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Chymotrypsin MechanismStep 5: De-acylation
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Chymotrypsin MechanismStep 6: Serine hydroxyl restored
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Chymotrypsin
Mechanism
Step 7: ProductDissociates
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Peptidoglycan and Lysozyme
Peptidoglycan is a
polysaccharide found in
many bacterial cell walls
Cleavage of the cell wallleads to the lysis of
bacteria
Lysozyme is an
antibacterial enzyme
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General Acid-Base + Covalent Catalysis:
Cleavage of Peptidoglycan by Lysozyme
X-ray structures of
lysozyme with bound
substrate analogs show
that the C-1 carbon is
located between Glu 35
and Asp 52 residues.
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Cleavage of Peptidoglycan by
Lysozyme: Two Successive SN2
Steps ModelAsp 52 acts as a nucleophileto attack the
anomeric
carbon in the first SN2 step
Glu 35 acts as a general acidand protonates theleaving group in
the transition state.
Water hydrolyzes the covalent glycosyl-enzyme
intermediate
Glu 35 acts as a general baseto deprotonate water
in the second SN2 step
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Enzyme Regulation
Allosteric regulation,
heterotropic ligand binding modulates substrate
binding and catalysis,
Feedback regulates metabolic pathways
Homotropic regulation Multisubunit
Covalent modification Reversible
Phosphorylation, nucleotides, lipid anchors
Proteolysis converts inactive pro-enzymes
(zymogens) to active
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Allosteric Regulation; ATCase
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Chapter 6: Summary
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
In this chapter, we learned about:
