Enzyme mechanisms

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Lecture 12

• Enzyme mechanisms

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Common enzyme reactions
Oxidation and reductions (cofactors are involved!)
(Oxidation of an alcohol to a ketone)


B
NAD
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Common enzyme mechanisms
Isomerizations
B
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More common enzyme mechanisms
Making and breaking C-C bonds
Aldol condensation
O
B
H
C
C
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Example of reactions
Phosphorylation/ dephosphorylation
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Lysozyme

• Discovered by Fleming, 1922
• Lyses the cell wall of bacteria by cleaving the
  polysaccharides in bacterial cell walls

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Lysozyme specificity

• Hexamer (or longer) of sugars binds
• 4th sugar residue must be distorted
• Cleaves between the 4th and 5th
• sugar

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Lysozyme mechanism
General acid base catalysis Stabilization of
carbocation
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Lysozyme mechanism
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Covalent Catalysis by Enzymes

• Formation of acylserine intermediate by
  chymotrypsin

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Covalent Catalysis by Enzymes
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Identifying Covalent Catalysis
Identical rates reflect rate-limiting breakdown
of a common intermediate
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Mechanism and rate
ENZYME
fast
O
ENZYME
O
C
Acyl-enzyme intermediate
H2O
slow
H
-

ENZYME
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Identification of catalytic residues
ENZYME

ENZYME
Only serine 195 reacts with DIPF (no other serine
in the protein reacts)
Irreversible reaction inactivates enzyme
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Catalytic Triad

• Ser195 - Nucleophile
• His57
• Asp102

General acid and base catalysis
Serine proteases (esterases) all have similar
mechanisms.
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Catalytic Triad
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Chymotrypsin

• pH-rate profile

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Chymotrypsin Mechanism
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Hexokinase

• Mr 100,000
• Glucose gtgt H2O 106
• ATP Glucose ADP
  Glucose-6-Phosphate

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Hexokinase Mechanism

• Induced fit
• Glucose unbound