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Voet - Chapt - 11 Enzymes PDF
Voet - Chapt - 11 Enzymes PDF
Introduction
1. Enormous variety of chemical reactions within a cell
2. Mediated by Enzymes
3. Enzymology, the study of enzymes
(coined 1878; Greek: en, in; zyme, yeast),
fermentation: glucose -> ethanol
12 enzyme-catalyzed steps
4. James Summer, 1926, crystallized urease
from jack bean, shown to be a protein
5. Other catalysts, i.e. ribozymes (peptide-bond
formation; RNA-world), only for units
6. Proteins more versatile, 20 functional units
Introduction
Enzymes increase the rate of chemical
reactions by lowering the free energy
barrier that separates the reactants
and products
Table 11-1
A) Classification of Enzymes
- naming: -ase, urease, alcohol dehydrogenase
but no rules,
- systematic: IUBMB: 6 Classes acc. to the nature of
the chemical reaction that is catalyzed
(http://expasy.org/enzyme/)
An Enzyme-Substrate complex
Geometric and
electrostatic
complementarity
Stereospecificity in
substrate binding
Prosthetic groups
Permanently associated with enzyme, often by
covalent bonds, example heme is bound to proteins
called cytochromes
Holoenzyme = enzyme+cofactor complex, active
Apoenzyme, lacks cofactor, inactive
Substrate
Product
Free energy
of activation
Free energy
of reaction
bottleneck
3) Catalytic Mechanisms
Enzymes lower the free energy of the
transition state (G) by stabilizing the
transition state
Learn about enzymatic reactions mechanisms
by examining the corresponding non-enzymatic
reactions of model compounds
Catalytic Mechanisms
Curved arrow convention to trace electron pairs
At all times, rules of chemical reasons apply to
the system, i.e. never five bonds on C, or 2 on H
etc.
pH Optimum of Fumarase
Decarboxylation of acetoacetate
Nucleophilicity of a substance is
related to its basicity:
24-times
faster
Inhibitors
4) Lysozyme
Lysozyme is an enzyme that degrades bacterial cell
walls.
Hydrolyzes (1->4) glycosidic bond from N-acetylmuramic
(NAM) acid to N-acetylglucosamine (NAG) in cell wall
peptidoglycan
also hydrolyzes chitin: (1->4) NAG
Lysozyme occurs widely as bactericidal agent, best
characterized: hen egg white lysozyme, 14.3 kD, single
129 Aa polypeptide chain, 4 disulfide bonds, rate
enhancement 108-fold
(1->4)
D-ring remains
anomer
4) Serine Proteases
Class of proteolytic enzymes,
Active site reactive Ser-residue (cut after Ser !)
digestive enzymes,
developmental regulation
blood clotting
inflammation
many other cellular processes
Focus on chymotrypsin, trypsin, elastase
Diisopropylphosphofluoridate (DIPF)
Diisopropylphosphofluoridate (DIPF)
A second important residue, His 57, was identified
by affinity labeling
Substrate analog bearing reactive groups reacts with
nearby residues, Trojan horses
Chymotrypsin specifically binds tosyl-L-phenylalanine
chloromethylketone (TPCK), resembles Phe, reacts
with His 57
Nerve Poisons
Use of DIPF as enzyme inhibitor based on discovery that
organophosphorous compounds, such as DIPF, acts as potent
nerve poisons.
Inactivate acetylcholinesterase, catalyzes hydrolysis of
acetylcholine, active site Ser
Nerve Poisons
Acetylcholine is a neurotransmitter: transmits nerve
impulses across certain types of synapses (junctions
between nerve cells)
Acetylcholinesterase in the synaptic clevt normally degrades
acetylcholine to terminate nerve impulse.
Acetylcholine receptor, which is a Na+-K+ channel, remains
open for longer than normal, toxic to humans (inability to
breathe)
DIPF so toxic that it has been used as military nerve gas.
Related compound such as parathion and malathion are
used as insecticides
Tetrahedral phosphate
= transition state analog
2. Decomposition of the
tetrahedral intermediate
Decomposition to the acylenzyme intermediate and
scission of the peptide bond
Driven by donation of proton
from N3 of His 57 (general
acid catalysis)
Helped by polarizing effect
of Asp 102 on His 57
(electrostatic catalysis)
5. Reversal of step 1
Yields the carboxylate product, that is the new Cterminus of the peptide, and regenerates the
active enzyme
2.
3.
4.
5.