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Study of enzymatic processes is the oldest field of biochemistry, dating back to late 1700s Study of enzymes has dominated biochemistry in the past and continues to do so
Classification of Enzymes
Each enzyme is assigned a four-part classification number and a systematic name, which identifies the reaction it catalyzes.
The enzyme chymotrypsin, with bound substrate in red (PDB ID 7GCH). Some key active-site amino acid residues appear as a red splotch on the enzyme surface.
Rate Acceleration
Enzymes affect reaction rate, not equilibria. A favorable equilibrium S P does not mean a detectable rate. The rate of a reaction depends on the activation energy G: a higher activation energy corresponds to a slower reaction. Catalysts enhance reaction rates by lowering activation energies.
How to Lower G?
Enzymes organize reactive groups into proximity
Uncatalyzed bimolecular reactions:
two free reactants single restricted transition state
Largely H effect
acid-base catalysis: give and take protons covalent catalysis: change reaction paths metal ion catalysis: use redox cofactors, pKa shifters electrostatic catalysis: preferential interactions with TS
HO N O
O S O O
O N O
k1
KS =
k-1 k1
E+S
k1 k-1
ES
k2
E+P
Enzyme-Substrate Complex
[Etot] = [E] + [ES] f = k1 [E] [S] = k1 ([Etot] - [ES]) [S] d = k-1 [ES] + k2 [ES] f = d k1 ([Etot] - [ES]) [S] = (k-1 + k2) [ES]
k-1 + k2 k1
= Km
Michaelis-Menten Equation
The rate of formation of product is V0 = k2 [ES]
V0 =
V0 =
Michaelis-Menten Equation
The final form in case of a single substrate is
E+S
k1 k-1
ES
k2
E+P
v=
k [ E ][ S ] K + [S ]
cat tot m
kcat (turnover number): how many substrate molecules can one enzyme molecule convert to product per second when the enzyme is saturated Km (Michaelis constant): an approximate measure of substrates affinity for enzyme Microscopic meaning of Km and kcat depends on the details of the mechanism
V0 =
Deviations due to:
Limitation of measurements Substrate inhibition Substrate prep contains inhibitors Enzyme prep contains inhibitors