biochemistry lecture 8. why enzymes? higher reaction rates greater reaction specificity milder...
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Biochemistry
Lecture 8
Why Enzymes?• Higher reaction rates• Greater reaction specificity• Milder reaction conditions• Capacity for regulation
COO
OH
O COO
COO
O COO
NH2
OOCCOO
O
OH
OH
COO
NH2
COO
-
-
-
-
-
-
--
Chorismate mutase
• Metabolites have many potential pathways of decomposition
• Enzymes make the desired one most favorable
Enzymatic Substrate Selectivity
No binding
OOC NH3
H
OOC NH3
H
HNH
HOH
OH
H
OH
CH3
OOC NH3
H
OH
--
-
+
+
+
Binding but no reaction
Example: Phenylalanine hydroxylase
How to Lower G?Enzymes organizes reactive groups into
proximity
How to Lower G?Enzymes bind transition states best
How is TS Stabilization Achieved?
– 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
End result? Rate enhancements of 105 to 1017!
How is TS Stabilization Achieved?
– covalent catalysis: change reaction paths
CH3O
O
CH3
O
CH3O
O
CH3O
O
H+- -+
H2O
slow + 2
CH3O
O
CH3
O
N
CH3O
O
N CH3
O
OH H
N CH3
O
OHN
CH3O
O
H+
..fast
-+ +
..
+
-
-+..
Enzyme Kinetics
• Kinetics is the study of the rate at which compounds react
• Rate of enzymatic reaction is affected by– Enzyme– Substrate– Effectors– Temperature
How to Do Kinetic Measurements
What equation models this behavior?
Michaelis-Menten Equation
Meaning of Vmax and Km
Simple Enzyme Kinetics
• The final form in case of a single substrate is
• kcat (turnover number): how many substrate molecules can one
enzyme molecule convert per second
• Km (Michaelis constant): an approximate measure of
substrate’s affinity for enzyme
• Microscopic meaning of Km and kcat depends on the details of
the mechanism
][
]][[
SK
SEkv
m
totcat
Two-substrate Reactions
• Kinetic mechanism: the order of binding of substrates and release of products
• When two or more reactants are involved, enzyme kinetics allows to distinguish between different kinetic mechanisms
– Sequential mechanism– Ping-Pong (Double Displacement) mechanism
Distinguishing Mechanism
Ping-PongTernary Complex
Enzyme Inhibition
Inhibitors are compounds that decrease enzyme’s activity
• Irreversible inhibitors (inactivators) react with the enzyme- one inhibitor molecule can permanently shut off one enzyme molecule- they are often powerful toxins but also may be used as drugs
• Reversible inhibitors bind to, and can dissociate from the enzyme - they are often structural analogs of substrates or products - they are often used as drugs to slow down a specific enzyme
• Reversible inhibitor can bind:
– To the free enzyme and prevent the binding of the substrate
– To the enzyme-substrate complex and prevent the reaction