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Lecture 2: Biochemistry of Enzyme (How is TS stabilization achieved? (end…
Lecture 2: Biochemistry of Enzyme
Enzymes
Advantages
Greater reaction
specificity
Milder reaction
conditions
Higher reaction
rates
Capacity
for regulation
Metabolites have many potential pathways of decomposition; enzymes make the desired one most favorable
How to lower G ?
Enzymes organizes reactive groups into proximity
Enzymes bind transition states best
How is TS stabilization achieved?
(end result: rate enhancement
10^5 - 10^17
)
Covalent catalysis
- change reaction paths
Metal ion catalysis
- use redox cofactors, pKa shifters
Acid-base catalysis
- give and take protons
Electrostatic catalysis
- preferential interactions with TS
Enzyme kinetics
Kinetics
- study of the rate at which compounds react
Rate of enzymatic reaction is affected by:
enzyme, substrate, effectors, temperature
Kinetic measurements
Michaelis-Menten equation derivation
Rate of ES formation = k1([Et] - [ES])[S]
([Et] is total concentration of enzyme E and k-2 is considered neglible)
Rate of ES breakdown to product = k1[ES] + k2[ES]
Enzyme inhibition
Inhibitors
- compounds that decrease enzyme's activity
Irreversible inhibitors
(inactivators)
one inhibitor molecule can
permanently shut off
one enzyme molecule
often
powerful toxins
but also may be used as drugs
Reversible inhibitors
bind to, and can dissociate from the enzyme
often structural analogs of substrates or products
often used as drugs to slow down a specific enzyme
can bind
to the free enzyme and prevent the binding of the substrate
to the enzyme-substrate complex and prevent the reaction
