DBT2117: Biochemistry (I)
Lecture 19
Enzymes
• Understanding the function of an enzyme
• Why it speeds up reaction
• How it speeds up reaction
• Importance of substrate binding to enzyme
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Enzymes
•
Enzymes are biological catalysts
•
A catalyst is a compound that increases rate of a chemical reaction
• Catalyst is never consumed in the reaction
•
Types of enzymes
•
Enzymatic proteins (vast majority)
•
Ribozyme – catalytic RNA
•
Abzyme – antibody
•
The most important question is:
•
How does an enzyme catalyze a chemical reaction?
國立交通大學生物科技學系蘭宜錚老師
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Chemical reactions
•
Before we talk about enzymes, we need to understand chemical reactions
•
Ultimately, all biological reactions are chemical reactions!
•
In any chemical reaction, there is its:
•
Thermodynamics: ΔG’°: does the reaction happen spontaneously? Release energy vs. require energy
•
Kinetics: how FAST does the reaction happen?
MOST importantly!! A Catalyst does NOT change the thermodynamics of a
reaction. Reaction does NOT become more favorable. Instead, reaction just
finishes more quickly.
•
Chemical reaction thermodynamics
•
Reaction of chemicals or compounds can release or require energy
•
Thermodynamics demands that:
• Energy is conserved
• universe favors increase in entropy (disorder)
•
Gibbs free energy (ΔG)
• Tells us whether a particular reaction will be spontaneous
•
ΔG = ΔH – TΔS
H
S
will reaction occur spontaneously?
‐
+
always
‐
‐
only at low temperature
+
+
only at high temperature
+
‐
never
國立交通大學生物科技學系蘭宜錚老師
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What parameters affect thermodynamics of a reaction
•
Temperature and pressure can be looked at as “energy”
•
Increasing temperature & pressure  increases the energy of a system
•
In biochemistry, we look at:
•
ΔGo′: “delta – naught – prime”
• Substrate & production concentration = 1M
• Temperature 25oC
• Pressure 100 kPa (close to 1 atm)
•
•
pH: 7
So in biochemistry, we look at the “nature” of the reaction!
(since most other factors are constant now)
What does ΔGo′ tell us?
•
•
ΔGo′ = ‐ R*T*ln(Keq)
•
•
R is a constant
T is a constant at 298K
•
Keq is the equilibrium constant Keq = [product]eq
[reactant]eq
This equation gives us the
relationship between ΔGo′ and Keq
Lehninger’s Principles of Biochemistry, fourth edition, by David Nelson and Michael Cox
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Thermodynamics vs. kinetics...
•
While some reactions in nature are VERY favorable with VERY negative ΔGo′.
•
But they are not happening “spontaneously”
•
For example, oxidation (combustion) of glucose:
C6H12O6 + 6O2  6CO2 + 6H2O ∆G0' = –2870 kJ/mol
A lot of potential chemical energy is stored in sugar
Oxidation of glucose is a spontaneous process because it releases heat…
However, while the thermodynamics is favorable, the kinetic barrier is too large for this reaction to happen fast enough.
Reaction kinetics
Lehninger’s Principles of Biochemistry, fourth edition, by David Nelson and Michael Cox
•
While some reactions in nature are VERY favorable with VERY negative ΔGo′.
•
But they are not happening “spontaneously”
Fast enough
Rate = k*[Reactant]m
ΔG‡uncat
Arrhenius equation
A is a constant
Ea is activation energy
(commonly written as ΔG‡)
ΔG‡cat
Lower Ea (ΔG‡cat)
Higher the k
ΔGo’
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Some common biological reactions
Reaction rates
Rate of reaction depends on:
•
Numbers of collisions
•
Energy of molecules
•
Orientation of molecules
•
Reaction pathway (transition state)
How do enzymes increase reaction rate without changing temperature?
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How an enzyme works
Substrate movement is restricted in enzyme
Promotes substrate into shape of transition state (which is stabilized by the enzyme)
Stabilization of transition state, lowers the activation energy!
Lehninger’s Principles of Biochemistry, fourth edition, by David Nelson and Michael Cox
Enzymatic reaction property
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Enzymes are catalysts! So it only changes the RATE of reaction
•
Enzymes lower the activation energy from both direction of the reaction.
•
•
Enzymes accelerate reaction rate of both forward and reverse reaction!
Enzymes accelerate reaction towards equilibrium
• (remember that at equilibrium ΔG = 0)
•
It does NOT change the equilibrium!
•
ΔΔGo‡ = ΔGo‡uncatalyzed ‐ ΔGo‡catalyzed
•
ΔGo‡catalyzed will always be lower than ΔGo‡uncatalyzed
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Enzymatic catalysis model
•
Lock & key hypothesis (1894): Enzymes is lock, substrate is a key. Explains specificity of
enzyme, but does not explain the actual catalysis
•
Induced fit hypothesis (1958): both enzyme and substrate are distorted to fit the transition
state.
•
Knowing what we discussed…
•
Which do you think is more accurate to
our current understanding of enzymes?
•
How to lower ΔGo‡catalyzed ? That is, how do we make catalysis happen?
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ΔGo‡catalyzed = ΔHo‡catalyzed – T*ΔSo‡
Enthalpic and entropic effect increases catalysis
How enzyme stabilizes (binds) transition state
•
How enzyme directs substrate to the preferred orientation
Just remember, the ultimate GOAL for catalysis is
to reduce activation energy ΔGo‡.
國立交通大學生物科技學系蘭宜錚老師
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