Enzymes (Ch. 6)
• Intro
• Basics of catalysis
• General types of catalysis
• Quantification of catalysis– enzyme kinetics and inhibition
• Specific examples
• Allostery and enzyme regulation
EN
ER
GY
(G
°)
REACTION PROGRESS
G < 0
Reaction should bespontaneous
Equil should favorproducts
Biological reaction:sugar + oxygen ↔ CO2 + water
Reactants (R)
Activation energy
EA
Kinetic barrier to reaction
High energy “Transition state”Intermediate between R & P
Products (P)
The energy barrier is critical for life
• Potentially deleterious reactions are blocked by EA
– Complex molecule degrading to simpler constituents
http://asm.wku.eduhttp://encyclopedia.quickseek.com/
DNAnucleotide
How do enzymes speed up reactions?
• New reaction pathway
• Lower activation energy
• Decreased energy barrier
2H2O2 → 2H2O + O2
Isolated: EA ~ 86 kJ/molIn the presence of catalase: EA ~ 1kJ/mol
Hydrogen peroxide
Binding of substrate to enzyme creates a new reaction pathway
http://w3.dwm.ks.edu.tw/
An enzyme changes EA NOT G
Affects RATE, not EQUILIBRIUM
Without enzyme
With enzyme
EA = G‡
How is EA lowered?
• Enzyme’s ‘goal’ is to reduce G‡
• Two ways enzymes can affect G
– Improve H– Improve S
EA =G‡ = H - TS
G‡ = Gtrans.state – Greactants
Enzymes alter the free energy of the
transition state
enthalpy entropy
-
Example: More favorable H
A B
AOHBH
A BH+
+ H2O
+OH-
+
Charge unfavorableUnstable transition st.
A BH+
Ionic interaction stabilizesthe positive charge
OH-
Example: More favorable S
Two moleculesMore ‘freedom’Higher disorder (high S)
One moleculeLower disorder (low S)Unfavorable entropically
ENZYME
Example: More favorable S
Enzyme/Reactant COMPLEX
Essentially a single molecule
ENZYME
Enzyme/Transition state complex
Still a single molecule
Not much difference entropically
Remember
1. Enzymes lower the energy barrier
2. Decrease EA (G‡)
3. Provide an environment where:
• Transition state is stabilized (lower enthalpy)• Change of disorder (entropy) is minimized
Enzymes create a new reaction pathway
Go vs. G‡ transition state vs. reaction intermediates rate limiting step
Factors contributing to enzyme catalysis
• Weak interactions between enzyme and transition state
• Transient covalent bonds between S and E
• Entropy optimization in ES complex formation
• Solvation shell surrounding S & E (entropy/hydrophobic interactions)
• Substrate distortion upon binding to noncomplementary E
• Proper alignment of catalytic functional groups
Common catalytic mechanisms
• General acid/base catalysis– Proton transfer– Reactions with charged
intermediates/AAs• Fumarase
– Precise positioning of acid/base: reaction occurs faster than specific acid/base reactions
• Free H+/OH-
Common catalytic mechanisms
• Covalent catalysis– Covalent bond formation
between E and S– Reaction path is altered
and new path has lower Ea
– Chymotrypsin (combination)
Common catalytic mechanisms
• Metal catalysis (metalloenzymes)– Ionic interactions
• Stabilize charged TS or orient charged substrate for reaction
• Carboxypeptidase
– Oxidation/reduction• Reversible changes in oxidation state of the metal• Electron transfer reactions • Transition metals• Catalase ezample