Enzyme kinetics and mechanisms

Question 1

catalysts

Answer 1

• Increase the rate of chemical reactions
• Participates in the chemical reaction but is overall unchanged
• Changes the rate of reaction but not position of equilibrium
  
  • equilibrium is just approached more rapidly
• most biological catalysts are enzymes

Question 2

First order reaction

Answer 2

A reaction that proceeds at a rate that depends linearly on only one reactant concentration

r=k[A]¹

ln[A]=-kt+ln[A]_o

Question 3

second order reaction

Answer 3

A reaction in which the sum of the exponents in the rate law is equal to 2

r=k[A]¹[B]¹

(1/[A])=k(t)+(1/[A]_o)

Question 4

transition state

Answer 4

The state with the highest energy along the reaction coordinate

more energy than the subtrate or product, therefore it is the least stable

Enzymes lower the activation energy by binding and stabilizing transition state structures

Question 5

Example of a transition state

Answer 5

a molecule going from boat conformation to half chair and finally to chair formation.

Question 6

How do enzymes lower activation energy?

Answer 6

• Increase fraction of molecules with sufficient energy
• Increase rate of reaction in both directions

Question 7

How does a catalyst lower energy barrier?

Answer 7

• Lower energy by forcing reacting molecules into state resembling the transition state but lower in energy
  
  • Lower energy state as a result of binding to the catalyst
• Effect proper orientation of reacting molecules
• Enzymes may provide intermediate state

Question 8

Two models for enzyme-substrate interaction

Answer 8

• Lock and key model
• Induced fit model

Question 9

For a simple enzymatic reaction involving one reactant and one product…

Answer 9

we can write an equation like

E + S ⇔ ES ⇔ EP ⇔ E + P

All of the double arrows have associated k’s and k_-1’s

• Often the first step, binding of the substrate, is reversible k₁ and k_-1 >> k₂
• The second step, conversion of ES to EP, lies far to the right k_{2 >>} k_-2
• The third step, release of product, is rapid compared to the catalytic step k₃ >> k₂

Question 10

Initial rate kinetics

Answer 10

The initial rate corresponds to the kinetics before a significant amount of product is formed

Question 11

Enzymes may bind two or more substrates

Answer 11

most biochemical reactions involve more than one substrate

Question 12

Classify based on order of substrate binding

Answer 12

• Random substrate binding
• Ordered substrate binding
• Ping pong mechanism
  *

Question 13

Inihibition

Answer 13

• Reversible - noncovalent binding of inhibitor
• Irreversible - covalent binding of inhibitor
  
  • typically toxic substances
  • may react with amino acid residue of active site
    
    • serine
    • histidine
  • may react with metal ion cofactors
  • may block active site so substrate cannot bind

Question 14

Substrate specificity

Answer 14

• Substrate binding is stabilized by the same noncovalent forces that stabilize the structure of proteins
• Stereospecificity
• geometric specificity
• physical complementarity
  *

Question 15

Cofactors

Answer 15

• Enzyme functional groups can participate in limited types of reactions
  
  • Acid-base reactions
  • formation of some covalent bonds
  • charge-charge interactions
• To participate in other types of reactions enzymes need helpers called cofactors
  
  • Metal ions
  • Organic molecules (often called coenzymes