Enzymatic Catalysts

Question 1

What are some general properties of enzymes?

Answer 1

• High reaction rates
• Mild reaction conditions: can catalyze reactions at low temperatures and close to neutral PH
• Greater specificity
• Can be regulated through allostery

Question 2

Cofactors

Answer 2

• Non-protein molecules
• Provide different types of chemistry (tools) that allows enzyme to catalyze different reactions

Question 3

What are the two types of cofactors?

Answer 3

• Metal ions
• Coenzymes

Question 4

Metal ions

Answer 4

Cations that help orient negatively charged molecules on substrate accordingly (stabilizes negatively charged molecules)

Question 5

Coenzyme

Answer 5

Organic molecules that bind to enzymes and expand their tool kit
- Protetic groups
- Cosubstrates

Question 6

Prosthetic Groups

Answer 6

Bind irreversibly to enzyme

Question 7

Cosubstrates

Answer 7

Bind reversibly to enzyme

Question 8

Apoenzyme

Answer 8

Enzyme is inactive because it is not yet bonded to its cofactor

Question 9

Haloenzyme

Answer 9

Enzyme is active / bound to its cofactor

Question 10

At what point is an enzyme at its lowest concentration and highest free energy?

Answer 10

The transition state

Question 11

What is the free energy of activation (aka activation energy)?

Answer 11

The barrier that you must overcome to get to the transition state
*This determines the kinetics of the reaction (the larger the free energy of activation the slower the reaction will occur)

Question 12

What is a catalyst (enzyme)?

Answer 12

Enzymes are proteins that lower the free energy of the transitions state (speeding up the reaction)

Question 13

What is the rate enhancement?

Answer 13

Rate of the catalyzed reaction / rate of the uncatalyzed reaction
This is proportional to the stabilization of the activation energy by the enzyme

Question 14

Enzyme catalytic mechanisms

Answer 14

• Acid-base catalysis
• Covalent catalysis
• Metal ion cofactors
• Entropy reduction
• Preferential binding to the transition state
  An enzyme can use more than one of these methods to catalyze a reaction

Question 15

Acid-Base Catalysis

Answer 15

• The goal is to avoid creating a transition state species which has a positive charge O2 (why?: O2 does not like to have a positive charge which results in a high free energy and activation energy)
• Charged amino acids = capable of acid-base catalysis

Question 16

Covalent Catalysis

Answer 16

• Forming a covalent bond between the nucleophile on an enzyme and part of the substrate
• Covalent intermediate has low free energy and low activation energy
• Nucleophilicity = related to basicity (stronger base = stronger nucleophile)
  If nucleophile = too good the covalent bond between the nucleophile on the enzyme and the substrate will be too difficult to break

Question 17

Entropy Reduction

Answer 17

• Enzyme acts as a platform to bring two substrates together and orient groups in a way to make productive interactions (most reactive orientation)
• Rate enhancement is increased (lower activation energy)

Question 18

Preferential binding to the transitions state

Answer 18

• The free energy difference between the ES complex and the E-transition state complex is less than the substrate and transition state (activation energy = lower / reaction will go faster)