Chapter 6 (Exam 2)

Question 1

What are enzymes?

Answer 1

Biological catalysts: increase reaction rates without being used up.
Most enzymes are globular proteins.
- Some RNA (ribozymes and ribosomal RNA) also catalyze reactions.

Question 2

By how much can an enzyme accelerate the rate of a reaction?

Answer 2

By factors of as much as a million or more.

Question 3

What is Carbonic Anhydrase?

Answer 3

An enzyme that catalyzes hydration reactions.
One of the fastest known enzymes: can hydrate 10^6 molecules of carbon dioxide per second.
Catalyzed reaction is 10^7 times as fast as the uncatalyzed one.

Question 4

What are substrates?

Answer 4

Reactants in enzyme-catalyzed reactions.

Question 5

What are Proteolytic enzymes?

Answer 5

Also known as proteases.
Catalyze hydrolysis of peptide bonds.
Hydrolysis reaction.

Question 6

What is papain?

Answer 6

An enzyme from papaya plants that cleaves any peptide bond.
Exhibits broad specificity.

Question 7

What do proteolytic enzymes have?

Answer 7

Different degrees of specificity

Question 8

What is trypsin?

Answer 8

Cleaves on the carboxyl side of arginine and lysine residues.

Question 9

What is thrombin?

Answer 9

Cleaves Arg-Gly bonds in particular sequences only (high specificity)

Question 10

What are the 6 major classes of enzymes?

Answer 10

1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases

Question 11

What are oxidoreductases?

Answer 11

Involved in oxidation and reduction

Question 12

What are transferases?

Answer 12

Transfer functional groups between molecules

Question 13

What are hydrolases?

Answer 13

Cleaves molecules by addition of water; catalyze hydrolysis of a substrate.
Proteases papain, trypsin, and fibrinogen.

Question 14

What are lyases?

Answer 14

Add atoms or functional groups to a double bond or remove them to form double bonds.

Question 15

What are isomerases?

Answer 15

Catalyze rearrangements of atoms within a molecule.

Question 16

What are ligases?

Answer 16

Join 2 molecules.

Question 17

What do many enzymes require for activity?

Answer 17

Non-protein cofactors.

Question 18

What falls under cofactors?

Answer 18

Metal ions: ex. Fe2+, Cu2+, Zn2+.
Coenzymes: organic molecules.
- Cosubstrates: transiently associated with the enzyme (ex. NADH)
- Prosthetic groups: permanently associated with the enzyme (often covalently bound); ex. Heme, some FADH2 enzymes.

Question 19

What are the 2 groups of cofactors?

Answer 19

1. Coenzymes: organic molecules derived from vitamins.
2. Metals

Question 20

What is a holoenzyme?

Answer 20

An enzyme with its cofactor.

Question 21

What is an apoenzyme?

Answer 21

An enzyme without its cofactor.

Question 22

What are prosthetic groups?

Answer 22

Tightly bound coenzymes.

Question 23

What do properties of the reaction depend on?

Answer 23

Free-energy differences.

Question 24

What is Gibbs free energy (G)?

Answer 24

Measure of useful energy.

Question 25

What does the free-energy change of the reaction (delta G) tell us?

Answer 25

Whether the reaction can take place spontaneously.

Question 26

Do enzymes alter the delta G of a reaction?

Answer 26

No.

Question 27

What does the free-energy change provide information about?

Answer 27

The spontaneity but not the rate of a reaction.

Question 28

What is an exergonic reaction?

Answer 28

Reaction will occur without the input of energy, or spontaneously, only if delta G is negative.

Question 29

What is an endergonic reaction?

Answer 29

Reaction will not occur spontaneously if the delta G is positive.

Question 30

What happens at equilibrium in a reaction?

Answer 30

There is no net change in the amount of reactant or product.
Delta G = 0.

Question 31

What does the delta G of a reaction depend on?

Answer 31

Only on the free energy difference between reactants and products and is independent of how the reaction occurs.

Question 32

What does the delta G of a reaction not provide information about?

Answer 32

The rate of the reaction.

Question 33

What do enzymes do to activation energy?

Answer 33

Decrease it.

Question 34

Do enzymes affect equilibrium?

Answer 34

No, so enzymes cannot affect delta G.
Slow reactions face significant activation barriers that must be surmounted during the reaction.
Enzymes increase reaction rate (k) by decreasing delta G plus (catalyzed delta G), the free energy of activation.

Question 35

How do enzymes facilitate the formation of the transition state?

Answer 35

Enzyme-catalyzed reactions take place in the pocket on the enzyme called active site.
The molecule that is bound in the active site and acted upon by the enzyme is called the substrate.
Enzymes bring substrates together to form an enzyme-substrate complex on the active site.
formation of enzyme-substrate complex drive selectivity.
Interaction of the enzyme and substrates at the active site promotes the formation of the transition state.
Active sites may include distance residues.

Question 36

What are common features of active sites of enzymes?

Answer 36

1. Active site is a 3-dimensional surface created by amino acids from different parts of primary structure.
2. Active site constitutes a small portion of the enzyme volume.
3. Active sites create unique microenvironments.
4. Interaction of the enzyme and substrate at the active site involves multiple weak interactions.
5. Enzyme specificity depends on the molecules architecture at the active site.