Lecture 12, Catalysis (Ford)

Question 1

What do enzymes do?

Answer 1

Lower activation energy and stabilize transition state

Question 2

T or F: Enzymes alter the thermodynamics of a reaction.

Answer 2

False. Enzymes do not change the deltaG of a reaction.

Question 3

Can enzymes irreversible change shape?

Answer 3

No

Question 4

What is a catalyst?

Answer 4

Increases the rate of a reaction but does not undergo any permanent chemical change as a result

Question 5

What is Gibbs Free Energy equation?

Answer 5

deltaG = deltaH - T*deltaS

Question 6

Describe what happens when there is a negative deltaH value.

Answer 6

Energy is released from the system

Question 7

Describe what happens when there is a positive deltaH value.

Answer 7

Energy is added to the system

Question 8

Describe what happens when there is a negative deltaS value.

Answer 8

Disorder decreases

Question 9

Describe what happens when there is a positive deltaS value.

Answer 9

Disorder increases

Question 10

Describe what a negative deltaG value indicates.

Answer 10

Free energy released, exergonic reaction, favorable reaction, spontaneous reaction

Question 11

Describe what a positive deltaG value indicates.

Answer 11

Free energy required, endergonic reaction, unfavorable reaction, driven reaction

Question 12

Describe what deltaG = 0 means.

Answer 12

Equilibrium

Question 13

How would you calculate deltaG when the reaction is not at equilibrium?

Answer 13

deltaG = deltaG’ + RT*lnQ

Question 14

How would you calculate deltaG when the reaction is at equilibrium?

Answer 14

deltaG = deltaG’ + RT*lnK

Question 15

What is the unit for temperature when used in the Gibbs Free Energy reaction?

Answer 15

Kelvin

Question 16

What are some biochemical strategies to drive an unfavorable reaction?

Answer 16

Maintain Q < K; Couple it to a highly favorable reaction

Question 17

What does it mean to couple an unfavorable reaction to a highly favorable one?

Answer 17

Reactions and deltaG values can be summed; Couple with ATP hydrolysis

Question 18

What is the transition state?

Answer 18

High energy, unstable form of the reactants that is ready to form products

Question 19

What is the activation energy?

Answer 19

Energy barrier that must be overcome for the reaction to proceed

Question 20

How can a reaction be sped up?

Answer 20

1. Raise temperature

2. Stabilize the transition state with an enzyme

Question 21

Describe the induced fit model.

Answer 21

When a substrate binds, the enzyme changes shape so that the substrate is forced into the transition state

Question 22

Give the 4 ways catalysis is achieved.

Answer 22

1. Substrate orientation
2. Sustaining substrate bonds
3. Creating a favorable microenvironment
4. Covalent/noncovalent interactions between enzyme and substrate

Question 23

Describe covalent catalysis.

Answer 23

Enzyme covalently binds the transition state

Question 24

T or F: Covalent catalysis is a transfer of electrons.

Answer 24

True.

Question 25

Describe acid-base catalysis.

Answer 25

Partial proton transfer to the substrate

Question 26

Describe catalysis through approximation.

Answer 26

If electrons/protons must be exchanged, proper spatial orientation and close contact (proximity) of the reactant molecules must occur; "entropy reduction"

Question 27

Describe electrostatic catalysis.

Answer 27

Stabilization of unfavorable charges on the transition state by polarizable side chains in the enzyme/metal ions

Question 28

Why are proteases needed?

Answer 28

Recycling, regulation, defense

Question 29

What are the various applications of carbonic anhydrases?

Answer 29

Physiological (pH regulation, enzyme pathway regulation), medical (artificial lungs), industrial (CO2 scrubbers for reduction of greenhouse gases)

Question 30

Describe the active site of chymotrypsin.

Answer 30

Catalytic triad: serine = nucleophile, histidine = base (proton acceptor), aspartic acid = acid (proton donor)

Question 31

In chymotrypsin, what stabilizes the tetrahedral intermediate (transition state)?

Answer 31

Oxyanion hole

Question 32

Regarding chymotrypsin, what determines the placement of the cut?

Answer 32

Specificity pocket

Question 33

What does the active site of carbonic anhydrases contain? What is it coordinated to?

Answer 33

Zn2+ ion; Coordinated to 3 histidines and a water

Question 34

Regarding carbonic anhydrases, what is the importance of water?

Answer 34

Facilitates the transition state (deprotonated)

Question 35

Which catalytic strategy does water use for the transition state of a carbonic anhydrase?

Answer 35

Approximation

Question 36

Regarding carbonic anhydrases, what determines the size of the substrate?

Answer 36

Entry channel

Question 37

What is the reaction mechanism for a carbonic anhydrase?

Answer 37

1. Water binds to Zn2+ 2. Approximation strategy as substrate enters site 3. Nucleophilic addition (adds functional group to CO2) 4. Release of product and regeneration of enzyme (histidine proton shuttle)

Question 38

During the carbonic anhydrase reaction mechanism, what is the significance of water binding to Zn2+?

Answer 38

Lowers pKa (at physiological pH, water loses a proton)