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Biochemistry > Lecture 12, Catalysis (Ford) > Flashcards

Lecture 12, Catalysis (Ford) Flashcards

1
Q

What do enzymes do?

A

Lower activation energy and stabilize transition state

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2
Q

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

A

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

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3
Q

Can enzymes irreversible change shape?

A

No

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4
Q

What is a catalyst?

A

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

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5
Q

What is Gibbs Free Energy equation?

A

deltaG = deltaH - T*deltaS

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6
Q

Describe what happens when there is a negative deltaH value.

A

Energy is released from the system

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7
Q

Describe what happens when there is a positive deltaH value.

A

Energy is added to the system

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8
Q

Describe what happens when there is a negative deltaS value.

A

Disorder decreases

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9
Q

Describe what happens when there is a positive deltaS value.

A

Disorder increases

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10
Q

Describe what a negative deltaG value indicates.

A

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

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11
Q

Describe what a positive deltaG value indicates.

A

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

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12
Q

Describe what deltaG = 0 means.

A

Equilibrium

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13
Q

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

A

deltaG = deltaG’ + RT*lnQ

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14
Q

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

A

deltaG = deltaG’ + RT*lnK

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15
Q

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

A

Kelvin

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16
Q

What are some biochemical strategies to drive an unfavorable reaction?

A

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

17
Q

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

A

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

18
Q

What is the transition state?

A

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

19
Q

What is the activation energy?

A

Energy barrier that must be overcome for the reaction to proceed

20
Q

How can a reaction be sped up?

A
  1. Raise temperature

2. Stabilize the transition state with an enzyme

21
Q

Describe the induced fit model.

A

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

22
Q

Give the 4 ways catalysis is achieved.

A
  1. Substrate orientation
  2. Sustaining substrate bonds
  3. Creating a favorable microenvironment
  4. Covalent/noncovalent interactions between enzyme and substrate
23
Q

Describe covalent catalysis.

A

Enzyme covalently binds the transition state

24
Q

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

A

True.

25
Q

Describe acid-base catalysis.

A

Partial proton transfer to the substrate

26
Q

Describe catalysis through approximation.

A

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

27
Q

Describe electrostatic catalysis.

A

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

28
Q

Why are proteases needed?

A

Recycling, regulation, defense

29
Q

What are the various applications of carbonic anhydrases?

A

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

30
Q

Describe the active site of chymotrypsin.

A

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

31
Q

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

A

Oxyanion hole

32
Q

Regarding chymotrypsin, what determines the placement of the cut?

A

Specificity pocket

33
Q

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

A

Zn2+ ion; Coordinated to 3 histidines and a water

34
Q

Regarding carbonic anhydrases, what is the importance of water?

A

Facilitates the transition state (deprotonated)

35
Q

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

A

Approximation

36
Q

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

A

Entry channel

37
Q

What is the reaction mechanism for a carbonic anhydrase?

A
  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)
38
Q

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

A

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

Biochemistry (10 decks)

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