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CHE 541 > 12 - Enzyme Kinetics I > Flashcards

12 - Enzyme Kinetics I Flashcards

1
Q

What does it mean to understand enzyme kinetics qualitatively?

A

How enzymes serve as catalysts and have specificity

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2
Q

What does it mean to understand enzyme kinetics quantitatively?

A

How reaction rates change with mechanisms, mutants, substrates, etc.

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3
Q

How do enzymes work?

A

They decrease energy to make product

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4
Q

What do enzymes do?

A

Enhance reaction rate under physiological temperature, pressure, and pH

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5
Q

In a reaction coordinate diagram, what parts are based on kinetics?

A

The peaks, and differences in energy between valleys and peaks

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6
Q

What determines the rate of a reaction?

A

The transition state

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7
Q

In a reaction coordinate diagram, what represents thermodynamics?

A

The difference in energy between the valleys (equilibrium)

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8
Q

What is the transition state?

A

The highest energy species on the reaction coordinate

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9
Q

In a multistep reaction, what determines the rate of the reaction?

A

The biggest energy gap (bottleneck)

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10
Q

What is the difference between a transition state and an intermediate?

A

Transition states have partial bonds and cannot be isolated, while intermediates have full bonds and can be isolated

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11
Q

What is an example of a transition state?

A

An Sn2 reaction with partial bonds with the leaving group and nucleophile

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12
Q

What is an example of an intermediate?

A

A planar carbocation from an Sn1 reaction

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13
Q

What types of molecules bond very tightly to enzymes?

A

Molecules that mimic the transition state

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14
Q

What is activation energy?

A

Energy required to form the transition state during a collision between reactants

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15
Q

What does the activation energy do?

A

It controls the rate of the reaction

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16
Q

How are metabolics coupled in a cell?

A

Through rates (kinetics)

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17
Q

What is the rate of a reaction?

A

How fast reactants / products change over time (dC/dt)

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18
Q

What is the Arrhenius equation?

A

k = A exp(-Ea/RT) (relate k to Ea)

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19
Q

In the Arrhenius equation, what is A?

A

Frequency factor (how long collisions occur, proper geometry needed)

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20
Q

What is a rate law?

A

An expression that reveals the effect of reactant concentrations on the reaction (at a constant temperature)

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21
Q

What is rate proportional to?

A

Frequency of collisions (concentrations)

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22
Q

How are the order of the reaction determined?

A

Experimentally

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23
Q

For A –> P, what is the rate law?

A

dP/dt = kA (dA/dt = -kA)

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24
Q

What is the relationship between A and P at t = 0, and t = n?

A

At t = 0, [A0] = [A]
At t = n, [A0] = [A] + [P]
(conservation of mass)

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25
Q

What are the units of rate?

A

M/s

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26
Q

For a 0th order reaction, what are the units of k?

A

M/s

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27
Q

For a 1st order reaction, what are the units of k?

A

1/s

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28
Q

For a 2nd order reaction, what are the units of k?

A

1/(Ms)

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29
Q

What is the rate law for a second order reaction (in terms of product)?

A

dP/dt = k[A][B] = k(A0-P)(B0-P)

30
Q

How can a second order reaction be simplified?

A

If B0&raquo_space; A0, then B0&raquo_space; P

31
Q

What is the simplified second order reaction?

A

P = A0(1-exp(-kB0t)) (pseudo 1st order)

32
Q

What is the rate law for a reversible reaction?

A

dP/dt = k1(A0-P) - k-1(P)

33
Q

In a multistep reaction, what is the rate limiting/determining step?

A

The slowest rate (the only rate you need to consider)

34
Q

How does an active site assist in a reaction?

A

Acid/base catalysis, nucleophilic catalysis, increasing effective concentration, stabilize intermediates/transition states

35
Q

How does an enzyme increase effective concentration?

A

Bring reactants close together

36
Q

What is the general formula for enzyme catalysis?

A

E + S ES –> EP

37
Q

What is the Michaelis complex?

A

The ES complex

38
Q

What is measured from a P vs t graph?

A

Initial velocity (v0)

39
Q

Why is initial velocity measured?

A

The rate changes over time (less S interacts), and it is linear initially

40
Q

What is the shape of the P vs t curve?

A

Hyperbolic (saturation)

41
Q

What is the shape of the v0 vs. S curve?

A

Hyperbolic (saturation)

42
Q

At low S, how does V0 vary?

A

It is 1st order linear (more S is more v0)

43
Q

At high S, how does v0 vary?

A

It does not change (enzyme is saturated)

44
Q

What is the rapid equilibrium assumption?

A
  1. E and S are in rapid equilibrium with ES (k-1&raquo_space; k2)

2. E &laquo_space;S, so Sf = S

45
Q

What is Ks?

A

Dissociation constant of ES

46
Q

What is the formula for Ks?

A

Ks = [Ef][Sf]/[ES]

47
Q

What is ES under the rapid equilibrium assumption?

A

[ES] = [E][S] / (Ks + [S]) ([Ef] = [E] - [ES], [Sf] = [S])

48
Q

What is kcat?

A

k2 (rate of catalysis from ES –> E + P)

49
Q

What is the rate of the enzyme equation under therapid equilibrium assumption?

A

v0 = k2[ES] = kcat([E][S]/(Ks + [S]))

50
Q

What is the formula for vmax?

A

vmax = kcat[E]

51
Q

What is the steady state assumption?

A

ES reaches a constant value soon after the enzyme is mixed (d[ES]/dt = 0, d[E]/dt = 0)

52
Q

What formula is derived from the steady state approximation?

A 
Synthesis = degradation
k1[Ef][Sf] = (k-1 + k2)[ES]
53
Q

What is the formula for [ES] under the steady state assumption?

A

[ES] = [Ef][Sf] / Km

54
Q

What is Km?

A

Michaelis Menten constant

55
Q

What is the formula for Km?

A

Km = (k-1 + k2)/k1

56
Q

What is the Michaelis Menten equation?

A

v0 = kcat[E][S] / (Km + [S]) (note vmax = kcat[E])

57
Q

In a vo vs. S curve, where is Km?

A

At v0 = vmax/2, Km = [S]

58
Q

Which is more generally applicable: rapid equilibrium or steady state assumption?

A

Steady state assumption

59
Q

What are the units of Ks?

A

M

60
Q

What are the units of Km?

A

M

61
Q

What are the units of kcat?

A

1/s

62
Q

What happens if k-1&raquo_space; k2?

A

Km = Ks (k-1/k1)

63
Q

What does Kd represent (in terms of enzyme catalysis)?

A

A system with no catalysis (only dissociation)

64
Q

What is Km a measure of?

A

Substrate binding affinity

65
Q

What is kcat a measure of?

A

Turnover number of enzyme, number of chemical steps

66
Q

What is the formula for enzyme efficiency?

A

kcat/Km

67
Q

What are the units of kcat/Km?

A

1/(Ms) (same as 2nd order reaction rate)

68
Q

What does kcat/Km represent?

A

Free energy differences between free E and S, and transition state

69
Q

What experiment can be done to determine the effect of an H-bond on catalysis?

A
  1. Measure kcat/Km for wild type and mutant enzyme

2. Calculate delta delta G (-RT ln(ratio of kcat/Km for both))

70
Q

What assumptions are present for seeing if an H-bond is important for catalysis?

A
  1. Is H-bond only thing changing?

2. Any changes in partial structure or folded structure?

CHE 541 (20 decks)

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