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CHE 541 > 12 - Enzyme Kinetics I > Flashcards

12 - Enzyme Kinetics I Flashcards

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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
What are the units of rate?
M/s
26
For a 0th order reaction, what are the units of k?
M/s
27
For a 1st order reaction, what are the units of k?
1/s
28
For a 2nd order reaction, what are the units of k?
1/(Ms)
29
What is the rate law for a second order reaction (in terms of product)?
dP/dt = k[A][B] = k(A0-P)(B0-P)
30
How can a second order reaction be simplified?
If B0 >> A0, then B0 >> P
31
What is the simplified second order reaction?
P = A0(1-exp(-kB0t)) (pseudo 1st order)
32
What is the rate law for a reversible reaction?
dP/dt = k1(A0-P) - k-1(P)
33
In a multistep reaction, what is the rate limiting/determining step?
The slowest rate (the only rate you need to consider)
34
How does an active site assist in a reaction?
Acid/base catalysis, nucleophilic catalysis, increasing effective concentration, stabilize intermediates/transition states
35
How does an enzyme increase effective concentration?
Bring reactants close together
36
What is the general formula for enzyme catalysis?
E + S ES --> EP
37
What is the Michaelis complex?
The ES complex
38
What is measured from a P vs t graph?
Initial velocity (v0)
39
Why is initial velocity measured?
The rate changes over time (less S interacts), and it is linear initially
40
What is the shape of the P vs t curve?
Hyperbolic (saturation)
41
What is the shape of the v0 vs. S curve?
Hyperbolic (saturation)
42
At low S, how does V0 vary?
It is 1st order linear (more S is more v0)
43
At high S, how does v0 vary?
It does not change (enzyme is saturated)
44
What is the rapid equilibrium assumption?
1. E and S are in rapid equilibrium with ES (k-1 >> k2) | 2. E << S, so Sf = S
45
What is Ks?
Dissociation constant of ES
46
What is the formula for Ks?
Ks = [Ef][Sf]/[ES]
47
What is ES under the rapid equilibrium assumption?
[ES] = [E][S] / (Ks + [S]) ([Ef] = [E] - [ES], [Sf] = [S])
48
What is kcat?
k2 (rate of catalysis from ES --> E + P)
49
What is the rate of the enzyme equation under therapid equilibrium assumption?
v0 = k2[ES] = kcat([E][S]/(Ks + [S]))
50
What is the formula for vmax?
vmax = kcat[E]
51
What is the steady state assumption?
ES reaches a constant value soon after the enzyme is mixed (d[ES]/dt = 0, d[E]/dt = 0)
52
What formula is derived from the steady state approximation?
``` Synthesis = degradation k1[Ef][Sf] = (k-1 + k2)[ES] ```
53
What is the formula for [ES] under the steady state assumption?
[ES] = [Ef][Sf] / Km
54
What is Km?
Michaelis Menten constant
55
What is the formula for Km?
Km = (k-1 + k2)/k1
56
What is the Michaelis Menten equation?
v0 = kcat[E][S] / (Km + [S]) (note vmax = kcat[E])
57
In a vo vs. S curve, where is Km?
At v0 = vmax/2, Km = [S]
58
Which is more generally applicable: rapid equilibrium or steady state assumption?
Steady state assumption
59
What are the units of Ks?
M
60
What are the units of Km?
M
61
What are the units of kcat?
1/s
62
What happens if k-1 >> k2?
Km = Ks (k-1/k1)
63
What does Kd represent (in terms of enzyme catalysis)?
A system with no catalysis (only dissociation)
64
What is Km a measure of?
Substrate binding affinity
65
What is kcat a measure of?
Turnover number of enzyme, number of chemical steps
66
What is the formula for enzyme efficiency?
kcat/Km
67
What are the units of kcat/Km?
1/(Ms) (same as 2nd order reaction rate)
68
What does kcat/Km represent?
Free energy differences between free E and S, and transition state
69
What experiment can be done to determine the effect of an H-bond on catalysis?
1. Measure kcat/Km for wild type and mutant enzyme | 2. Calculate delta delta G (-RT ln(ratio of kcat/Km for both))
70
What assumptions are present for seeing if an H-bond is important for catalysis?
1. Is H-bond only thing changing? | 2. Any changes in partial structure or folded structure?

CHE 541 (20 decks)

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