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bio1332 - biochemistry > Enzyme Kinetics > Flashcards

Enzyme Kinetics Flashcards

1
Q

What is the difference between kinetics and thermodynamics?

A
  • Kinetics: how fast the reaction

- Thermodynamics: does the reaction happen or how far does it proceed

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2
Q

Why is the rate of biological reactions important?

A
  • Most cellular chemicals are unstable, rely on rate of their breakdown
  • Some disease are cause by imbalances in rate at which a reaction takes place
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3
Q

What does change in G of a reaction equal to?

A

free energy of the products (final) - the free energy of the reactants (initial)

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4
Q

Does change in G provide information about the rate of reaction?

A

No

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5
Q

What is change in G independent on?

A

Path of the transformation

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6
Q

What is the rate of reaction dependent on?

A

Free energy of activation

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7
Q

What is the sign for free energy of activation?

A

change in G double daggers

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8
Q

if change in G reaction < 0 for a spontaneous reaction, how is it possible to reach a transition state that is at a higher value of G?

A

Have to consider individual molecule properties rather than bulk properties that change in G refers to

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9
Q

Will a mixture of molecules have all the same amount of energy as one another?

A

No

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10
Q

How is the distribution of energy of molecules shown?

A

On a Maxwell-Boltzmann distribution

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11
Q

Define activation energy:

A

Energy that a molecule requires to overcome the transition state free energy barrier

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12
Q

How many molecules can overcome the activation energy?

A

Only a certain proportion of molecules in a mixture

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13
Q

What does the Arrhenius equation show?

A

Rate of reaction is related to activation energy

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14
Q

What is the Arrhenius equation?

A

k = Ae^-(change in G double dagger/RT)

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15
Q

What is k in the Arrhenius equation?

A

Rate constant

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16
Q

What is T in the Arrhenius equation?

A

Temperature in kelvin

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17
Q

What is A in the Arrhenius equation?

A

Pre-exponential factor (constant for each chemical reaction that defines the rate due to frequency of collisions the correct orientation)

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18
Q

What is change in g double dagger in the Arrhenius equation?

A

Activation energy for the reaction in joules

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19
Q

What is R in the Arrhenius equation?

A

universal gas constant

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20
Q

How to speed up a chemical reaction?

A
  • Increase the temperature
  • Increase the pressure
  • Change the pH
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21
Q

What are enzymes?

A

Macromolecules whose function is to increase the rate of reactions

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22
Q

How do enzymes generally increase the rate of reaction?

A

By reducing the transition state energy for a reaction

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23
Q

What are the general properties of an enzyme?

A
  • Catalytic
  • Specific
  • Fast
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24
Q

What is meant by catalytic in terms of enzymes?

A

Enzyme ends in the state that it started

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25
Q

What is meant by specific in terms of enzymes?

A

Change the rate of a limited set of reactions

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26
Q

What is meant by fast in terms of enzymes?

A

Most reactions need to be speeded up by many orders of magnitude

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27
Q

Why are enzymes made of proteins?

A
  • 20 amino acids offer a wide range of difference on shape (SPECIFIC)
  • Very different chemical properties (SPEED)
  • Good at accommodating different reactants so proteins itself is not changed in the reaction (CATALYTIC)
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28
Q

What do enzymes for form with substrates?

A

Enzyme-substrate complexes

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29
Q

What substrate does enzyme cytochrome P450 bound to?

A

Camphor

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30
Q

What doe enzymes decrease?

A

The activation energy

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31
Q

How is the transition state barrie reduced?

A
  • Stabilise the unfavourable intermediated

- Make possible a less favourable reaction

32
Q

What are the unfavourable intermediates?

A
  • Charge-charge interactions
  • Hydrogen bonding
  • Protecting hydrophobic groups
33
Q

How do you make a less favourable reaction?

A
  • Provide acid/base-like conditions
  • Allow oxidation/reduction
  • Provide a small vacuum
  • Provide an attacking group (covalent catalysis)
  • Provide a metal ion
34
Q

What is the reaction kinetics in terms of S and P with no enzyme?

A

An equilibrium of S to P

35
Q

What is the reaction kinetics in terms of S and P with an enzyme?

A

Equilibrium of E + S to ES to EP to E + P

36
Q

What is rate constant?

A

Constant temperature, elementary reaction is proportional to the frequency with the reacting molecules come together

37
Q

What should you assume for enzyme kinetics??

A
  • Release of product is vert fast

- Reverse reaction is sufficiently slow that we can ignore it

38
Q

When applying the enzyme kinetics assumptions we can use what equation?

A

Michaelis-Menten equation

39
Q

What is the Michaelis-Menten equation?

A

Vo = Vmax ([S]/Km + [S])

40
Q

What is Vmax in the Michaelis-Menten equation?

A

Maximal rate

41
Q

What is [S] in the Michaelis-Menten equation?

A

Substrate concentration

42
Q

What is Km in the Michaelis-Menten equation?

A

Michaelis constant

43
Q

What is Vo in the Michaelis-Menten equation?

A

Reaction velocity

44
Q

What is the x-axis label of the Michaelis-Menten?

A

Substrate concentration

45
Q

What is the y-axis label of the Michaelis-Menten?

A

Reaction velocity

46
Q

Do Km values of enzymes a little or wide range?

A

Wide range

47
Q

What range does Km lie between?

A

10^-1 and 10^7M

48
Q

What does Km range depend on?

A

Substrate and conditions such as pH

49
Q

What is Km?

A

Concentration of substrate at which hall the active sites are filled

50
Q

What does Km provide?

A

A measure of the substrate concentration required for significant catalysis to occur

51
Q

What does Km provide for in vivo?

A

Approximation of the substrate concentration

52
Q

What does Km measure other than substrate concentration?

A

The strength of the ES complex

53
Q

What does a high Km indicate?

A

Weak ES binding

54
Q

What does a low Km indicate?

A

Strong ES binding

55
Q

When does Km indicate the affinity of the ES complex?

A

When k-1 is much greater than k2

56
Q

What does Vmax show?

A

The turnover number

57
Q

What is another work for turnover number?

A

Kcat

58
Q

What must you have to calculate the Michaelis-Menten constants?

A
  • Obtain at least 5 values of [S]
  • Values of [S] should be both sides of the Km for a good result
  • Constants of enzyme then can be calculated
59
Q

How do you calculate the Michaelis-Menten constants?

A

-Proper statical package and non linear regression to solve equation
OR
-Rearrange the equation to give a linear equation

60
Q

What is the rearrange equation of Michaelis-Menten equation to present y = mx + c?

A

1/v = ((Km/Vmax)*(1/[x]) + 1/Vmaz

61
Q

What is the consequence of Michaelis-Menten equation?

A

When the substrate concentration drops, so does the rate

62
Q

How can you solve the problems of when the substrate concentration drops, so does the rate relating to the Michaelis-Menten equation?

A

Record initial rate

or use stopped assay

63
Q

How will kinetics differ?

A
  • Enzyme is affect by concentration of some other compounds
  • Reaction is more complicated
  • Enzyme has multiple subunits
  • Law of mass action do not apply
64
Q

What is Kcat/Km?

A

A measure of catalytic efficiency

65
Q

What does Kcat/Km take into account?

A

Rate of catalysis and strength of ES

66
Q

What is the x-axis of the line weaver-burk plot?

A

1/[S]

67
Q

What is the y-axis of the line weaver-burk plot?

A

1/V

68
Q

What is the x-axis intercept of the line weaver-burk plot?

A

-1/Km

69
Q

What is the y-axis intercept of the line weaver-burk plot?

A

1/Vmax

70
Q

What is the slope of the line weaver-burk plot?

A

Km/Vmax

71
Q

What is the x-axis of the Hanes-woolf plot?

A

[S]

72
Q

What is the y-axis of the Hanes-woolf plot?

A

[S]/V

73
Q

What is the x-axis intercept of the Hanes-woolf plot?

A

-Km

74
Q

What is the y-axis intercept of the Hanes-woolf plot?

A

Km/Vmax

75
Q

What is the slope of the Hanes-woolf plot?

A

1/Vmax

76
Q

Can enzymes tightly bind to either substrate of products?

A

No - bad for catalysis

77
Q

When can enzymes tightly bind?

A

During transition state

bio1332 - biochemistry (19 decks)

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