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BIOS4007 - Enzyme Kinetics > Enzyme Kinetics > Flashcards

Enzyme Kinetics Flashcards

1
Q

What are the proportions of reactants and products when Kc > 1?

A

Products exceed reactants
- much greater than 1, reaction almost at completion

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2
Q

What are the proportions of reactants and products when Kc < 1?

A

Reactants exceed products

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3
Q

What factor affects Kc?

A

Temperature

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4
Q

What factors do not affect Kc?

A
  • pressure
  • catalyst
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5
Q

Zeroth law of thermodynamics

A

If 2 thermodynamic systems are in thermal equilibrium with a 3rd, then they’re in thermal equilibrium with each other.

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6
Q

First law of thermodynamics

A

Energy can’t be created/destroyed - can only be transferred.

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7
Q

Second law of thermodynamics

A

The entropy of an isolated system not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium.

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8
Q

Third law of thermodynamics

A

As temperature approaches absolute zero, the entropy of a system approaches a constant minimum.

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9
Q

Define enthalpy ΔH

A

The change in heat associated with a chemical reaction.

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10
Q

What reactions take place when ΔH<0 or ΔH>0?

A
  • Spontaneous exothermic reactions ΔH<0 (negative)
  • Non-spontaneous endothermic reactions ΔH>0 (positive)
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11
Q

Define entropy ΔS

A

The degree of disorder
- Matter changes from a more ordered to a less ordered state.
(randomness in a system)

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12
Q

What reactions take place when ΔS<0 or ΔS>0?

A
  • Spontaneous reaction ΔS>0 (positive)
  • Not spontaneous reaction ΔS<0 (negative)
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13
Q

Gibbs Free Energy equation

A

ΔG° = -RTln(Kc)

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14
Q

What does the Gibbs Free Energy equation calculate?

A

Measures the difference in free energy between the products and reactants of a reaction.
- it is a thermodynamic property
(determines whether reaction is spontaneous or non-spontaneous)

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15
Q

What is the relationship between ΔG and standard-state to equilibrium?

A
  • The smaller the value of ΔG, the closer the standard-state is to equilibrium.
  • The larger the value of ΔG, the further the reaction has to go to reach equilibrium.
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16
Q

When do exergonic reactions occur?

A
  • Spontaneously
  • ΔG is negative
    reactants E > products E
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17
Q

Draw an energy profile for an endergonic reaction

A

Slide 16 (part 1)

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18
Q

What factors affect reaction rate?

A
  • temperature
  • concentration
  • addition of catalyst
  • SA
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19
Q

Under what conditions can a reaction spontaneously occur?

A
  • thermodynamically favourable
  • kinetically favourable
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20
Q

What is the Collision Theory?

A

Reactions occur when molecules collide with:
- sufficient energy
- correct orientation

So bonds can be broken/made

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21
Q

How can the rate of a reaction be increased on a energy profile?

A

Increase number of successful collisions:
- change shape of curve
- move activation energy further to the left

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22
Q

What factors affect reaction rate explained by collision theory?

A
  • increase in temp
  • increase in conc of reactants
  • addition of catalyst
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23
Q

How does the collision theory explain temperature as a factor?

A

Increase temp, rate of reaction increases.
- molecules move faster
- collide more often
- increase in number of high energy collisions

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24
Q

How does the collision theory explain concentration as a factor?

A
  • higher concentration of reactants
  • chances of collision are greater
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25
Q

How does the collision theory explain catalysis as a factor?

A

Increases rate by increasing number of successful collisions.
- remains unchanged whilst providing lower activation energy

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26
Q

Does a catalyst change equilibrium state?

A

No - ΔG° and Kc remain the same.

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27
Q

What are enzymes?

A

Proteins that act as catalysts - biological catalysts that increases reaction rate.

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28
Q

How do enzymes function?

A
  • temporarily binding
  • specifically activating a substrate
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29
Q

What are the 6 types of enzymes (we need to familiarise with)?

A
  • oxidoreductases
  • transferases
  • hydrolases
  • lyases
  • isomerases
  • ligases
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30
Q

What type of reaction do oxidoreductases catalyse?

A

oxidation-reduction reactions

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31
Q

What type of reaction do transferases catalyse?

A

transfer of functional groups

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32
Q

What type of reaction do hydrolases catalyse?

A

hydrolysis reactions

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33
Q

What type of reaction do lyases catalyse?

A

group elimination to form double bonds

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34
Q

What type of reaction do isomerases catalyse?

A

isomerization

35
Q

What type of reaction do ligases catalyse?

A

bond formation coupled with ATP hydrolysis

36
Q

What is a kinase (enzyme)?

A

An enzyme that catalyses the transfer of a phosphate group from ATP to a specified molecule.

37
Q

What is the enzyme-substrate equation?

A

E + S ⇌ ES

38
Q

What is the 1st step at the active site of an enzyme?

A

S binds to active site to form ES

39
Q

What is the 2nd step at the active site of an enzyme?

A

As S binds to active site:
- enzyme adjusts its conformation
- so active site & S take the shape of the transition state

40
Q

What is the 3rd step at the active site of an enzyme?

A

The transition state-enzyme complex gives rise to product.

41
Q

What is the 4th step at the active site of an enzyme?

A
  • product released from active site
  • enzyme is returned unchanged to its native conformation
  • ready to bind to another S
42
Q

What are the characteristics of enzymes?

A
  • Increase speed of reaction: 10^6 - 10^14 rate enhancements
  • very selective
  • very specific
    = responds to regulation
43
Q

How much do enzymes increase rate of reaction?

A

Factors of 10^7-14

44
Q

What is meant by Enhancement Factors?

A

Enhancement Factors refer to various strategies or factors that can increase the rate or efficiency of a chemical reaction.

45
Q

What are the enhancement factors in enzyme catalysis?

A
  • distortion of substrate
  • provision of functional group
  • provision of microenvironment in active site
  • controlling the orientation of reactants
  • reducing unfavourable interactions between reactants in multi-substrate reactions
  • proximity effect
46
Q

How does distortion of the substrate affect the rate of a chemical reaction?

A
  • distortion of the substrate towards the shape & electronic structure of the transition state
  • increases the rate of a chemical reaction by lowering the Ea required for the reaction to occur
47
Q

How can the provision of a functional group affect the rate of a chemical reaction?

A
  • provision of a functional group for an alternative reaction mechanism
  • increases the rate of a chemical reaction by providing an alternative, lower-energy pathway for the reaction to occur
48
Q

How can the microenvironment in the active site of an enzyme affect the rate of a chemical reaction?

A
  • provision of a microenvironment in the active site - affects the rate of a chemical reaction
  • by favouring a particular reaction pathway
  • through factors such as pH, ionic strength, and electrostatic interactions
49
Q

How can controlling the orientation of reactants affect the rate of a chemical reaction?

A
  • controlling the orientation of reactants can increase the probability of a chemical reaction occurring
  • by bringing the reactive groups into closer proximity
  • & minimizing non-reactive interactions
50
Q

How can Enhancement Factors reduce unfavourable interactions between reactants in multi-substrate reactions?

A
  • reduce unfavourable interactions between reactants in multi-substrate reactions
  • by stabilizing the transition state
  • & minimizing repulsion between reactants
51
Q

What is the proximity effect in relation to Enhancement Factors?

A
  • proximity effect increases probability of a chemical reaction occurring
  • by bringing the reactants into close proximity
  • thereby increasing the likelihood of productive collisions
52
Q

How can the average rate of reaction be measured?

A

Measure change in reactant/product over a given time period.
- slope between two points

53
Q

How is the instantaneous rate of a reaction found?

A

Particular point - tangent of slope

54
Q

What is the equation for rate of reaction?

A

rate = k[A]^x

55
Q

What is k in the rate of reaction equation?

A

k = rate constant

56
Q

What is ^x in the rate of reaction equation?

A

the order of reaction with respect to a particular reactant

57
Q

What is the overall order of reaction?

A

Add the powers

58
Q

What is a zero order reaction?

A

x = 0 so
rate = k[A]^0
rate = k x 1
rate = k

59
Q

What is the half-life of a reaction (t1/2)?

A

Time taken for concentration of reactant to fall to 50%?

60
Q

How does half-life decrease in a zero order reaction?

A

Half life decreases as concentration of reactant decreases
- so half-life dependent on concentration

61
Q

What is the relationship between half-life and concentration in a first order reaction?

A

Half-life is independent of concentration of reactant
- half-life remains constant.

62
Q

What is V0?

A

Initial velocity / rate of reaction

63
Q

What is measured instead when [ES] is difficult to measure?

A

Measure V0:
- with fixed amount of enzyme
- and excess substrate
- when product is at a minimum

64
Q

What graph is the rate of an enzyme reaction shown on?

A

[P] against time graph

65
Q

How is initial velocity (V0) measured on a graph?

A

When [S] is a maximum at:
- time = 0
- and [P] is at minimum

66
Q

What happens to V0 when [E] is constant and [S] increases?

A
  • [E] constant
  • [S] increased
  • V0 increases
67
Q

What curve is shown on a V0 vs [S] graph?

A
  • hyperbolic curve
  • approaches a maximum value of V0
  • approaches Vmax asymptomatically
    (part 2, slide 22)
68
Q

What is Vmax?

A

Maximum rate/velocity of the enzymatic reaction where all enzyme is bound to substrate (saturated with substrate).
- theoretical maximum rate of reaction
- never achieved in reality
- units = μmol / mL / s

69
Q

How is Vmax approached on a V0 against [S] graph?

A

Asymptomatically approached as [S] is increased.

70
Q

What is the Michaelis-Menten Equation?

A

Graph resulting from plot of V0 against [S]

71
Q

What is the Michaelis Constant (Km)?

A

[S] at 1/2 Vmax
- half of enzyme is bound to substrate
- units = moles L-1

72
Q

What is Km used to evaluate about an enzyme?

A

The specificity of an enzyme for its substrate.

73
Q

What else does Km measure of an enzyme?

A

Measures affinity of the enzyme for the substrate.

74
Q

What does a high Km suggest?

A

Weak association between E and S
- high Km = low affinity

75
Q

What does a small Km suggest?

A

Enzyme binds strongly to its substrate
- low Km = high affinity
- Enzyme works at low [S]

76
Q

How are the characterisations of enzymes determined?

A

By measuring these parameters:
- Vmax
- Km
- turnover number (kcat)

77
Q

Define turnover number (kcat)

A

Measure of catalytic activity
- maximal number of S molecules
- catalysed per unit of time
- by a S saturated enzyme

78
Q

What is the Lineweaver-Burke plot?

A

Straight line graph
- 1/[S] (x) against 1/V0 (y)
- X-intercept = -1/Km
- Y-intercept = 1/Vmax
- m = Km/Vmax

79
Q

What is the Lineweaver-Burke equation?

A

1/V0 = (Km/Vmax)1/[S] + 1/Vmax

80
Q

What is a con of a Lineweaver-Burke plot?

A

Puts unneeded emphasis on the data corresponding to small values of [S].

81
Q

What is a Hanes-Woolf plot?

A

Straight line graph
- [S]/v (y) against [S] (x)

82
Q

Why is the Hanes-Woolf plot used more frequently than the Lineweaver-Burke plot?

A
  • gives more reliable values of Km and Vmax
  • when experimental methods prone to errors
  • error distribution better in H-W than L-B
83
Q

What are the limitations of Michaelis-Menten

A
  • only applicable to single substrate & single product reactions, so does not allow reversibility of product formation, P & S inhibition
  • assumes that the reaction is irreversible
  • assumes that enzyme concentration is much smaller than substrate concentration
  • does not account for enzyme cooperativity (where the binding of 1 S molecule affects the binding of subsequent S molecules)

BIOS4007 - Enzyme Kinetics (2 decks)

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