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Biochemical Methods > Enzyme Kinetics > Flashcards

Enzyme Kinetics Flashcards

1
Q

What are biological catalysts?

A

Enzymes

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2
Q

Except for some RNA or RNA/protein complexes (Ribozymes) most enzymes are what?

A

Proteins

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3
Q

The name of an enzyme usually ends with what?

A

-ase

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4
Q

What does the name of an enzyme describe?

A

Its function

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5
Q

What does sucrase do?

A

breaks down sugars

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6
Q

What do proteases do?

A

break down proteins

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7
Q

What do lipases do?

A

break down lipids

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8
Q

What does DNA polymerase do?

A

builds DNA

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9
Q

What do oxidases do?

A

catalyze oxidation reactions

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10
Q

Sometimes common names are used particularly for which enzymes

A

digestion

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11
Q

Most names describe the substrate and the what?

A

function (alcohol dehydrogenase)

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12
Q

What is a molecule that enzymes work on called?

A

substrate

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13
Q

What do we call the molecule that is produced by an enzymatic reaction?

A

Product

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14
Q

What is the part of the enzyme where the substrate binds and a reaction takes place?

A

Active-site

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15
Q

Enzymes are not what during the reaction

A

changed

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16
Q

What changes during a catalyzed reaction?

A

the activation energy

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17
Q

What do catalysts do to the rate of a specific reaction?

A

accelerate

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18
Q

What don’t catalysts do?

A 
Alter the reaction (change thermodynamic)
Get consumed (remain the same/regenerated)
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19
Q

Catalysts affect the rate of the forward and reverse reactions by what?

A

the same factor

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20
Q

Do catalysts affect the position of equilibrium?

A

No

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21
Q

What do catalysts lower for a reaction?

A

the activation energy required

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22
Q

What is the Arrhenius equation?

A

k=Ae^(-Ea/RT)

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23
Q

In the Arrhenius equation, what is A?

A

Frequency factor (frequency of collision)

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24
Q

What is activation energy?

A

The minimum energy required to start a reaction (to reach the transition state from the reactants)

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25
Q

What is the region within an enzyme that binds substrate molecules

A

Active site

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26
Q

What are the two proposed models of Enzyme-substrate interaction?

A

Lock-and-Key

Induced Fit Model

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27
Q

With Lock-and-Key, the active site has what kind of shape?

A

rigid

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28
Q

The specificity of enzymes can be explained by which model, but does not work for all enzymes?

A

Lock-and-Key

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29
Q

With Induced Fit Model, the active site is what shape?

A

flexible (the shapes of the enzyme, active site, and substrate adjust to maximize the fit, which improves catalysis) (greater range of substrate specificity)

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30
Q

Substrates are held in active site by weak interactions such as what?

A

hydrogen bonds and hydrophobic interactions

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31
Q

What does lowering the activation energy do?

A
  1. Stabilizes the transition state
  2. Provides a favorable microenvironment
  3. participation directly in the catalytic reaction
  4. speeds up the reaction
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32
Q

What affects the enzyme activity?

A
  1. Environmental Conditions (Temperature, pH)
  2. Cofactors and Coenzymes
  3. Enzyme Inhibitors
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33
Q

Using the optimum temperature allows for what?

A

greatest number of collisions between enzyme and substrate.

too high (denature protein-unfolded)
too low (molecules move slower-fewer collisions)
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34
Q

pH affects what?

A

protein structure (activity)

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35
Q

What are two types of cofactors?

A 
metal ions (inorganic) Zn Fe Mg Mn Cu Co
small organic molecules (coenzymes)
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36
Q

Are cofactors proteins?

A

no

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37
Q

What is a non-protein component that is loosely bound to the apoenzyme by non-covalent bonds?

A

coenzyme (PLP, FMN, FAD, NAD+)

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38
Q

What is a non-protein component that is tightly bound to the apoenzyme by covalent bonds?

A

prosthetic group (Heme)

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39
Q

What do we call an enzyme without its cofactor or ligands?

A

Apoenzyme (inactive)

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40
Q

What do we call an enzyme that is active with its non protein component?

A

Holoenzyme

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41
Q

As the substrate concentration increases, the rate of the reaction does what?

A

increases

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42
Q

when does the maximum activity occur?

A

enzymes are saturated

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43
Q

What bring reactants to close proximity and align them in the proper orientation fro the reaction to happen via lowering the reaction activation energy?

A

Enzymes

44
Q

Are enzymes reusable?

A

Yes

45
Q

What is the change in concentration of a reactant/product divided by the time interval during which this change is observed called?

A

speed/rate of a chemical reaction

46
Q

What sign is placed in front of the definition for reactants?

A

negative (being consumed)

47
Q

what is the reaction rate of A + B -> C + D

A

rate = (-delta A/delta t)= (-delta B/delta t)=(delta C/delta t)=(delta D/delta t)

48
Q

If there is a coefficient in front of a compound where does it show up in the rate equation?

A

the denominator

49
Q

What is determined by taking the slope of a line tangent to the curve at that particular point?

A

instantaneous rate (first derivative of the function)

50
Q

What is the change of concentration over a period of time?

A

Average rate

51
Q

The larger the time interval used to find the average rate, the more the what?

A

deviation from the instantaneous rate

52
Q

To measure the reaction rate, what do you need?

A

the ability to measure the concentration of at least one component in the mixture at different points in time

53
Q

What often depends on the concentration of one or more of the reactants molecules?

A

the rate

54
Q

The equation relating the concentrations of reactants to rate is called what?

A

The Rate Law

55
Q

What would be the Rate Law of A -> Products?

A

rate = k[A]^n

k is the rate constant
n is the order (determines the rate dependence on reactant concentration)

56
Q

The sum of the exponents on the reactants is called the what?

A

order of the reaction

57
Q

What is the order of the following reaction: k[NO]^2[O2]?

A

3

58
Q

If a reaction is zero order the rate of the reaction is what?

A

always the same rate = k[A]^0 = k

59
Q

If a reaction is first order, the rate is directly proportional to what?

A

The reactant concentration, rate = k[A]

60
Q

If a reaction is second order, the rate is directly proportional to what?

A

the square of the reactant concentration rate = k[A]^2

Doubling [A] will quadruple the rate of the reaction.

61
Q

What must be determined experimentally?

A

The rate law

62
Q

What method is the data from different experiments with varying starting concentrations of reactants used?

A

method of initial rates

63
Q

What can be determined if you change the initial concentration of one reactant but keep the other reactant at saturation concentration?

A

the rate

64
Q

What is k’?

A

the pseudo first-order rate constant

65
Q

What is kcat?

A

how well the enzyme completes one cycle

kcat = Vmax/[E]t

66
Q

What is Km?

A

How well the substrate and enzyme interact

67
Q

what is kcat/Km?

A

Specificity constant: How fast does the enzyme turnover

68
Q

Catalysts affect both the forward and reverse reaction. (T/F)

A

T

69
Q

What are the common environmental conditions under which an enzyme (biological catalyst) performs?

A

Temperature (35-40 C)

pH (6-8)

70
Q

What is the difference between cofactors and prosthetic groups?

A

prosthetic groups are tightly bound or covalently bound cofactors (small organic molecules)

71
Q

The reaction rate is directly proportional to what?

A

The concentration of the reactants

72
Q

Why are enzyme kinetics studied?

A
  1. understand effects of experimental conditions
  2. understand mechanism of enzyme
  3. investigation of metabolic pathways
  4. understand regulation of biochemical reactions (up or down regulation of catalyst)
  5. Describes its catalytic power, substrate affinity, and its response to inhibitors (helps design drugs)
73
Q

What did Victor Henry do in 1903?

A

Proposed that an enzyme combines with its substrate molecule to form an ES complex as a necessary step in enzyme catalysis

74
Q

What did Leonor Michaelis and Maud Menton do in 1913?

A

Expanded on the idea of Victory Henry into a general theory of enzyme actions.

75
Q

How is steady state approximation (SSA) used to study enzymes?

A

It assumes the concentration of the intermediate is constant.

rate of ES = 0

76
Q

If [S] is&raquo_space;»> than km, what do we find?

A

km can be ignored in the Michaelis-Menton equation and the rate = vmax=k2[Eo]

77
Q

If [S] is ««<

A

rate = (k2[E0][S])/km

78
Q

If [S] = km, what do we find?

A

rate = Vmax/2

79
Q

Vmax is commonly referred to as the what?

A

limiting rate

80
Q

Is there a rate controlling step when [S] «<

A

no

81
Q

Km is the substrate concentration when the limiting rate is what?

A

Half its value

82
Q

What is a measure of affinity of enzyme for S and can be a measure for substrate affinity if k2

A

km

83
Q

What does a low km indicate?

A

A fast formation of ES/tight ES complex (hard for it to dissociate)

84
Q

What is the initial reaction velocity when the substrate concentration is very high compared to km?

A

Vmax

85
Q

What is the maximum velocity independent enzyme concentration known as the catalytic constant (turnover number)?

A

kcat = Vmax/[Eo]=k2[Eo]/[Eo]=k2

86
Q

What two things contribute to the maximum velocity limit?

A
  1. amount of enzyme

2. ability of enzyme (catalytic constant) kcat

87
Q

What measures the affinity of an enzyme for a specific substrate?

A

kcat/km (enzyme efficiency or specificity constant)

88
Q

The specificity constant is useful when what?

A

comparing primary substrate to other substrates (e.g. ethanol vs. propanol in alcohol dehydrogenase

89
Q

Efficient enzymes have large what?

A

kcat/km (specificity constants)

large kcat and/or small km

90
Q

What is considered the maximum efficiency of enzymes and is controlled by the diffusion limit of the substrate?

A

10^8 or 10^9 1/(M*s)

91
Q

What is the rate at which the ES complex is formed?

A

kcat/km = (k1*k2)/(k-1+k2)=k1k2/k2=k1

92
Q

Enzymes with efficiencies in the range of 10^8 to 10^9 (1/(M*s)) are said to have reached what?

A

Catalytic/kinetic perfection

93
Q

How do we conduct kinetic experiments?

A
  1. Find out a reasonable amount of enzyme for the reaction
  2. Do an experiment with varying starting material and keeping the second substrate at a very high concentration
  3. measure product formed per second (plot [P] vs time)
  4. measure initial rate
  5. plot initial rate versus substrate concentration
94
Q

What do you plot in a Lineweaver and Burk plot?

A

1/v vs 1/[S]

95
Q

In a Lineweaver and Burk plot what is the y-intercept?

A

1/vmax

96
Q

In a Lineweaver and Burk plot what is the x-intercept?

A

-1/km

97
Q

In a Hanes-Wolf plot what do you plot?

A

[S]/v vs [S}

98
Q

In a Hanes-Wolf plot what is the slope

A

1/vmax

99
Q

In a Hanes-Wolf plot what is the x-intercept?

A

-km

100
Q

What do you plot in an Eadie-Hofstee plot?

A

vo vs vo/[S]

101
Q

What is the y-intercept of an Eadie-Hofstee plot?

A

vmax

102
Q

What is the slope of an Eadie-Hofstee plot?

A

-km

103
Q

What do you do to the Michaelis-Menton Equation to form the Lineweaver and Burk equation?

A

take the inverse

104
Q

What do you do to the Lineweaver and Burk Equation to form the Hane-Wolf equation?

A

Multiply through with [S]

105
Q

What do you do to the Michaelis-Menton Equation to form the Eadie-Hofstee plot?

A

rearrange the equation by:

1) multiply both sides by the denominator
2) distribute v0 on the left side
3) move the vokm term back to the right side
4) divide both sides by [S]

Biochemical Methods (5 decks)

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