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Structural Biochemistry > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What is Km?

A

The Michaelis Menten constant. It is the concentration of substrate at which the reaction rate is at half maximum. When Km = [S], Vmax = 1/2

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2
Q

What would a low Km indicate?

A

High affinity of substrate for enzyme

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3
Q

What would a low Km indicate?

A

Low affinity of substrate for enzyme

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4
Q

What is graphed in a Michaelis Menten plot?

A

Velocity of reaction (product concentration/time) vs substrate concentration

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5
Q

What is the Michaelis Menten equation?

A
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6
Q

What affect does cool temperate have on an enzyme?

A

results in low molecular motion and therefore slows catalysis

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7
Q

What affect does heat have on an enzyme?

A

It causes denaturation of the enzyme due to excessive molecular motion and therefore catalysis stops.

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8
Q

What affect does pH have on enzymes?

A

Enzymes have specific ionization states in their active sites. Altering the ion concentration can alter the ionization state and therefore denature the enzyme

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9
Q

What is enthalpy?

A

The measure of types and number of chemical bonds.

Represented by the letter, H

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10
Q

What is entropy?

A

The measure of disorder.

Represented by the letter S

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11
Q

What is the second law of thermodynamics?

A

Entropy of the universe is ever increasing

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12
Q

What does a - ΔG reaction indicate?

A

It is an exergonic reaction - Free energy is released be the reaction and therefore it will proceed spontaneously towards product formation.

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13
Q

What does a reaction with + ΔG indicate?

A

It is an endergonic reaction - Free energy input is required in order for the reaction to proceed toward product formation. Without free enery input, the reaction favors substrate formation.

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14
Q

What is energy coupling?

A

Combining a exergonic reaction with an endergonic reaction to overcome energy barriers

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15
Q

What does a large Keq indicate?

A

most of the substrate has been converted to product and therefore the reaction is more likely to go to completion

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16
Q

What does a small Keq indicate?

A

Little substrate has been converted to product therefore ther reaction is less likely to go to completion.

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17
Q

What is the equilibrium constant?

A

The constant that reflects the molar concentration of product/substrate at equilibrium

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18
Q

At equilibrium, what happens to potential energy?

A

It is balanced

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19
Q

What does an unbalanced potential energy create?

A

A driving force towards equilibrium

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20
Q

The magnitude of ΔG is dependent on what?

A

how far from equilibrium the system is

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21
Q

What does ΔGº reflect?

A

Free energy change of reaction under standard conditions: pH = 7, 1 atmosphere and no influence of water

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22
Q

What equation quantifies the likelihood that substrate will proceed to product?

A

ΔGº =-RTlnKeq

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23
Q

What proves that ES exists before release of product and enzyme?

A
  1. high specificity of enzyme for substrate
  2. ES can be isolated
  3. physical properties of enzyme change with binding
  4. EM and X-ray crystalography confirm it
24
Q

What does ΔG¥ reflect?

A

Activation energy/energy barrier - the amount of free energy required to convert E + S to ES complex

25
Q

What affect do enzymes have on ΔG¥?

A

Substrate binding to the active site of an enzyme lowers ΔG¥.

26
Q

How is ΔG¥ reduced by enzymes?

A

multiple weak non-covalent bonds release energy upon substrate:active site binding and induced fit.

27
Q

How does the ES complex stability compair to other steps of an enzymatic reaction?

A

It is more stable that the initial E + S encounter because the enzyme is most complementary to the transition state.

It is less stable that product, making ES transitory and favoring product formation

28
Q

What roles to non-covalent bonds play in enzymes?

A

They give rise to enzyme specificity and are the driving force of catalysis

29
Q

What is a “super polar” residue?

A

It is a polar residue in a non-polar microenvironment of the active site, giving it special catalytic and binding properties

30
Q

What is the significance of the 3D structure of enzymes and unsequencial AA active sites?

A

gives active site more range of motion for orientation with substrate

31
Q

What is a zero order reaction?

A

A reaction whose rate is independent of substrate

-usually when [substrate] >>>> [enzyme]

32
Q

What is the steady state assumption?

A
  1. consider only the forward reaction ES⇒P, not ES ⇒E+S
  2. measure rate from initial introduction of enzyme, t=0
  3. Enzyme concentration is constant
  4. [substrate] >>> [enzyme] creating zero order reaction
  5. ES concentration is constant
  6. Vmax cannot be obtained because of diffusion, temp, pressure, etc.
33
Q

How would high enzyme concentration affect the steady state assumption and enzyme kinetics?

A

The rate of product formation would appear faster.

34
Q

What is the rate limiting step of enzymatic reactions?

A

The formation of product due to slower reaction rate of ES to P, therefore overall reaction rate is proportional to the concentration of ES

35
Q

In MM kinetics, when KM = [S], what does Vmax equal?

A

1/2

36
Q

Lineweaver-Burk equation

A
37
Q

What does the Y intercept of a Lineweaver Burk Plot show?

A

1/Vmax

38
Q

What does the X-intercept of a Lineweaver Burk plot show?

A

-1/KM

39
Q

What is the slope of the Lineweaver Burk plot?

A

KM/Vmax

40
Q

What does KM reflect in MM vs LB kinetics?

A

In MM kinetics, it reflects affinity of an enzyme for substrate

In LB kinetics, is a measurement of when catalysis will occur because it is a numerical representation of 1/2 Vmax

41
Q

What is kcat?

A

a measure of the overall rate of catalysis, turnover number

it is useful in enzyme kinetics with different rate limiting step

42
Q

What is kcat/KM?

A

measure of catalytic efficiency (rate of catalysis/affinity)

-used in comparing enzyme preference for substrate

43
Q

How would a heterotropic stimulator affect Vmax?

A

1/2 Vmax would be achieved with less substrate

44
Q

How would a heterotropic inhibitor affect Vmax?

A

more substrate would be required to reach 1/2 Vmax

45
Q

Describe phosphorylation

A

A chemical modification of an enzyme - transfer of phosphoryl group from ATP or another neucleotide to Ser, Thr, Tyr or His via protein kinase. This can have a stimulatory or inhibitory affect on enzymes. Phosphatases reverse the reaction

46
Q

Inhibitor that binds to the active site of an enzyme?

A

competitive inhibitor

47
Q

Characteristics of competitive inhibitors?

A
  • resemble the substrate
  • reaction slows because no product forms while inhibitor is bound
  • Vmax is unchanged because increasing [substrate] will overcome inhibition
  • KM has an apparent increase although affinity of substrate for enzyme has not changed, the reaction is just slowed by inhibitor
48
Q

What kind of inhibition is represented here?

A

competitive inhibition

  • Vmax unchanged
  • apparent KM increase
49
Q

What kind of inhibition is represented here?

A

uncompetitive inhibition

-Vmax and KM decrease proportionally

50
Q

What kind of inhibition is represented here?

A

non competitive inhibition

  • Vmax decreases
  • KM unchanged
51
Q

Characteristics of non competitive inhibition?

A
  • inhibitor and substrate bind at different sites
  • inhibitor can bind E or ES
  • Vmax decreases because fuctional enzyme is depleted
  • KM is unchanged because active site is unaltered
52
Q

Characteristics of uncompetitive inhibition?

A
  • inhibitor binds ES complex only
  • inhibitor binds at site distinct from active site
  • Vmax decreases because functional enzyme is depleated
  • KM has apparent increase less active enzyme is available
53
Q

A compoud that binds to the active site of an enzyme and form a irreversible bond?

A

Suicide inhibitor

54
Q

Why do allosteric enzymes not obey MM kinetics?

A
  • multiple binding sites
  • show cooperative binding and structure change
  • bind in non-hyperbolic pattern
55
Q
A

Structural Biochemistry (7 decks)

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