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CHEM-3502 > Chapter 12: Enzymatic Kinetics > Flashcards

Chapter 12: Enzymatic Kinetics Flashcards

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1
Q

Describe the michaelis menton steady state assumption

A

MM assumes that the rate of formation of the E-S complex equals its rate of breakdown

k1[E}{S}= K-1[ES] + K2[ES]

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2
Q

For a one-substrate enzymatic reaction, what’re the rate of formation and breakdown of ES equations?

A

V formation= k1[E}{S}

V breakdown= K-1[ES] + K2[ES]

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3
Q

What is the michaelis complex

A

the enzyme-substrate complex

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4
Q

What is the equilibrium assumption? when is this truly valid?

A

the assumption that E+S via K1/K-1 –>ES is only disturbed by ES via K2–>Product. this is only valid is the dissociation constant K2 of the ES complex (Michaelis complex) is ««&laquo_space;K1

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5
Q

What is the equation for the michaelis constant Km?

A

Km= (K-1 + K2)/ K1

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6
Q

What is Km?

A

the michaelis constant, the substrate concentration at which the reaction velocity is at half the max

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7
Q

What would happen if a reaction had a small Km?

A

it would achieve maximal catalytic efficiency at a low substrate amount.

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8
Q

What is Ks?

A

Ks is the dissociation constant of the michaelis ES complex (first step in enzymatic reaction) Ks=( [E]{S])/ {ES}

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9
Q

What would happen if Ks is high?

A

means that the enzyme has a low affinity for the substrate, will easily dissociate. Therefore, as the Ks decreases, the substrate affinity increases

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10
Q

What is Kcat?

A

the catalytic constant, the turnover number of an enzyme/ the number of reaction processes that each active site catalyzes per unit time (amount of times product is formed).

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11
Q

In what kind of system would Kcat=K2? what would the equation for Vmax be?

A

in a simple system. Vmax=kcat[enzyme total] or Vmax=K2[enzyme total]

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12
Q

When is Vmax is achieved

A

the maximal velocity of an enzyme. Occurs at increased substrate concentration when the enzyme is saturated and entirely in ES form.

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13
Q

As total enzyme concentration increases, Vmax ____

A

increases

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14
Q

If the substrate concentration is «&laquo_space;than Km, ____ ES is formed, and E= Et

A

very little enzyme substrate complex is formed cause theres not a lot of substrate. Thus, the free enzyme concentration is essentially the total enzyme concentration.

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15
Q

What does it mean when Kcat/Km is high?

A

the enzyme has reached catalytic perfection. 1

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16
Q

General equation for Kcat?

A

Kcat= Vmax/[Et]

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17
Q

What kind of curve does a michaelis-menton enzyme present?

A

hyperbolic

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18
Q

In an MM enzyme reaction, Vo=Vmax when [S] is ____

A

when substrate concentration is HIGH. When [S] is low, which is the linear portion of the graph, there is essentially no ES and thus [E]=[Et].

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19
Q

If the concentration of substrate=Km, what does Vo equal?

A

When [S]=Km, Vo=1/2Vmax because Km is literalyl defined as the concentration of substrate in which the rate of teh reaction is at 1/2 the max.

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20
Q

In terms of Km and Ks, what is the equilibrium assumption?

A

Km=Ks (dissociation constant of ES back into the E+S form) when K2«<

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21
Q

The lower the Km, the _____ the fit between the enzyme and the substrate

A

the lower the Km, the better the fit between the enzyme and the substrate. An enzyme with a high Km has a low affinity for its substrate, and requires a greater concentration of substrate to achieve Vmax.

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22
Q

In a lineweaver burke plot, how do you determine Vmax and Km?

A

1/V0 intercept= 1/Vmax

1/S intercept= -1/Km

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23
Q

What in a lineweaver-burke equation?

A

1/Vo= (km/Vmax)(1/[S])+ (1/Vmax)

24
Q

difference between an inhibitor and an inactivator

A

inactivator binds irreversibly via covalent bonds to the enzyme. Aka suicide substrates

25
Q

What does DIPF do to chymotripsin? what amino acid does it interact with?

A

DIPF interacts with Ser195 active site of chymotripsin and irriversibly inactivates the serine protease by forming a stable adduct via covalent bonds.

26
Q

what is an acetylcholineesterase?

A

an enzyme that catalyzes the hydrolysis of acetylcholine, a neurotransmitter

27
Q

Compare and contrast serine protease vs serine esterases

A

Esterases: hydrolyze ester linkages, have a ser active site, use covalent catalysis, can be modified covalently via DIPF.

Proteases: hydrolyze PEPTIDE bonds, have an active ser site, can use covalent catalysis as well as other mechanisms such as acid base catalysis, can also be modified covalently by DIPF

28
Q

How does DIPF or Sarin act as a nerve poison?

A

they inactivate acetylcholine esterase which prevents the closing of Na-K+ ion channels, interfering with regular nerve impulses. It is effective because its a tetrahedral phosphate group makes this compound a transition state

29
Q

Define competitive inhibitor

A

A sbustance that competes directly with a normal substrate for an enzyme’s substrate-binding site. Usually resembles the substrate so that it specifically binds to the active site but differs from the substrate enough so that it cannot react as the substrate does to form product.

30
Q

How can the effects of a competitive inhibitor be overcome to still reach Vmax?

A

by increasing the substrate concentration

31
Q

In competitive inhibition, the Km _____ and Vmax_____. Explain in terms of line weaver burke plot

A

Km is higher because it requires more substrate to achieve Vmax, and Vmax stays the same.

In line weaver burke plot, the Y intercept would stay the same but the X intercept would be close to the origin/higher

32
Q

How does an uncompetitive inhibitor bind to the enzyme?

A

It does not bind to the active site like a competitive inhibitor, it binds to the substrate-enzyme complex or an alternative position on the enzymes which renders the active site inactive due to distortion.

33
Q

In uncompetitive inhibition, increasing substrate concentration will:

A

not change the effect. If the active site is distorted, no amount of substrate will make the reaction improve

34
Q

In uncompetitive inhibition, the Km _____ and Vmax ____. Explain in terms of line weaver burke plot

A

Km would lower because it would not take much substrate for Vmax to be achieved, since VMax would essentially be 0, and the Vmax will lower.

In line weaver burke plot, the Y intercept of the inhibited enzyme would raise because it is the inversion of Vmax, thus if the y intercept is higher the true Vmax is lower (y int= 1/Vmax). The X intercept would also lower, or become more negative in the x axis.

35
Q

Define pure non competitive inhibition, how does Km and Vmax change?

A

The enzyme and the ES complex bind the inhibitor with equal affinity. The Km remains the same (X int) but the Vmax reduces.

36
Q

Define Flux. In equilibrium, where is flux at?

A

rate of flow through a pathway. At equilibrium, flux=0 because there is no net flow through the pathway.

37
Q

What’re the two main methods of regulating enzymatic activity?

A

1) controlling enzymatic availability- the body can control how fast the enzyme degrades and how fast enzymes are built.
2) controlling enzyme activity- using allosteric effectors or covalent regulation.

38
Q

What is the value of flux in a healthy individual’s body

A

Flux=0 in a biological system because the body’s mechanisms keep everything in equilibrium for optimal function

39
Q

Name covalent methods of enzymatic activity controls. Which ones are irreversible? reversible?

A

1) Phosphorylation: reversible
2) Activation by Cleavage: Irriversible
3) Protein Methylation: reversible

40
Q

T/F Allosteric effectors bind to the active site

A

false, they bind to sites other than the active site.

41
Q

What type of enzymatic regulation is feedback inhibition?

A

allosteric regulation.

42
Q

If an enzyme could be allosterically regulated, would it still show a michaelis-menton binding pattern?

A

no, it would show a sigmoidal curve because its allosteric effectors make it a cooperative molecule

43
Q

Name three main features of activation by cleavage covalent modification process and an example of this

A

1) can occur outside the cell
2) does not require ATP
3) Requires safeguards to prevent premature activation because cleavage can be amplified.

example: zymogens are activated by cleaving the bonds to render an active digestive enzyme. this process is irreversible as the cleaved peptide chain cannot be added back on.

44
Q

How does the blood clotting cascade get activated by cleavage?

A

thrombin, a serine protease, activates fibrinogen in the blood stream to form fibrin (scab)

45
Q

Equation for Vo

A

Vo=K[A]

46
Q

Explain why it is usually easier to calculate an enzyme’s reaction velocity from the rate of appearance of product rather than the rate of disappearance of a substrate.

A

Enzyme activity is measured as an initial reaction velocity, the velocity before much substrate has been depleted and before much product has been generated. It is easier to measure the appearance of a small amount of product from a baseline of zero product than to measure the disappearance of a small amount of substrate against a background of a high concentration of substrate.

47
Q

How would diisopropylphosphofluoridate-affect the apparent KM and Vmax of a sample of chymotrypsin?

A

By irreversibly reacting with chymotrypsin’s active site, DIPF would decrease [E]T. The apparent Vmax would decrease since Vmax = kcat[E]T・ KM would not be affected since the uninhibited enzyme would bind substrate normally.

48
Q

In order to construct a Vo vs [S] graph, E must be > or < to [s}

A

E concentration needs to be much less than substrate concentration to make a Vo vs S graph to ensure that you are not running out of substrate, which would limit the speed of the reaction.

49
Q

equation for rate of ES formation

A

k1[E][S]

50
Q

Equation for rate of product formation

A

k2[ES]

51
Q

equation of ES degredation

A

K-1[ES]+K2[ES]

52
Q

Vmax rate equation

A

Vmax=kcat[Et]

53
Q

T/F: Michaelis menton kinetics assume that the enzyme and substrate first bind to form and enzyme substrate complex

A

true, E+S= ES

54
Q

T/F: Michaelis menton kinetics assume that, at extremely high substrate concentrations, the initial velocity is no longer affect by substrate concentration

A

true. V0 will no longer be limited to the concentration of substrate if the substrate concentration is very high. Vo=Vmax when substrate concentration approaches infinity

55
Q

T/F: the michaelis menton kinetics describe single substrate enzyme

A

true

CHEM-3502 (8 decks)

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