Enzymes Flashcards

1
Q

Not all enzymes exhibit these specificities

A

Substrate specificity: only bind & react a single substrate/group of substrates

Reaction specificity: only catalyze one type of reaction

Tissue specificity, others are ubiquitous

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2
Q

How do enzymes cause reactions to reach quilibrium more quickly?

A

they accelerate the rate without changing the thermodynamics

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3
Q

How do enzymes accelerate rxn rates?

A

They form weak bonds (hydrogen, hydrophobic, ionic, vdw) between the enzymes and the substrate that puts the substrate in a favorable position for hte reaction

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4
Q

If a reaction is to proceed from substrate to product, it’s thermodynamically favorable and the ground state of the ___ is lower than that of the ___.

A

Product’s ground state is lower than that of the substrate

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5
Q

Enzymes lower

A

the energy required to achieve the transition state

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6
Q

Change in free energy of activation(delta G*)- what is it and how do enzymes impact it?

A

The change in E required to reach the transition state

Enzymes lower it

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7
Q

deltaG‘o is the total change in the reaction from substrate, through transition state, and to product.

Favorable reactions have a

A

negative deltaGo’

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8
Q

Transition state analogues as pharmacological agents- how do they work and what are 2 examples?

A

May bind the enzyme more tightly than the actual substrate o product –> can act as competitive inhibitors

<strong>HIV protease inhibitors</strong>

<strong>Tamiflu</strong> on neuraminidase

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9
Q

The most important reaction for metabolism is done by what class of enzymes? What does it do?

A

Oxidoreductases transfer electrons (H- or H atoms)

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10
Q

Oxidation-reduction

A

change in electron density around carbon, nitrogen, and sulfur

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11
Q

An atom that gained electrons is

A

reduced

OIL RIG

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12
Q

An atom that lost electrons is

A

oxidized

OIL RIG

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13
Q

Name some electron carriers

A
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14
Q

Velocity

A

The RATE (unit per time) of appearance of P or disappearance of S

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15
Q

Initial velocity (v0 or vi)

A

velocity at the beginning of an enzyme-catalyzed reaction at time zero

This exhibits the “true” rate of reaction before the substrate becomes limiting

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16
Q

Describe the relationship between V0 and [enzyme]

A

V0 increases linearly with enzyme concentration

note: Reaction rate decreases (curves on the graph) once the enzyme depletes the substrate pool

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17
Q

Why does the left graph flatten out? Why does the right graph flatten out?

A

The left graph plots velocity - it’s reaching equilibrium.

The right graph plots initial velocity - enzymes are becoming saturated with substrate, so you’ve already reached Vmax

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18
Q

Vmax

A

The velocity at infinitely high [substrate], when all enzymes are occupiied in the E-S complex

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19
Q

Km

A

the [substrate] at which velocity is 1/2 maximal.

Thus if [S]=Km, then V0=1/2Vmax

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20
Q

this is the michaelis menten equation. How does it change at low [substrate]? At high [substrate]?

A

At low substrate, the “+[S]” disappears. –> V0 = (Vmax/Km)[S]

At high substrate, V0=Vmax

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21
Q

Relationship between Km and affinity

A

Lower Km = high enzyme affinity

22
Q

Hexokinase I in the brain/muscle

vs

Hexokianse IV in the liver

A

Hexokinase I has a much lower Km for glucose –> high affinity for glucose –> readily saturated with glucose to phosphorylate it.

23
Q

Kcat/turnover number

A

kcat = Vmax/[total enzyme]

It is a rate constant = the number of substrate converted to product each second on a single enzyme when the enzyme is saturated with substrate

in sec-1

24
Q

Competitive inhibition

A

Inhibitor binds the active site, thus blocking the substrate from binding so catalysis can’t occur

Reverse by simply increasing [S]

25
Q

Mixed inhibition

A

Inhibitor binds to a site on either the enzyme or E-S, distant from the active site

26
Q

Uncompetitive inhibition

A

Inhibitor binds to a site distance from the active site on the ES complex only

27
Q

The lineweaver burke double reciprocal plot is just an extrapolation of the mcihaelis menten.

What does the y-intercept mean? What does the x-intercept mean? What does the slope mean?

A
28
Q

What kind of inhibition is this?

A

Competitive inhibition.

  • Km increases as [I] increases - the more inhibitor, the more substrate needed to reach 1/2 Vmax
  • Vmax stays the same - infinitely high [S] will outcompete the inhibitor
29
Q

What kind of inhibition is this?

A

Mixed inhibition

  • Km increases as you increase [I]
  • Vmax decreases as you increase [I]
30
Q

Allosteric inhibitors often display what kind of inhibition>

A

Mixed

Mixed inhibition is the msot common type of inhibition

31
Q

What kind of inhibition is this?

A

Noncompetitive inhibition (a type of mixed inhibition) : both E and ES have the same affinity for binding the inhibitor

Super rare

  • No effect on Km
  • Decreases Vmax
32
Q

What kind of inhibition is this?

A

Uncompetitive inhibition

parallel lines

  • Both Km and Vmax decrease as inhibitor increases
33
Q

Irreversible inhibitors work by

A

forming a covalent bond with a specific active site residue; may resemble the substrate or transition state for the reaciton

34
Q

Mechanism-based / suicide inhibitors

A

An irreversible inhibitor that is inactive until it’s acted upon by the enzyme and converted to a reactive intermediate that can then form a covalent bond with the enzyme –> enzyme kills itself by activating the inhibitor

35
Q

Serpins

A

suicide inhibitors of cellular proteases

Ex) Alpha 1-antitrypsin, Antithrombin III

36
Q

Alpha 1-antitrypsindeficiency(A1AD) can result in

A

emphysema and liver failure

Because A1A inhibits inflammatory cells’ enzymes to protect tissues

37
Q

Antithrombin III deficiency

A

Can cause excessive clotting

Beccause antithrombin III inhibits coagulation by neutralizing thrombin

38
Q

Oxygen is a __ for hemoglobin

A

Allosteric activator - it changes the structure of hemoglobin to bind more oxygen

39
Q

Negative feedback inhibition

A

The product of a pathway accumulates and turns that pathway off

40
Q

Would transition state analogues be stronger or weaker inhibitors than substrate analogues?

A

TS analogues are stronger because they make more molecular contacts with the enzyme

41
Q

At what point of a metabolic pathway is it most important to control enzyme activity?

A

The first committed step in the pathway, after which it can’t funnel into any other alternative metabolic pathway in the cell

42
Q
A

Transferase

43
Q
A

Lyase

44
Q
A

Ligase

45
Q
A

Enzyme conc

46
Q
A

0.4mM

47
Q
A

0.4 umoles/min

48
Q

What enzyme modifications are associated with the process of angiogenesis?

A

Prolyl and asparaginyl hydroxylation

49
Q

What enzyme modifications are associated with cholera toxin and how does it cause cholera symptoms?

A

ADP ribosylation of Ga in intestinal epithelial cells –> constitutive cAMP production –> Na & K production

–> Cl- and HCO3- into the lumen of the small intestine

50
Q

Loss of Ras prenylation is a

A

cancer therapy

51
Q

Cleavage of a peptide bond is

A

irreversible