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BIO1332 - Biochemistry > Allosteric enzymes and Inhibitors > Flashcards

Allosteric enzymes and Inhibitors Flashcards

1
Q

What is an inhibitor?

A

Any molecule that acts to reduce the rate of an enzymatic reaction

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2
Q

What can inhibitors be composed of?

A

Small chemicals or larger polymers (including other protein)

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3
Q

What can act as competitive inhibitor?

A

Drugs

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4
Q

What does a good inhibitor do?

A

Increase the Km of an enzyme

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5
Q

What substrate does sildenafil mimic?

A

Phosphodiesterase 5

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6
Q

What is a competitive inhibitor?

A

Resembles the substrate so if can bind to the active site but doesn’t react like the actually substrate

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7
Q

Can a competitive inhibitor undergo a reaction with the enzyme?

A

No

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8
Q

Finish the sentence:

The enzyme-inhibitor complex, is catalytically…

A

inactive

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9
Q

What does competitive inhibitors reduce?

A

The concentration of free enzyme available for substrate binding

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10
Q

Can a higher concentration of substrate over come the effects of the competitive inhibitor?

A

Yes

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11
Q

Why does the inhibitor make the Km look larger on a Michaelis-Menten?

A

As the binding of the inhibitor and the substate to the enzyme are mutually exclusive

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12
Q

What is v equal in the Michaelis-menten equation?

A

V = Vmax x [S] / aKm + [S]

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13
Q

What is the double reciprocal of V = Vmax x [S] / aKm + [S]?

A

1/v = (aKm/Vmax)1/[S] + 1/Vmax

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14
Q

What remains constant with competitive inhibitor on a line weaver burn plot?

A

Vmax

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15
Q

What is an uncompetitive inhibitor?

A

Inhibitor binds directly to the enzyme-substrate complex but not to the free enzyme. (active site)

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16
Q

What does uncompetitive inhibitors rely on?

A

Inhibitor affects the catalytic function the enzyme not the its substrate binding

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17
Q

What is Kis?

A

The dissociation constant and has the units M

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18
Q

What is Ki?

A

The dissociation constant and has units M

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19
Q

What is Ki equal to?

A

[E][I]/[EI]

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20
Q

What is Kis equal to?

A

[ES][I]/[ESI]

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21
Q

Finish the sentence:

The enzyme-substrate-inhitibor complete, is catalytically…

A

inactive

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22
Q

When are uncompetitive inhibition significant in?

A

Multi-substrate enzymes

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23
Q

What does a uncompetitive inhibition do to Vmax/Km?

A

Nothing remains constant

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24
Q

What does uncompetitive inhibition do to Km and Vmax?

A

Decrease

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25
Q

Is Vmax reversed by increasing the concentration of substrate when uncompetitive inhibition is occurring?

A

Nothing - Cant to be reversed

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26
Q

What is a mixed inhibitor?

A

Binds to enzyme sites that participate in both substrate binding and cataslyse

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27
Q

What is non-competitive inhibition?

A 
Ki = Kis 
a = a'
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28
Q

Is a non-competitive inhibitor the same an uncompetitive inhibitor?

A

No

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29
Q

Why is non-competitive inhibitor the different to an uncompetitive inhibitor?

A

Decrease in Vmax
Constant Km
No-competitive is irreversible

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30
Q

What does irreversible inactivation resemble?

A

Non-competitive inhibition

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31
Q

What do you call an inhibitor which binds to irreversibly to an enzyme?

A

Inactivator

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32
Q

What do inactivators reduce?

A

Level of [E]T = Vmax without changing Km

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33
Q

What is similar between non-competitive and inactivators on the double reciprocal plot?

A

Lines intersect on the 1/[S] axis

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34
Q

How can amino acids be inactivators?

A

Specific amino acid residues which have be chemical modified by reagents

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35
Q

What effect does competitive inhibition have on Km?

A

Increase

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36
Q

What effect does uncompetitive inhibition have on Km?

A

Decrease

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37
Q

What effect does mixed inhibition have on Km?

A

Increase

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38
Q

What effect does non-competitive inhibition have on Km?

A

None

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39
Q

What effect does competitive inhibition have on Vmax?

A

None

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40
Q

What effect does uncompetitive inhibition have on Vmax?

A

Decreases

41
Q

What effect does mixed inhibition have on Vmax?

A

Decreases

42
Q

What effect does non-competitive inhibition have on Vmax?

A

Decreases

43
Q

How can we identify what types of inhibitors are present?

A

Using Lineweaver-Burk plot

44
Q

What are multi-subunit enzymes?

A
  • Made from more than one protein chain
  • Can be identical to different chains
  • The binding of one chain can influence the binding to other subunits
  • Leadings to co-operativity between the subunits
45
Q

Give an example of multi-unit enzymes:

A

Aspartate transcarbamoylase (ATCase)

46
Q

How can you regulate enzyme activity?

A
  • Control of enzyme availability

- Control of enzyme activity

47
Q

How do you control enzyme availability?

A
  • Amount depends on rate of synthesis and rate of degradation
  • Rate controlled by cell and can change dramatically over time
48
Q

How do you control enzyme activity?

A

Directly regulated by structural alterations which influence substrate binding affinity
-Allosteric mechanism

49
Q

What is an active site?

A

The region where the binding of substrate and catalysis takes place

50
Q

What is the average size of an enzyme?

A

300 amino acids

51
Q

What do the rest of the proteins present in the enzyme which aren’t involve in the active site do?

A
  • overall structure
  • Ensure correct shape
  • Allow for regulation
52
Q

What are allosteric effectors?

A

Any molecule that can bind to an enzyme away from the active site and change the enzyme’s activity for its substrate

53
Q

What do allosteric activators do?

A

Increase the rate of reaction

54
Q

What do allosteric inhibitors do?

A

Reduce the rate of reaction

55
Q

What molecules have inherent flexibility?

A

Proteins

56
Q

What is inherent flexibility?

A

Small changes in the structure in one part of the protein can be communicated throughout the entire structure.

57
Q

What can inherent flexibility affect?

A

The fit of the active site to substate and transition state

58
Q

What does allostery refer to?

A

The situation where a chemical binds to an enzyme away from the active site and influence the kinetic properties of the enzyme

59
Q

Where doe the catalysis take place with an enzyme and a substrate?

A

Active site

60
Q

What is the first step in the biosynthesis of pyrimidines?

A

ATCase catalyses

61
Q

What does carbamoyl donate in the pathways leading to arginine as well as pyrimidines?

A

Carbamoyl group

62
Q

What does aspirate and carbamoyl phosphate produce which is only used in synthesis of pyrimidine nucleotides?

A

CTP -Cytidine triphosphate

63
Q

What is the allosteric behaviour of ATCase?

A

Substates bind cooperatively to the enzyme

  • Allosterically inhibited
  • Allosterically activated
64
Q

How is ATCase allosterically inhibited?

A

By Cytidine triphosphate

65
Q

How is ATCase allosterically activated?

A

By adenosine triphosphate

66
Q

What is the curve for ATCase?

A

Sigmoidal

67
Q

What does CTP do to ATCase enzyme’s catalytic rate?

A

Decreases

68
Q

What does ATP do to ATCase enzyme’s catalytic rate?

A

Increases

69
Q

What are allosteric effecters called when comparing to competitive inhibitors?

A

K-system effectors

70
Q

What is the difference of allosteric effecters to competitive inhibitors?

A

-Affect Km and not Vmax

71
Q

How is ATCase regulated?

A

By ATP and CTP

72
Q

What is the structure of ATCase?

A
  • Subunit composition C6R6
  • Arranged as two sets of trimers of the catalytic subunits
  • 3 sets of regulatory dimers
  • Each dimer joins two trimers
73
Q

What is r in the ATCase structure?

A

Regulatory subunit

74
Q

What is c in the ATCase structure?

A

Catalytic subunit

75
Q

What type of inhibitor is PALA?

A

Competitive Inhibitor

76
Q

Describe the active site of ATCase:

A
  • Crystal strutcure
  • Substate bound to subunit interface
  • Site lying at boundaries between pairs of c chains within catalytic trimer
  • Each trimmer contributes three active sites
77
Q

What does the binding of PALA cause to an enzyme?

A

Major changes in the quaternary structure

78
Q

What two distinct quaternary forms do ATCase have?

A

-Absence of substrate or substrate analogous
OR
-Substrates or substrate analogous are bound

79
Q

What are the forms of ATCase referred to?

A

T state

R state

80
Q

What is R state?

A

Relaxed when substate bound

81
Q

What is T state?

A

Tense when no substrate

82
Q

How do you go from a T state to and R state transition?

A
  • Cataltyic trimers separate along molecular three fold axis by 12A
  • Rotate around three fold axis by 10 degrees
  • The regulatory dimers rate clockwise around the two fold axis by 15 degree
  • Separate by 4A along the three fold axis
83
Q

Where do CTP and ATP bind to on ATCase?

A

Outer edge of regulatory subunit about 50A away from catalytic site

84
Q

In which state (T OR R) does CTP bind to increase stability?

A

T-state

85
Q

In which state (T OR R) does ATP bind to increase stability?

A

R-state

86
Q

What happens when CTP binds to R-state?

A

Induces contraction in r dimer that cause c trimers to come together by 0.5A becoming less active

87
Q

What happens when ATP binds to T-state?

A

Causes c trimers to move apart by 0.4 A becoming more active

88
Q

Finish the sentence:

The T state and R state are in….

A

equilibrium

89
Q

What does the binding of CTP do to the equilibrium?

A

Shifts the equilibrium to T-State which decreases the net enzyme activity and reducing the rate of N-carbamoylaspartate generation

90
Q

Do allosterically regulated enzymes follow the Michaelis-Menten kinetics?

A

No

91
Q

What curve do allosterically regulated enzymes make?

A

Sigmoidal curve

92
Q

Why do allosterically regulated enzymes make sigmoidal curve?

A

The biding of substrate to one active site favours the conversion of the entire enzyme in to R-State increasing the activity at the other active sites

93
Q

What are the basis for sigmoidal curve?

A

Mixture of two Michaelis-Menten enzymes

  • One with high Km (low affinity) for substrate (T-state)
  • One with low Km (high affinity) for substrate (R-state)
94
Q

Does a high Km have a low or high affinity for substrate?

A

Low

95
Q

Does a low Km have a low or high affinity for substrate?

A

High

96
Q

What is positive cooperatively?

A

Binding of substrate to one unit increases likelihood of other subunits binding substrate

97
Q

What is negativity cooperatively?

A

Binding of substrate to one subunit to reduce the likelihood of other subunits binding substrate

98
Q

Which is more likely negative or positive cooperatively?

A

Positive cooperatively

BIO1332 - Biochemistry (19 decks)

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