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BMSC 200 > module 6: enzymes > Flashcards

module 6: enzymes Flashcards

1
Q

what is the most important feature about enzymes?

A

their catalytic power & specificity

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2
Q

what is vitalism?

A

the belief that things are fundamentally different from non-living things

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3
Q

who developed vitalism?

A

Edward Buchner

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4
Q

what are co-factors?

A

non-protein factor & activator

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5
Q

what are examples of co-factors?

A

inorganic ions (Mg, Fe)

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6
Q

what are co-enzymes?

A

complex organic molecules for activity

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7
Q

what is an example of a co-enzyme?

A

vitamins- required by the body but cannot be produced

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8
Q

what is a holoenzyme made of?

A

apoenzyme + co-factor/co-enzyme

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9
Q

what is a holoenzyme?

A

whole enzyme that represents a biologically active form

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10
Q

what is an apoenzyme?

A

inactive protein portion

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11
Q

what is a prosthetic group?

A

co-enzyme or co-factor that is highly associated with the enzyme

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12
Q

what is the difference between a co-enzyme / co-factor and a prosthetic group?

A

the degree of association

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13
Q

what are 2 functions of catalysts?

A
  1. lower amount of energy required for a reaction to occur
  2. speed up attainment of equilibrium but do not change it
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14
Q

are enzymes or catalysts faster?

A

enzymes

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15
Q

enzymes or catalysts: which functions under physiological conditions & which requires complex extreme conditions?

A

enzymes: physiological conditions
catalysts: complex & extreme conditions

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16
Q

enzymes or catalysts: which has a higher degree of specificity?

A

enzymes

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17
Q

enzymes or catalysts: which are responsive to changing conditons?

A

enzymes

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18
Q

what are catabolic reactions?

A

breaks stuff down & are less specific

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19
Q

what are anabolic reactions?

A

builds stuff up

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20
Q

what is the Circe effect?

A

ability of some enzymes to catalyze reactions faster than diffusion-controlled rate limits through electrostatic interactions

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21
Q

what is a substrate?

A

the molecule acted upon by the enzyme

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22
Q

what is the product?

A

the molecule produced by the enzyme

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23
Q

what is the active site?

A

the portion of the enzyme responsible for binding the substrate to ES complex

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24
Q

what is the ES complex equilibrium equation?

A

E + S <–> ES <–> E + P (goes both ways)

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25
Q

what kind of environments are active sites?

A

micro-environments

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26
Q

what can substrate binding cause?

A

induced fit

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27
Q

what is a lock & key enzyme?

A

the substrate fits into enzyme without changing its confirmation

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28
Q

what is a hand in glove enzyme?

A

substrate changes its confirmation to fit into the enzyme (induced fit)

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29
Q

what will be favoured in free energy graphs?

A

substrate/product using lower energy

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30
Q

what causes a more skewed equilibrium in free energy graphs?

A

greater difference between free energies

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31
Q

what does the difference between free energies in substrate & product mean?

A

shows where equilibrium lies but not the rate it is reached

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32
Q

what does a higher barrier tell us on a free energy graph?

A

slower rate of equilibrium

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33
Q

what does a lower energy path do on a free energy graph?

A

increases the rate of reaction but equilibrium remains the same

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34
Q

the reaction is spontaneous only if G is…

A

negative

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35
Q

does G provide information about the rate of a reaction?

A

no

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36
Q

what does G depend on?

A

free energy of the product - free energy of the reactants

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37
Q

what do enzymes do in free energy graphs?

A

provide a lower energy pathway which increases rate of reaction & decreasing activation energy

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38
Q

what does the binding of a substrate do?

A

provides specificity & catalytic power

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39
Q

how much can catalytic mechanisms increase reaction rates?

A

by a 10,000 fold

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40
Q

what is the most difficult moment to achieve?

A

transition state stabilization

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41
Q

what is transition state stabilization?

A

an increased interaction of the enzyme substrate occurs in the transition state

42
Q

the active site is ( ) to the transition state in shape & chemical character

A

complementary

43
Q

enzymes bind to their transition states ( ) more tightly than their substrates

A

10^10 - 10^15

44
Q

what are transition state analogs?

A

stable compounds that resemble unstable transition states

45
Q

what are competitive inhibitors?

A

molecules that bind to the active state of an enzyme (tend to resemble the substrate molecule)

46
Q

what is prevented when transition state analogs bind with high affinity?

A

substrate binding

47
Q

what does the active site often contain?

A

polar, ionizable side chains

48
Q

what is acid-base catalysis?

A

enzyme donates or accepts proton & changes protonation state of substrate

49
Q

what amino acid is often involved in acid-base catalysis?

A

histidine

50
Q

what is the pKa of a functional group is influenced by?

A

chemical microenvironment

51
Q

what is covalent catalysis?

A

covalent intermediate is formed between the enzyme & the substrate molecule

52
Q

what does a steep drop off mean on a graph?

A

all enzyme is unfolded at max temp & there is no more activity

53
Q

what do K1 & K-1 represent?

A

rapid, non-covalent interactions between enzyme & substrate

54
Q

what does K2 represent?

A

rate constant of formation of product from ES

55
Q

how to calculate initial velocity?

A

Vo= [ES] K2

56
Q

how to calculate velocity?

A

V= delta P / delta t

57
Q

steady state assumption equation?

A

[E] [S] K1 = [ES]K-1 + [ES]K2

58
Q

what is the michaelis-menten graph?

A

relationship between substrate concentration & initial velocity

59
Q

what is the michaelis-menten equation?

A

Vo= Vmax [S] / Km + [S]

60
Q

what is Km?

A

the concentration of substrate required to reach 1/2 Vmax

61
Q

[S] < Km

A

enzymes are highly sensitive to changes, but have little activity

62
Q

[S] > Km

A

enzymes have high activity but are insensitive to changes

63
Q

[S]=Km

A

enzyme has significant activity & is responsive to changes

64
Q

Thrombin cleaves…

A

Arg-Gly bonds

65
Q

Trypsin cleaves by…

A

Lys & Arg

66
Q

Chymotrypsin cleaves by…

A

Phe, Tyr & Met

67
Q

Elastase cleaves by…

A

Gly & Ala

68
Q

what does Papain do?

A

cuts all peptide bonds

69
Q

what is the catalytic triad made of?

A

Asp, His & Ser

70
Q

what does His do in the catalytic triad?

A

accepts & donates a proton at each stage of acid-base catalysis

71
Q

what does Asp do in the catalytic triad?

A

stabilizes positively charged His to facilitate serine ionzation

72
Q

what does Ser do in the catalytic triad?

A

attacks carbonyl group of peptide bond to be cleaved

73
Q

what function does Ser cause in the catalytic triad?

A

covalent catalysis

74
Q

is changing amount of enzyme long term or short term?

A

long

75
Q

3 factors of covalent modifcation

A
  1. phosphorylation
  2. methylation
  3. glyosylation
76
Q

what is the mechanism used for non-covalent modification?

A

allosteric regulation

77
Q

what type of feedback are enzymatic pathways controlled by?

A

negative feedback

78
Q

what are allosteric enzymes?

A

slow, information sensors that coordinate cellular metabolism

79
Q

what shape of data are allosteric enzymes represented by?

A

sigmoidal curve

80
Q

what structure level do allosteric enzymes have?

A

quaternary

81
Q

how are allosteric enzymes regulated?

A

by allosteric modulators that bond non-covalently at sites that are NOT active sites

82
Q

allosteric enzymes transition from an ( ) active state to a ( ) active state within a ( ) range of concentration

A

less active –> more active in narrow range

83
Q

what is the threshold effect?

A

below a certain substrate concentration there is little activity & after threshold has been reached, activity increases rapidly

84
Q

what does Phosphopfructokinase 1 (PFK1) do?

A

catalyzes an early step of glycolysis

85
Q

what is Phosphoenolpyruvate (PEP)?

A

an intermediate near the end of the pathway & is an allosteric inhibitor of PK1

86
Q

ADP is a ( ) of PK1

A

allosteric activator

87
Q

When the ratio [PEP] / [ADP] is high, what is inhibited?

A

PFK1 is inhibited

88
Q

When the ratio [PEP] / [ADP] is low, what happens?

A

PFK1 is activated & glycolysis produces more ATP from ADP

89
Q

what do concentrations of PEP & ADP do?

A

act allosterically through PKF1 to regulate activity

90
Q

how are enzymes regulated?

A

covalent linkage of a modifying group to change protein behaviour

91
Q

what is the most common post-translational covalent modification?

A

through phosphorylation

92
Q

are modifications reversible?

A

yes

93
Q

what is glycogen synthase?

A

anabolic production of glycogen from glucose
(Glucose -> Glycogen)

94
Q

what is glycogen phosphorylase?

A

catabolic breakdown of glycogen into glucose
(glycogen -> glucose)

95
Q

what hormone is regulated when you are hungry?

A

glucagon

96
Q

what is phosphorylation?

A

activates the catabolic enzyme & inactivates the anabolic enzyme

97
Q

what does phosphorylation favour?

A

breakdown of glycogen into glucose

98
Q

when is the breakdown of glycogen into glucose favoured?

A

when both are un-phosphorylated

99
Q

where do un-competitive inhibitors bind to?

A

only ES complex

100
Q

where do non-competitive inhibitors bind to?

A

either ES or E

101
Q

what are zymogens activated by?

A

activated by selective proteolysis

BMSC 200 (10 decks)

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