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BIOCH 320 > 7-enzymes C > Flashcards

7-enzymes C Flashcards

1
Q

what kind of curve is the michaelis-menten kinetics curve

A

logarithmic

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2
Q

do allosteric enzymes follow the michaelis-menten kinetics curve

A

no

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3
Q

what kind of curve does allosteric enzymes folloe

A

sigmoidal curves

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4
Q

what kind of allostery is cooperative substrate binding

A

positive allostery

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5
Q

what are the two states called in the allostery cooperative stuff

A

R and T states

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6
Q

what does the T state mean

A

tense and low affinity for substrate

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7
Q

what does the R state mean

A

relaxed state and high affinity for substrate

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8
Q

do effects bind covalently or non-covalently to regulatory sites

A

non-covalently

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9
Q

what is homoallostery

A

the substrates act as effects (like oxygen on hemoglobin)

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10
Q

where to homoallosteric effectors bind

A

to active sites or regulatory sites

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11
Q

what is heteroallostery

A

when the substrates are not the effectors (like BPG on hemoglobin)

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12
Q

where to heteroallosteric enzymes bind

A

to regulatory sites

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13
Q

what kind of structure do many allosteric enzymes have

A

quaternary

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14
Q

where can regulatory sites be (2 options we learned)

A

their own subunit but they may be on catalytic subunits

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15
Q

what can effects do to activity

A

increase (positive) or decrease (negative)

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16
Q

what do positive effectors do to the graph

A

shift to the left

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17
Q

which state do positive effects favor

A

the R state

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18
Q

what is Km

A

concentration of substrate it takes to get to 50% of Vmax

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19
Q

what do negative effectors do to the graph

A

shift it to the right

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20
Q

which state do negative effects favor

A

the T state

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21
Q

what is a generalization of the symmetry model of allostery

A

that the enzyeme can either be only in R or T state, no inbetween

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22
Q

what kind of structures do allosteric proteins in symmetry model of allostery have

A

quaternary structure

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23
Q

what are the states that each oligomer can exist in in symmetry model of allostery

A

in R or T state

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24
Q

what causes a shift in equilibrium in T and R states in symmetry model of allostery

A

when ligands/substrates bind (with different addinities)

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25
Q

what state is the enzyme in when there is no substrate bound (in symmetry model of allostery)

A

almost exclusively T state

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26
Q

which state in symmetry model of allostery is high activity

A

R state

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27
Q

which state in symmetry model of allostery is low activity

A

T state

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28
Q

what is the sequential model of allostery

A

when binding of substrate causes a conformational change which makes other subunits switch to the R state

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29
Q

what is in the symmetry model of allostery

A

binding of substrate affects the probability that the enzyme is in R or T state (the entire enzyme as a whole)

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30
Q

what kind of structure do the enzymes in sequention model of allostery have

A

quaternary structure

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31
Q

what are the states that each subunit can exist in in symmetry model of allostery

A

T or R state

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32
Q

is it the subunit or oligomer that can be in either T or R state in sequential model of allostery

A

subunits

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33
Q

is it the subunit or oligomer that can be in either T or R state in symmetry model of allostery

A

oligomer (whole enzyme, not just subunits)

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34
Q

is symmetry maintained in the sequential model of allostery

why

A

no, the subunits are not necessarily in the same conformation

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35
Q

what happens once a ligand binds in the sequential model of allostery

A

1 subunit becomes R state, there is an increased affinity for substrate in the other subunits

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36
Q

what is ATCase (what does it stand for)

A

aspartate transcarboamoylase

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37
Q

what kind of structure does ATCase (aspartate transcarboamoylase) have

A

quaternary

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38
Q

how many catalytic subunits does ATCase (aspartate transcarboamoylase)

A

6

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39
Q

how many regulatory subunits does ATCase (aspartate transcarboamoylase)

A

6

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40
Q

what is the symmetry for ATCase (aspartate transcarboamoylase)

A

D3

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41
Q

what is the role of ATCase (aspartate transcarboamoylase)

A

first step in CTP synthesis

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42
Q

what activates ATCase (aspartate transcarboamoylase)

A

ATP

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43
Q

which model of allostery does ATCase (aspartate transcarboamoylase) follow

A

symmetry

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44
Q

what inhibits ATCase (aspartate transcarboamoylase)

and how (which mechanism)

A

CTP, feedback inhibited

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45
Q

what composes the protomers in ATCase (aspartate transcarboamoylase)

A

1 catalytic and 1 regulatory subunit

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46
Q

how many protomers in ATCase (aspartate transcarboamoylase)

A

6

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47
Q

what is feedback inhibition

A

when the concentration of the end product of a pathway often signals the amount of activity required in the pathway

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48
Q

what kind of modulation are most feedback inhibitors

A

allosteric (because they have little resemblance to the origional substrate)

49
Q

what is the T state of ATCase (aspartate transcarboamoylase) look like

A

the aspartate binding domain is blocked off

50
Q

what is the R state of ATCase (aspartate transcarboamoylase) look like

A

the aspartate binding domain is not blocked off

51
Q

is CTP binding favored in the R or T state of ATCase (aspartate transcarboamoylase)

A

favored in T state because its the inhibitor (T is closed off and compressed)

52
Q

what does PALA do to the R state in ATCase (aspartate transcarboamoylase)

why

A

it stabilizes it because it looks like the intermediate for ATCase

53
Q

is PALA an inhibitor or potentiatory and why

A

inhibitor because it mimics the intermediate for ATCase so it wont allow the enzyme to work

54
Q

what does ATP do to the curve (Vo vs [S]) of ATCase

A

shifts it to the left

55
Q

what does CTP do to the curve (Vo vs [S]) of ATCase

A

shifts it to the right

56
Q

what does CTP do to ATCase

A

inhibit

57
Q

what kind of inhibitor is CTP and why

A

heterotropic

58
Q

what is a homotropic modulator

A

substrate for its target enzyme, as well as a regulatory molecule of the enzyme’s activity

59
Q

what is a heterotropic modulator

A

regulatory molecule that is not the enzyme’s substrate

60
Q

what kind of modulator is CTP to ATCase (2)

A

heterotropic inhibitor

61
Q

what kind of modulator is ATP to ATCase (2)

A

heterotropic activator

62
Q

what kind of modulator is aspartate to ATCase (2)

A

homotropic activator

63
Q

why does CTP shift the ATCase graph to the right

A

because it makes it stay in the T state a little longer

64
Q

why does ATP shift the ATCase graph to the left

A

because it makes it stay in the R state a little longer

65
Q

is the catalytic and regulatory part on the same subunit in ATCase

A

no

66
Q

is the catalytic and regulatory part on the same subunit in phosphofructokinase

A

yes

67
Q

what kind of enzyme class is phosphofructokinase

A

transferase

68
Q

what kind of symmetry does phosphofructokinase have

A

D2

69
Q

what does each subunit in phosphofructokinase contain

A

an active AND a regulatory site

70
Q

what is a homotretramer

A

protein complex made up of four identical subunits

71
Q

what kind of protein is PFK (what are the subunits like and how many)

A

homotetramer

72
Q

what happens to phosphofructokinase activity without AMP

why

A

it stays in the T state for longer

AMP is its activator

73
Q

what happens to phosphofructokinase activity with AMP present

why

A

it goes into the R state faster because AMP is its activator

74
Q

what happens to phosphofructokinase activity without ATP

why

A

there is high activity

ATP inhibits PFK

75
Q

what happens to phosphofructokinase activity with ATP

why

A

it makes an inverted U shape curve because ATP starts to decrease activity (it is a negative regulator)

76
Q

what kind of molecule is ATP to PFK

A

homotropic inhibitor

77
Q

what kind of molecule is fructose-6-phosphate to PFK

A

homotropic activator

78
Q

what kind of graph relationship does fructose-6-phosphate have to PFK

A

a sigmoidal relationship

79
Q

where does fructose-6-phosphate bind to PFK

A

active site

80
Q

where does ATP bind to PFK

A

it has 2 binding sites, active site and regulatory site

81
Q

what kind of molecule is AMP to PFK

A

heterotropic activator

82
Q

where does AMP bind to PFK

A

the same regulatory site as ATP

83
Q

what kind of molecule is PEP to PFK

A

heterotropic inhibitor

84
Q

what state does PFK shift to when AMP binds

why

A

to the R state

because its an activator

85
Q

what is the nucleophile in the PFK reaction

A

fructose-6-phosphate towards the phosphate

86
Q

what is the most common type of reversible covalent modification

A

phosphorylation

87
Q

where can phosphorylation occur (which residues)

A

Ser, Thr, Tyr, His

88
Q

what is the general formula for phosphorylation

A

Enzyme + ATP –> Enzyme-P + ADP

89
Q

what are 2 types of reversible covalent modification

A

phosphorylation and adenylylation

90
Q

which residues can get adenylylation

A

Tyr

91
Q

what is the general formula for adenylylation

A

Enzyme + ATP –> Enzyme-AMP + PPi (pyrophosphate)

-it takes the adenosine

92
Q

is adenylylation or phosphorylation a bigger physical change

A

adenylylation because thats taking an adenosineMP instead of just a phosphate

93
Q

what are 2 conditions for the target sequence to act as a substrate for kinase

A

sequence must match the kinase active site and be available on protein surface

94
Q

can some proteins have multiple targets/ protein kinases

A

yes

95
Q

what do multiple targets/ protein kinases allow for in protein kinases

A

finer control of activity

96
Q

what is the role of glycogen synthase

A

catalyzes glycogen synthesis (anabolic process)

97
Q

does glycogen synthesis only get phosphorylated at phosphorylate 1 site

A

no it can be phosphorylated at multiple sites

98
Q

what activates glycogen phosphorylase

A

phosphorylated by a kinase (it becomes phosphorylated to be active)

99
Q

which state of glycogen phosphorylase is active (is it phosphorylated or not)

A

phosphorylated is the active state

100
Q

what happens with phosphorylation of glycogen synthase

A

it becomes less active

101
Q

what does multiple phosphorylations of glycogen synthase do

A

act in concert to reduce its activity

102
Q

overall, how does phosphorylation effect glycogen synthase vs glycogen phosphorylase

A

reduction in glycogen synthase activity

increase in glycogen phosphorylase activity

103
Q

what is irreversible covalent modification

A

a covalent change in PRIMARY structure

104
Q

what are zymogen

A

unaltered inactive enzymes

105
Q

what activates zymogen

A

modifications by other enzymes, like a proteinase

106
Q

how do you turn off an activated zymogen

A

you need to destroy it or inactivate it

107
Q

what happens when you phosphorylate isocitrate dehydrogenase and why

A

it is inactive because the phosphase (negative) interacts at the same site as the substrate (negative)

108
Q

what activates trypsinogen

A

enteropeptidase

109
Q

what is the active form of trypsinogen

A

trypsin

110
Q

what does trypsin do

A

activates chymotrypsinogen into pi-chymotryipsin

111
Q

what does pi-chymotryipsin di

A

cleaves and activates itself to become alpha-chymotryipsin

112
Q

what kind of enzyme is enteropeptidase

A

proteinase

113
Q

what kind of enzyme is trypsinogen

A

zymogen

114
Q

what kind of enzyme is trypsin

A

proteinase

115
Q

what kind of enzyme is chymotripsinogen

A

zymogen

116
Q

what kind of enzyme is pi-chymotrypsin

A

proteinase

117
Q

what kind of enzyme is alpha-chymotrypsin

A

proteinase

118
Q

what happens in chymotrypsin maturation

A

trypsin cleaves it, exposes +ve N terminal which pulls back into an Asp group which stabilizes the negative charge

119
Q

can aa far in 1ary structure be close in 3D space

A

yes

BIOCH 320 (16 decks)

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