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biochem > biochem lectures 6 & 7 pt 2 > Flashcards

biochem lectures 6 & 7 pt 2 Flashcards

1
Q

what is ATP synthase

A

multisubunit transmembrane protein

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2
Q

another name for ATP synthase

A

complex V

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3
Q

what is ATP synthase made of

A

2 subunits, F1 and F0

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4
Q

what is F0

A

water insoluble transmembrane proton pore

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5
Q

why is F0 water insoluble complex

A

cuz the parts of the transmembrane proton pore that forms interacts w/ inner mitochondrial membrane, so there’s a lot of interactions w/ hydrophobic fatty acid side chains

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6
Q

what does complex IV do

A

uses energy of reduction of O2 (to H2O) to pump one H+ into the intermembrane space for each e- that passes through

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7
Q

how much NADH to reduce one O2

A

2 NADH

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8
Q

how much H+ is used to reduce O2

A

4 H+

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9
Q

is F0 subunit free floating or embedded

A

it’s embedded within inner mitochondrial membrane

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10
Q

what pore structures do protons diffuse thru

A

this F0 subunit of ATP synthase

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11
Q

basically what is F0

A

pore structure, what protons will diffuse thru

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12
Q

what is F1

A

catalytic component

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13
Q

describe F1

A

water soluble peripheral membrane protein complex

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14
Q

what carries out the actual synthesis of ATP

A

F1

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15
Q

how does ATP synthase work

A

by coupling facilitated diffusion of protons thru F0 w/ catalytic mechanism underlying synthesis of ATP via F1 component

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16
Q

how much ATP does ATP synthase generate

A

1 ATP per every 3 protons

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17
Q

what happens to F0 as proteins diffuse thru it

A

begins to rotate

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18
Q

where does rotation of F0 occur

A

within inner mitochondrial membrane

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19
Q

what does rotation of F0 complex affect

A

gamma protein

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20
Q

what is gamma protein

A

a part of F1; physically connecting thru other accessory proteins

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21
Q

what happens as F0 turns

A

causes gamma protein subunit to turn with it

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22
Q

what happens as gamma subunit turns

A

causes conformational changes to alpha and beta subunits in F1 catalytic complex

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23
Q

describe alpha-beta units

A

3 sets of alpha-beta dimers or pairs in F1; each is capable of synthesizing ATP

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24
Q

what is rotational catalysis or binding chain mechanism

A

rotation of F0 drives movement of central gamma chain, gamma chain tweaks alpha-beta pairs of F1 that helps drive conformational change in catalytic subunits needed to make ATP

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25
Q

what is F0 again?

A

transmembrane proton pore; part of ATP synthase thru which protons will diffuse through

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26
Q

what does this pore structure enable

A

enables protons to, via facilitated diffusion and PMF, to pass thru F0

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27
Q

what is atomic force microgaphy

A

type of electron microscope, allows you to look at C subunits in F0

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28
Q

what are C subunits

A

form pore structure of F0

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29
Q

what is F1

A

catalytic subunit of ATP synthase

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30
Q

describe structure of F1

A

alternating a-b pairs/dimers around a central gamma subunit

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31
Q

where is gamma subunit located

A

in center of F1

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32
Q

how many sets of alpha-beta pairs or dimers in F1

A

3 sets

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33
Q

at any given time, what can each of those alpha-beta pairs assume

A

1 of 3 conformations; b-ATP, b-ADP, b-empty

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34
Q

what does each conformation represent

A

a diff step or ability/function of those alpha beta pairs to do something relevant to ATP synthesis

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35
Q

b-ADP

A

not catalytically active

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36
Q

what does b-ADP bind

A

ADP and Pi

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37
Q

b-ATP

A

catalytically active

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38
Q

what does b-ATP bind

A

ATP

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39
Q

what is b-empty

A

low affinity for ATP or ADP

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40
Q

which conformation has a high affinity of alpha beta pairs for ADP and Pi

A

beta-ADP

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41
Q

what is catalytically active form

A

beta-ATP

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42
Q

what form of alpha-beta do we get ATP synthesis

A

beta-ATP

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43
Q

what is beta-empty

A

as it transitions from beta-ATP to beta empty, we get release of ATP thats just been formed

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44
Q

what happens as central gamma subunit turns

A

causes each alpha-beta pair to go thru b-ADP, b-ATP, and then beta empty conformation

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45
Q

what is order of sequence of conformations

A

b-ADP, b-ATP, beta-empty

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46
Q

at any give point, describe each of the alpha-beta dimers

A

each is in one of those three states or conformations

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47
Q

why do we call it beta-whatever

A

because its beta subunit that is important for catalysis

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48
Q

what is alpha subunit needed for

A

functionality

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49
Q

what is rotational catalysis

A

free E generated w/ proton movement is harnessed to interconvert the conformation states to make and release ATP

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50
Q

what are the conformational changes driven by

A

rotation of rotor relative to aB subunits

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51
Q

how much H+ used for each 120* turn

A

each 120* turn uses 3 H+

52
Q

conversion of what is related to synthesis of ATP

A

beta-ADP –> beta-ATP

53
Q

conversion of what is related to release of ATP

A

b-ATP to b-empty

54
Q

how does beta ADP transition to beta ATP conformatoin

A

as gamma subunit rotates (cuz F0 rotates), brings about conformational changes within three sets of alpha-beta pairs

55
Q

what results in movement of central gamma subunit

A

diffusion of protons thru F0, causes rotational catalysis to occur, results in movement of central gamma subunit

56
Q

what do we have at any given time

A

we will have each of these alpha-beta pairs in one of these 3 conformational change

57
Q

how much does it rotate

A

120* increments

58
Q

what happens w/ each 120* turn of subunit

A

brings about conformational change in each of the three alpha-beta pairs

59
Q

what is each rotation driven by

A

thru diffusion of protons thru F0

60
Q

what happens to an alpha-beta pair that was in b-ADP conformation after a 120* rotation of gamma subunit

A

converted to b-ATP conformation

61
Q

what happens after another 3 protons diffuse thru (after b-ATP)

A

beta-empty conformation

62
Q

what happens after it releases ATP

A

resets

63
Q

what happens when one b-subunit assumes b-empty

A

one neighbor assumes b-ADP, one assumes b-ATP

64
Q

what does one complete rotation of gamma cause

A

causes each b to assume all 3 conformations

65
Q

what happens per 360* turn

A

produces 3 ATP

66
Q

who came up w a way to visualize rotational catalysis

A

japanese scientists; used recombinant proteins tagged w/ histidine, and nickel coated glass

67
Q

what else did japanese scientists notice

A

120* increments

68
Q

yield of cell respiration

A

3 ATP per NADH, 2 ATP per FADH2

69
Q

what do we get from anaerobic fermentation

A

only 2 ATP per glucose

70
Q

total yield per glucose for cell respiration

A

30/32

71
Q

why do we utilize more PE in glucose thru cell respiration

A

because we synthesize greater numbers of ATP in cell respiration vs. fermentation rxns

72
Q

what is efficiency of ATP production from PE stored in glucose

A

30-40%

73
Q

how much of PE stored in glucose are we losing, and to what

A

60%, in form of heat

74
Q

what gives us body temperature

A

metabolic activities of body

75
Q

how much PE from glucose is released in form of heat

A

greater than 50%

76
Q

what is 40% harnessed to make ATP sufficient for

A

enough for necessary biochemical rxns; we need to consider additional E sources (fats, proteins, etc)

77
Q

what is ox phos coupled to

A

electron transport

78
Q

what happens if you block electron transfer

A

block ATP synthesis

79
Q

what do you need in order for ATP synthesis

A

electron flow; source of electrons

80
Q

can we uncouple ATP synthesis from electron transport

A

yup

81
Q

what drugs can uncouple this

A

oligomycin or venturicidin

82
Q

what are oligomycin and venturicidin

A

ATP synthase inhibitors; enzymes that block ATP synthase’s ability to do what it does

83
Q

what happens if you treat ATP synthase with these ddrugs

A

not only fails to allow diffusion of protons thru F0, but prevents synthesis of ATP

84
Q

what happens if you block diffusion of protons thru F0

A

concentration of protons builds up, levelling off of O2 consumption

85
Q

why do we see leveling off of o2 consumption and atp synthesis

A

when u block ATP synthase’s ability to allow diffusion of protons thru F0, you prevent further flow of electrons. stuff builds up, more and more accumulation, electrons back up, no further electron transport along ETC, everything stops. leveling off of O2 consumption

86
Q

describe how we showed ATP synthesis (ox phos) and ETC are linked

A

not enough just to have reactants for ATP or just electron, we need BOTH

87
Q

what happens if you block diffusion of protons

A

also block electron transport

88
Q

how do wee see this blocking of electron transport

A

leveling off of O2 consumption

89
Q

what is an uncoupler of electron flow

A

separates/uncouples process of electron transport from ATP synthesis

90
Q

example of uncoupler

A

dinitrophenol (DNP)

91
Q

what happens if you block electron transfer

A

block ATP synthesis

92
Q

what do we need to get respiration AND ATP synthesis

A

need both a source of electrons (succinate) and ADP + Pi

93
Q

how do we know electron transport and ox phos are dependent?

A

experiments; isolated mitochondria from muscle. measure O2 consumption and ATP synthesis

94
Q

what happens if you just add reactants for ATP synthesis (ADP and Pi)

A

nothing; tiny increase in O2 consumption, no increase in ATP synthesis

95
Q

when do you get increase in both ATP synthesis and O2 consumption

A

when you add ADP & Pi AND succinate (source of electrons)

96
Q

what do you see when you block electron transport

A

leveling off of ATP synthesis and O2 consumption

97
Q

what blocks ATP synthase

A

venturicidin and oligomysin

98
Q

describe how uncouplers work

A

venturicidin/oligomycin block ATP synthase, H builds up. takes too much energy to pump H across gradient. uncouplers dissipate the gradient (carry protons from P to N), allows ETC to begin again

99
Q

can you have ETC without ATP synthesis

A

yup

100
Q

what is DNP

A

hydrophobic, dissociable proton

101
Q

what can DNP do

A

dissipate H+ gradient by carrying H+ across inner mitochondrial membrane

102
Q

what happens if you add DNP

A

destroy proton gradient

103
Q

what happens if you destroy gradient

A

ETC can continue

104
Q

how do we see this uncoupling of DNP on the graph

A

increase in O2 consumption, but ATP synthesis is still same line (levels off)

105
Q

when does uncoupling of ETC from ATP synthesis occur in real world

A

hibernation in mammals (some plants also)

106
Q

do hibernating bears have DNP

A

nope

107
Q

what do bears have

A

brown fat

108
Q

what is brown fat

A

high in mitochondria [called brown fat cuz of cytochromes present in mitochondria causing it to look brown]

109
Q

when does brown fat accummulate

A

winter approaches, temperature drops

110
Q

what else do bears have

A

important protein called thermogenin

111
Q

what does thermogenin do

A

uncouples ATP synthesis from ETC

112
Q

why does this matter in hibernating animals?

A

aren’t expending as much energy, but they need heat.

113
Q

what does natural uncoupling lead to

A

allows more E derived from flow of e- thru ETC, to be released as heat

114
Q

what else is brown fat in

A

babies

115
Q

what does brown fat serve as

A

significant heat source

116
Q

what protein does uncoupling involve

A

thermogenin

117
Q

what happens as winter approaches

A

hibernating mammals increase expression of thermogenin

118
Q

what is thermogenin

A

proton pore protein

119
Q

what does pore protein thermogenin do

A

allows protons to flow down gradient

120
Q

how does thermogenin function

A

functions like F0, but doesn’t have F1 component (so not synthesizing ATP)

121
Q

what does lack of F1 mean

A

it’s not synthesizing ATP

122
Q

what does thermogenin essentially function as

A

a bypass proton pore

123
Q

what does increasing thermogenin expression do

A

more proteins will diffuse thru thermogenin vs ATP synthase, simply b/c there’s more thermogenin around

124
Q

what does thermogenin do

A

dissipate the gradient (like DNP)

125
Q

how does thermogenin dissipate gradient

A

by its proton pore function

126
Q

what happens as more protons diffuse thru thermogenin

A

more E from electron flow is generated in form of heat

biochem (15 decks)

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