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Biochemistry II > Exam 3.2 > Flashcards

Exam 3.2 Flashcards

1
Q

What is an anapleuotic reaction?

A

replenishing CAC cycle intermediates that have been extracted for biosynthesis

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2
Q

Is oxaloacetate considered a catalyst?

A

Yes

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3
Q

Anapleurotic reactions off set the loss of _________ taken for biosynthesis

A

intermediates

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4
Q

Decreased [catalysts] = INCREASED/DECREASED rate?

A

decreased

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5
Q

If an intermediate of CAC is withdrawn what happens to the rate of the CAC?

A

slows

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6
Q

what is the most important anapleurotic reaction?

A

pyruvate –> oxaloacetate

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7
Q

what enzyme catalyzes the most important anapleurotic reaction?

A

pyruvate carboxylase

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8
Q

what cofactor is involved in the most important anapleurotic reaction?

A

biotin

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9
Q

What molecule activates the most important anapleurotic reaction?

A

acetyl coA

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10
Q

what are the 2 domains of pyruvate carboxylase?

A
  1. BC (biotin carboxylase)
  2. CT (carboxytransferase)
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11
Q

what is the P/O ratio for NADH?

A

2.5 (NADH comes from matrix)
1.5 (using G3P pathway)

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12
Q

Which Complex is NOT involved in succinate oxidation?

A

Complex I

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13
Q

What is the P/O ratio fro NADH generated in the cytosol?

A

1.5 (FAD dependent)
2.5 (malate/aspartate)

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14
Q

Why are the 2 issues involving NADH in the cytosol?

A
  1. cannot cross the inner membrane
  2. can only enter the RETC via Complex I which is on the matrix side
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15
Q

How many ATP are generated and H+ translocated using the FADH dependent method?

A

1.5 ATP
6 H+

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16
Q

How many ATP a generated and H+ translocated using the malate/aspartate dependent method?

A

2.5 ATP
10 H+

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17
Q

Including the actions of respiratory electron transport and F1F0 ATPase, how many ATPs will be generated as a result of converting one pyruvate to an acetyl coA

A

2.5

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18
Q

T/F almost all oxidoreductases require a cofactor to function

A

True

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19
Q

NADH is an obligate _______ donor

A

hydride (2e-)

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20
Q

What is the only Complex involving NADH?

A

Complex I

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21
Q

Flavins are __e- acceptors and ___e- donors

A

2e- acceptors
1e- donor

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22
Q

What are the 4 obligate 2e- (hydride) donors?

A
  1. NADH (Complex I)
  2. succinate (Complex II)
  3. glycerol-3-P
  4. fatty acetyl coA
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23
Q

What allows flavins to be obligate 1e- donors?

A

semiquinone intermediate

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24
Q

Fe/S clusters are obligate ___e- donors/acceptors

A

1e-

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25
Q

What are the 2 oxidative states of 2Fe/2S and 4Fe/4S?
Ferric/ferrous?

A

Fe II (ferrous)
Fe III (ferric)

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26
Q

Rieske Fe/S clusters are ________ to reduce and ________ to oxidize

A

easier
harder

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27
Q

What coenzyme are highly hydrophobic?

A

UQ

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28
Q

What coenzyme freely moves in the inner membrane?

A

UQ

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29
Q

UQ is a obligate ___e- donor/acceptor?

A

1e-

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30
Q

What coenzyme shuttles e- between donors/acceptors?

A

UQ

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31
Q

What is the Q-cycle?

A

as UQ is reduced H+ is pumped into the IMS

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32
Q

Hemes are prosthetic groups for __________

A

cytochromes

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33
Q

Hemes are obligate ___e- donor/acceptor

A

1e-

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34
Q

What is special about cytochrome a3?

A

it is penta so the 6th spot is open for O2 binding

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35
Q

What is the only complex with Cu?

A

Complex IV

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36
Q

What are the 2 types of Cu and what do they do?

A

CuA: electron transfer
CuB: assists cytochrome a3 in O2 reduction

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37
Q

Rieske 4Fe/4S is easier to reduce, what is its delta G?

A

positive (easier to reduce)

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38
Q

How is partial reduction of O2 prevented?

A

keeping cofactors near each other

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39
Q

What is another name from Complex I?

A

NADH ubiquinone oxidoreductase

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40
Q

What is another name for Complex II?

A

succinate ubiquinone oxidoreductase

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41
Q

What is another name for Complex III?

A

ubiquinol cytochrome c oxidoreductase

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42
Q

What is another name for Complex IV?

A

cytochrome c oxidase

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43
Q

What is the largest Complex?

A

Complex I

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44
Q

In complex I, where are all the cofactors found?

A

soluble portion (points into matrix)

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45
Q

How many H+ are translocated from Complex I?

A

4

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46
Q

What are 2 inhibitors of Complex I?

A

Rotenone
Amytal

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47
Q

How does Rotenone and Amytal inhibit Complex I?

A

blocks UQ binding site

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48
Q

What happens to the RETC when Complex I inhibitors are present?

A

NADH accumulates = lactate accumulation (lactate DH) = CAC inhibited

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49
Q

Exposure to rotenone will lead to an increase in __________ production

A

lactate

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50
Q

What cofactor does Complex II have that doesn’t participate in e- transfer and we are not sure why its there

A

heme b

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51
Q

How many H+ are translocated at Complex II?

A

none

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52
Q

What is an inhibitor of Complex II?

A

thenoyl trifluoroacetone carboxin
TTC

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53
Q

Complex III has 2 sets of 11 subunits, the side oriented towards the IMS is Q__ and the side oriented near the matrix is Q____

A

Q P (IMS) (positive)
Q N (Matrix) (negative)

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54
Q

How many H+ are translocated at Complex III?

A

4

55
Q

What cycle is used also in Complex III to translocated H+?

A

Q cycle

56
Q

What are 3 inhibitors of Complex III?

A
  1. myxothiazol
  2. antimycin A
  3. stigmatellin
57
Q

How does myxothiazol inhibit Complex III?

A

binds to Q P site preventing e- transfer from UQH2 to Rieske Fe/S or Cyt. bL

58
Q

How does Antimycin A inhibit Complex III?

A

binds to Q N site preventing e- transfer from Cyt. bH to UQ

59
Q

How does stigmatellin inhibit Complex III?

A

binds to Q P site and forms a hydrogen bond disrupting its bond with UQH2 and binding to a His residue (reducing potential of Rieske Fe/S)

60
Q

In Complex IV, what does subunit I do?

A

O2 reduction

61
Q

What cofactors are in Complex IV’s subunit I?

A

Cyt. a
Cyt. a3
Cu B

62
Q

In Complex IV, what does subunit II do?

A

site of Cyt. c binding

63
Q

What cofactor is in Complex IV’s subunit II?

A

Cu A

64
Q

In Complex IV, what does subunit III do?

A

hydrophobic channels to direct O2 to subunit I

65
Q

What cofactor is in Complex IV’s subunit III?

A

none

66
Q

How many H+ are translocated across Complex IV?

A

2 (per e- pair)

67
Q

What are the 3 channels of Complex IV?

A

K channel
D channel
H channel

68
Q

Complex IV’s K channel’s H+ comes from _______

A

Cu B

69
Q

Complex IV’s D channel’s H+ comes from _______

A

Cyt. a3

70
Q

Complex IV’s H channel’s H+ comes from _______

A

matrix

71
Q

Which Complex IV channel is vectoral?

A

H channel (matrix to IMS physically)

72
Q

I am an electron transport complex, I have no Rieske Fe/S, no hemes and no FAD.

A

Complex I

73
Q

I am an electron transport complex, I have Fe/S and hemes but no flavins.

A

Complex III

74
Q

There is a __________ gradient and a ___________ gradient across the inner membrane

A

concentration
charge

75
Q

RETC’s goal is to pump H+ into ________ for ATPase to make ATP

A

IMS

76
Q

The pH in the IMS is _______ than the pH in the matrix

A

lower (more H+)

77
Q

The delta G pushing against the gradient is POSITIVE OR NEGATIVE?

A

positive

78
Q

The delta G at the end of RETC is POSITIVE OR NEGATIVE?

A

negative

79
Q

Who created the chemiosmotic hypothesis?

A

peter mitchell

80
Q

What is the chemiosmotic hypotheisis?

A

Free E (-G) delivered from H+ passage across the membrane with the gradient provides the driving force for ADP phosphorylation

81
Q

What is 5 pieces of evidence to support the chemiosmotic hypothesis?

A
  1. intact membrane
  2. inpermiable inner membrane
  3. e- transport = H+ transport out of matrix
  4. increasing acidity outside = increase ATP production
  5. compounds that increase permiability prevent ATP synthesis
82
Q

What is an uncoupling agent?

A

able to cross the mitochondrial inner membrane (in protonated state), the deprotonates once across (INCREASE PERMIABILITY)

83
Q

What are 4 examples of uncoupling agents?

A
  1. 2,4-dinitrophenol
  2. Fluorocarbonyl cyanide phenylhydrazine
  3. Dicoumarol
  4. Thermogenin
84
Q

The coupling agent, ___________, is expressed in brown fat of mitochondria

A

Thermogenin

85
Q

What is brown fat?

A

uses proton gradient to generate heat to protect CNS and organs (babies)

86
Q

T/F Introduction of a K+ channel in the mitochondria inner membrane will disrupt ATP synthesis by F1F0.

A

True

87
Q

T/F introduction of a K+ channel in the mitochondria inner membrane will result in lactate accumulation.

A

False (uncoupling agents are not inhibitors so they are no inhibiting the e- flow they are only affecting “downstream” ATP synthesis)

88
Q

What couples the H+ generated by RET and ADP phosphorylation?

A

F1F0 ATPase

89
Q

Where is F1F0 ATPase located?

A

F0 - inner membrane
F1 - matrix

90
Q

What is F1 refered to as?

A

the generator

91
Q

What are the subunits of F1?

A

3 alpha
3 beta
1 gamma
1 delta
1 epsilon

92
Q

What does the alpha subunit do of F1?

A

binds ATP but DOES NOT catalyze

93
Q

the alpha subunit of F1 provides an ______ residue to the beta subunit

A

Arginine

94
Q

What are the 3 binding options for the beta subunit of F1?

A

AMP PNP (ATP)
ADP + Pi
empty

95
Q

When (AMP PNP) ATP is bound to the beta subunit of F1, is the KD high or low?

A

low (high association)

96
Q

The center of the alpha/beta orange of F1 is very _________ made of ___________

A

hydrophobic
3 alpha helices

97
Q

In the presence of ATP and the absence of F0, the gamma subunit rotates in the ____________ direction

A

counter clockwise

98
Q

Which subunit of F1F0 ATPase is in the matrix? F1 or F0?

A

F1

99
Q

What is a name for F0?

A

turbine

100
Q

How many alpha helices is the c ring of F0 made of?

A

12

101
Q

c ring of F0 has Asp61 on each subunit, what is special about the last one?

A

It is partially off the subunit because of helical unwinding which allows H+ to bind and be dropped off in the matrix

102
Q

subunit a of F0 has a _______ residue

A

Arg 210

103
Q

What subunit of F0 has a half channel for H+?

A

a subunit

104
Q

Which complex does dicoumarol bind to?

A

none

105
Q

Which complexes activity is inhibited by dicoumarol?

A

F1F0 ATPase

106
Q

Consider an F1F0 ATPase who has 9 c subunits, how many H+ across the mitochondria inner membrane will result in one full revolution of the c ring?

A

9

107
Q

Consider a F1F0 ATPase who has 9 c subunits. Passage of how many H+ across the mitochondria inner membrane will result in one full revolution of the gamma subunit?

A

9

108
Q

How many ATP are made for every gamma revolution?

A

3

109
Q

What is the purpose of the Complexes in the RETC?

A

build a high concentration of H+ in the IMS

110
Q

H+ in the IMS enters ATPase where?

A

F0 (a subunit)

111
Q

What structurally distinguishes heme a, b, and c

A

a: long tail
b: normal
c: S-protein

112
Q

T/F: under standard conditions, malate oxidation by NAD+ is energetically favored

A

false

113
Q

T/F: almost all hemes found in the ETC are hexacoordinate

A

true

114
Q

T/F: In the context of the citric acid cycle, oxaloacetate can be viewed as a catalyst

A

true

115
Q

What electron transport complex contains a Reiske Fe/S center?

A

complex III

116
Q

What electron transport complexes do not contain hemes?

A

complex I

117
Q

Which about stigmatellin is true?
a. It binds to QP site
b. Interrupts Q cycle
c. Prevents conformational change in Complex III
d. All are true

A

d. All are true

118
Q

What is the order of electron transfer in Complex I?

A

NADH, FMN, 2Fe/S, 4Fe/S, UQ

119
Q

In Complex I, what would happen if conformational change is not possible?

A

no H+ transfer but e- would still happen

120
Q

What would happen if UQ binding is affected in Complex I?

A

no e- transfer and no H+ transfer stopping all other complexes after I

121
Q

Would someone with no e- transfer or with e- would have more pyruvate DH kinase activity/lactate accumulation?

A

the one with NO e- transfer because NADH would accumulate and Pyruvate DH would have to deal with it ramping up glycolysis

PDK is activates by NADH

122
Q

The RETC moves towards the more _____ direction

A

positive (reduced)

123
Q

Why are the cofactors in the specific orders they’re in in the RETC?

A

reduction potential and obligate donor/acceptors

124
Q

How does CN affect succinate DH?

A

decreases succinate DH (COMPLEX II) activity b/c it affects O2 ability to be a final e- acceptor which will back up the cycle

125
Q

How does CN affect pyruvate DH?

A

DECREASES pyruvate DH activity b/c it affects O2 ability to be a final e- acceptor which will ACCUMULATE NADH WHICH IS AN INHIBITOR FOR IR

126
Q

How does CN affect glycogen phosphorylase?

A

increase because RETC is backed up and glycogen needs to be broken down to up regulate glycolysis to take care of accumulated NADH

127
Q

T/F: in the absence of F0, F1 catalyzes ATP synthesis

A

false (catalyzes ATP hydrolysis)

128
Q

T/F: The identity of the fatty acyl-CoA dehydrogenase used in -oxidation depends upon the carbon chain length of the fatty acyl-CoA substrate.

A

true

129
Q

Carboxin is an inhibitor for which complex?

A

Complex II (inhibits succinate)

130
Q

What is the visual difference between NADH and FAD?

A

NADH has 1 N ring
FAD has 2 N rings

131
Q

What is the visual difference between FAD and FMN?

A

FAD has a bunch of stuff at the bottom
FMN looks just like it without the clutter at the bottom

132
Q

What is visual difference between CuA and CuB?

A

CuA is more complicated looking (makes a square)

133
Q

How does stigmatellin affect Rieske Fe/S clusters?

A

affects the reduction potential

Biochemistry II (6 decks)

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