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Biochemistry Exam III material > Oxidative phosphorylation I > Flashcards

Oxidative phosphorylation I Flashcards

1
Q

What are the three large protein complexes that transfer electrons from NADH to O2

A
  • NADH Q oxido reductase (complex 1)
  • Q cytochrome c oxidoreductase (complex 3)
  • Cytochrome C oxidase (complex 4)
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2
Q

What large protein complex transfers electrons from FADH2 to O2

A

Succinase Q reductase (complex 2)

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3
Q

Ubiquinone is the ____ form of of coenzyme Q

A

Oxidized

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4
Q

Ubiquinol is the ______ form of Coenzyme Q

A

Reduced

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5
Q

size of a mitochondria

A

about the size of bacterium— 2 micrometers long and 0.5 micrometers wide

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6
Q

Outer mitochondrial membrane is permeable due to presence of

A

porin aka VDAC (voltage-dependent anion channel) a 30-35 kDa pore forming protein

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7
Q

What is the most prevalent protein in the outer mitochondrial membrane, and plays a role in the regulated flux of metabolites

A

VDAC (voltage-dependent anion channel)

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8
Q

What can cross the VDAC

A

phosphate, chloride, organic anions, and the adenine nucleotides

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9
Q

what is needed to move metabolites such as ATP, pyruvate, and citrate across the inner mitochondrial membrane

A

Metabolite Transporters

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10
Q

The mitochondria has how many compartments

A
  • intermembrane space

- Matrix (site of TCA cycle and fatty acid oxidation)

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11
Q

Where does the TCA cycle and fatty acid oxidation occur

A

in the Mitochondrial matrix

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12
Q

The inner mitochondrial membranes permeability

A

Impermeable, has metabolite transporters to shuttle substances such as (ATP, Pyruvate and citrate across)

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13
Q

Where does oxidative phosphorylation occur

A

inner mitochondrial membrane

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14
Q

The membrane potential on the matrix side is ____ and on the cytoplasmic side of the mitochondria it is ___

A

negative, positive

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15
Q

Mitochondria are ____ autonomous organelles

A

semi

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16
Q

Mitochondria are a ______ relationship with host cell

A

endosymbiotic

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17
Q

Mitochondria are a result of an endosymbiotic event in which a free living organism, with the ability of oxidative phosphorylation, was engulfed by

A

another cell

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18
Q

Mitochondrial genomes _______ between species

A

range in size

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19
Q

Sequence data shows that all mitochondria derived from ________ due to a single endosymbiotic event

A

R. Prowazekii

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20
Q

Mitochonria have their own ____ and are able to make

A

DNA, and are able to make proteins and RNAs

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21
Q

The human mitochondrial DNA has ______ bp and encodes _____ respiratory chain proteins, rRNAs, tRNAs

A

16,569 bp, 13

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22
Q

Electrons in the ETC reduce molecular O2 to

A

water

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23
Q

how many of the ETC complexes pump protons from matrix to inter membrane space

A

3

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24
Q

Protons return to matrix by flowing through another complex called ________ powering the synthesis of ____

A

ATP synthase, ATP

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25
Q

Electron flow in the ETC is ____

A

exergonic

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26
Q

electrons from FADH2 enter the electron-transport chain at

A

Q-cytochrome C oxidoreductase

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27
Q

Does Succinate-Q reductase pump protons

A

No!!!

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28
Q

Complexes I, III, and IV appear to be associated in a supramolecular complex termed the

A

Respirasome

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29
Q

Transferes electrons from NADH Q oxidoreductase (complex I) and succinate Q reductase (complex II) to Q cytochrome oxidoreductase (complex III)

A

Coenzyme Q (ubiquinone)

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30
Q

Coenzyme Q has a long tail made of _____ units which makes is

A

5-Carbon isoprene units, hydrophobic

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31
Q

Most common mammalian form of Coenzyme Q (ubiquinone)

A

CoQ 10

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32
Q

Fully reduced form of Coenzyme Q is named

A

ubiquinol

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33
Q

ubiquinol holds protons

A

more tightly than the oxidized form (ubiquinone)

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34
Q

What are the two electron carriers of the ETC

A
  • Coenzyme Q (ubiquinone)

- cytochrome C

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35
Q

Shuttles electrons from Q cytochrome c oxidoreductase to cytochrome C oxidase

A

Cytochrome C

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36
Q

final component of ETC

A

-Complex IV (cytochrome C oxidase)

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37
Q

Catalyzes the reduction of O2

A

Cytochrome C oxidase

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38
Q

Prosthetic group(s) of Complex I (NADH-Q oxidoreductase)

A
  • FMN

- Fe-S

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39
Q

Prosthetic group(s) of Complex II (Succinate-Q reductase)

A
  • FAD

- Fe-S

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40
Q

Prosthetic group(s) of Complex III (Q-cytochrome c oxidoreductase)

A
  • Heme bH
  • Heme BL
  • Heme C1
  • Fe-S
41
Q

Prosthetic group(s) of Complex IV (Cytochrome C oxidase)

A
  • Heme a
  • heme a3
  • CuA and Cu8
42
Q

_____ clusters are common components of the ETC

A

Iron-Sulpher

43
Q

simplest of Fe-S cluster structure

A

a single iron ion is tetrahedrally coordinated to the sulfhydryl groups of four cysteine residues of the protein

44
Q

Explain the structure of 2Fe-2S

A

Contains 2 iron ions, two inorganic sulfides, and usually four cysteine residues

45
Q

Explain the structure of 4Fe-4S

A

contains 4 iron ions, 4 inorganic sulfides, and four cysteine residues

46
Q

NADH-Q contains what two iron-sulfide clusters

A

2Fe-S and 4Fe-4S

47
Q

unlike quinones and flavor, iron-sulfer clusters generally undergo oxidation-reduction reactions without

A

releasing or binding protons

48
Q

What is Friedreich’s Ataxia

A
  • Mutations in the protein Frataxin lead to its loss of function
  • small mitochondrial protein is crucial for the synthesis of Fe-S clusters
  • Affects the CNS, PNS, as well as the heart and skeletal system
  • most common mutation is trinucleotide expansion in frataxin gene
49
Q

Frataxin is crucial for

A

the synthesis of Fe-S clusters

50
Q

small mitochondrial protein is crucial for the synthesis of Fe-S clusters

A

Frataxin

51
Q

What is the most common mutation in friedreich’s ataxia

A

trinucleotide expansion in frataxin gene

52
Q

Complex I name

A

NADH dehydrogenase (NADH-Q oxidoreductase)

53
Q

Size of Complex I

A

-large protein (>900 kDa, with 46 polypeptide chains)

54
Q

Complex I is encoded by

A

nuclear and mitochondrial genes

55
Q

Shape of Complex I (NADH-Qoxidoreductase)

A

L-shaped with the horizontal arm lying in the inner membrane and the vertical arm that projects into the matrix

56
Q

What is the reaction catalyzed by complex 1

A

NADH+ Q + 5 H+ (matrix)—-> NAD(+) + QH2+ 4H+(cytoplasm)

57
Q

What is the initial step in complex I

A

the binding of NADH and the transfer of its two high-potential electrons to the flavin mono nucleotide (FMN) thus yielding the reduced form FMNH2

58
Q

What is the electron receptor of FMN

A

isoalloxazine ring

59
Q

The electron acceptor of FMN is identical to that of

A

FAD

60
Q

in complex I electrons from FMNH2 are transferred to

A

a series of Iron-sulfur clusters (the second prosthetic group in complex I)

61
Q

Is complex I a proton pump

A

Yes

62
Q

The membrane-embedded part of complex I has ____ proton half-channels consisting, in part, of vertical helices. 1 set of half-channels is exposed to the matrix and the other to the inner membrane space

A

4

63
Q

The vertical helices on the matrix side of complex one are linked by ________ that connects the matrix half-channels

A

a long horizontal helix (HL)

64
Q

The cytoplasmic half-channels of complex I are joined by

A

a series of Beta-hair pin helix connecting elements (BH)

65
Q

Does FADH2 leave complex II

A

No

66
Q

Electrons from FADH2 are transferred to

A

FE-S and then to Q to form QH2

67
Q

Does the oxidation of FADH2 synthesize less ATP than NADH

A

Yes

68
Q

Electrons from QH2 are passed on to cytochrome C by _______

A

Complex III (cytochrome c reductase/ Q-cytochrom c oxireductase)

69
Q

Reaction equation for complex III

A

QH2 + 2 cytochrome C(oxidized) + 2H+ (matrix) —-> Q + 2 Cytochrome c (reduced) + 4 H+ cytoplasm

70
Q

Cytochrome c can only accept electrons

A

1 at a time

71
Q

The flow of a pair of electrons through complex III leads to the effective net transport of ____ H+ to the cytoplasmic side

A

4( half the yield obtained with Complex I because of a smaller thermodynamic driving force)

72
Q

Complex I, III, and IV are encoded by

A

genes residing in both the mitochondria and nucleus

73
Q

What is the final electron acceptor of the ETC

A

Oxygen

74
Q

Catalyzes the transfer of electrons from reduced cytochrome C to molecular oxygen

A

Cytochrome C oxidase (Complex IV)

75
Q

How many electrons in complex IV are funneled to oxygen to reduce it to water

A

4

76
Q

____ molecules of cytochrome c sequentially transfer electrons to Cu8 and heme a3

A

two

77
Q

Pathological conditions that may entail free-radical injury

A
  • Parkinson’s disease**
  • Ischemia; reperfusion injury**
  • Atherogenesis
  • Emphysema;bronchitis
  • Duchenne muscular dystrophy
  • cervical cancer
  • Alcoholic liver disease
  • Diabetes
  • Acute renal failure
  • Down syndrome
  • Retrolental fibroplasia
  • Cerebrovascualr disorders
78
Q

complete oxidation of oxygen forms

A

water

79
Q

Partial reduction of oxygen forms

A

Free radicals (dangerous species)

80
Q

Transfer of a single electron to oxygen forms

A

superoxide anion and hydroxyl radical

81
Q

Transfer of 2 electrons to oxygen forms

A

hydrogen peroxide and hydroxyl radical

82
Q

Two was to form a hydroxyl radical

A
  • transfer of a single electron to oxygen

- transfer of 2 electrons to oxygen

83
Q

What is the Q cycle

A

The mechanism for the coupling of electron transfer from Q to cytochrome c to transmembrane proton transport

  • Two QH2 molecules bind to the complex consecutively, each giving up two electrons and two H+ (these protons are released to the cytoplasmic side of the membrane)
84
Q

Explain the Q cycle

A
  • The first QH2 to exit the Q pool binds to the first Q binding site (Q0) and its two electrons travel through complex III to different destinations.
  • one electron flows, first, to the Riske 2Fe-2S cluster; then, to cytochrome c1; and, finally to a molecule of oxidized cytochrome c, converting it to it reduced form.
  • Reduced cytochrome c is free to diffuse away form the enzyme to continue down the respiratory chain
  • The second electron passes through two heme groups of cytochrome b to an oxidized ubiquinone in a second Q binding site (Qi)
  • The Q in the second binding site is reduced to a semiquinone radical anion (Q-) by the electron form the first QH2. The now fully oxidized Q leaves the first Q site, free to reenter the Q pool
  • A second QH2 binds to Q0 and repeats the cycle
85
Q

What makes humans breath

A

Cytochrome C oxidase (complex IV)

86
Q

equation for complex IV

A

4 cyt c(reduced) + 8 H+ (matrix) + O2 —-> 4 cyt c (oxidized) + 2 H2O + 4 H+ (cytoplasm)

87
Q

The cycle in Complex IV begins and ends with all prosthetic groups in their _____ forms

A

oxidized

88
Q

What forms the peroxide bridge in complex IV

A

Reduced CuB and Fe in heme a3 bind to O2 which forms a peroxide bridge

89
Q

What cleaves the peroxide bridge in complex IV

A

The addition of two more electrons and two more protons cleaves the peroxide bridge

90
Q

four protons are taken up from the matrix side to reduce one molecule of O2 to ___ molecules of H2O

A

2

91
Q

What is the strategy for the safe reduction of O2

A

the catalyst does not release partly reduced intermediates (cytochrome C oxidase meets this criteria by holding O2 tightly between Fe and Cu ions)

92
Q

ROS

A

Reactive oxygen species

93
Q

Superoxide dismutase (SOD)

A
  • cellular defense against oxidative damage by ROS

- catalyzes the conversion of two free radicals into hydrogen peroxide and molecular oxygen

94
Q

Catalase

A

hydrogen peroxide formed by SOD and other processes is scavenged by catalase to form water and molecular oxygen

2H2O2—-> O2 + 2 H2O

95
Q

Eukaryotes contain ____ forms of SOD

A

2 (a maganese-containing version in the mitochondria)and(a copper and zinc dependent cytoplasmic form)

96
Q

The oxidized form of SOD is reduced by supported to form

A

oxygen

97
Q

The reduced from of SOD reacts with

A

a second superoxide ion to form peroxide, which takes up two protons along the reaction path to yield hydrogen peroxide.
Note that this regenerates the oxidized form of SOD

98
Q

The rate of electron transfer decreases as the electron donor and electron acceptor

A

move apart

99
Q

The conformation of cytochrome c has remained essentially

A

constant for more than a billion years

Biochemistry Exam III material (13 decks)

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