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Biochemistry Exam III material > Oxidative phosphorylation I > Flashcards

Oxidative phosphorylation I Flashcards

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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
Electron flow in the ETC is ____
exergonic
26
electrons from FADH2 enter the electron-transport chain at
Q-cytochrome C oxidoreductase
27
Does Succinate-Q reductase pump protons
No!!!
28
Complexes I, III, and IV appear to be associated in a supramolecular complex termed the
Respirasome
29
Transferes electrons from NADH Q oxidoreductase (complex I) and succinate Q reductase (complex II) to Q cytochrome oxidoreductase (complex III)
Coenzyme Q (ubiquinone)
30
Coenzyme Q has a long tail made of _____ units which makes is
5-Carbon isoprene units, hydrophobic
31
Most common mammalian form of Coenzyme Q (ubiquinone)
CoQ 10
32
Fully reduced form of Coenzyme Q is named
ubiquinol
33
ubiquinol holds protons
more tightly than the oxidized form (ubiquinone)
34
What are the two electron carriers of the ETC
- Coenzyme Q (ubiquinone) | - cytochrome C
35
Shuttles electrons from Q cytochrome c oxidoreductase to cytochrome C oxidase
Cytochrome C
36
final component of ETC
-Complex IV (cytochrome C oxidase)
37
Catalyzes the reduction of O2
Cytochrome C oxidase
38
Prosthetic group(s) of Complex I (NADH-Q oxidoreductase)
- FMN | - Fe-S
39
Prosthetic group(s) of Complex II (Succinate-Q reductase)
- FAD | - Fe-S
40
Prosthetic group(s) of Complex III (Q-cytochrome c oxidoreductase)
- Heme bH - Heme BL - Heme C1 - Fe-S
41
Prosthetic group(s) of Complex IV (Cytochrome C oxidase)
- Heme a - heme a3 - CuA and Cu8
42
_____ clusters are common components of the ETC
Iron-Sulpher
43
simplest of Fe-S cluster structure
a single iron ion is tetrahedrally coordinated to the sulfhydryl groups of four cysteine residues of the protein
44
Explain the structure of 2Fe-2S
Contains 2 iron ions, two inorganic sulfides, and usually four cysteine residues
45
Explain the structure of 4Fe-4S
contains 4 iron ions, 4 inorganic sulfides, and four cysteine residues
46
NADH-Q contains what two iron-sulfide clusters
2Fe-S and 4Fe-4S
47
unlike quinones and flavor, iron-sulfer clusters generally undergo oxidation-reduction reactions without
releasing or binding protons
48
What is Friedreich's Ataxia
- 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
Frataxin is crucial for
the synthesis of Fe-S clusters
50
small mitochondrial protein is crucial for the synthesis of Fe-S clusters
Frataxin
51
What is the most common mutation in friedreich's ataxia
trinucleotide expansion in frataxin gene
52
Complex I name
NADH dehydrogenase (NADH-Q oxidoreductase)
53
Size of Complex I
-large protein (>900 kDa, with 46 polypeptide chains)
54
Complex I is encoded by
nuclear and mitochondrial genes
55
Shape of Complex I (NADH-Qoxidoreductase)
L-shaped with the horizontal arm lying in the inner membrane and the vertical arm that projects into the matrix
56
What is the reaction catalyzed by complex 1
NADH+ Q + 5 H+ (matrix)----> NAD(+) + QH2+ 4H+(cytoplasm)
57
What is the initial step in complex I
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
What is the electron receptor of FMN
isoalloxazine ring
59
The electron acceptor of FMN is identical to that of
FAD
60
in complex I electrons from FMNH2 are transferred to
a series of Iron-sulfur clusters (the second prosthetic group in complex I)
61
Is complex I a proton pump
Yes
62
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
4
63
The vertical helices on the matrix side of complex one are linked by ________ that connects the matrix half-channels
a long horizontal helix (HL)
64
The cytoplasmic half-channels of complex I are joined by
a series of Beta-hair pin helix connecting elements (BH)
65
Does FADH2 leave complex II
No
66
Electrons from FADH2 are transferred to
FE-S and then to Q to form QH2
67
Does the oxidation of FADH2 synthesize less ATP than NADH
Yes
68
Electrons from QH2 are passed on to cytochrome C by _______
Complex III (cytochrome c reductase/ Q-cytochrom c oxireductase)
69
Reaction equation for complex III
QH2 + 2 cytochrome C(oxidized) + 2H+ (matrix) ----> Q + 2 Cytochrome c (reduced) + 4 H+ cytoplasm
70
Cytochrome c can only accept electrons
1 at a time
71
The flow of a pair of electrons through complex III leads to the effective net transport of ____ H+ to the cytoplasmic side
4( half the yield obtained with Complex I because of a smaller thermodynamic driving force)
72
Complex I, III, and IV are encoded by
genes residing in both the mitochondria and nucleus
73
What is the final electron acceptor of the ETC
Oxygen
74
Catalyzes the transfer of electrons from reduced cytochrome C to molecular oxygen
Cytochrome C oxidase (Complex IV)
75
How many electrons in complex IV are funneled to oxygen to reduce it to water
4
76
____ molecules of cytochrome c sequentially transfer electrons to Cu8 and heme a3
two
77
Pathological conditions that may entail free-radical injury
- 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
complete oxidation of oxygen forms
water
79
Partial reduction of oxygen forms
Free radicals (dangerous species)
80
Transfer of a single electron to oxygen forms
superoxide anion and hydroxyl radical
81
Transfer of 2 electrons to oxygen forms
hydrogen peroxide and hydroxyl radical
82
Two was to form a hydroxyl radical
- transfer of a single electron to oxygen | - transfer of 2 electrons to oxygen
83
What is the Q cycle
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
Explain the Q cycle
- 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
What makes humans breath
Cytochrome C oxidase (complex IV)
86
equation for complex IV
4 cyt c(reduced) + 8 H+ (matrix) + O2 ----> 4 cyt c (oxidized) + 2 H2O + 4 H+ (cytoplasm)
87
The cycle in Complex IV begins and ends with all prosthetic groups in their _____ forms
oxidized
88
What forms the peroxide bridge in complex IV
Reduced CuB and Fe in heme a3 bind to O2 which forms a peroxide bridge
89
What cleaves the peroxide bridge in complex IV
The addition of two more electrons and two more protons cleaves the peroxide bridge
90
four protons are taken up from the matrix side to reduce one molecule of O2 to ___ molecules of H2O
2
91
What is the strategy for the safe reduction of O2
the catalyst does not release partly reduced intermediates (cytochrome C oxidase meets this criteria by holding O2 tightly between Fe and Cu ions)
92
ROS
Reactive oxygen species
93
Superoxide dismutase (SOD)
- cellular defense against oxidative damage by ROS | - catalyzes the conversion of two free radicals into hydrogen peroxide and molecular oxygen
94
Catalase
hydrogen peroxide formed by SOD and other processes is scavenged by catalase to form water and molecular oxygen 2H2O2----> O2 + 2 H2O
95
Eukaryotes contain ____ forms of SOD
2 (a maganese-containing version in the mitochondria)and(a copper and zinc dependent cytoplasmic form)
96
The oxidized form of SOD is reduced by supported to form
oxygen
97
The reduced from of SOD reacts with
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
The rate of electron transfer decreases as the electron donor and electron acceptor
move apart
99
The conformation of cytochrome c has remained essentially
constant for more than a billion years

Biochemistry Exam III material (13 decks)

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