Exam 2 Ch 18 Flashcards

1
Q

What is ch 18 about

A

Oxidative Phosphorylation & Electron Transport Chain

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2
Q

How many electrons are captured by glucose oxidation?

A

24 electrons from oxidation of 1 glucose are sequestered in 2 FADH2 and 10 NADH

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2
Q

WHat are the major ETC events

A
  1. Regeneration of FAD+ and NAD+
  2. Reduction of O2 to H2O
  3. Synthesis of ATP through oxidative phosphrylation
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3
Q

What is the site of eukaryotic oxidative metabolism

A

Mitochondrion

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4
Q

WHat is endosymbiosis

A

theory that mitochondria originated from a symbiotic relationship between an ancestral eukaryotic cell and a prokaryote

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4
Q

What is eukaryotic oxidative metabolism

A

A group of metabolic processes that use oxygen for energy. Crucial metabolic processes:
Acetyl-CoA synthesis enzyme
Citric Acid Cycle Enzymes
Fatty Acid Oxidation enzymes
Electron Transport Chain enzymes
Oxidative Phosphorylation enzymes

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5
Q

Theories that resulted from Endosymbiosis

A

 Merger between archaea and prokaryotes (an early eukaryotic cell merged with a prokaryotic cell, specifically an α-proteobacterium, which evolved to become the mitochondrion.)
 Mitochondria are descendants of α-
proteobacteria that are Gram-negative
o Gram-negative bacteria contain a thin layer of
peptidoglycan between an inner & outer
membrane
 All mitochondrial DNA in humans is exclusively
maternally inherited

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6
Q

What are α-proteobacteria

A

Gram negative bacteria

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7
Q

What do gram-negative bacteria contain?

A

a thin layer of peptidoglycan between an inner & outer membrane

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8
Q

What is the cristae

A

inner membrane folds (site of ETC & oxidative phosphorylation)

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9
Q

Where is the site of ETC and Oxidative Phosphorylation

A

Cristae

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10
Q

what is the Matrix

A

inner membrane folds (site of ETC & oxidative phosphorylation)

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11
Q

what happens in the Intermembrane space

A

region between membranes where metabolite transport occurs

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12
Q

Where does metabolite transport occur?

A

Intermembrane space

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13
Q

Spaces of the mitochondira

A

Matrix, Intermembrane space

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14
Q

Membranes of the mitochondria

A

Outer membrane
Inner membrane
Cristae (folds of the inner membrane, not a space themselves, but they increase the surface area of the inner membrane, providing more area for the enzymes involved in oxidative phosphorylation and the electron transport chain.)

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15
Q

Outer Mitochondrial Membrane (OMM)

A

Porins: allow for diffusion of
molecules up to 10 kDa
o Metabolite concentrations are
equivalent between the cytosol &
intermembrane space

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16
Q

Inner Mitochondrial Membrane (IMM)

A

 Contains more protein than the
OMM (75% by mass)
o 2× denser than the outer membrane
 Only permeable to O 2 , CO 2 , and
H2 O
 Impermeability is controlled by
transporter proteins

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17
Q

The IMM is only permeable to:

A

O2 , CO2 , and H2O

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18
Q

What is the impermeability of the IMM controlled by?

A

Transporter proteins

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19
Q

Is the metabolite concentraion between the cytosol and intermembrane space equivalent or not equivalent?

A

Equivalent

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20
Q

Which (OMM or IMM) contains more proteins?

A

IMM (75% by mass)

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21
Q

Which (OMM or IMM) contains porins

A

OMM

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22
Q

IMM lacks an NADH transporter, what significance does this have?

A

Since the inner mitochondrial membrane (IMM) lacks a direct transporter for NADH, alternative shuttle systems are used to transfer the electrons from NADH into the mitochondrion for use in the electron transport chain (ETC).
1.Malate-aspartate Shuttle
2.Phosphoglycerate Shuttle

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23
Describe the Malate-aspartate Shuttle
Transfers Electrons from cytosol NADH into the mitochondria. Malate dehydrogenase is the key enzyme. How it works: In the cytosol, NADH is oxidized by oxaloacetate to form NAD+ and malate. The enzyme is malate dehydrogenase. The malate is transported into the mitochondria. Malate is oxidized back to oxaloacetate, reducing NAD+ to NADH in the mitochondria.
24
Where is the Malate-aspartate shuttle most used?
Liver, heart, and kidney cells
25
Describe the phosphoglycerate shuttle
Catalyzed by 3-phosphoglycerol dehydrogenase and Flavoprotein dehydrogenase. NADH is oxidized by DHP in the cytosol to yield NAD+ for glycolysis and 3-phosphglycerol. This reaction is catalyzed by 3-phosphoglycerol dehydrogenase. The 3-phosphoglycerol (3PG) is then moved into the mitochondria where it donates electrons to FAD, yielding FADH2 in the mitochondria. This is catalyzed by Flavoprotein dehydrogenase. The FADH2 is then oxidized by ETC.
26
When is Flavoprotein dehydrogenase used?
In the second step of phosphoglycerate shuttle. It takes the electron of 3PG and puts it on FAD forming FADH2 which can be oxidized by the ETC
27
WHat are the enzyems used to transport NADH into the mitochondria?
Malate dehydrogenase, 3-phosphoglycerol dehydrogenase, and flavoprotein dehydrogenase.
28
What is Adenine Nucleotide Translocase (ATP/ADP Translocator)
it's a transport protein that exchanges ATP produced within the mitochondria with ADP produced in the cytosol
29
What is the general electron transfer pathway?
NADH  Complex I  Coenzyme Q (CoQ)  Complex III  Cytochrome C (Cyt c)  Complex IV
30
WHat are the ETC enzymes?
Metalloproteins (metal cofactors)
31
Where did the mitochondria come from?
Ancestral proteobacteria Endosymbiosis with archaea to yield eukaryotic cell
32
Tell me about the OMM
Highly permeable due to porins (proteins) that allow for diffusion of metabolites (< 10 kDa) into the intermembrane space from the cytosol
33
Tell me about the IMM
- Highly impermeable except for CO 2 , O 2 , and H2 O - Requires use of transporter proteins to move metabolites between the intermembrane space and the mitochondrial matrix 1. Malate-Aspartate Shuttle 2. Phosphoglycerate Shuttle 3. ATP / ADP Translocator - Contains electron transfer chain
34
Which membrane is more permeable?
OMM
35
Which membrane requires transporter proteins to move metabolites to move metabolites between the intermembrane space and the mitochondrial matrix and what are the transporter proteins
IMM Malate-Aspartate Shuttle Phosphoglycerate Shuttle ATP/ADP Translocator
36
List the order in the ETC
With NADH: Glycolysis/AcetylCoA/TCA Cycle - (NADH) - Complex I - (CoQ) - Complex III - (Cyt c) - Complex IV With FADH2: TCA Cycle - (FADH2) - Complex II (CoQ) - Complex III - (Cyt c) - Complex IV
37
is the ETC endergonic or exergonic?
Exergonic and sequential
38
What is complex I?
(NADH-Ubiquinone Oxidoreductase)
39
What is the classification of complex I?
Translocase
40
What are the reactions of the complex I?
1. Reduction of Ubiquinone by NADH through a series of electron transfers 2. Translocation of protons across the inner mitochondrial membrane
41
What does the Electron transfer arm contain? WHat are the "arms" and where are they in the cycles?
The electron transfer arm is made up of the 7 subunits of complex I that are matrix exposed
42
What does the proton translocation arm consist of?
7 subunits of the complex one embedded in the inner mitochondrial membrane. Pumps the protons from the mitochondrial matrix to the intermembrane space
43
Essentially, what does complex 1 do?
is responsible for initiating the electron transport chain by accepting electrons from NADH, passing them through a series of electron carriers, and reducing coenzyme Q (CoQ) to ubiquinol (CoQH₂).
44
What are the cofactors in complex I?
[4Fe-4S] clusters & FMN (flavin mononucleotide) cofactors
45
How many electron transfers does Nicotinamides (primarily) undergo?
2-electron transfers
46
How many electron transfers does Iron-Sulfur clusters undergo?
1 electron transfers
47
How many electron transfers does quinones undergo?
either 2 or 1 electron transfers
48
how many electrons transfer in the Hydride transfer from NADH to FMN yields FMNH2
(2 e− transfer)
49
how many electron transfer: FMNH2 undergoes sequential outer sphere electron transfer to the [Fe-S] clusters that ultimately reduce CoQ to CoQH2
(1 e− transfer)
50
What is the electron transfer mechanism (2 steps) from NADH to CoQ through complex 1
1. Hydride transfer from NADH to FMN yields FMNH2 (2 e− transfer) 2. FMNH2 undergoes sequential outer sphere electron transfer to the [Fe-S] clusters that ultimately reduce CoQ to CoQH2 (1 e− transfer)
51
Porphyrins: aromatic or not aromatic?
11 double bonds = 22 pi e- N = 5 (aromatic) Pi bonds= 4(N) + 2 22= 4(5) +2 If N is a whole number, it's aromatic
52
Chlorins: aromatic or not aromatic?
not aromatic 10 double bonds = 20 pi e- N = 4.5 (not aromatic)
53
Corrins: aromatic or not aromatic?
not aromatic 6 double bonds = 12 pi e- N = 2.5 (not aromatic)
54
Where is the ETC located
Along the inner mitochondrial membrane.
55
Why is the ETC exergonic?
o Incrementally increasing reduction potentials o Allows for directionality & utilization of energy to pump protons across the IMM (matrix to intermembrane space)
56
what is the direction protons flow across the IMM
matrix to intermembrane space
57
How many enzyme complexes are part of the ETC
4
58
What does complex 1 do?
Transfers electrons from NADH to CoQ & pumps protons
59
What does complex 2 do?
Transfers electrons from FADH2 to CoQ (Kreb's cycle)
60
What does complex 3 do?
Transfers electrons from CoQ to Cyt c & pumps protons
61
What does complex 4 do?
Transfers electrons from Cyt c to O2 & pumps protons
62
Give an overview of what all four enzymes complexes in the ETC do
1. Complex 1: transfers electrons from NADH to CoQ & pumps protons 2. Complex 2: transfers electrons from FADH2 to CoQ (Kreb’s Cycle) 3. Complex 3: transfers electrons from CoQ to Cyt c & pumps protons 4. Complex 4: transfers electrons from Cyt c to O 2 & pumps protons
63
What are the two mediators used to transfer electrons between complexes?
1. Coenzyme Q 10 (CoQ) 2. Cytochrome c (Cyt c)
64
Name this complex: transfers electrons from Cyt c to O 2 & pumps protons
complex 4
65
Name this complex: transfers electrons from CoQ to Cyt c & pumps protons
Complex 3
66
Name this complex: transfers electrons from FADH2 to CoQ (Kreb’s Cycle)
Complex 2
67
What is Huckel's rule of aromaticity?
1. Cyclic 2. Planar 3. Fully conjugated 4. 4N +2 = # π electrons
68
Give reaction for complex 2
Succinate + CoQ → Fumarate + CoQH2
69
Give Reaction for complex 1
NADH + H+ + CoQ + 4H+(matrix) → NAD+ + CoQH2 + 4H+(IMS)
70
What is the name of complex II
Succinate-Coenzyme Q Oxidoreductase
71
What is the form of complex II? What and where are A and B for? where and WHat are C and D for?
a heterotetramer (140 kDa) - 2x matrix exposed subunits (A & B). THe oxidation of succinate happens here. - 2x membrane embedded subunits (C & D). The reduction of CoQ happens here.
72
Where does the oxidation of succinate happen?
Complex II. 2x matrix exposed subunits.
73
where does the reduction of CoQ happen?
Complex II. 2x membrane embedded subunits.
74
What is the classification of complex II
Oxidoreductase
75
What are the cofactors in Complex II
o SDHA: FAD (cross-linked to His) o SDHB: 3× [Fe-S] o SDHC: heme b (cross-linked to His/Cys) AKA cytochrome b560 o SDHD: CoQ
76
What does SDH (succinate dehydrogenase) mean?
TCA cycle
77
WHat is the cofactor for the A subunit of complex 2? (SDHA)
FAD (cross-linked to His) Fast Flyers, Heights Cleared
78
What is the cofactor for subnit B of complex 2? (SDHB)
3x [Fe-S]
79
What is the cofactor for subnit C of complex 2? (SDHC)
heme b (cross-linked to His/Cys AKA cytochrom b560)
80
What is the cofactor for subnit D of complex 2? (SDHD)
CoQ
81
What are the reactions in complex II
1. Oxidation of Succinate to Fumarate 2. Reduction of CoQ to CoQH 2
82
List the three reactions in the Electron Transport Chain Complex II
(similar mechanism to complex I) 1. Hydride transfer from Succinate to FAD yields FADH2 . 2. FADH2 undergoes sequential outer sphere electron transfer to the [Fe-S] clusters 3. CoQ is sequentially reduced to CoQH2 a) directly by [Fe-S] clusters b) indirectly by Heme b  Mitigates reactive oxygen species formation
83
Which of the cofactors in complex II directly transfers electrons?
[Fe-S] clusters. The Fe-S clusters directly transfer electrons to CoQ, reducing it to CoQH₂. Each electron from FADH₂ travels through the Fe-S clusters and is passed onto CoQ.
84
Which cofactor in complex II indirectly transfers electrons?
heme b. It does not directly transfer electrons but helps mitigate the formation of reactive oxygen species (ROS) during electron transfer.
85
Which cofactor in complex II helps mitigate reactive oxygen species formation
heme b
86
Reaction of complex III
CoQH2 + 2Fe(III) CytC + 2H(matrix)+ → CoQ + 2Fe(II)CytC + 4H+(IMS)
87
How many subunits does complex III have?
Contains 11×2(may exist in duplicate) subunits (~420 kDa)
88
what is complex III known as?
cytochrome bc1 complex. It plays a crucial role in transferring electrons from ubiquinol (CoQH₂) to cytochrome c, while also pumping protons across the membrane to contribute to the proton gradient used for ATP synthesis.
89
where are the subunits of complex III?
transmembrane. They are in the inter mitochondrian membrane with parts in the intermembrane space and the matrix
90
What is complex III classified as?
translocase
91
what are the cofactors involved in complex III?
-heme b (for cytochrom b. membrane embedded) -[2Fe-2S] (for iron-sulfer protein. partially membrane embedded) -heme c1 (cytochrome c1, intermembrane space exposed)
92
What are the reactions in complex III
Reactions 1. Oxidation of CoQH 2 to CoQ / CoQ*− 2. Reduction of Fe(III)CytC to Fe(II)CytC
93
what is the Q cycle
The Q cycle is a process that occurs in Complex III (Cytochrome bc₁ complex) of the electron transport chain. It describes how electrons are transferred from ubiquinol (CoQH₂) to cytochrome c and how protons are pumped across the mitochondrial inner membrane, contributing to the proton gradient needed for ATP synthesis.
94
what initially accepts the electrons in the Q cycle
The cofactors. Heme b and [Fe-S]. THen they are passed to produce cytochrome c and b from cytochrome c1 and heme bH
95
Give the general steps of cycle 1 of the Q cycle
1.Reduction of CoQ to CoQH2 by complex 1. 2. CoQH2 binds to complex III 3. CoQH2 gives up an electron to ISP and then to cytochrom c1 and ultimately cytochrom c. Two protons are released across the membrane. 4. The other electron on CoQH2 goes to cytochrome b1 making CoQH2 turn into CoQ. 5. CoQ migrates to the Qi site 6.The electron from cytochrome b1 is transferred to cytochrome bH. 7. The electron from cytochrome bH is transferred to CoQ at the Qi site, reducing it back to CoQ
96
What is CoQ CoQH2 CoQ-
CoQ: ubiquinone CoQH2: ubiquinol CoQ-: semi-quinone
97
Give the overview of Q cycle cycle 2:
1. reduction of CoQ to CoQH2 by complex I. 2. CoQH2 binds to complex III 3.One electron oxidation of CoQH 2 to CoQ*− via ISP and cytochrome c1 and ultimately cytochrome c - Two protons are released across the membrane 4. One electron goes from CoQ- to cytochrom b1 prducing CoQ 5. CoQ dissociates 6. One electron transfers from cytochrom b1 to cytochrom bH 7. electron from cytochrome bH goes to CoQ- and two protons from the matrix making it CoQH2. Then CoQH2 dissociates from complex III
98
Summery of the Q cycle
Summary (Simply): Cycle 1: Ubiquinol (CoQH₂) donates electrons, and the CoQ formed remains bound to Complex III. Two protons are pumped. Cycle 2: Another ubiquinol (CoQH₂) donates electrons, but the CoQ formed dissociates from Complex III, and CoQH₂ is regenerated at the Qi site before leaving the complex. Two protons are pumped again.
99
is cytochrome c a big or small protein
small protein (~12 kDa) with around 100 amino acids.
100
Ideal for small proteins, studied in a solution (liquid phase).
NMR spectroscopy
101
Best for large proteins and protein complexes, studied in a frozen solution.
Cryo Electron Microscopy (cryo-EM)
102
Good for most proteins and requires a crystal lattice of the protein.
X-ray crystallography
103
Reaction for complex IV
4Fe(II)CytC + 8H+(matrix + O2 → 4Fe(III)CytC + H2O + 4H+(IMS)
104
WHat is complex IV known as
Cytochrome c oxidase
105
What subunits are in complex IV
11 x2 subunits 10 are transmembrane and 3 are encoded by mitochondrial DNA
106
What is complex IV classified as
oxidoreductase
107
What cofactors are in complex IV (subunit 1 and 2)
Subunit 1: heme a heme a3 Cu(B) Subunit 2: Cu(A) Mg2+
108
Reactions in complex IV
o Reduction of O 2 by Fe(II) Cyt c o Proton translocation across the IMM
109
Tell me about the proton gradient associated with complex IV (Cytochrome C Oxidase (CcO))
positive side is in the IMS and has a high concentration of protons. The negative side is in the matrix, low conc. of H+
110
What form of Cytochrom c oxidase (CcO) is the active form?
Monomeric form of the enzyme. It is primarly seen as such.
110
Give simply the electron transfer of complex I
NADH →FMN → [Fe-S] →→→ CoQ
111
Give electron transfer of complex II
FADH 2 → [Fe-S] →→→ CoQ and/or heme b
112
Give electron transfer of complex III
CoQH 2 → Q-cycle (bifurcated electron transfer) Path A: → [Fe-S] → Cyt c1 → Cyt c Path B: → Cytc b1 → Cyt bH → CoQ
113
Give the electron transfer of complex 4
Cyt c → Cu A → heme a → [heme a3 + Cu b ] → O2
114
How are path A and B and the Q cycle 1 and 2 related?
The Q cycle is the entire process of electron transfer and proton pumping, involving two rounds of electron transfer (cycle 1 and cycle 2). Path A and Path B refer specifically to the two distinct electron transfer pathways that occur during each cycle of the Q cycle.
115
Explain path A of the complex III
CoQH2 donates one electron to ISP. fThe electron then passes through cytochrome c1 and is transferred to cytochrome c(which shuttles the electrons to complex IV)
116
Explain path B of complex III
The second electron of CoQH2 is transferred to cytochrom b1, then to cytochrome bH. Then passed back to CoQ-, making it in it's oxidized form.
117
Where is proton translocation in complex III?
Path A
118
How may CoQH2 enter the complex III?
two, one for each Q cycle. Each CoQH2 goes through path A and B in each cycle. In both cycle 1 and 2, two protons are pumped across membrane.
119
Electron transfering of complex IV
Cyt c → Cu A → heme a → [heme a3 + Cu b ] →O2
120
What is the proton translocation of complex 4?
H-channel establishes gradient through proton loading site (Mg2+ ), K- channel supplies protons for oxygen reduction, & D-channel supplies both
121
IS the inner mitochondrial membrane permeable or impermeable to ions?
Impermeable
122
What does electron transport result in?
H+ out of the matrix (N-side) and into the intermembrane space (P-side) establishing an electrochemical potential
123
Where is ETC located in gram negative?
inner membrane
124
Where is ETC locatred in gram-possitive bacteria
cell membrane
125
What does the oxidation of NADH(FADH2 ) by O 2 supply?
The energy needed to synthesize ATP. Energy is stored in proton gradient across the inner mitochondrial membrane.
126
ATP Synthase catalyzes the synthesis of ATP from the proton gradient (F0 F1 -ATPase). Multisubunit transmembrane protein (450 kDa). Where is the F0 region? Where is the F1 region?
F0: membrane embedded F1: solvent exposed
127
How many subunits are in F0?
Membrane embedded. 3 subunits.
128
How many subunits in F1?
Solvent exposed. 5 subunits
129
Which region of ATP synthase has a cofactor?
F1 solvent exposed.
130
What does F0 do?
catalyzes proton translocation
131
What does F1 do?
Catalyzes synthesis & hydrolysis of ATP
132
What is the mechanism for complex 4 (Cytochrom c oxidase)?
heme a3 cycles through Ferrous (Fe2+ ), Ferric (Fe 3+ ), and Ferryl (Fe 4+ ) states o The Ferryl state is Compound II (Fe 4+ =O). These different oxidation states of iron are essential for the electron transfer process and the reduction of oxygen in the final step of the electron transport chain in cytochrome c oxidase.
133
What is oxidative phosphorylation?
Coupling of the electron transport chain to ATP synthesis
134
What are the three hypotheses of oxidative phosphorylation?
Chemiosmotic hypothesis (most widely accepted) Chemical coupling hypothesis Conformation coupling hypothesis.
135
What is the Chemiosmotic hypothesis of oxidative phosphorylation?
Conservation of ETC free energy by a proton gradient. (The proton gradient created by the ETC drives ATP synthesis via ATP synthase (the most widely accepted hypothesis).
136
What is the chemical coupling hypothesis
Breakdown of reactive intermediates generated by ETC (The ETC produces reactive intermediates that directly facilitate ATP production (less widely accepted today).
137
What is the conformation coupling hypothesis of oxidative phos?
High energy protein conformation states generated by ETC. (The energy from proton movement drives conformational changes in ATP synthase, allowing it to make ATP (also less widely accepted).
138
What is complex 5
ATP Synthase (F0F1-ATPase)
139
What is the F0 region
membrane embedded and translocates protons
140
F1 region
Matrix exposed and synthesizes ATP
141
What are the three protomer conformations for ATP synthase and what do they mean?
 L-state (loose)  T-state (tight)  O-state (open)
142
Formating ATP involves energy-dependent changes in the conformation states of ATP synthase, which are driven by the flow of protons. What is the flow
L to T to O
143
What are the conformation changes driven by?
flow of protons
144
What are the synthesis steps of ATP synthase
1. ADP & Pi bind to the L state 2. ATP is synthesized in the T state 3. ATP is released in the O state
145
GIve the proton channel for ATPase rotary engine
1. Enters through subunit a on the intermembrane space side 2. Binds to subunit c which induces a turn o Generates 3 ATP per full turn o Four protons per ATP 3. Releases through subunit a on the matrix side
146
How many protons per ATP is needed in ATP synthase?
4 per ATP
147
How many ATP are generated per each full turn?
3
148
Where do protons enter and exit the rotary engine?
enter subunit a on intermembrane space side and leave through subunit c on matrix side
149
WHat drives the reversal of ATP synthase?
Hydrolysis of ATP drives reversal of ATP synthase with near 100 % efficiency.
150
How much ATP does it cost to reverse ATP synthase
3
151
How much ATP does oxidation of one NADH yield?
3
152
How much ATP does oxidation of one FADH2 yield?
2
153
How much ATP does oxidation of one TMPD (nonphysiological compound) yield?
1
154
What is a P/O ratio?
Relates the amount of ATP (P) synthesized to the amount of oxygen reduced (O)
155
Oxidation of one glucose yields what?
32 ATP
156
What does the F0 region mainly do
proton translocation a → cn → protonation of Asp breaking Asp-Arg interaction → turn Asp in subunit c and Arg in subunit a
157
WHat does F1 region mainly do
ATP synthesis (αβ) 3 protomer; L → T → O (conformation change induced by proton translocation)
158
Which complex reaction is irreversible
Complex IV. Complex I (II) ⇌ Complex III ⇌ Complex IV → Complex V ⇌ ATP
159
Where do the NADH sources that feed into oxidative phosphorylation originate from?
GLycolysis, TCA cycle, and fatty acid catabolism
160
What regulate ETC and Oxidaive phosphorylation
ATP and NADH
161
What does Decoupling of ETC from oxidative phosphorylation produce and allow for?
Produces heat Allows for ETC to continually function under low energy
162
What does coupling of ETC and Oxidative phosphorylation depend on?
impermeability of IMM. It needs proton channel proteins to facilitate diffusion acorss membrane
163
Which is more efficient, aerobic or anaerobic gllycolysis?
Aerobic respiration is 16x more efficient than anaerobic glycolysis
164
What can aerobic respiration lead to the formation of?
ROS Reactive oxygen species
165
What are the primary ROS in biological systems?
Superoxide and hydroxyl