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Biochemistry II > Ch. 19 Oxidative Phosphorylation > Flashcards

Ch. 19 Oxidative Phosphorylation Flashcards

1
Q

What is the purpose of oxidative phosphorylation?

A

To capture the energy produced in glycolysis, pyruvate dehydrogenase, β-oxidation, and citric acid cycle. (mostly produces NADH and FADH₂)

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2
Q

What gets reduced and what gets oxidized in OxPhos/ETC?

A

Oxidize NAHD and FADH₂ back to NAD⁺ and FAD so they can be reused (pool).

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3
Q

Where does OxPhos/ETC take place (2 ish)?

A

Happens in the mitochondria. Reactions are either embedded in the inner membrane or associated with the inner membrane.

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4
Q

How many mitochondria do cells have?

A

Lots. 100s to 1000s. The higher the energy demand, the more mitochondria the cell will have.

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5
Q

Which mitochondrial membrane is permeable? Impermiable?

A

Outer membrane is permeable and has porins.
Inner membrane is impermeable and has very specific transport proteins.

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6
Q

What are porins?

A

Transmembrane protein pore in the outer mito. membrane that lets anything smaller than a protein (<10,000 Da) pass through.

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7
Q

What is the net reaction of OxPhos (w/o ATP/ADP/Pᵢ) and its ΔG?

A

NADH + H⁺ + ½O₂ → H₂O + NAD⁺

ΔG = ﹣219 kJ/mol (massive!)

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8
Q

Why is the ΔG of OxPhos/ETC a problem and how does the cell solve it?

A

It is too much energy to be released at one time (explosive). It needs to be broken into discrete steps.

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9
Q

What kind of reactions are OxPhos/ETC?

A

Redox reactions.

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10
Q

What is the highest energy electron form? Lowest?

A

Highest energy electron form is NADH.
Lowest energy electron form is water.

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11
Q

How do electrons flow in redox reactions/half reactions?

A

Electrons flow from negative redox potentials to positive redox potentials.

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12
Q

What happens to electron energy levels as they go through the ETC?

A

electrons go DOWNHILL in energy each step

aka: ΔG is negative and the ETC is unidirectional

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13
Q

Is the ETC regulated?

A

No. Despite its negative ΔG, it is NOT regulated. If NADH and oxygen are present, it will occur.

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14
Q

What is Complex Ⅰ of the ETC?

A

(NADH-CoEnzyme Q oxidoreductase) integral membrane protein in the inner mito. membrane that accepts two electrons from NADH (which only has 2).

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15
Q

What does Complex Ⅰ tie the ETC to?

A

any pathway that produces NADH

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16
Q

What does Complex Ⅰ contain? (2)

A

It has cofactor FMN.
It also has Fe-S Centers.
(its a big complex)

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17
Q

What are Fe-S Centers and how many are in Complex Ⅰ?

A

A center that can carry an electron because of the Fe. Complex Ⅰ has many Fe-S Centers.

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18
Q

What are the steps of ETC Complex Ⅰ electron movement? (3)

A
  1. two electrons from NADH are transferred to FMN to produce FMNH₂ and NAD⁺
  2. FMNH₂ transfers the two electrons through a SERIES of Fe-S Centers
  3. Fe-S Centers transfer the two electrons to CoEnzyme Q/ubiquinone
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19
Q

What is ubiquinone?

A

An electron carrier that can accept two electrons and carry them from Complex Ⅰ to Complex Ⅲ. It is called ubiquinol when it is carrying two electrons.

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20
Q

What is the big picture reactants and products of Complex Ⅰ?

A

Start with NADH and end with NAD⁺ and uniquinol.

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21
Q

What does Complex Ⅰ do in addition to moving electrons?

A

It pumps H⁺ out of the mitochondrial matrix into the intermitochondrial membrane space creating a H⁺ gradient.

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22
Q

Where does Complex Ⅰ get the energy to pump protons?

A

energy comes from the electron movement from FMNH₂ → series of Fe-S centers → ubiquinone

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23
Q

What is the estimate of how many protons are pumped by Complex Ⅰ per NADH oxidized and why is it an estimate?

A

It is estimated that 4 protons are pumped per NADH oxidized.
It is an estimate because it is NOT stoichiometric.

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24
Q

What is ETC Complex Ⅱ?

A

(succinate dehydrogenase) It produces FADH₂ and is also a part of the citric acid cycle.

25
What does Complex Ⅱ contain? (1)
It has several Fe-S centers.
26
How to electrons flow in Complex Ⅱ?
electrons flow from FADH₂ → a SERIES of Fe-S centers → ubiquinone which becomes ubiquinol once bound to electrons.
27
What is the shorthand for ubiquinone? Ubiquinol?
Ubiquinone is Q. Ubiquinol is QH₂
28
How does Complex Ⅱ differ from Complex Ⅰ ?
Complex Ⅱ doesn't pump protons because FADH₂ doesn't provide enough energy. (less energetic than NADH)
29
What is ETC Complex III?
(Coenzyme Q - cytochrome C reductase) A complex that accepts electrons from ubiquinone and passes them to cytochrome C
30
What does Complex III contain? (2)
Contains an Fe-S center and cytochromes.
31
What are cytochromes?
Proteins that absorb light
32
What are the steps of the Q cycle? (9)
1. reduced ubiquinone (QH₂) binds to the QP site of Complex III 2. one electron leaved reduced ubiquinone (QH₂), moves through the Fe-S center, is passed to cytochrome c1, and finally ends up on cytochrome C 3. ubiquinone is semiquinone state (QH) still occupying QP site 4. second electron from this semiquinone (QH) transferred through B cytochromes to an oxidized ubiquinone (Q) at the QN site 5. oxidized ubiquinone in semiquinone (QH) state still occupying QN site 6. a new (3rd) reduced ubiquinone (QH₂) binds at the now empty QP site 7. one electron leaves this reduced ubiquinone, moves through Fe-S center, is passed to cytochrome c1, and finally ends up on cytochrome C 8. second electron is transferred through B cytochromes to the oxidized semiquinone (QH) at the QN site which produces a fully reduced ubiquinone (QH₂) 9. fully oxidized (Q) and fully reduced (QH₂) ubiquinones are free to leave Complex III
33
Where does the reduced and oxidized Q come from?
There is a pool of both reduced and oxidized ubiquinone.
34
What is cytochrome C?
A peripheral protein in the intermitochondrial membrane space that carries one electron. (free to leave and does)
35
What does the Q cycle produce overall? (2)
Q cycle has oxidized one ubiquinone and has reduced two cytochrome C
36
What happens to cytochrome C once it receives its electron?
It leaves Complex III and carries its electron to Complex IV
37
What is ETC Complex IV?
(cytochrome C oxidase) a protein made of 13 subunits
38
What does Complex IV contain? (3)
It contains cytochromes, a copper cofactor similar to the Fe-S centers, and heme
39
What does Complex IV do?
It takes in two electrons from two cytochrome C's and uses existing oxygen and two existing hydrogen ions to produce water.
40
What is special about Complex IV?
It is the only enzyme to utilize oxygen!
41
What are the steps of electron movement through Complex IV? (4)
1. oxygen binds to Complex IV 2. one electron at a time enters on cytochrome C 3. electron is transferred through copper centers 4. oxygen, hydrogen, and electrons combine to produce water
42
What complexes pump hydrogen?
Complex I Complex III Complex IV
43
What is the problem with electrons entering Complex IV one at a time via cytochrome C?
It leads to the production of free radicals ( ̇O₂⁻) which will destroy anything they come in contact with, aka destroy the mitochondria
44
Why don't the free radicals destroy the whole cell as soon as they form?
They are stuck in the mitochondria because of the mitochondrial membrane. Membrane protects the rest of the cell.
45
How are free radicals removed (2)?
Superoxide dismutase Glutathione
46
What does superoxide dismutase do?
It is an enzyme that catalyzes the reaction 2 ̇O₂⁻ + 2 H⁺ → H₂O₂ + O₂ to remove free oxygen radicals.
47
What does glutathione do and where does the energy come from?
It quickly degrades hydrogen peroxide to water. Hydrogen peroxide is reduced to form water. The reductive power comes from NADH.
48
Why does diffusion of electron carriers happen quickly in the ETC?
The four complexes and two mobile electron carriers are in very high concentrations in the inner mitochondrial membrane. (don't have to go far before running into one)
49
How many protons can each proton pumping ETC Complex move per NADH?
Complex I: 4 H⁺ per NADH Complex III: 4 H⁺ per NADH Complex IV: 2 H⁺ per NADH (total of 10 H⁺)
50
What does the active transport of H⁺ produce and what is it?
It forms a chemiosmotic gradient: chemical and pH gradient, along with a charge gradient.
51
What are the consequences of the chemiosmotic gradient? (2)
Inner mitochondrial membrane space is much more positively charged than the matrix. There is a "﹣"ΔG associated with eliminating this gradient (aka eliminating the gradient is a spontaneous process).
52
Where does all of the energy collected from glycolysis, citric acid cycle, β-oxidation, pyruvate dehydrogenase, etc. end up?
All the energy ends up in this gradient and is then harvested.
53
How is the chemiosmotic gradient energy harvested?
The F₀F₁ ATPase, aka ATP Synthase, harvests the energy stored in the gradient.
54
What is the net reaction of ATP Synthase?
ADP + Pᵢ → ATP + H₂O
55
What are the two parts of ATP Synthase?
F₀ part/subunit and F₁ part/subunit.
56
What is the F₀ subunit and what does it do (2)?
It is a proton pore embedded in the inner membrane. It allows H⁺ to flow across the inner mitochondrial membrane back into the matrix. It also rotates like a carousel.
57
What is the F₁ subunit and what does it do?
It is a peripheral protein that has catalytic properties. It synthesizes ATP.
58
How does ATP Synthase make ATP and why does it work thermodynamically?
The enzyme binds ADP and Pᵢ so tightly that catalysis occurs. This is works because ATP that is BOUND (not is solution) is actually "low energy".
59
What problem does the energy of bound ATP pose and how is it corrected?
Releasing the ATP is a problem because it is an increase in energy. The energy to release ATP comes from F₀ rotation (H⁺ coming back into the matrix and spinning the rotor).

Biochemistry II (11 decks)

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