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Flashcards in Week 3 - Oxidative Phosphorylation Deck (20)
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1

Give an overview of what happens during the process of oxidative phosphorylation.

It is all based around the respiratory chain / electron transfer chain (complexes I - IV), which is embedded in the inner membrane of the mitochondria. Energy carriers pass through this respiratory chain, and finally become phosphorylated in complex 5 (ATP synthase), and this process is where the majority of ATP is produced. It is also where oxygen is consumed and converted into H2O.

2

Which of the 5 protein complexes in oxidative phosphorylation is the largest?

Complex I - NADH dehydrogenase.

3

Which complexes in the electron transport chain are responsible for pumping protons?

Complexes I, III and IV.

4

What is another name for Coenzyme Q? What is it responsible for?

Also known as Ubiquinone, this is the first electron carrier in the electron transport chain. It is responsible for carrying electrons from complexes I and II, over to complex III (i.e. it is reduced at complexes I and II, and is oxidised at complex III). It is quite hydrophobic, and can flow through the lipid bilayer of the inner mitochondrial membrane to get there. It is capable of carrying two electrons, as opposed to something like Cytochrome C, which is only capable of carrying one.

5

What is Cytochrome C? What is its function?

Cytochrome C is the second electron carrier in oxidative phosphorylation. It is a soluble heme-containing protein in the intermembrane space. It carries a single electron from complex III to complex IV (i.e. it is reduced at complex III and is oxidised at complex IV), and ultimately these electrons get passed onto water.

6

What is complex I called? What does it do?

NADH dehydrogenase. The biggest of the 5 complexes, it looks a bit like an upside down boot. Here, NADH gets oxidised, and electrons get passed onto Coenzyme Q, to be sent off to complex III. There is a channel running through the complex for the conduction of electrons, which includes a flavin mononucleotide (FMN) and a series of intermediates such as Fe-S complexes. Complex I also participates in pumping protons.

7

What is complex II called? What does it do?

Succinate dehydrogenase. It contains Fe-S centres, and there are also haeme groups and various phospholipids buried in the complex. Much like complex I, this complex contains Coenzyme Q, which is used to carry electrons to complex III. This consists of the oxidation of FADH2. It is the 6th step of the TCA cycle, and is therefore also responsible for the conversion of succinate to fumarate. The protein complex itself looks like a bust (statue), and it does not participate in pumping protons.

8

What is complex III called? What does it do?

Ubiquitone: Cytochrome C oxidoreductase. This is where the reduced forms of Coenzyme Q (produced by complexes I and II) transfer their electrons to Cytochrome C (a small haeme-containing protein), which binds at the Cytochrome C binding site, takes up an electron, and leaves again, i.e. carries it to complex IV. The protein complex itself looks like a person meditating. It does participate in pumping protons.

9

What is complex IV called? What does it do?

Cytochrome oxidase. Here we have the transfer of electrons from Cytochrome C to oxygen to form water. Cytochrome C comes from complex III with its one electron, gets reoxidised at complex IV, and can then be recycled, i.e. shuttled back and forth between these complexes transporting electrons. Complex IV contains copper ions which are coordinated to cysteine residues within the protein complex. It does participate in pumping protons. The protein complex itself looks a bit like the crowned portcullis (the official emblem / logo of the UK Parliament. It is an image of a grilled gate of the type found on medieval castles with a crown on top).

10

What is complex V called? What does it do?

ATP synthase, or ATPase. It is used to synthesise large amounts of ATP. So we have ADP and Pi, and this protein uses the H+ gradient to drive the conversion of these substrates to ATP. It can sort of be thought of as a turbine of sorts.

11

In which complexes are Fe-S centres found?

They are found in complexes I, II and III of the respiratory chain. They are one-electron carriers coordinated by cysteine residues in the protein. These Fe-S complexes are important for conducting electrons through the respiratory chain, as are haeme groups.

12

How does the electrical potential of electrons change as they go through the respiratory chain?

Electrons flow from a level of higher potential to a level of lower potential. The excess energy is used in proton pumping. And ultimately, the electrons end up on the oxygen to form water, and there's no more energy that can be extracted at that stage.

13

Which part of the electron transport pathway is blocked by the following inhibitors:
1. Rotenone?
2. Antimycin A?
3. CN- or CO?

1. Rotenone blocks the transfer of electrons from NADH to Coenzyme Q.
2. Antimycin A blocks the transfer of electrons from Cyt B to Cyt C.
3. CN- and CO block cytochrome oxidase, i.e. the transfer of electrons to oxygen to form water.

14

Summary equation of electron transport from :
1. Complex I to complex IV?
2. Complex II to complex IV?

1. NADH + 11H+ (M) + ½O2 ——> NAD+ + 10H+ (IMS) + H2O, where (M) = the mitochondrial matrix, and (IMS) = the inter membrane space. This means we have transfer of electrons from NADH to oxygen, and 11 electrons are pumped for every equivalent of NADH. Some of these protons find their way onto water, hence the mismatch in the equation.
2. FADH2 + 6H+ (M) + ½O2 ——> FAD + 6H+ (IMS) + H2O. In complex II, we produce FADH2. Again, those electrons are eventually transferred over to oxygen to form water. We don't get quite as much energy out of this reaction, we get 6 protons pumped for every equivalent of FADH2, and it's these protons that have been pumped across the membrane that are used to drive ATP synthesis.

15

How does electron transport lead to ATP synthesis?

So this whole process of ATP synthesis that we've been talking about is called chemiosmotic coupling. Electron transport is “coupled” with the phosphorylation
of ADP to form ATP. The coupling has been explained by
the chemiosmotic coupling hypothesis. So we have a coupling, but it's indirect. We have a TCA cycle happening in the mitochondrial matrix, and this is not directly synthesising ATP but the electrons are used to pump hydrogen ions across the membrane and out of the mitochondrial matrix, meaning there is a high concentration of H+ ions in the inter membrane space, and a low concentration in the mitochondrial matrix. This causes an electrochemical gradient in which the H+ ions to flow back into the mitochondrial space via the ATP synthase complex, and those hydrogen ions are ultimately used to drive ATP synthesis.

16

What are the Fo and F1 components of ATP synthase?

In the ATP synthase complex, we have a coupling of a mechanical process (rotation) and a biochemical process of ATP synthesis. “F” comes from “phosphorylation Factor". The two subunits are joined by an axle and a stator.
* The Fo subunit is a membrane spanning domain. It transports H+ from the IMS to the matrix, dissipating the proton gradient. The “o” in Fo (not zero!) comes from
Oligomycin sensitivity.
* The energy is transferred to F1. This is the ATP synthesizing domain, and F1 catalyzes phosphorylation of ADP. It is a soluble complex in the matrix, and it pushes an ADP and an inorganic phosphate together to form the ATP molecule. ATP synthases are present in bacteria, mitochondria and chloroplasts.

17

How many H+ ions are required to generate one molecule of ATP?

A total of 3 H+ are transported per ATP generated by ATPase. Another H+ is used to transport phosphate (H2PO4), which is required for ATP synthesis). Therefore, the net yield is 4H+ per ATP.

18

What is the binding-change model in regards to ATP synthase?

• The proton-motive force causes rotation of the central shaft—the γ subunit.
• Contacts each αβ subunit pair in succession.
• This produces a conformational change which ejects ATP from the β-ATP site. The β-ADP site is then converted to the β-ATP conformation, which promotes condensation of bound ADP + Pi to form ATP. Finally, the β-empty site becomes a β-ADP site, which loosely binds ADP + Pi entering from the solvent.
• At least two of the three catalytic sites alternate in activity; ATP cannot be released from one site unless and until ADP and Pi are bound at the other.

19

Total ATP yield from oxidative phosphorylation?

• For each NADH oxidized in oxidative phosphorylation, ~2.5 ATP are produced.
• For each FADH2 oxidised in oxidative phosphorylation, ~1.5 ATP are produced.
• ~30 to 32 ATPs are produced by the full oxidation of glucose.

20

What is the NADH and FADH2 that is formed via the TCA cycle used for?

To pump H+ ions from the matrix to the inner-membrane space.