M2: ETC and OXPHOS 1 L12

Question 1

Describe the inner and outer mitochondrial membrane and the matrix.

Answer 1

Outer membrane: Porous to allow diffusion of ions
Inner membrane: invaginations for surface area increase and it is impermeable to passive ion transport.
Matrix: (inside the inner membrane) houses citric acid cycle, mitochondrial DNA, mitochondrial ribosomes (protein synthesis machinery)

Question 2

What is the proton motive force and how is it formed?

Answer 2

The ETC (complexes 1,3 &4) generates a chemical gradient: more protons in the inter membrane space than in the matrix. 
The ETC also generates an electrical gradient: more positive charge in the inter membrane space (H+)
This electrochemical gradient is also referred to as the proton motive force.

Question 3

Which ETC complexes have Flavo proteins, and specify which kind.

Answer 3

Coplex 1: FMN (flavin mono nucleotide)

Complex 2: FAD (flavin adenine dinucleotide)

Question 4

Which ETC complexes have cytochromes?

Answer 4

Complex 2, complex 3, complex 4.

Question 5

Which ETC complexes have iron sulfur centers?

Answer 5

complex 1, complex2 , complex 3.

Question 6

What is complex 1 called?

Answer 6

NADH-Coenzyme Q Reductase

Question 7

Describe what happens in complex 1. How many protons are pumped?

Answer 7

1) NADH donates 2 electrons to FMN (reduces it).
2) The electrons are passed down the iron sulfur centers until they’re donated to CoQ (Q) which reduces it (QH2).
3) Reduction of CoQ causes a conformational change of the transmembrane arm which drives the pump of protons across the membrane from the matrix into the inter membrane space. The protons travel through translocation channels (Nqo 12, 13, & 14) which open when the transmembrane arm forces them into a conf. change.
4) Complex 1 pumps a net of 4 protons.

Question 8

How does CoQ get electrons from complex 1?

Answer 8

CoQ binds to Complex 1.

Question 9

What is the name of complex 2?

Answer 9

Succinate-Coenzyme Q reductase

Question 10

Explain what happens in complex 2.

Answer 10

Complex 2 is part of the CAC. Succinate comes in from CAC, and gets oxidized to fumarate and FADH2 is formed. The electrons from FADH2 reduce FAD, get passed down through the iron sulfur clusters, and then reduce CoQ. Complex 2 does not pump protons.

Question 11

What are pathways other than complex 1 and 2 that reduce CoQ?

Answer 11

1) Electrons from the matrix: There are FAD containing dehydrogenases that can donate electrons to ETF. Electron transfer flavo protein (ETF) receives the electrons. ETF-QO takes electrons from ETF and puts them onto Coenzyme Q.
2) Electrons from the cytosol of inter membrane space: Glycerol 3 phosphate dehydrogenase is located in the cytosol of the intermembrane space facing the inner mitochondrial membrane. The enzyme oxidizes a molecule of Glycerol-3-P to DHAP. The electrons from Glycerol-3-P can get donated to FAD which can donate to CoQ.

Question 12

What is the name of complex 3?

Answer 12

Coenzyme Q-cytochrome c reductase.

Question 13

How many protons are pumped from complex 3? What cycle takes place in Complex 3?

Answer 13

Pumps 2 net protons.

The Q cycle.

Question 14

Why do we need the Q cycle?

Answer 14

Because coenzyme Q can accept 2 electrons but Cytochrome C can only accept one.

Question 15

How does the Q cycle work?

Answer 15

PHASE 1

1. Fully reduced CoQ (QH2) binds to the Qo site (in complex 3).
2. 2 protons pumped to inter membrane space.
3. Cyt C can only accept one of the 2 electrons from QH2. So QH2 (ubiquinol) gives one electron to Cyt C.
4. Q (ubiquinone) binds to Q1 site and receives the second electron to make QH (semi-quinone).

PHASE 2

1. QH2 Binds Qo site
2. 2 protons go to inter membrane space.
3. One electron reduces Cyt C
4. The other electron binds semi-quinone (QH) in the Q1 site and makes a fully reduced QH2.

NET OF 2 PROTONS PUMPED. (2 protons are used in the process)

Question 16

What is the end result of the Q cycle?

Answer 16

1) 2 QH2’s (ubiquinol) are fully oxidized to Q (ubiquinone)
2) 1 Q is reduced to QH2
3) 2 Cyt C molecules are reduced.

Question 17

What is the name of complex 4?

Answer 17

Cytochrome c oxidase

Question 18

Describe what happens in complex 4 of the ETC. How many protons does it pump?

Answer 18

It pumps 4 net protons.
Catalyzes the transfer of 4 electrons from 4 molecules of reduced Cytochrome C. (Oxidizes Cyt C) Generates 2 water molecules.

Question 19

How many protons are pumped through the ETC per NADH?

Answer 19

10.

Question 20

What is the respirasome?

Answer 20

It is a supercomplex containing an aggregate of all the ETC complexes. The complexes touch one another. This is a possibility that allows for more efficiency of electron transport, it reduces byproducts of reactive oxygen species, and limits crystallization.

Question 21

How is the reduction potential involved in the ETC?

Answer 21

The lower a reduction potential is, the more likely a molecule is to give up its electrons. The higher the reduction potential, the more likely a molecule is to accept electrons. NADH has a low reduction potential compared to oxygen which is high. So electrons want to go to oxygen. We know the electron path is taken bc the reduction potential increases as it goes along the ETC.

Question 22

Why does the body use the ETC (biological oxidation) rather than combustion to generate energy?

Answer 22

Combustion is a one step reaction but a lot of energy would be lost as heat.
Biological oxidation: If you separate the oxidation reactions into many smaller reactions you can more efficiently harness the energy. It also allows you to fine tune the reaction. More efficient.

Question 23

What are the two ways to shuttle NADH to the mitochondria?

Answer 23

1) the dihydroxyacetone phosphate/glycerol-3-phosphate shuttle (DHAP/ Glyerol-3-P)
2) the malate/aspartate shuttle

Question 24

How does the DHAP/G3P shuttle work?

Answer 24

1. NADH reduces DHAP to make G3P (glycerol-3-phosphate) in the cytosol of the cell.
2. G3P can diffuses through the outer mitochondrial membrane into the inter membrane space.
3. Re-oxidation of G3P to DHAP by G3P dehydrogenase found in the inner membrane.
4. G3P dehydrogenase also reduces FAD to FADH2.
5. Transfer of electron pair from FADH2 to CoQ, CoQ goes to complex 3.
6. DHAP returns to the cytosol.

Question 25

How does the malate/aspartate shuttle work?

Answer 25

1. Oxaloacetate is reduced by NADH in the cytosol to malate.
2. Malate diffuses theough the outer AND inner membrane to get into the mitochondrial matrix.
3. Malate is re-oxidized to oxaloacetate and gives its electrons to NAD to make NADH.
4. NADH is oxidized by complex 1.
5. Oxaloacetate doesn’t have a transporter so it undergoes a transamination rxn. It gets an amino group from glutamate and turns into spartic acid. Since glutamate releases an amino group it turns into alpha keto glutarate. alpha keto glutarate and spartic acid (aspartate) have specific transporters, they cdiffues back to the cytosol.
6. A reverse transamination rxn occurs to re-make oxaloacetate from aspartate and a-ketoglutarate..

Question 26

Define the P/O ratio.

Answer 26

How many ATP molecules are made for every oxygen that is consumed.

Question 27

What is the P/O ratio starting from complex 1?

What is the P/O ratio starting from complex 2?

Answer 27

From Complex 1: 10/3.7 = 2.5

From complex 2: 6/3.7 = 1.5

Question 28

How is the P/O ratio for complex 1 calculated?

Answer 28

Step 1: how many protons do you need to make one ATP?
8 protons from the Fo subunit + 3 protons from AAC transporter to balance import of inorganic phosphate. 11 protons/3ATP = 3.7 protons/ ATP

Step2: How many ATP’s can you make per oxygen molecule that’s reduced?
to reduce 1 oxygen molecule, 10 protons need to be pumped via the ETC. So finally, 10 protons pumped to reduce O / 3.7 protons needed to make 1 ATP = 2.5 ATP’s per oxygen molecule reduced.