Metabolism part 3

Question 1

What is the basic cell biology of the mitochondria?

Answer 1

Outer membrane, inter membrane space, inner membrane, cristae, matrix

Question 2

Outline the mitochondrial genome

Answer 2

Single circular chromosome in the matrix - 16,500 base pairs which is 37 genes in total (13 protein encoding, 2 rRNA and 22 tRNA)

Question 3

What is mitochondrial fusion and fission?

Answer 3

Fusion- 2 mitochondria fuse to form 1
Fission - 1 mitochondria splits into 2

Question 4

What are mitochondrial ribosomes?

Answer 4

rRNA forms the subunits of ribosomes
12S and 16S rRNA forming a 55S mitochondrial ribosome

Question 5

What does S mean when describing ribosomes?

Answer 5

Svedberg unit - level of a particles sedimentation - the time taken to move to the bottom of a tube during centrifugation

Question 6

What is endosymbiosis?

Answer 6

A symbiotic relationship where one organism, the endosymbiont, lives inside the cells or body of another organism, called the host. This relationship can be mutually beneficial

Question 7

How are proteins transported into the mitochondria?

Answer 7

If a protein contains a specific signal sequence then the cell knows that it needs to enter the mitochondria
Firstly, it will pass through the TOM complex of the outer membrane and then through the TIM complex on the inner membrane and into the matrix

Question 8

How is pyruvate transported into the mitochondria?

Answer 8

Can enter through the outer mitochondrial membrane through porins or VDAC (channel protein) - small molecules up to 5000 Da
Passes into the matrix via mitochondrial pyruvate carriers - these require a change in pH to function
Pyruvate is then decarboxylated to form acetyl CoA

Question 9

How is NADH transported into the mitochondria using the Malate Aspartate Shuttle?

Answer 9

1. NADH from glycolysis is used to reduce oxaloacetate to malate in the cytosol
2. Malate crosses into the matrix by an antiporter - alpha ketoglutarate goes out
3. Malate is then oxidised to form oxaloacetate and NAD+ is reduced
   Malate carries NADHs electrons into the mitochondria

Question 10

How is NADH transported into the mitochondria via the G3P Shuttle?

Answer 10

1. NADH from glycolysis is used to reduce DHAP converting it to G3P in the cytosol
2. This enters the mitochondria and is oxidised back to DHAP on the inner membrane
3. This generates FADH2
4. G3P transfers electrons from NADH to FADH2

Question 11

How are fatty acids transported into the mitochondria?

Answer 11

Carnitine transports (shuttles) fatty acyl CoA into the matrix
Acyl CoA is converted to Acyl carnitine by CPT1
Acyl Carnitine is transported via the Acyl Carnitine Translocase
Acyl carnitine is converted back to acyl CoA by CPT2
Carnitine is regenerated

Question 12

What is the definition of cellular respiration?

Answer 12

The generation of high energy electrons with transfer potential (NADH and FADH2), the flow of these electrons through the respiratory chain (electron transfer chain) and the subsequent synthesis of ATP.

Question 13

What is the definition of oxidative phosphorylation?

Answer 13

The energy in the electrons carried by NADH and FADH2 is used to form ATP.
This is highly exergonic

Question 14

Why do electrons pass readily along the ETC?

Answer 14

Redox potential
More negative - prefers to donate electrons
More positive - prefers to accept
This dictates

Question 15

Outline the role of complex 1 in the respiratory chain

Answer 15

1. NADH binds to flavin mononucleotide (FMN) and donates 2 electrons to form FMNH2
2. FMN is a prosthetic group for complex 1 FMN passes electrons to iron sulphur clusters through the complex
3. 2 electrons are ultimately passed to coenzyme Q to form QH2

4 H+ are pumped across the inner membrane and NAD is regenerated

Question 16

What is an iron sulphur cluster?

Answer 16

prosthetic clusters play important roles in redox reactions
Iron ions Fe3+ are bound to sulphur atoms of cysteine residues of proteins they are reduced to form Fe2+, never takes a proton

Question 17

Outline the role of complex 2 in the respiratory chain?

Answer 17

1. Succinate dehydrogenase converts succinate to fumarate and generates FADH2
2. Then transfers the electrons to the iron sulphur clusters which pass the electrons to Co Q

Not enough energy to pump any protons across the membrane

Question 18

Outline the role of complex 3 in the respiratory chain?

Answer 18

Co Q binds to Q0 site on complex 3 and releases its electrons to cytochrome C but this can only carry 1 electron
Cytochromes contain heme which is iron based
Use the Q cycle
QH2 arrives one electrons goes upwards to cytochrome C the other goes down to the Qi site
A second QH2 arrives and repeats the process
So the partially reduced Q has 2 electrons and can leave to come back into complex 3
When QH2 transfers its electrons its H gets released into the intermembrane space
Per Q cycle 4 H are released into intermembrane space

Question 19

Outline the role of complex 4 in the respiratory chain

Answer 19

1. Cytochrome C arrives with 1 electron so 2 of these arrive together and pass electrons into the complex.
2. The electrons are passed through the complex which reduces ferrous and copper ions.
3. Oxygen arrives and accepts the 2 electrons causing it to become a free radicle (peroxide)
4. Complex 4 holds on to this peroxide
5. 2 more cytochrome c arrive and 2 protons arrive forming hydroxyl groups
6. 2 more protons arrive forming water

4 H are pumped across the membrane

Question 20

What is the electrochemical proton gradient?

Answer 20

Termed the proton motive force via the respiratory chain the cell uses this to generate ATP

Question 21

Outline the structure of ATP synthase

Answer 21

Fo- in the membrane consists of 12 identical subunits (C) it has a gamma subunit which protrudes into the cytoplasm and F1
F1 - has 3 pairs of alpha and beta subunits - subunits a and b are on the side and connect the F1 subunit to the membrane

Question 22

How does ATP synthase form ATP?

Answer 22

1. Proton gradient causes Fo to rotate - protons enter through a channel in subunit a and enter subunit c causing Fo rotates 120 degrees at a time.
2. Protons are released into the cytoplasm.
3. F1 is held in place but the axle moves causing F1 to change conformation which catalyses the formation of ATP

1 ATP = 4 protons

Question 23

Outline the different types of conformation

Answer 23

Loose confirmation - binds ADP and Pi
Tight confirmation - ATP synthesised
Open confirmation - releases ATP

Rotation of ATP synthase does not drive ATP synthesis it enables ATP release

Question 24

How is ATP transported out of mitochondria?

Answer 24

ADP-ATP translocase (an antiporter)
ATP leaves whilst ADP leaves