MMT: oxidative phosphorylation

Question 1

Define oxidative phosphorylation.

Answer 1

Process in which ATP is formed from the transfer of electrons from NADH and FADH2 to O2 by a series of electron carriers

Question 2

Identify the initial electron donors and terminal electron acceptor of the electron transport chain

Answer 2

Initial: NAD+ and FAD+

Terminal: oxygen

Question 3

complex I of the ETC: what it takes its electrons from, how many protons it pumps, and how it works

Answer 3

• NADH
• 4 protons
• Contains iron-sulfur clusters that bind to cysteine residues in the protein. FMN first accepts the electrons from NADH, and then transfers them onto iron-sulfate clusters. A molecule of CoQ gets reduced to CoQH2 by the electrons

Question 4

complex II of the ETC: what it takes its electrons from, how many protons it pumps, and how it works

Answer 4

• FADH2
• 0 (it does not span the membrane!)
• donates electrons from FADH2 to CoQ. also forms fumarate from succinate.

Question 5

complex III of the ETC: what it takes its electrons from, how many protons it pumps, and how it works

Answer 5

• CoQH2
• 4 protons
• it donates electrons from CoQH2 to cytochrome c.

Question 6

describe the electron transfer from CoQH2 to cytochrome c

Answer 6

CoQH2 carries two electrons, by cytochrome C can only accept one. Thus, it uses the Q cycle to fix this. One electron bounces through iron-sulfur cluster, cytochrome C1 unit, and then to cytochrome C. this electron can immediately go to complex IV. the other electron comes through cytochrome b electron node and finds a separate CoQ molecule sitting in complex III. It waits for another cycle to receive a second electron to become CoQH2, when can then go and re-enter the cycle

Question 7

Describe complex IV of the ETC: what it takes its electrons from, how many protons it pumps, and how it works

Answer 7

• cytochrome c
• 2 protons
• donates electrons to oxygen to form water

Question 8

Relate myocardial infarction induced cardiac cell death to oxidative phosphorylation.

Answer 8

The decreased oxygen supply impacts our ability to form ATP. In the ETC. ATP is needed for cellular processes and energy, causing the cells to dysfunction and damage. This is a huge issue.

Question 9

How does the structure of the mitochondria allow for the proton gradient to form?

Answer 9

The outer mitochondrial membrane is permeable to protons due to VDACs, while the inner membrane is largely impermeable. This allows for a proton gradient along the surface (cytosolic side) of the inner mitochondrial membrane.

Question 10

Identify the energetic link between oxidation in the electron transport chain and ATP
generation

Answer 10

A proton motive force

Question 11

What are E’ and G’

Answer 11

E’: electron transfer potential, also known as the reduction potential or redox potential

G’: phosphoryl transfer potential

Question 12

As we move through the ETC, we move from ___ to ___ reduction potential, and ___ to ___ free energy

Answer 12

Negative to positive; higher to lower

We gain energy as we go!

Question 13

Compare and contrast Coenzyme Q and Cytochrome C

Answer 13

• Cytochrome c is water soluble and moves in the intermembrane space of the mitochondria. it contains a heme covalently linked to the protein by 2 cysteine residues.
• CoQ is a mobile electron carrier that shuttles between complexes I and II and complex III. it is not bound to protein and is hydrophobic.

Question 14

explain the transfer of electrons through Complex IV: cytochrome c oxidase.

Answer 14

-Two cytochrome C molecules enter. 2 electrons bounce from a copperA center to heme a, to heme a3, and to copperB. The first molecule will reduce the CuB, and the second will reduce the heme a3.

-The reduced centers form a peroxide bridge by accepting an oxygen molecule

-Two more electrons cytochrome C molecules enter. This allows two more electrons to enter the cycle and break the peroxide bridge. Two protons are used to stabilize the oxygen to form hydroxyl groups.

-Two more protons are pulled in to form water that can dissociate and leave

Question 15

Describe the mechanism of cyanide toxicity.

Answer 15

Cyanide can bind to heme a3, which blocks complex IV and shuts down the ETC. if we cannot reduce water we cannot accept electrons. TCA will then shut down and we rely on glycolysis, and our tissues cannot be sustained off of glycolysis only. We die pretty fast.

Question 16

List the types of electron carriers in the electron transport chain.

Answer 16

FADH2, NADH, FMN, CoQ, cytochrome C, FeS, hemes, copper ions

Question 17

Calculate the number of protons pumped into the intermembrane space per acetyl entering the TCA cycle.

Answer 17

36!
3 NADH in TCA, 1 FADH2
10 protons per 2e NADH, 6 protons per 2e FADH2

Question 18

Describe the mechanism by which the ETC generates reactive oxygen species

Question 19

how does the body clear ROS

Answer 19

Superoxide dismutase can neutralize superoxide to form oxygen and hydrogen peroxide. Glutathione peroxidase can convert the hydrogen peroxide into water.

Question 20

Identify each subunit of ATP synthase and their functions.

Answer 20

F0: proton channel; motor portion
F1: ATPase; stator portion
Exterior column (a, b2, delta) and Gamma-epsilon stalk connect F0 and F1

Question 21

describe subunit a in ATP synthase

Answer 21

has two proton half channels that do not span the membrane; one channel opens to the cytosol, and one opens to the intermembrane space

Question 22

describe subunit c in ATP synthase

Answer 22

: when a proton enters the cytosolic half channel on a, it interacts with c. the c subunit is largely hydrophobic and has a central aspartic acid residue. The aspartate gets protonated/deprotonated to drive rotation of the c subunit

Question 23

describe the gamma-epsilon stalk in ATP synthase

Answer 23

tightly connected to c ring, so when the c ring rotates so does gamma-epsilon. This rotation leads to conformational changes that help form ATP

Question 24

Describe the open, loose, and tight phases of the beta subunits.

Answer 24

Open: release ADP/ATP
Loose: binds ADP and Pi but can’t release ADP
Tight: converts ADP and Pi to ATP, but has high affinity for ATP and cannot release it

Question 25

describe the G3P shuttle and its ATP yield

Answer 25

transfer electrons from NADH to DHAP to form G3P. the electrons from G3P are transferred to a membrane-bound enzyme that reduces FAD+ to FADH2. These will ultimately go to CoQ. This takes an energy hit…only 1.5 ATP per NADH as opposed to 2.5

Question 26

describe malate-aspartate shuttle and its ATP yield

Answer 26

used in liver and heart cells. Aspartate converts to oxaloacetate then malate. The malate enters the matrix, then converts back to aspartate. The reduction from malate to oxaloacetate turns NAD+ to NADH. This system does not take an energy hit, but it can only function in equilibrium

Question 27

Describe ATP-ADP translocase and the energy cost of translocating ATP out of the mitochondrial matrix.

Answer 27

ATP-ADP translocase binds ADP in the intermembrane space, then changes its conformation and allows ADP into the matrix. The ATP then binds, and the conformation changes again to allow ATP into the intermembrane space. This process cuts into the protein gradient and requires some energy, but we take the hit.

Question 28

how much ATP do we make when oxidizing glucose?

Answer 28

30-32, depending on which NADH shuttle system is active.

Question 29

Identify mechanisms that regulate activity of the TCA cycle and oxidative phosphorylation

Answer 29

Energy charge: high ADP will spike the ETC, low ADP will mean less ETC activity
An active ETC lowers NADH, which activates the TCA cycle

Question 30

Describe biological and chemical mechanisms to uncouple the ETC from ATP synthase and explain the effects of uncoupling

Answer 30

Uncoupling proteins transport protons from the intermembrane space into the matrix. This is favorable, so it produces energy. This energy produces heat. This is an adaptive process…if we move to cold areas, we can upregulate this. The process disrupts the proton gradient, uncoupling the gradient from the synthase

Question 31

Describe DNP’s impact on oxidative phosphorylation

Answer 31

DNP: a chemical uncoupler; if we have too much of it, we can reach an internal body temperature that is too high

Question 32

How do CN-, N3, and CO impact oxidative phosphorylation

Answer 32

CN- N3 and CO react with compound IV, preventing the reduction of oxygen and the functioning of the ETC

Question 33

Explain how inheritance of mutations in oxidative phosphorylation enzymes can vary depending on nuclear or mitochondrial encoding of the gene

Answer 33

Mutations can be accumulated in mitochondrial DNA over time. When DNA separates into eggs, more defect mitochondria genes can separate into some cells than others. This leads to different inheritance patterns

Question 34

Describe leighs syndrome

Answer 34

mutation in pyruvate dehydrogenase, mutation is pyruvate dehydrogenase phosphatase, or F0 subunit of ATP synthase. The F0 mutation is mitochondrially inherited, and may show this different distribution due to the way we inherit mitochondria

Question 35

which amino acid is found in the c ring of ATP synthase

Answer 35

Asp 61