MMT: oxidative phosphorylation Flashcards
Define oxidative phosphorylation.
Process in which ATP is formed from the transfer of electrons from NADH and FADH2 to O2 by a series of electron carriers
Identify the initial electron donors and terminal electron acceptor of the electron transport chain
Initial: NAD+ and FAD+
Terminal: oxygen
complex I of the ETC: what it takes its electrons from, how many protons it pumps, and how it works
- 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
complex II of the ETC: what it takes its electrons from, how many protons it pumps, and how it works
- FADH2
- 0 (it does not span the membrane!)
- donates electrons from FADH2 to CoQ. also forms fumarate from succinate.
complex III of the ETC: what it takes its electrons from, how many protons it pumps, and how it works
- CoQH2
- 4 protons
- it donates electrons from CoQH2 to cytochrome c.
describe the electron transfer from CoQH2 to cytochrome c
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
Describe complex IV of the ETC: what it takes its electrons from, how many protons it pumps, and how it works
- cytochrome c
- 2 protons
- donates electrons to oxygen to form water
Relate myocardial infarction induced cardiac cell death to oxidative phosphorylation.
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.
How does the structure of the mitochondria allow for the proton gradient to form?
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.
Identify the energetic link between oxidation in the electron transport chain and ATP
generation
A proton motive force
What are E’ and G’
E’: electron transfer potential, also known as the reduction potential or redox potential
G’: phosphoryl transfer potential
As we move through the ETC, we move from ___ to ___ reduction potential, and ___ to ___ free energy
Negative to positive; higher to lower
We gain energy as we go!
Compare and contrast Coenzyme Q and Cytochrome C
- 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.
explain the transfer of electrons through Complex IV: cytochrome c oxidase.
-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
Describe the mechanism of cyanide toxicity.
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.
List the types of electron carriers in the electron transport chain.
FADH2, NADH, FMN, CoQ, cytochrome C, FeS, hemes, copper ions
Calculate the number of protons pumped into the intermembrane space per acetyl entering the TCA cycle.
36!
3 NADH in TCA, 1 FADH2
10 protons per 2e NADH, 6 protons per 2e FADH2
Describe the mechanism by which the ETC generates reactive oxygen species
how does the body clear ROS
Superoxide dismutase can neutralize superoxide to form oxygen and hydrogen peroxide. Glutathione peroxidase can convert the hydrogen peroxide into water.
Identify each subunit of ATP synthase and their functions.
F0: proton channel; motor portion
F1: ATPase; stator portion
Exterior column (a, b2, delta) and Gamma-epsilon stalk connect F0 and F1
describe subunit a in ATP synthase
has two proton half channels that do not span the membrane; one channel opens to the cytosol, and one opens to the intermembrane space
describe subunit c in ATP synthase
: 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
describe the gamma-epsilon stalk in ATP synthase
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
Describe the open, loose, and tight phases of the beta subunits.
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
describe the G3P shuttle and its ATP yield
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
describe malate-aspartate shuttle and its ATP yield
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
the malate-aspartate shuttle is used in which cell types?
liver and heart
Describe ATP-ADP translocase and the energy cost of translocating ATP out of the mitochondrial matrix.
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.
how much ATP do we make when oxidizing glucose?
30-32, depending on which NADH shuttle system is active.
Identify mechanisms that regulate activity of the TCA cycle and oxidative phosphorylation
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
Describe biological and chemical mechanisms to uncouple the ETC from ATP synthase and explain the effects of uncoupling
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
Describe DNP’s impact on oxidative phosphorylation
DNP: a chemical uncoupler; if we have too much of it, we can reach an internal body temperature that is too high
How do CN-, N3, and CO impact oxidative phosphorylation
CN- N3 and CO react with compound IV, preventing the reduction of oxygen and the functioning of the ETC
Explain how inheritance of mutations in oxidative phosphorylation enzymes can vary depending on nuclear or mitochondrial encoding of the gene
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
Describe leighs syndrome
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
which amino acid is found in the c ring of ATP synthase
Asp 61
