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135 Cards in this Set

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What is the final stage of cellular respiration?
Oxidative phosphorylation
Where does oxidative phosphorylation take place?
In the mitocondria (the "energy-factory").
What does oxidative phosphorylation essentially do?
it couples the oxidation of NADH or FADH2 to the reduction of O2 (to H2O) and the formation of ATP (from ADP) in the process.
What would the oxidation of NADH result in?
NAD+
How many membranes does the mitochondria have?
1. Outer membrane

2. Inner membrane
Most of the components of the respiratory chain are in which membrane of the mitochondrion?
Most are in the inner membrane.
Remember glycolysis takes place where?
In the cytosol.
Give a 3 step outline of the respiratory process in the mitochondria?
1. Electrons flow through a chain of membrane-bound carriers.

2. This process results in the movement of protons (H+) from the matrix to the inter-membrane space

3. The proton gradient drives the synthesis of ATP.

(This all occurs in the inner membrane)
What leads up to oxidative phosphorylation in the mitochondria?
(Recall from previous chapters)

1. Electrons are transferred from a substrate to one of the universal electron acceptors. (NAD+, NADP+, FMN, or FAD)

2. NAD+ (or sometimes NADP+) accepts H- and releases a proton.

3. FMN or FAD can accept and transfer one or two electrons at a time
The respiratory chain is a series of what?
It is a series of sequentially acting electron carriers.
In addition to NAD and the flavoproteins name three electron carriers involved in the respiratory chain?
1. Hydrophobic quinone (ubiquinone [Q])

2. Cytochromes (contain iron)

3. Iron-sulfur proteins
Ubiquinone may also be known as what?
It may also be known as Coenzyme Q or Q.
Ubiquinone is ?, ?, and ?.
It is lipid soluble, small, and freely diffusible.
Ubiquinone is fully ?.
It is fully oxidized. It has no extra electrons and is in a low energy form.
What can ubiquinone accept?
It can accept one or two electrons. (only one at a time though)
What does ubiquinone also carry with every electron it accepts?
It will carry a proton with each electron.
What does ubiquinone become after accepting one electron?
It becomes a semiquinone radical (QH+). This is not seen much and it doesn't exist for long periods of time.
What does ubiquinone become after accepting two electrons?
It become ubiquinol (QH2). This is the fully reduced form. (2 extras e-s, and 2 hydrogen ions).
How many classes of cytochromes exist?
Three exist; a, b, and c.
All cytochrome classes have a what?
All have an iron-containing heme prosthetic group.
What is the distinguishing characteristic of the different cytochrome groups?
They all have different side R-groups.
In cytochromes what state is iron found in? What does this mean?
It can be in the Fe2+ or Fe3+ oxidation state. This means it can either accept or donate an electron. Fe3+ can accept to become Fe2+. Fe2+ could donate to become Fe3+.
Class a and b cytochromes (and some of c) are ? proteins; cytochrome c for the most part is ? and ?.
Class a and b cytochromes (and some of c) are INTEGRAL (INNER MEMBRANE) proteins; cytochrome c for the most part is SOLUBLE and MOBILE (OUTER SURFACE OF THE MEMBRANE).
MOST cytochromes are what?
Most are INTEGRAL (in the membrane). A and B are always stable in the membrane.
Cytochrome c is soluble. What does this mean?
This means it is hydrophilic and moves in a soluble environment. So it does escape from the membrane sometimes and moves out into the intermembrane space.
What part of an iron-sulfur protein can be oxidized or reduced?
The iron part.
What does iron associate with in an iron-sulfur protein? What does it participate in?
Fe associates with inorganic S, cysteine, or both. They all participate in one electron transfers.
The electron carriers of the respiratory chain are organized into what? What can these be separated into?
They are organized into SUPRAMOLECULAR COMPLEXES that can be separated into 4 INDIVIDUAL COMPLEXES & ATP SYNTHASE.
Complex I is a ? complex.
It is a multicomponent complex.
What docks and surrenders its electrons on complex I?
NADH docks and surrenders its electrons on complex I. So complex is the receptor of the electrons from NADH.
What does complex II accept?
FADH2 electrons from the CAC.
What is the common intermediate of complex I and II?
Q (ubiquinone) is the common intermediate.
FADH2 is ? not ?.
FADH2 is FIXED not MOBILE. So electrons go from succinate to FAD which becomes FADH2.
The electrons from complex I and II are all ultimately passed to what?
They are all ultimately passed to coenzyme Q to form ubiquinol (QH2).
Once the electrons are received by ubiquinone to form ubiquinol what can occur?
Ubiquinol can then move onto the next complex. While this occurs 4 hydrogen ions are moved from the intracellular to extracellular space.
In complex I NADH can be referred to as what?
"ubiquinone oxidoreductase"
In complex I the intermembrane space is the ? side.
It is the p side (positive side).
In complex I the matrix is the ? side.
It is the n side (negative side).
QH2 is easily ?.
It is easily diffusible.
How many peptides are involved in complex I?
It contains 42 polypeptides. We just need to remember that there are many.
Complex I involves an NADH reduction couple to a what?
It involves an NADH reduction coupled to 4 H+ movement.
What enzyme is involved in complex II?
Succinate dehydrogenase (from the CAC).
The electrons transferred in complex II come from where?
They come from the FADH2 of the CAC.
Where do the electrons in complex II end up?
They go to Q, which becomes QH2 (ubiquinol).
Unlike complex I, complex II has no movement of what?
Complex II has no movement of hydrogen ions.
QH2 is the ? form of coenzyme Q.
QH2 is the reduced form of coenzyme Q.
In the CAC what happens to succinate?
Succinate is oxidized to fumarate.
Once succinate is oxidized to fumarate, what is it coupled to?
This is coupled to the reduction of FAD to FADH2. The electrons are transferred from succinate to FAD. These electrons are then transferred from FADH2 to Q.
What goes in to complex I and what comes out?
FAD goes in and QH2 comes out.
What is the ultimate outcome of complex I and complex II?
Ubiquinol (QH2).
Where can ubiquinol diffuse to?
It can diffuse to complex III.
What two processes are coupled when QH2 diffuses to complex III from complex I or II?
1. The movement of electrons from QH2 to cytochrome (c1)

2. Transport of H+ across the membrane.
Complex III is aka what?
Cytochrome bc1
Where is complex III situated relative to the membrane?
It is partially in and partially out.
What occurs during the Q cycle of complex III?
Ultimately a molecule of QH2 will be oxidized back to ubiquinone. In the process 4 H+ ion are passed along the membrane, 2 at a time, from the matrix (N side) side to the intermembrane space (P side).
What is the net result of complex III?
1. 1 molecule of QH2 is oxidized

2. 2 molecules of cyt c1 are reduced (each with an electron waiting for the next step)

3. 4 H+ enter the inter-membrane space
What "docks" with complex III? What occurs once it is docked?
Cyt c "docks" with the complex (transiently), and an electron is transferred from cyt c1 to cyt c.
Once an electron has been transferred from cyt c1 to cyt c what can occur?
Cyt c (hydrophilic) can then diffuse to complex IV.
What is complex IV aka?
It is aka cytochrome oxidase.
What is the input into complex IV for 4e-? What is the input for 2e-?
The input for 4e- is 1 O2 and 4 Cyt c.

The input for 2e- is 1/2 O2 and 2 Cyt c.
How many subunits does complex IV have?
It is a large, 13 subunit, complex.
What does complex IV transfer electrons to?
It transfers electrons from cyt c to O2.
What does complex IV couple?
It couples the oxidation of cyt c to reduction of O2.
In complex IV, how many H+ ions move across the membrane per 4 cyt c?
4 H+ ions (and 4 e-s) move across the membrane per 4 cyt c. Pumped from matrix out.
What marks the end of electron transport through the complexes?
In complex IV 4 cyt c deposit an e- one at a time into the complex. The e- then reduce 1 O2 to 2 H2O. (This is the end of e- transport)
Respiratory chain has 4 complexes but electrons will always only pass through ? of them. What are the possible paths?
Electrons can only pass through three. They can either go from 1 to 3 to 4 OR 2 to 3 to 4.
What is the carrier between complex III and complex IV?
Cytochrome C
What allows the protons moved into the intermembrane space by the complexes to enter back into the matrix? What does this drive?
A "hole"/channel in the membrane allows them to move back. This drives the synthesis of ATP. This channel is part of ATP synthase. This process is known as chemiosmotic coupling.
How many processes are coupled in ATP formation? Name them. What are they coupled by?
Three.

1. Substrate oxidation (NADH, succinate [FADH2]).

2. O2 consumption/reduction

3. ATP synthesis/formation

(If you stop one, you stop all of them...if one goes they all go)

These are all coupled by e- and H+ translocation.
What is the evidence for the coupling of the following 3 processes :

1. Substrate Oxidation

2. O2 reduction

3. ATP synthesis
Evidence:

A. Inhibiting/blocking O2 reduction stops ATP formation


B. Inhibiting/blocking ATP formation stops O2 reduction.

C. With ATP formation blocked, O2 reduction can proceed if it is uncoupled from ATP formation.
What is the docking site for NADH in e- transport?
complex I
List 3 examples of how to block oxidation/reduction (e- transport) through the complexes.
1. Rotenone

2. Antimycin A

3. Cyanide
How does rotenone block oxidation/reduction (e- transport?
It is observed in insects. It blocks movement from complex I.
How does antimycin A block oxidation/reduction (e- transport)?
It blocks movement through complex III. It is an antibiotic that tends to effect bacterial respiratory synthesis. Electrons can't go further than cyt b. So everything to the left accumulates electrons and gets reduced. The right side gets oxidized. (SEE FIG. 19-6)
How does cyanide and carbon monoxide block oxidation/reduction (e- transport)?
Electrons can't go to oxygen and everything to the left accumulates in a reduced state. (see 19-6)
What are the inhibitors of e- to O2 also responsible for?
Inhibitors of e- to O2 (CN-, CO, etc.) also block atp synthesis. This illustrates the idea of coupling.
What is oligomycin?
An inhibitor of ATP synthase. So it also blokcs the passage of e- to O2. This is another illustration of coupling.
What does blocking ATP synthase also block?
It also blocks O2 consumption.
List 3 ways in which ATP synthesis can be UNCOUPLED from electron transport?
1. Disrupting the mitochondria

2. Adding molecules that can move H+ (eg. DNP, FCCP are hydrogen ion movers by active transport)

3. Adding ionophores (eg. valinomycin) which reduce the electrical component of the gradient. It is essentially a channel in the membrane that allows for passive transport.
What is valinomycin?
An uncoupler of ATP synthesis from electron transport. Basically, a channel in a membrane.
If ATP is uncoupled from e- transport, what is allowed to happen?
The e- can still move and still reduce O2 to H2O. There is just no ATP synthesis.
Where is ATP synthase located?
It is located in the inner mitochondrial membrane.
List the 2 distinct components of ATP synthase?
1. Fo

2. F1
Describe the Fo component of ATP synthase?
It is INTEGRAL to the membrane. It is an H+ pore. The "o" stands for oligomycin-sensitive, because this portion of ATP synthase is blocked by oligomycin.
Describe the F1 component of the ATP synthase?
It is peripheral to the membrane. It catalyzes ATP synthesis (if coupled to Fo) or ATP hydrolysis. The old name for this F1 ATPase.
On the surface of F1 of ATP synthase what is the ^G for ATP synthesis from ADP? How does this compare to the standard ^G for ATP? Explain why this is observed?
On the surface of F1, the ^G for ATP synthesis from ADP is close to 0. The standard ^G for ATP synthesis is +30.5 kj/mol.

This happens because once it is formed, the ATP is very tightly bound, so that it cannot be hydrolyzed to ADP + Pi. So there is a reduction of entropy and it is more likely to react.
F1 structure is inside the ? while Fo is in the ?.
F1 is inside toward the mitochondria and Fo is in the membrane.
When an H+ moves through the Fo complex what does it cause?
It essentially causes F1 to turn. This casue ATP to turn and increases ATP synthesis.
What indicates how many molecules of ATP are formed per atom (half molecule) of O2 consumed?
The P/O or P/2e- ratio (x).


xADP + xPi + 1/2O2 + H+ + NADH --> xATP + H2O + NAD+
In P/O or P/2e- ratio (x)...what did researchers assume for years?
They assumed that the ratio had to be an integer. Most experiments suggested a number a bit greater than 2 if the electrons came from NADH and a bit greater than 1 if succinate (FADH2) was their source.
What is the chemiosmotic model?
The idea that the formation of ATP is more like work being done by a water mill. The current best estimate is that 4H+ must pass back through the membrane (Fo) to form 1 ATP from ADP+Pi.
What is the actual valueS of the P/O ratio?
2.5 ATPs are formed per NADH.

1.5 ATPs are formed per succinate (FADH2).
Explain why the P/O ratio per NADH is 2.5 ATPs.
If 10 H+ are translocated (4 + 4 + 2) when the 2 e- from NADH pass through the respiratory chain, this means that 10/4 = 2.5 ATPs are formed per NADH.
Explain why the P/O ratio per succinate (FADH2) is 1.5 ATPs.
If 6 H+ (no e- from complex 1) are translocated (4 + 2) when the 2 e- from 1 succinate (1 FADH2) pass through the respiratory chain, this means that 6/4 = 1.5 ATPs are formed per succinate (FADH2).
List the three general situations that may effect oxidative phosphorylation.
It can occur

1. Normally

2. In the presence of an inhibitor

3. In the presence of an uncoupler.
What is antymycin A?
It is an example of an electron transfer inhibitor. It inhibits electron transfer from cyt b to cyt c1.
What is 2,4-Dinitrophenol?
It is an example of an electron transfer uncoupler.
List 4 inhibitors of ATP synthesis?
1. Antymycin A

2. CO, CN-

3. 2,4 dinitrophenol (DNP)

4. Oligomycin
How does antimycin A inhibit ATP synthesis?
It blocks Complex III.
How does CO, CN- inhibit ATP synthesis?
They block the reduction of O2 in the final step.
How does 2,4-dinitrophenol (DNP) inhibit ATP synthesis?
It is an uncoupler.
How does oligomycin inhibit ATP synthesis?
It directly inhibits ATP synthASE which leads to an inhibition of ATP synthesis.
The H+ gradient present during oxidative phosphorylation also drives what essential transport processes?
1. Transports ADP + Pi into the matrix

2. Transports ATP out of the matrix.
What are translocases essential for?
They are essential for the continuing formation of ATP.
Name two translocases that are essential for the continuing formation of ATP?
1. Adenine nucleotide translocase (ANT)

2. Phosphate translocase
What is an antiporter?
A translocase that translocates in two different directions. Into the matrix and out of the matrix.
What is a symporter?
A translocase that transports in one direction. (ie. only into the matrix)
Give an example of an antiporter? Explain.
Adenine nucleotide translocase (ANT). It transports ATP out of the matrix into the intermembrane space AND it transports ADP out of the intermembrane space and into the matrix. So ATP4- out of matrix and ADP3- into matrix.
What drives the adenine nucleotide translocase transporter (ANT)?
It is driven by the electrochemical gradient (so electrical charge). It moves ATP4- and ADP3-. So as it moves one in and one out of the matrix is is moving a net of 1 electron into the intermembrane space.
Does the intermembrane space or the matrix have excess H+?
The intermembrane space has excess H+ and the matrix has less H+.
Give an example of a symporter? Explain.
Phosphate translocase. It moves both H2PO4- and H- into the matrix. This partially reduces the gradient.
What drives the phosphate translocase?
The H+ gradient (excess in intermembrane space) drives the simultaneous transport of Pi and H+.
How do the translocases help form ATP?
The H2PO4- that is moved into the matrix by phosphate translocase can react with the ADP that is brought into the matrix by ANT to make new ATP, which can then be brought out of the matrix by ANT.
When the translocases are considered together what is the net charge difference between the intermembrane space and the matrix?
There is no net charge difference.
NADH cannot cross the ? ? or the mitochondrion but it can cross the ? ?.
NADH cannot cross the inner membrane but it can cross the outer membrane of the mitochondrion.
How do we solve the dilemma of NADH (the fact that it cannot cross the inner membrane)?
We can move an NADH reducing equivalent. ('virtual NADH').
List the two shuttles for moving an NADH reducing equivalent.
1. Malate-Aspartate Shuttle

2. Glycerol 3-phosphate Shuttle
What organs are associated with the malate-aspartate shuttle?
The Liver, Kidney, and Heart (LKH).
What organs are associated with the glycerol 3-phosphate shuttle?
The Skeletal muscle and the brain.
What does the malate-aspartate shuttle use to shuttle electrons into the interior of the mitochondria?
It uses malate.
Describe how the malate-aspartate shuttle works
?
In the intermembrane space NADH (usually from glycolysis) can't go any further, but the electrons can go to malate and malate CAN move across and deliver electrons inside of the matrix and you can reform oxaloacetate.
What link is the malate-aspartate shuttle also a part of?
It is also part of the UC-CAC link.
Explain how the glycerol 3-phosphate shuttle works?
It bypasses complex I. This means that only 6H+ (instead of 10) are translocated per NADH from the matrix to the intermembrane space. This explains why there are only 1.5 ATPs per NADH from glycolysis.

It essentially takes electrons from NADH to FADH2. When they go to FADH2 they are worth less.
The final ATP count from glycolysis could be either 3 or 5. Explain.
The variability is due to whether it occurs in LKH (5) or skeletal muscle (3). This is why the final ATP count from glucose could be either 30 or 32.
It is very important to match ATP formation to what?
To the cell's needs.
The rate of O2 consumption in oxidative phosphorylation is generally limited by what?
It is generally limited by ADP availability ('acceptor control').
In oxidative phosphorylation a change in ? can change the rate of O2 consumption by as much as 10-fold.
A change in [ADP] can change the rate of O2 consumption by as much as 10-fold.
What is the mass-action ratio for oxidative phosphorylation?
[ATP]/[ADP]...The changed rate keeps the ratio relatively constant.
What does a high mass-action ratio do to oxidative phosphorylation?
It slows it down.
What does a low mass-action ratio do for oxidative phosphorylation?
It speeds it up.
Is uncoupled oxidative phosphorylation always bad? Explain.
No, there are situations when it is not always bad. For instance, "brown fat" in the adipose tissue of newborn mammals is present in high concentration of mitochondria. The 'brown' color is due to cytochromes in the high mitochondria concentration. ATP is not formed but heat is generated and this is a good thing.
What is thermogenin?
It is an uncoupling protein synthesized in newborns for their first couple of weeks. It is essentially a restricted 'hole' in the membrane. It is not an unhealthy situation. The ATP is not formed but heat is generated. If this were to occur later in life it would be considered unhealthy.
What plays a key role in the overally regulation of ATP-producing pathways to help maintain a relatively constant [ATP], homeostasis?
ATP, ADP, and AMP.
What is the general trend of the presence of ATP on ATP-producing pathways. What is the general trend of ADP or AMP.
ATP slows them down. AMP or ADP speeds them up.
Explain the origin of the mitochondrion.
1. The 1st organisms capable of aerobic metabolism were prokaryotes

2. These invaded other organisms

3. The invaded organisms thus acquired the ability to metabolize aerobically.

This is an example of endosymbiosis.