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Proton motive force
Force created from the pumping of protons across the mitochondrial inner membrane; couples the oxidation of fuels and the phosphorylation of ADP; consists of a chemical gradient (pH gradient) and a charge gradient (positive charge on the unequally distributed protons forming the chemical gradient)
When the electron-transfer potential of NADH and FADH2 is converted into phosphoryl-transfer potential of ATP; production of ATP through flow of electrons through the ETC
Coenzyme Q (CoQ)
Aka: ubiquinoneHydrophobic quinone that diffuses rapidly within the inner mitochondrial membrane, carrying electrons from NADH-Q oxidoreductase to Q-cytochrome c oxidoreductase. Can exist in three forms—oxidized ubiquinone, semiquinone, and reduced ubiquinol; contains a long tail with five-carbon isoprene units
Enormous with 46 chains; L-shaped with the vertical arm in the matrix and the horizontal arm in the membrane; takes electrons from NADH and transfers them to FMN to give the redued form FMNH2, which then transfers its electrons to Fe-S clusters; from FE-S, they go to coenzyme Q; this movement leads to the pumping of four electrons fromt eh matrix to the intermembrane space
Succinate-Q reductase complex
An integral membrane protein of the inner mitochondrial membrane with a bound FADH2; electrons from FADH2 get transferred to Fe-S centers and then to Q; no protons are pumped
Q-cytochrome c oxidoreductase
Catalyzes the transfer of electrons from QH2 to oxidized cytochrome c and pump protons out of the matrix; 2 protons get transferred; contains cyt b and cyt c1, which have a total of three hemes: heme bL and heme bH, and one heme within cytochrome c1; also contains an 2Fe-2S center (Rieske center)
An electron-transferring protein that contains a heme prosthetic group
The 2Fe-2S center of Q-cytochrome c oxidoreductase, which contains one iron ion tha tis coordinated by two histidine residues rather than two cysteine residues
Cytochrome c oxidase
Catalyzes the transfer of electrons from the reduced form of cytochrome c to molecular oxygen
Electron transport and ATP synthesis are coupled by a proton gradient acros the inner mitochondrial membrane; the transfer of electrons through the respiratory chain leads to the pumping of protons from the matrix to the cytoplasmic side of the inner mitochondrial membrane; the H+ concentration becomes lower in the matrix, and an electric field with the matrix side negative is generated. Protons then flow back intot he matrix to equalize the distribution. This flow back drives ATP synthesis
An antiporter protein that couples the transport of ATP out of the matrix and ADP into the matrix. It has three repeats of 100- amino acids, each of which appears has two transmembrane segments; the helices form a tepeelike structure with the nucleotide-bindig site lying in the center.
1) Explain the permeability of the two membranes of the mitochondrion.
a. The outer membrane is permeable because it contains many copies of porin, which is VDAC. The inner membrane is impermeable to nearly all ions and polar molecules.
1) Explain the charges of each side of the inner membrane.
a. The matrix side is negative; and, the cytoplasmic side is positive—0.14 V more positive
1) What is the relationship between mitochondria and bacteria?
a. Mitochondria have several similarities to bacteria and are said to have arose from endosymbiosis. Bacterial mitochondrial genomes of Reclinomas Americana contains all the protein-coding genes found in all sequenced mitochondrial genomes. Therefore, 2% of bacterial genes are found in all mitochondria.
1) How does one measure the redox potential?
a. They use an apparatus with a sample half-cell (contains an electrode immersed in a solution of 1M oxidant and 1M reductant) and a standard reference half-cell *contains an electrode immersed in a 1 M H+ solution in equilibrium with H2 gas at 1 atm of pressure. The electrodes are connected to a voltmeter, and an agar bridge allows ions to move from one half-cell to the other, establishing electrical continuity. Electrons flow from the sample to the standard reference half-cell; and the samlple cell electrode is negative. This was useful in understanding that a strong reducing agent donates electrons and has a negative reduction potential, whereas a strong oxidizing agent is ready to accept electrons and has a positive reduction potential.
1) What is the flow of electrons in the ETC? Briefly mention it.
a. The electrons go from NADH to NADH-Q oxidoreductase, Q-cytochrome c oxidoreductase, and cytochrome c oxidase. FADH2 is linked to succinate-Q reductase. Its electrons are transferred to Q-cytochrome oxidoreductase.
1) What is the problem when transferring electrons from CoQ to cytochrome c? What is the solution?
- a. CoQ is a two electron carrier; cyt C is a one electron carrier. The Q cycle is utilized.
- b. Two QH2 molecules bind to the complex consecutively, each giving up two electrons and two H+. These protns are released to the cytoplasmic side of the membrane.
- i. The first QH2 binds to the first Q binding site, and releases two electrons. One electron flows first to the Rieske 2Fe-2S cluster; then, to cytc1 and then to a cytochrome c. The second electron passes through two heme groups cytb to an oxidized Q in another Q binding site, reducing it to a semiquinone radical anion.
- ii. The second QH2 binds to the Q binding stie of Q-cytochrome c oxidoreductase and reacts similarly, transferring one electron to cytC and transferring the second to the semiquinone radical anion I the Q binding site, reducing it to QH2. This radical ion takes up two protons from the matrix side to form QH2.
- c. In sum, four protons are released on the cytoplasmic side, and two protons are removed from the matrix.
1) What is the structure of cytochrome c oxidas?
- a. It has 13 subunits, 3 of which are encoded by the mitochondrion’s own genome. It contains two hemes and three copper ions. One center, CuA/CuA, accepts electrons from reduced cyt C. The CuB is coordinated to three histidine residues, which accepts and donates electrons. Heme a andheme a3 are the two hemes.
- b. Electrons flow from cycCà CuA/CuAà heme aà heme a3à CuBà O2
- i. Heme a3 and CuB form the active center.
1) Explain the flow of electrons through Complex IV.
a. Electrons from two molecules of reduced cyt C flow down the electron transfer pathway, one stopping at CuB and the other at heme a3. Together, they bind an oxygen molecule, which forms a eroxide bridge between the two. Two more moelcules of cyt C bind and release electrons that travel tot eh active center. The addition of an electron as well as H+ to each oxygen atom reduces the two ion-oxygen groups to CuB2+--OH and Fe3+--OH. Reaction with two more H+ ions allows the release of two molecules of H2O and resets the enzyme
1) What are some hazards of molecular oxygen and its reduction? How is this prevented?
- a. It can undergo partial reduction with a single electron to form a superoxide anion or two electorns to yield peroxide.
- b. This is prevented by the catalyst, which does not release partly reduced intermediates. Also, superoxide dismutase scavenges superoxide radicals by catalyzing the conversion of two of tehse radicals into hydrogen peroxide and molecular oxygen. The hydrogen peroxide is then scavenged by catalase.
1) What is special about cytochrome c?
a. Its function has been conserved and it functions similarly, if not the same, in other organisms. The resemblance extends to the amino acid sequence. 21 of 104 residues have been invariant for more than 1.5 billion years of evolution.
1) What is the structure of ATP synthase?
- a. It is a large complex with an F0 and an F1 subunit, which has the catalytic activity of the synthase.
- b. The F1 subunit consists of five types of polypeptide chains (alpha3, beta3, gamma, delta, and epsilon
- i. The alpha and beta are arranged in a hexameric ring. Both bind nucleotides, but only beta participates in catalysis.
- ii. Below the alpha and beta subunits is a central stalk consisting of the gamma and epsilon proteins. The gamma subunit includes a long helical coiled coil that extends intot eh center of the alpha3beta3 hexamer, breaking its symmetry
- c. The F0 subunit is hydrophobic and spans the inner mitochondrial membrane. It contains the proton channel, which consists fo a ring comprising from 10 to 14 c subunits that are embedded in the membrane.
- i. A single a subunit binds to the outside the ring.
- d. The F1 and F0 subunits are connected by the central gamma-epsilon stalk and by the exterior column, consisiting of one a subunit, two b subunits, and the delta subunit
1) What is interesting about ATP production?
a. In the absence of a proton-motive force, ATP is still produced and hydrolyzed. However, it is not released; and so, the role of the proton motive force is to release the ATP from the synthase.
1) Explain the proton-motive force in terms of the beta subunit.
- a. The proton motive force causes the tree active sites to change functions as protons flow through the membrane-embedded component of the enzyme. The Beta subunit performs three steps: binding of ADP and Pi, ATP synthesis, and ATP release.
- b. Interactions with the gamma subunit make the three beta subunits unequivalent; and, at any given moment, one beta subunit will be in the L (loose), T (tight), or O (open).
- i. The loose conformation binds ADP and Pi. The tight binds ATP with great avidity, coverting bound ADP and Pi to ATP. The open conformation can bind or release adenine nucleotides.
1) Explain the rotation of the ATP synthase that results in ATP production.
- a. In the T state will be an ADP and Pi that is being converted to ATP. A 120 degree counterclockwise rotation transforms the T into the O conformation, releasing the ATP and replacing it with ADP and Pi. This O site then undergoes rotation to form an L site, which binds the substrates more tightly.
- b. Essentially, rotation causes conversion from T to O to L.
- i. T has the ATP that is tightly bound. To release it, it undergoes rotation to become an O form, which releases the bound ATP and replaces it with ADP and Pi. It then rotates to become L, binding more tightly to it.
1) How did they determine this structure?
- a. The Beta subunits were engineered to certain tags and allows the alpha3beta3 assembly to be immobilized on a glass surface. With a fluorescently labeled actin, they added ATP to view the effect. It caused the actin filament to rotate unidirectionally in a counterclockwise direction. The gamma subunit was rotating, driven by the hydrolysis of ATP.
- b. Each 120 rotation results in the formation of a single ATP molecule.
1) What does the proton motive force have to do with ATP synthesis?
- a. Essentially, the movement of protons through the half-channels from the high proton concentration to the cytoplasm to the low proton concentration of the matrix powers the rotation of the c ring. Its rotation is favored by the ability of the newly protonated aspartic acid residue to occupy the hydrophobic environment of the membrane. Thus, the c subunit with the newly protonated aspartic acid moves from contact with the cytoplasmic half-channel into the membrane, and the other c subunits move in unison. The a unit remains stationary as the c ring rotates. Each protn that enters the cytoplasmic half-channel of the a unit moves through the membrane by riding around on the rotating c ring to exit throught he matrix half-channel intot eh proton poor environment
What is the structure of the c subunit?
a. Te structure of the c subunit is two transmembrane alpha helices with an aspartic residue in the middle of one of the helices. In a proton rich environment, a proton enters the channel and binds to the aspartic acid, neutralizing its charge and allowing it to now enter the membrane with ease. This causes rotation of the c subunit, which rotates until the aspartate residue is in a proton-poor environment and releases the proton to the other side of the membrane.
What is the structure of the a subunit?
a. The stationary a subunit abuts the membrane-spanning ring formed by 10 to 14 c subunits. The a subunit has two hydrophilic half channels that don’t span the membrane. So, protons cannot move completely across the membrane. They go halfway. The a subunit is positioned such that each half-channel directly interacts with one c subunit.
1) How does the rotation fot e c ring lead to the synthesis of ATP?
- a. The c ring is tightly linked to the gamma and epsilon subnits. Thus, as the c ring turns, the gamma and epsilon subunits are turned inside the alpha3beta3 hexamer unit of F1. The rotation of the gamma subunit in turn promotes the synthesis of ATP through the binding-change mechanism. The exterior column formed by the two b chains and the delta subunit prevents the a3b3 hexamer from rotating.
- b. Each 360 degree rotation leads to the synthesis of three ATP mlecules.
1) How do we get rid of the problem of the extra NADH in the cytoplasm?
- a. NADH transfers its electrons to a glycerol 3-phosphate shuttle.
- i. The first step is the transfer of a pair of electrons from NADH to dihydroxyacetone phosphate to form glycerol 3-phosphate, catalyzed by glycerol 3-phosphate dehydrogenase. G3P is reoxidized to dihydroxyacetone phosphate on the outer surface of the inner mitochondrial membrane by a membrane-bound isozyme of glycerol 3 phosphate dehydrogenase. An electron pair from glycerol 3-phosphate is transferred to an FAD prosthetic group in this enzyme to form FADH2, which transfers its electrons to CoQ. This resuls in 1.5 ATP being formed.
1) How do we deal with ADP and ATP not being able to cross the membrane? What helps?
- a. We use ATP-ADP translocase, which enables the molecules to traverse the barrier. ADP enters the matrix only if ATP exits. The translocase is an antiporter.
- b. Because the matrix side is negative compared to the cytoplasmic side, and ATP has one more negative chrge than ADP, an actively respiring mitochondrion with a positive membrane potential favors ATP transport out of the matrix and ADP into the matrix.
1) How is oxidative phosphorylation controlled?
a. Electrons flow through the ETC if ADP is simultaneously phosphorylated to ATP. When ADP concentrations rise, the rate of oxidative phosphorylation increases to meet the ATP needs of the muscle. This is respiratory/ acceptor control. The amount of oxygen consumed increases markedly when ADP is added and then returns to its initial value whenadded ADP has been converted to ATP.
a. Some organisms can uncouple oxidative phosphorylation from ATP synthesis to generate heat, which occurs in hibernating animals. Rown adipose tissue is rich in mitochondria; and, the inner mitochondrial membrane contains a large amount of uncoupling protein (thermogenin), which forms a pathway for the flow of protons from the cytoplasm to the matrix. It generates heat by short-circuiting the mitochondrial proton battery