Suggested problems from the end of chapter 20: 1 (standard reduction potential of the FAD half-reaction can be taken to be 0.02V), 3 ( this question deals with a half reaction, at pH=8 Ehalf reaction =0.153V), 4,5,6,7, 8 (CoQ is UQ in Tables 20.1, and 3.5; the calculation in part c is for 25°C) 9 (the calculation in part c is for 25°C) 10, 13 (calculation is for 25°C, ∆Goverall = ∆Gimport + ∆Gsynthesis), 20. Electron transport and oxidative phosphorylation in the mitochondrion The mitochondria contains: • pyruvate dehydrogenase. • the enzymes involved in fatty acid oxidation. • the citric acid cycle enzymes. • the redox proteins involved in electron transport and oxidative phosphorylation. Thus the mitochondria can be viewed as a cellular “power plant” for ATP production. A eukaryotic cell can have 1000’s of mitochondria. By volume, the mitochondria can take up to 20% of the cell. The presence of mitochondria in cells can be viewed as an example of cellular “symbiosis” by an early bacterium with the eukaryotic cell. 1 Mitochondrion organization mitos = thread, chondros = granule Outer membrane Inner membrane Cristae ( = crests) Matrix Freeze-fracture and freeze-etch electron micrographs of the mitochondrial membranes The inner membrane contains about twice as many particles as the outer membrane. Electron transport and oxidative phosphorylation proteins are found within the inner membrane. There is an asymmetric distribution of particles between the inner and outer faces of the membrane. The concentration of protein and DNA in the matrix is very high, probably on the order of 100 mg/ml. The viscosity is high, as expected. Mitochondrial DNA, RNA and ribosomes reside in the matrix. Porin proteins reside within the outer membrane. 2 The inner mitochondrion membrane does not contain an NADH transporter 1. A hydride and a proton are transferred to DHAP, forming 3- phosphoglycerol. 2. FAD is reduced to FADH2. 3. FADH2 is oxidized, and the electrons are transported to the reducing centers of the electron transport chain within the mitochondria inner membrane. ATP generated in the mitochondrion must be transported into the cytosol •The ADP-ATP translocator has 2 conformations. Both conformations have equal affinities to ADP and ATP. Would you predict that AMP, adenosine, or adenine could bind the transporter? •Ligand binding is required for conformational switches (unlike the glucose transporter). There is an overall charge difference across the membrane, where the inside of the membrane is kept more negative than the outside. How does this affect ATP transport? See redox worksheet 3 Electron transport sequence Four electron transport centers with (except for complex III) increasingly greater electron affinities (greater reduction potential) participate in electron transfer in the mitochondrial inner membrane. Complex I catalyzes oxidation of NADH by Coenzyme Q (CoQ, ubiquinone): NADH + CoQ (oxidized) ↔ NAD+ + CoQ (reduced) ∆E°’ = 0.360 V, ∆G°’ = -69.5 kJ/mol Complex III catalyzes oxidation of CoQ by cytochrome c: CoQ (reduced) + 2 cytochrome c (oxidized) ↔ CoQ (oxidized) + 2 cytochrome c (reduced) ∆E°’ = 0.190 V, ∆G°’ = -36.7 kJ/mol Complex IV catalyzes oxidation of cytochrome c by O2: 2 cytochrome c (reduced) + 0.5 O2 ↔ 2 cytochrome c (oxidized) + H2O ∆E°’ = 0.580 V, ∆G°’ = -112 kJ/mol Complex II catalyzes oxidation of FADH2 by cytochrome c (ATP is NOT produced in this step): FADH2 + CoQ (oxidized) ↔ FAD + CoQ (reduced) ∆E°’ = 0.085 V, ∆G°’ = -16.4 kJ/mol Electron transport sequence 4 Use of inhibitors to reveal the sequence of mitochondrial electron transport Mitochondrial membrane preparations were made by purifying mitochondria from enriched sources (bovine heart, insect flight muscle). The rate of NADH-dependent (or FADH2 - dependent) O2 consumption by this preparation can be measured. This measurement indicates the respiration rate. The effect of inhibitors on the O2consumption rate, then, can be measured. Rotenone and amytal block electron transport in complex I OCH3 H3CO O O CH2CH2CH(CH3)2 N CH2CH3 O O O N O O CH2 Rotenone C Amytal CH3 Use of inhibitors to reveal the sequence of mitochondrial electron transport Antimycin A inhibits complex III Cyanide inhibits complex IV O O H O C N CH3 -C N O H3C Cyanide O C CH2CH(CH3)2 OH O HN CHO (CH2)5CH3 O Antimycin A In some cases one can “rescue” the inhibited respiratory chain by introducing compounds that would supply electrons downstream of the inhibited complex. 5 Arrangement of the electron transport chain within the inner mitochondrial membrane These complexes are not arranged in higher-order structures. They seem to be able to diffuse freely within the membrane. Proton translocation as a consequence of electron transfer This is a hypothetical model for proton translocation across the mitochondrial inner membrane. Binding of protons and sunsequent reduction may induce a change in the protein transporter. The affinity for protons then is decreased, and a concomitant change in the overall structure of the protein makes proton release into the intermembrane space likely. Oxidation of the complex induces a switch to the starting conformation. 6 Electron transfer in complex I Complex I consists of 43 polypeptides and a total mass of 850 kDa. The groups that are active in electron transfer are 6 to 7 iron-sulfur clusters and one flavin mononucleotide. The free radical form of flavin mononulceotide (FMN) and the reduced (FMNH2) are stable. Thus FMN can transfer 2 electrons, whereas the iron-sulfur centers can transfer only one electron at a time. Because NADH can only transfer 2 electrons per reaction, FMN can serve as a conduit between the 2 - electron transfer reaction of NADH and the 1 - electron transfer reaction of the iron-sulfur centers. Electron transfer in complex I The iron-sulfur clusters can undergo a single electron transfer reaction. Overall the iron moieties can have either a +2 or a +3 charge. These groups cannot transfer more than one electron at a time. The exact sequence of reducing equivalent transfer is not known because the system “equilibrates” faster than it is possible to measure. 7 Electron transfer in complex I CoQ can accept and transfer 1 or 2 electrons because the semiquinone form is a stable free radical. It seems that only some of the time 2 electrons are transferred. CoQ has a hydrophobic tail that makes it soluble in the inner membrane. In contrast to FMN, CoQ is not tightly bound to the protein moiety of complex I. In mammalian cells the number of C5 isoprenoid units is 10 and is designated Q10CoQ. In plants and bacteria, this tail may only be a Q6 or Q8. Proton translocation as a consequence of electron transfer For each pair of electrons donated by NADH, 4 protons are pumped from the matrix across the mitochondrial inner membrane to the intermembrane space. The mechanism is not well understood, but almost certainly a conformational change within a trans-membrane protein is involved. Bacteriorhodopsin may have some structural similarities to the mitochondrial proton pump. When light is received by the retinal group, the protein conformation changes. There are two main conformations, and protons are driven across the membrane as a result of these conformational switches. In general, this system confirms that changes in one part of the protein can have profound consequences on the overall structure. 8 Complex II The reduction potential of complex II is not sufficient to drive ATP synthesis. Nevertheless, complex II serves to insert the electrons contributed by FADH2 into the electron transport chain. Complex II contains succinate dehydrogenase, with a covalently bound FAD group, three iron-sulfur clusters, and one cytochrome b560. Cytochromes are redox-active proteins containing heme groups. The electron transfer potential of the heme groups is very high and the protein moiety must be situated properly to prevent non-specific electron transfer. Complex III Complex III transfers electron from reduced CoQ to cytochrome c. Complex III contains two cytochrome b proteins, one cytochrome c, and one iron-sulfur center. Complex III’s function is to catalyze the transfer of 2 electrons from CoQH2 to two molecules of cytochrome c. This is done using the Q cycle (actually 2 cycles), which allows protons to be pumped across the mitochondrial inner membrane. The ISP is the iron-sulfur protein, and cytochrome c is reduced by the ISP. The other electron eventually is transferred to cytochrome bH. CoQ dissociates from site Q0 and rebinds to site Q1, where it accepts the electron from cytochrome bH. inter- membrane space matrix 9 Complex III In cycle 2, another CoQH2 repeats the steps of cycle 1. There is a free radical CoQ- bound at the Q1 site, and this free radical accepts the electron from cytochrome bH, as well as two protons from the mitochondrial matrix. Overall: two CoQH2 were consumed and one was re-generated. 2 cytochrome c1 were reduced. 4 protons were pumped across the membrane. This model depends on: 1. Stability of free-radical CoQ-. 2. The presence of 2 binding sites for CoQ, so-called Q0 and Q1. Structural evidence for 2 CoQ binding sites within Complex III •The crystal structure of Complex III is known, and different electron transport inhibitors were soaked into the crystal to identify their site of inhibition. - •Actimycin A has been shown to block electron flow from heme bH to CoQ or CoQ . This inhibitor binds near bH, and, most likely, at site Q1. •Myxothiazol has been shown to inhibit electron flow from CoQH2 to the ISP and to heme bL. This inhibitor binds near the ISP and heme bL. Most likely, this is site Q0. CH OCH3 OCH3 3 CH3 N N S CH3 H2N C CH3 S O Myxothiazol 10 Complex IV (cytochrome c oxidase) The overall oxidation of 4 cytochrome c molecules yields: 2+ + 3+ 4 cytochrome c (Fe ) + 4 H + O2 → 4 cytochrome c (Fe ) + 2 H2O The complex is a homodimer of 400 kDa.