Complex III of Electron Transport Chain: Difference between revisions
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<applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1' /> At the start of the cycle the Q<sub>P</sub> site of cytochrome b is empty and the Fe/S center of the Rieske protein is in the 'Int position'. (<scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1'>Reset initial scene.</scene>) With the binding of <scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_cycle/2'>ubiquinol</scene>, UQH<sub>2</sub>, to the Q<sub>P</sub> site (black arrow) of cytochrome b the Rieske protein moves to the 'cyto b position' by flexing at the hinge region and rotating the Fe/S head so that the His which is bound to the Fe/S also binds to <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle/1'>ubiquinol</scene> (<font color=red>stigmatellin</font> in this model)<ref name=1KYOmodified/>. Binding of the His to UQH<sub>2</sub> reduces its pK, and the UQH<sub>2</sub> loses a proton to become [http://en.wikipedia.org/wiki/Ubiquinol UQH<sup><big> -</big></sup>]. The position of Q<sub>P</sub> in the complex is such that the proton which is lost <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_arrow/1'>diffuses to the intermembrane space</scene>. After UQH<sub>2</sub> loses the proton and becomes UQH<sup> -</sup>, it passes an electron through the His to the Fe<sup>+3</sup> reducing it to Fe<sup>+2</sup>. With the loss of the electron the UQH<sup><big> -</big></sup> becomes UQH<big><sup> •</sup></big>, a [http://en.wikipedia.org/wiki/Ubiquinol semiquinone], which loses a proton and becomes UQ<sup><big> • -</big></sup>, the conjugate base of the semiquinone. The proton diffuses to the intermembrane space, as the first one did. (The fate of the semiquinone can be traced starting with the next paragraph.) After Fe in the Fe/S center is reduced by the UQH<sup><big> -</big></sup>, the Rieske head rotates & the Fe/S moves to cytochrome c1, <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_move_c1/1'>the "c1" position</scene>, so that the second His bound to Fe/S binds to the heme of cytochrome c1. When the His contacts the heme of cytochrome c1 an electron is rapidly passed from the Fe/S through the His to the Fe of the cytochrome c1 heme, and since it is now in the oxidized form, the Rieske protein returns to the "Int" position. The cytochrome c1 heme is now reduced, and when <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_2_cycle/1'>cytochrome c binds</scene> to it the electron is passed from the c1 heme to the c heme (black arrow). The cytochrome c then releases from the membrane and diffuses through the intermembrane space to Complex IV. | <applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1' /> At the start of the cycle the Q<sub>P</sub> site of cytochrome b is empty and the Fe/S center of the Rieske protein is in the 'Int position'. (<scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1'>Reset initial scene.</scene>) With the binding of <scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_cycle/2'>ubiquinol</scene>, UQH<sub>2</sub>, to the Q<sub>P</sub> site (black arrow) of cytochrome b the Rieske protein moves to the 'cyto b position' by flexing at the hinge region and rotating the Fe/S head so that the His which is bound to the Fe/S also binds to <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle/1'>ubiquinol</scene> (<font color=red>stigmatellin</font> in this model)<ref name=1KYOmodified/>. Binding of the His to UQH<sub>2</sub> reduces its pK, and the UQH<sub>2</sub> loses a proton to become [http://en.wikipedia.org/wiki/Ubiquinol UQH<sup><big> -</big></sup>]. The position of Q<sub>P</sub> in the complex is such that the proton which is lost <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_arrow/1'>diffuses to the intermembrane space</scene>. After UQH<sub>2</sub> loses the proton and becomes UQH<sup> -</sup>, it passes an electron through the His to the Fe<sup>+3</sup> reducing it to Fe<sup>+2</sup>. With the loss of the electron the UQH<sup><big> -</big></sup> becomes UQH<big><sup> •</sup></big>, a [http://en.wikipedia.org/wiki/Ubiquinol semiquinone], which loses a proton and becomes UQ<sup><big> • -</big></sup>, the conjugate base of the semiquinone. The proton diffuses to the intermembrane space, as the first one did. (The fate of the semiquinone can be traced starting with the next paragraph.) After Fe in the Fe/S center is reduced by the UQH<sup><big> -</big></sup>, the Rieske head rotates & the Fe/S moves to cytochrome c1, <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_move_c1/1'>the "c1" position</scene>, so that the second His bound to Fe/S binds to the heme of cytochrome c1. When the His contacts the heme of cytochrome c1 an electron is rapidly passed from the Fe/S through the His to the Fe of the cytochrome c1 heme, and since it is now in the oxidized form, the Rieske protein returns to the "Int" position. The cytochrome c1 heme is now reduced, and when <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_2_cycle/1'>cytochrome c binds</scene> to it the electron is passed from the c1 heme to the c heme (black arrow). The cytochrome c then releases from the membrane and diffuses through the intermembrane space to Complex IV. | ||
Returning to UQ<sup><big> • -</big></sup>, the conjugate base of the [http://en.wikipedia.org/wiki/Ubiquinol semiquinone], which was formed at Qp as described above and is shown <scene name='Complex_III_of_Electron_Transport_Chain/Focus_semiuq/1'>here</scene> as <font color=red>stigmatellin</font>, the UQ<sup><big> • -</big></sup> is oxidized to the full UQ when it <scene name='Complex_III_of_Electron_Transport_Chain/Electron_semi_to_hem_l/3'>passes an electron</scene> to heme b<sub>L</sub>. The <scene name='Complex_III_of_Electron_Transport_Chain/Electron_hem_l_to_hem_h/1'>electron</scene> is then passed from the Fe of heme b<sub>L</sub> to the Fe of Heme b<sub>H</sub>, and with Heme b<sub>H</sub> being next to UQ bound at the Q<sub>n</sub> site (Binding site is located on the <scene name='Complex_III_of_Electron_Transport_Chain/Hem_h_next_to_surface/3'> surface</scene> with a black arrow.), the <scene name='Complex_III_of_Electron_Transport_Chain/Electron_hem_h_to_uq/3'>electron</scene> is passed to UQ. With only one electron being passed in this series of reaction the UQ is reduced to UQ<sup><big> • -</big></sup>, and | Returning to UQ<sup><big> • -</big></sup>, the conjugate base of the [http://en.wikipedia.org/wiki/Ubiquinol semiquinone], which was formed at Qp as described above and is shown <scene name='Complex_III_of_Electron_Transport_Chain/Focus_semiuq/1'>here</scene> as <font color=red>stigmatellin</font>, the UQ<sup><big> • -</big></sup> is oxidized to the full UQ when it <scene name='Complex_III_of_Electron_Transport_Chain/Electron_semi_to_hem_l/3'>passes an electron</scene> to heme b<sub>L</sub>. The <scene name='Complex_III_of_Electron_Transport_Chain/Electron_hem_l_to_hem_h/1'>electron</scene> is then passed from the Fe of heme b<sub>L</sub> to the Fe of Heme b<sub>H</sub>, and with Heme b<sub>H</sub> being next to UQ bound at the Q<sub>n</sub> site (Binding site is located on the <scene name='Complex_III_of_Electron_Transport_Chain/Hem_h_next_to_surface/3'> surface</scene> with a black arrow.), the <scene name='Complex_III_of_Electron_Transport_Chain/Electron_hem_h_to_uq/3'>electron</scene> is passed to UQ. With only one electron being passed in this series of reaction, the UQ is reduced to UQ<sup><big> • -</big></sup>, and when it accepts a <scene name='Complex_III_of_Electron_Transport_Chain/Proton_matrix_in/1'>proton</scene> which comes from the matrix it becomes UQH<big><sup> •</sup></big>. The end products of the first half of the Q cycle are UQ at the Q<sub>p</sub> site, reduced cyt c and semi-ubiquinone at the Q<sub>n</sub> site. | ||
The second half of the Q cycle starts the same as the first half with the binding of UQH<sub>2</sub> at the Q<sub>p</sub> proceeding from there, it is the same as in the first half and is only different from the first half at the end of the cycle at the Q<sub>n</sub> site | The second half of the Q cycle starts the same as the first half with the binding of UQH<sub>2</sub> at the Q<sub>p</sub> proceeding from there, it is the same as in the first half and is only different from the first half in that at the end of the cycle at the Q<sub>n</sub> site the semi-ubiquinone is reduced to UQH<sub>2</sub> so that during a complete cycle at the Q<sub>n</sub> site UQ is reduced to UQH<sub>2</sub>. | ||
Q CYCLE | SUMMARY OF Q CYCLE REACTIONS:<br> | ||
2 ubiquinols oxidized to 2 ubiquinones<br> | 2 ubiquinols oxidized to 2 ubiquinones<br> | ||
2 cytochrome c's reduced<br> | 2 cytochrome c's reduced<br> | ||
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4 hydrogen ions moved from matrix to intermenbrane space<br> | 4 hydrogen ions moved from matrix to intermenbrane space<br> | ||
==View Interior of Q | ==View Interior of Q<sub>p</sub> and Q<sub>n</sub> Sites== | ||
<applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/4' />The applet on the right shows the surface of interior cavities of Complex III with the four substrate binding sites labeled.<ref name=1BGYmodified/> (<scene name='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/3'>Reset initial scene.</scene>) The PDB file used to generate the display has no cofactors binding at these sites so they are empty. After turning on the Slicer observe that | <applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/4' />The applet on the right shows the surface of interior cavities of Complex III with the four substrate binding sites labeled.<ref name=1BGYmodified/> (<scene name='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/3'>Reset initial scene.</scene>) The PDB file used to generate the display has no cofactors binding at these sites so they are empty. After turning on the Slicer observe that, | ||
<jmol> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
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</jmol> | </jmol> | ||
as the surface rotates its interior is exposed and that the empty binding sites are joined by connecting interior channels. These channels permit the UQ that is formed in Q<sub>p</sub> to diffuse to Q<sub>n</sub> where it is reduced to UQH<sub>2</sub>, and in turn the UQH<sub>2</sub> can diffuse to a Q<sub>p</sub> where it is oxidized to UQ. | as the surface rotates, its interior is exposed and that the empty binding sites are joined by connecting interior channels. These channels permit the UQ that is formed in Q<sub>p</sub> to diffuse to Q<sub>n</sub> where it is reduced to UQH<sub>2</sub>, and in turn the UQH<sub>2</sub> can diffuse to a Q<sub>p</sub> where it is oxidized to UQ. | ||
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