Sandbox Reserved 1600: Difference between revisions

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[[Image: CH462 overall mechanism 1.png|300 px|left|thumb|Figure 4. Overall oxidation-reduction mechanism summary.]]
[[Image: CH462 overall mechanism 1.png|300 px|left|thumb|Figure 4. Overall oxidation-reduction mechanism summary.]]
As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, yielding the overall reaction of O₂ + 4H<sup>+</sup> + 4e<sup>-</sup> → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the oxygen entry site to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene>. This pathway is depicted in <font color='orange'><b>orange</b></font> in Figure 4.
As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, yielding the overall reaction of O₂ + 4H<sup>+</sup> + 4e<sup>-</sup> → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the oxygen entry site to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene>. This pathway is depicted in <font color='orange'><b>orange</b></font> in Figure 4.
As shown above, the electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> and gets oxidized giving 4e<sup>-</sup> to <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>. Once at <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> the 4e<sup>-</sup> will be shuttled directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> to be used in the reduction of O₂. The electron pathway is depicted in <font color='blue'><b>blue</b></font> in Figure 4.


The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene> utilize amino acids with charges that help shuttle the protons from the intracellular side of the protein to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>. in the active site. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene> passes through the <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA subunit</scene>, and is shown in <font color='purple'><b>purple</b></font> in Figure 4. The <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene> proceeds through the <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB subunit</scene>, and is shown in <font color='green'><b>green</b></font> in Figure 4.
The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene> utilize amino acids with charges that help shuttle the protons from the intracellular side of the protein to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>. in the active site. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene> passes through the <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA subunit</scene>, and is shown in <font color='purple'><b>purple</b></font> in Figure 4. The <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene> proceeds through the <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB subunit</scene>, and is shown in <font color='green'><b>green</b></font> in Figure 4.
As shown above, the electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> and gets oxidized giving 4e<sup>-</sup> to <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>. Once at <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> the 4e<sup>-</sup> will be shuttled directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> to be used in the reduction of O₂. The electron pathway is depicted in <font color='blue'><b>blue</b></font> in Figure 4.


When all of these elements of the reduction aggregate in the active site, the protons and electrons are shuttled to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene>, where the actual reduction occurs. The 2H₂O molecules are then expelled, as seen in <font color='red'><b>red</b></font> in Figure 4. The shuttling of these electrons and protons also helps assist with the electric chemical potential in the [https://en.wikipedia.org/wiki/Cell_membrane cellular membrane].
When all of these elements of the reduction aggregate in the active site, the protons and electrons are shuttled to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene>, where the actual reduction occurs. The 2H₂O molecules are then expelled, as seen in <font color='red'><b>red</b></font> in Figure 4. The shuttling of these electrons and protons also helps assist with the electric chemical potential in the [https://en.wikipedia.org/wiki/Cell_membrane cellular membrane].
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