Structural Biochemistry/Oxidative Phosphorylation Cycle (Electron Transport Chain cycle)

Definition
Between mitochondrial matrix and intermembrane space, within the innermembrane, there are 5 complexes involved in the oxidative phosphorylation cycle, also known as electron transport chain cycle
 * 1) At complex I - NADH dehydrogenase: NADH is oxidized to NAD+: a process that releases electrons, which is transported by FMN (flavin mononucleotide to the Fe-S center (similar to heme group of hemoglobin) and reduce Q (ubiquinone) to QH2 (ubiquinol). Besides, 4 protons are pumped from matrix to intermembrane space.
 * 2) At complex II - Succinate dehydrogenase: succinate is oxidized to fumarate: a process that releases electrons to reduce FAD to FADH2, which carries the original electrons to reduce Q (ubiquinone) to QH2 (ubiquinol). Again protons are pumped into the intermembrane space
 * 3) At complex III - Ubiquinone Cytochrome c oxidoreductase: Q-cycle transfers electron from QH2 to cytochrome c (cyt c).
 * 4) At complex IV - cytochrome oxidase: cyt c transfer electrons to oxygen O2 (by the support of Cu-S center and hemes). This is where water is released and proves the role of oxygen in aerobic respiration. Again protons are pumped into the intermembrane space
 * 5) At complex V - ATP Synthase: with protons pumped into intermembrane space now return to the matrix, a rotary complex carries out the job of combining ADP and inorganic phosphate in mitochondria into ATP for cellular energy.



ATP Synthase
While the electron transport chain transports electrons and pumps H+ ions into the intermembrane space, the process of ATP synthesis does not occur until the ATP Synthase. The other part of the oxidative phosphorylation, after the electron transport chain, is the ATP synthase. ATP synthase is a transport protein that is consists of four parts, the Stator, the Rotor, the internal rod, and the Catalytic knobs.
 * 1) The H+ ions in the intermembrane space pumped by the electron transport chain will flow down their gradient first through the stator. The stator is anchored in the membrane.
 * 2) The H+ ion then binds onto the rotor, which is shaped somewhat like a waterwheel. This binding causes the rotor to change its shape and thus, makes it spin within the membrane.
 * 3) The spinning of the rotor causes the internal rod to spin, which leads the catalytic knob to spin. The spinning of the catalytic rod causes the catalytic sites in the rod to transform ADP and inorganic phosphate group into ATP in the mitochondrial matrix.

Overall, the ATP synthase functions like a waterwheel. When the concentration of H+ ions in the intermembrane space becomes higher than that of the matrix, the H+ ions will go down the ATP synthase and facilitate the rotor of the ATP synthase. This causes the other components of the ATP synthase to spin. As a result, ATP can be generated from the catalytic sites in the catalytic rod.

Chemiosmosis
Chemiosmosis is the movement of ions across a membrane down its gradient. It couples the electron transport chain and chemiosmosis in order to create ATP. In electron transport chain, the multiprotein structure pumps out H+ ions into the intermembrane space. As the H+ ions get pumped out, the concentration of H+ in the intermembrane space gets higher. As a result, H+ ions will start flowing down back to the chromosomes matrix through the ATP molecule. Through this movement, the cardiac rotor of the ATP synthase transforms the ADP into ATP.