In step 1, ubiquinol reduced by NaDh dehydrogenase docks to the cytochrome c reductase complex. Oxidation of the quinol produces two protons and two electrons. the protons are released into the cristae space. One electron passes via an iron-sulfur cluster to heme c1, and then to the soluble electron carrier protein cytochrome c on the membrane surface. the second electron passes via hemes bL and bh to a ubiquinone (red Q) bound at a separate site near the matrix side of the protein. Uptake of a proton from the matrix produces an ubisemiquinone radical (see Figure 14–17), which remains bound to this site (red Qh• in B).
In step 2, a second ubiquinol (blue Qh2) docks and releases two protons and two electrons, as described for step 1. One electron is passed to a second cytochrome c, whereas the other electron is accepted by the ubisemiquinone. the ubisemiquinone takes up a proton from the matrix and is released into the lipid bilayer as fully reduced ubiquinol (red Qh2).
On balance, the oxidation of one ubiquinol in the Q cycle pumps two protons through the membrane by a directional release and uptake of protons (see Figure 14–21), while releasing another two into the cristae space. In addition, in each of the two steps and (B), one electron is transferred to a cytochrome c carrier (Movie 14.4).
Figure 14–24 The structure of cytochrome c oxidase. the final complex in the mitochondrial electron-transfer chain consists of 13 different protein subunits, with a total mass of 204,000 daltons. (a) the entire dimeric complex is shown, positioned in the crista membrane. the highly conserved subunits I (green), II (purple), and III (blue) are encoded by the mitochondrial genome, and they form the functional core of the enzyme.
(B) the functional core of the complex. Electrons pass through this structure from cytochrome c via bound copper ions (blue spheres) and hemes (red) to an O2 molecule bound between heme a3 and a copper ion. the four protons needed to reduce O2 to water are taken up from the matrix; see also Figure 14–25. (C) this shows the symbol for cytochrome c oxidase used throughout this chapter. (pDB code: 2OCC.) 772 Chapter 14:  Energy Conversion: Mitochondria and Chloroplasts on to oxygen at a special bimetallic center, where it remains clamped between a heme-linked iron atom and a copper ion until it has picked up a total of four electrons. Only then are the two oxygen atoms of the oxygen molecule safely released as two molecules of water (Figure 14–25).
The cytochrome c oxidase reaction accounts for about 90% of the total oxygen uptake in most cells. This protein complex is therefore crucial for all aerobic life. Cyanide and azide are extremely toxic because they bind to the heme iron atoms in cytochrome c oxidase much more tightly than does oxygen, thereby greatly reducing ATP production.
the respiratory Chain Forms a Supercomplex in the Crista Membrane
By using cryoelectron microscopy to examine proteins that have been very gently isolated, it can be shown that the three protein complexes that form the respiratory chain assemble into an even larger supercomplex in the crista membrane. As illustrated in Figure 14–26, this structure is thought to help the mobile electron carriers ubiquinone (in the crista membrane) and cytochrome c (in the crista space) transfer electrons with high efficiency. The formation of the supercomplex depends on the presence of the mitochondrial lipid cardiolipin (see Figure 14–11), which presumably works like a hydrophobic glue that holds the components together.