Zac89s

well, its a friggin protein, of course there's a polypeptide chain, especially with a protein as complex as cytochrome c. It can't be solved looking at one piece as you said. Thats why I spoke of the changes in conformation of the protein itself which is of coure wholistic. That is it concerns the polypeptide chains and the attached prphyrin ring rom the haem and of coure the ligand and orbital interactions with the complex ion structure of the porphyrin ring.

This is how I believe it works. Cytochrome C as a protein has quite a complex conformation (shape/structure). This conformation can be changed by any slight change in the electron configuration of the orbitals of the central ion (in this case iron) of the porphyrin ring. Before the iron is reduced its own orbitals do actually extend outside of the protien just a tiny bit because it has many ligands and its orbitals are actually hybridized and shared by all of these ligands. When the reductase reduces the iron (III) to iron (II) the entire hyrbridization of all of these orbitals changes dramatically. The electron is now a part of the new hyrbridization of the compound and the hybridiztion change causes a change in conformation of the phyrin ring structure which slightly effects the conformation of the cytochrome. Together the change in hybridization and the slight change in conformation manipulate the position of the hybridized orbital containing the new electron so that the orbital is protruding slghtly outside of the other part of the protein from the porphyrin ring. This electron stresses the conformation and is loosely held so when the electron passes through this protruding portion of the orbital the oxidase (or some oxidizer, the substrate perhaps) snatches it away with ease and then cytochrome c returns to its original conformation with the protrusion on the other side. You are correct in saying that a channel isn't exactly what's formed here. Its more like the electron hops on a complex orbital rollercoaster that rebuilds itself during the ride so that it ejects the electron out to the substrate. It cruses on through changing orbitals and these changing orbitals are being moved because the conformation of the molecule is changing. Does that help? I'm pretty darn sure this is how it works but I'm a junior in highschool, so I could be wrong. we studied this in ap bio and my orbital mumbo jumbo and physiology comes from my ap chem background. Tell me if this makes any since to you. (by the way this definitely not inorganic chemistry. far from it.) By the way sweet picture.

I know this isn't relevant to the subject but why is this website calling me a type of subatomic particle? the thing in parentheses "lepton" next to my name

What he said. But also, as chemistry is basicly the pursuit of stability, the compound with a more stable hybridization of orbitals and a higher degree of ionization will form. Phosporic acid has a larger acid dissociation constant than Phosphorous acid. You don't even have to look this value up. The oxygen to hydrogen ratio in phosphoric acid is 4/3 and the oxygen to hydrogen ration in phosphorous acid is 1 to 1 (3/3). This is of course cased on the general rule that the more oxygens you have realative to the number of hydrogens the stronger te acid. In the PCl5 + H20 reaction we know that the more stable compound will generally be thone that forms so we can safely assume that the product will be Phophic acid rather than phosphorous acid. But this is just the reason why this is so. The statement made by woelen is what you should probably focus on as it is quicker and less complicated. However, learning to think like this will greatly help you with reaction prediction.