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I'm currently reviewing this concept in cellular respiration. The book which I'm using is Reece, Minorsky, Campbell's Biology and while it does a good job at explaining the process involved in the electron chain transport. I think it lacks of clearing out my doubts concerning initial protons.

Let me explain, the part where I'm stuck at is, where do originally the protons in the mitochondrial intermembrane space come from?. I understand that there is a proton gradient and the translocation of this protons in the proton pump is key during the electron shuttle process but, how did those initial protons come?. In other words, during the formation of the mitochondria in the cell, have they always been there? or are they part of some bigger molecule and that those protons are detached from them so that there is an initial gradient that triggers the process for the first time?. In other words, how does that initial spark or kick off begins?.

In most animations I've found, the explanations take for granted that the protons are freely moving in the intermembrane space such as here and also here but what do those videos lack is the explanation of how (as mentioned above) do those protons got there in the first place.

I'd like somebody could help me to clear out this doubt. I feel that as an addition to the answer, I'd like to know how does the mitochondria forms in the cell?. Since I believe there might be steps involved, I'd appreciate that the answer could explain those steps so I could easily understand, because as mentioned. I'm still confused on that part as well.

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    $\begingroup$ Well, proton gradient is set up by using protons of NADH2 and FADH2.Their proton is transported to the intermembrane space leaving behind NAD+ of FAD in matrix. Did I get your question correctly. You have asked about the source of protons I.e. which energy molecules provides them, haven't you?Also, the protons transported from NADH2 and FADH2 are more than what is coming out of F0-F1 particle so there is an excess of proton in intermembrane space. $\endgroup$
    – Abner Alfred Thompson
    Mar 26, 2019 at 3:04
  • $\begingroup$ @Abner Alfred Thompson Let me explain, I can understand that there might be protons due to water content in the cytosol from which during the formation of the organelles happens I believe in mitosis. But how does exactly there is an excess of protons so that a gradient is initially established in the intermembrane space?. I had believed that it was due to any terminal hydrogen from a peptide, aminoacid of protein contained in the intermembrane space and that when this gradient is held initially the process of electron chain can commence and go on in a cycle. $\endgroup$
    – Chris Steinbeck Bell
    Mar 27, 2019 at 20:09
  • $\begingroup$ @Abner Alfred Thompson As I mentioned every explanation takes for granted that initially there is a surplus of protons taking this intermembrane space as a pool of protons. But as I mentioned before, where do they come from?. Is it due water, any peptide, protein, aminoacid initially present in the intermembrane space?. You mentioned that the transported protons from NADH2 and FADH2 are more than what comes out from F0-F1 particle, but again this is when the cycle is happening. But what it was that initial surplus source?. This is my question?. Can you help me to clear out this doubt?. $\endgroup$
    – Chris Steinbeck Bell
    Mar 27, 2019 at 20:10
  • $\begingroup$ You can understand this if you consider the entire events of oxidative phosphorylation and electron transport chain.The amount of H+ from NADH2 and FADH2 going in is way more than what's coming out.This is what's the cause of proton gradient.You can see this video on YouTube to get your doubts clarified : youtu.be/wX7J2JtxM08 .Also,there is a minor error in this which is pinned in the comments section but it won't affect your understanding.Hope this helps $\endgroup$
    – Abner Alfred Thompson
    Mar 28, 2019 at 9:08
  • $\begingroup$ @Abner Alfred Thompson I understood the part that the amount of protons going in to be more than what is coming out but my question was more aimed at the ab-initio aspect. something more like Big Bang thing. I hope this makes clear my question. Probably this part isn't necessarily critical to understanding the process. But I felt that it is my general doubt. Come to think of it, if you put a sugar in a solution, you know there will be more oxigen due to its presence in the molecule, plus what it was in the water and probably from the air in the surroundings dissolved in that water. $\endgroup$
    – Chris Steinbeck Bell
    Mar 28, 2019 at 23:06

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