During cellular respiration in both mitochondria and aerobic prokaryotes, the Electron Transport Chain pumps H+ ions out of the matrix or cytoplasm to create a H+ concentration gradient. This forces the H+ ions back into the matrix or cytoplasm forcing ATP synthase into action.

I was wondering, however, why the H+ ions are pumped out of the matrix or cytoplasm, instead of into it. For aerobic prokaryotes, and the early mitochondria (which were prokaryotes living on their own) pumping the H+ ions out of the matrix or cytoplasm means pumping them into the outside world, a very uncontrolled environment. There is nothing to prevent the H+ ions from diffusing out, making the pumping completely inefficient, if not pointless. Wouldn't it make more sense to pump the H+ ions into the matrix or cytoplasm, where the H+ ions cannot diffuse, resulting in much higher efficiency?

  • $\begingroup$ But they aren't pumped out in the surroundings they are pumped between inner and outer membrane? Add some references about your statements $\endgroup$
    – KingBoomie
    Oct 27, 2016 at 15:15
  • $\begingroup$ @KingBoomie the OP is talking about when mitochondria were still free living bacteria $\endgroup$
    – John
    Apr 20, 2019 at 5:04

4 Answers 4


Mitochondria pumps out the H+ perhaps just because there is no disadvantage of it. Once they've evolved such a machinery with complex network; they weren't threatened to evolve any opposite-system.

Any opposite system too; would not plausibly disadvantageous; and really happens in case of chloroplast; another sort of cell-organelle.

  1. from Heldt

  2. whole

1: image from Plant Biochemistry, by Hans Walter Heldt, 3rd Edition.

2: picture including all chloroplast membranes.

But if any organelle used cytosol as the H+ pool; probably that would made cytosol acidic as wel disrupt metabolic processes on cytosol. (usually the cytosol have very mildly alkaline pH.)

Reference: Plant Biochemistry by Hans Walter Heldt, 3rd Edition, Academic Press.


Probably someone can dig up an answer that answers this question, but I'll just repeat it here shortly:

You'll get the same gradient if you pump protons out or in. You're not specifically decreasing the outside pH when you pump protons, you're mainly increasing the inside pH. As long as there is a gradient that can be used to achieve other things for the cell, it doesn't fundamentally matter if protons want to flow in or out the cell, as long as they want to flow across the membrane.

  • $\begingroup$ If the protons would flow into the cell the pH would rise here, this could be a problem for the protiens present here $\endgroup$
    – KingBoomie
    Oct 27, 2016 at 16:13
  • 1
    $\begingroup$ @RickBeeloo the reverse is also true, so your statement is not a valid argument. $\endgroup$
    – Liu Tianyi
    Nov 2, 2016 at 10:02
  • $\begingroup$ but the reverse is happening in the mitochondria.... and we all still live so what do you mean? @LiuTianyi? $\endgroup$
    – KingBoomie
    Nov 2, 2016 at 10:17
  • $\begingroup$ Because the proteins in the mitochondria have adapted for that reason? Evolution could very well occur such that proteins in the cell would be suited to work in low ph (ph decreases when protons flow into the cell, not rise) levels, which is the case for, eg lysosomes. You reject your hypothetical statement on the basis that it does not occur in the real world, exactly because it is hypothetical. That line of argument does not make sense. @RickBeeloo $\endgroup$
    – Liu Tianyi
    Nov 2, 2016 at 10:26
  • $\begingroup$ Coult you cite you reference on "Because the proteins in the mitochondria have adapted for that reason"? $\endgroup$
    – KingBoomie
    Nov 2, 2016 at 10:34

I don't know if this is a proper answer... and this answer is really late... but if I remember correctly, the mitochondria pump H+ out to better compartmentalize the activities of the TCA and other oxygen-dependent metabolic processes within the mitochondria. This compartmentalization helps further minimize the possibility of a process or reaction to take place before the cell is ready. It also helps keep proteins that have closely related functions (as in they function in the same or complementary pathway) spatially close to each other.

Interestingly, prokaryotes have been observed to localize cellular activities as well. It is hypothesized that this occurs for the same or a similar reason as described above for eukaryotic cells, albeit it is likely less effective. This is accomplished through intracellular scaffolding of some kind of cytoskeleton. My guess is that prokaryotic cells can utilize this cytoskeleton to localize their proteins, but can't use it to localize H+ due to a lack of "binding" region (speculative).

Also, majority of prokaryotic organisms will pump the H+ into their periplasm (inter membranous space, not the "chaotic" external environment) as Rick Beeloo mentioned. This periplasm is a smaller environment than the cytoplasm and is more densely filled with proteins (and possibly others molecules) as well. I think the periplasm is more viscous as well - whether a result of solvent composition, high protein or other molecule concentration, or something else entirely, I'm not sure (relatively unfounded statement). Regardless, all these factors actually make it more difficult H+ molecules to diffuse away in the periplasm than in the cytoplasm.

Another argument against why the H+ must be pumped to the side opposite of the proteins is that ATP inhibits the TCA and other oxygen dependent metabolic processes. The ATP synthase creates ATP on the side that the H+ ion passively flows to. This causes feedback inhibition is much more temporally sensitive as ATP synthase synthesizes ATP on the same side as the proteins involved in ATP synthesis. I think that ATP synthase cannot produce ATP on the same side as the H+ ions because their is no energy to make the ATP with until the H+ ion has flowed down the concentration gradient across the membrane; by this I mean the energy used to create ATP can only be harnessed on the low-energy side of membrane (I'm guessing on this last sentence...).

As a result of these reasons and maybe more, I'm led to believe these are some reasons that it is advantageous to pump H+ ions out of the cell/mitochondria interior than in. Although 2 years late and by no means a definitive answer, I hope this adds some new perspectives or ideas to the discussion on why this process occurs as it does.

  • 2
    $\begingroup$ Can you add sources to your answer to allow other users to background read on your material. +1 for the elaborate answer. $\endgroup$
    – AliceD
    Sep 10, 2018 at 9:14
  • $\begingroup$ Okay, I will work on that over time. It's been a while since I've gone through cell bio/biochemical engineering. It might take me a lot of time to pull stuff together, but I hope I can still find everything! $\endgroup$
    – SmallFish
    Sep 10, 2018 at 18:33
  • 1
    $\begingroup$ You don't have to add a zillion citations, but an image helps a lot and a few web-links here and there that back up your major claims and explain key terms would make a more satisfactory post and will give you your deserved #upvotes too. See the most upvoted answer above for example (not the best ever answer, but, well... better organized than yours for now :-). $\endgroup$
    – AliceD
    Sep 10, 2018 at 18:44

I cannot completely vouch for how accurately my answer does answer your question. I will however try to explain the best that I can.

Here is a picture: ATPase action
(source: els-cdn.com)

Firstly, in the electron transport chain the reactions that happen to metabolize the substrate are Redox reactions. As the complexes are oxidized by the release of electrons, protons are also released for counterbalancing. Statistically, the most effective route of ejection of the protons is through the H+ uniporters. There is a need for the protons to catalyze the reactions for synthesis of Hydrogen Sulfide which is required for stimulating the ATP synthase (you can check out the figure).

I am attaching some links which you can go through. http://www.sciencedirect.com/science/article/pii/S1043661816304820 (This paper gives a detail overview of the H2S mechanism.

You can also go through this wiki article. https://en.wikipedia.org/wiki/Electron_transport_chain

Hope I could clarify your question!



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