Submitted by Infinite-Flow7945 t3_yx71bm in askscience
I know the mechanism of oxidative phosphorylation but I still do not get where do protons come from. They are going between matrix and IMS but how did they end up in matrix? Are they from some cell reactions or something else?
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Like nearly everything in biology, water exists in a dynamic equilibrium. Constantly shifting between H2O and H+ & OH-. The mitochondrial matrix is an aqueous environment (IE watery) so there is a constant supply of H+ and OH-. The electron transport chain scoops these protons and sends them across the inner mitochondrial membrane to create the proton gradient.
Additional protons are also provided by the oxidation of NADH to NAD+ & H+.
Almost, but not quite. The proton gradient refers to the difference in concentration of H+ on each side of the membrane. It's ostensibly what allows for the ETC to transport those protons in the first place, by following their own gradient and harnessing some energy in the process to make ATP.
I think you may have the first 4 complexes of the ETC and ATP synthase mixed up (though ATP synthase is sometimes consider complex V). The ETC pumps protons** across the inner mitochondrial membrane from the matrix to the intermembrane space to create the proton gradient. The protons then flow down their gradient across the membrane (IMS to matrix) via ATP synthase which generates ATP in the process.
The first diagram from the Khan academy article about oxphos does a great job at showing how the protons flow and how each complex contributes. https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-respiration-ap/a/oxidative-phosphorylation-etc
EDIT: electrons -> protons
> The ETC pumps electrons across the inner mitochondrial membrane from the matrix to the intermembrane space to create the proton gradient.
This absolutely does not happen.
Electrons are transported from complex to complex arranged as a chain hence why it is called the ElectronTransport Chain. And indeed this is how it is illustrated in both the 1st two diagrams of your link, where the "path" of the electron(s) is between complexes within the membrane and not in to the intermembrane space. You'll note in the 2nd diagram that at the end the "free" electrons are passed from complex IV to Oxygen in the matrix because oxygen is the final acceptor of electrons in the ETC. This is where the electrons end up, not in the intermembrane space. Free electrons are not accumulated in the intermembrane space (I'm not even sure physics allows free electrons to accumulate outside of some exceptionally rarefied circumstances)
The oxidisation of free FADH and NADH provides high energy electrons at the start of the chain, as the electrons transition between complexes they lose energy and this free energy is "used" to move the H+ ions in "solution" within the matrix to the intermembrane space. That is, the ETC complexes pump protons across the inner mitochondrial member to the intermembrane space. This establishes a concentration gradient as H+ ions are highly concentrated in the intermembrane space.
Also the whole system wouldn't work if the intermembrane space was filled with free electrons while complexes I - IV were "pumping" H+ ions there. If that were the case the H+ ions would immediately neutralise and become hydrogen atoms. ATP Synthase works because it can make use of the concentration gradient between "free" H+ ions in the intermembrane space and the lack of "free" H+ ion in the mitochondrial matrix.
You're absolutely correct. I mistyped electrons instead of protons. I've edited my original comment!
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Ahhh, I see the problem. I had incorrectly assumed you were talking about ATP synthase, based on my very flimsy and rushed reading of your comment. Incidentally, I am of the camp that considers ATP synthase part of the ETC, but my critique of you was still based on my misperception of what you were trying to say.
Thanks for correcting my correction, science is hard and biology is confusing!
People are confusing electrons with protons here. The redox reaction between different complexes, which involves exchange of electron, generates energy to move protons in complex 1,2 and 4. That’s where the gradients are generated. As for where the protons are from, your bodies are full of water. Water is ionizable
To add to that, water undergoes constant autoprotolysis. You just have to move the protons, before they can recombine with sth else.
While it is that simple, accepting this statement as true will take years of study in chemistry/organic chemistry.
But yes. u/infinite-flow7945 the answer is water.
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From what I remember the H+ used in chemical/biochemical reactions is shorthand for a "solvated" proton. Nekkid protons don't really occur under normal conditions. For example, take two H20 molecules. One can donate a proton to the other. The first water then becomes an OH- ion and the latter a H3O+ "solvated" species, i.e. water with an extra proton. This species can then donate a free proton into reactions where you see an H+. See
https://escholarship.org/uc/item/9m11233k#page-1
for an in depth discussion.
Edit: wrong charge.
What happens to the hydroxide?
There are always OH- species in water from the self-ionization of water, i.e. 2H20 <--> H30+ and OH-. This adds a bit more. And this isn't a one way reaction. The reactions that require a proton are balanced out by the reactions that donate protons. Maybe not instant to instant but over the long term.
And you need something the balance out the charges. For example,
NADPH and H+ and acceptor <--> NADP+ and reduced acceptor
You need the OH- to charge balance the NADP+ and the H+. So maybe think
NADPH and H+ (and OH-) and acceptor <-->
NADP+ (and OH-) and reduced acceptor
You can't have loose charges running around all over the place-- that would be mayhem.
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Just like the electrons getting passed down the chain, they come from energy source molecules, like fats and sugars, and wind up getting passed on to oxygen at the end of the transport chain to form water.
The protons get passed through different chemical intermediates after they’ve been taken into the cell, but the overall equation C6H12O6 + 6O2 -> 6CO2 + 6H2O gives the idea. The H’s leave sugars and wind up in water.
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Perhaps a psych researcher can tell me why I'm doing this, even though I know better.
Mitochondrial protons come from mitochondrial quarks. I guess you need mitochondrial gluons as well.
That's just what they're made of. If you want to create one, leave a mitochondrial neutron in a sterile petri dish for about 15 minutes.
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UnhappyReporter3268 t1_iwnjjwf wrote
From what I understand, they come from the NADH and FADH2. They give electrons to the chain and get tranformed into NAD+ and FAD respectively. The hydrogen atoms get released and stay in the matrix before getting pumped out.