Talk:Proton pump

message: Oh God. ATP usually does *****NOT***** power the translocation of protons in these systems. Usually it is electron equivalents provided originally by NADPH or FADH2. God, The articles I originally authored are being attacked by a body of ignorance. I wish people would know something about bioenergetics before they edit these articles. Dwmyers 15:52 Feb 9, 2003 (UTC)
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More points to be made. the F1FO particle is a reversible ATP synthase. It can create ATP, or use ATP to create a gradient. More so, in the mitochondrion, there are 5 membrane bound complexes. Complex V is another name for the F1FO particle. Complexes I through IV are largely proton pumps, and none of them can use ATP directly to create a proton gradient. The only one of these that can is the F1FO particle itself. It's reversible, you see. And while there may be exogenous proton pumps that use ATP, they're uncommon in organelles that create electrochemical gradients to make ATP. Think about it. The biochemical point is to reduce glucose to carbon dioxide and water, and make ATP in the process. If the proteins in the electron transport chain had to consume ATP to make the gradient that then is used to create ATP, it wouldn't be an energy producing process, it would be a futile cycle, consuming energy and producing heat. Dwmyers 16:11 Feb 9, 2003 (UTC)
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Another point: the person who redirected ATP synthase to proton pump did noone a favor, as there is a lot of worthwhile chemistry about the particle that could be discussed in a separate article that has nothing to do with the general physical properties of proton pumps. Dwmyers 16:24 Feb 9, 2003 (UTC)
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Many of the electron transport chain proteins you call pumps I'd talk about as "in effect pumps" but not as pumps in the common sense. I don't know if I'm idiosyncratic in this regard, but when I hear "proton pump," I think "proton ATPase." Perhaps related to the fact that many people call the Na/K ATPase a pump and multidrug resistance transporter a pump and lots of other ATPases pumps. Bacteriorhodopsin "pumps," I would say, but I wouldn't call it a pump. I'd like to find out what the normal usage is. If it agrees with my sense, I think the ATPase pump belongs at the top of the article and the transport proteins should follow as elaboration. 
168... 22:23 Feb 12, 2003 (UTC)
* I think the pumps a particular individual would consider important depends on circumstance. If I'm a family practitioner dealing with ulcers, I'd have one orientation. If I were an emergency room physician dealing with a case of cyanide poisoning, I might not give a hoot about my patient's ulcers, but I might want to give my patient a mitochondrial uncoupler instead. You might consider the possibility that people will come at this post from multiple angles, and be careful about writing points of view that are not yours into tiny corners, or worse, out of existence. If you wish to expand on the things you know, I'm all for it. Just please be aware that your point of view isn't the only one. Dwmyers 14:58 Feb 13, 2003 (UTC)
* And just to elaborate on the difference in orientation, you don't think of the mitochondrial proteins as proton pumps, but the guy most instrumental in proving that they were proton pumps won a Nobel Prize for doing so. And this may be a generational thing, in that science students under the age of 30 may just take mitochondrial biochemistry for granted, but Peter Mitchell managing to prove himself right is one of the more striking examples of a maverick bucking the 20th century scientific establishment. Dwmyers 15:29 Feb 13, 2003 (UTC)
* This might help in terms of organizing how this article goes. 168, what for you is a "normal" proton pump? Does it have any common identifiable characteristics? Are those characteristics quantifiable? I guess the point is, if you can break down the kinds of proton pumps into classes of pumps, and then we go ahead and enunciate these classes, giving examples (I'd say give names and  PDB structure and EC numbers, when possible) then we have an article that benefits everyone, regardless of orientation. Dwmyers 16:05 Feb 13, 2003 (UTC)
Funny, we're discussing usage again. I wonder what principles dictionaries use to hierarchize their definitions. My gut feeling, point one, is that if mechanics call a radiator a radiator and if taxi drivers call a tire a radiator, then in explaining to someone who's never heard the term radiator one should start with the mechanic's usage. That's why I wanted to know whether bioenergeticists ever used "chemiosmotic potential." Point two is that it's a totally different challenge to definition when mechanics call a radiator a radiator and paleontologists call a dorsal fin a radiator (i.e. if they did). I think these two usages are more deserving of equal treatment than in the first scenario, and I think it's more challenging in this case to say which should come first. A natural basis to choose might be the date each usage arose, putting the older first--but I don't know. But this pump thing is closer to the first category, I think. Anyway, if a thing is not foremost a pump, if it is not inseparable from pumping in the minds of the people who pick it up and move it from place to place, and notably if it has other names for what it is that don't include "pump," then I think it belongs below the other pumps.  I suppose I should elaborate on "inseparable": An Earth "globe" is in effect a ball and a baseball is a ball and ballness might be _said_ to be inseparable from both, but a globe is not foremost a ball: foremost it's a kind of map. Maybe that's not the best example but I imagine you'll see what I'm getting at. 
"Transmembrane ATPases" are rarely referred to as such. Typically they are called pumps and exchangers and transporters. Foremost is that they transport. I'd say foremost in electron transport proteins is that they simply swap things laterally between each other and vaguely "participate" in oxidative phosphorylation--although I'm not a bioenergeticist, and barely remember this stuff, so that my intuition isn't worth much and I may just be displaying my ignorance here. But I do doubt that these are foremost pumps to bioenergetists, if only because they weren't first known as pumps and because they are talked about together and need to be distinguished when they are.
168... 18:12 Feb 13, 2003 (UTC)
* 168, My PhD was with a man who did hard core spectroscopy (electron spin resonance, circular dichroism, magnetically induced circular dichroism, and optical spectroscopy) on proteins in the electron transport system (among the things Graham Palmer did was determine what kinds of iron-sulfur clusters actually were in the complexes of the electron transport system; his use of magnetically induced circular dichroism with cytochrome oxidase was innovative and helped determine the coordinating ligands to cytochrome a and cytochrome a3 within the complex, all of which was a big deal in the days before crystal structures existed), and the functional mechanism of cytochrome c oxidase was a major focus of the lab I got my PhD in (we were working simultaneously on Complex III as well). I personally did not do laboratory work with cytochrome c oxidase, I worked with cytochrome c peroxidase for the most part, and then later I did computational studies of cytochrome c oxidase steady state mechanisms. <BR><BR>So I wouldn't call myself a bioenergeticist, but I'm a lot more familiar with what they do because my PhD was all about these kinds of proteins. To me a bioenergeticist is a guy who makes mitochondrial preparations and then uses Clark electrodes to study high energy phosphate production to oxygen consumption ratios. Guys like Al Lehninger or Peter Mitchell were bioenergeticists. Incidentally, unless you have fully coupled mitochondrial preparations with active proton pumping, how can you do quantitative bioenergetics at all? <BR><BR>If you think about it, though, what the large complexes of the electron transport system do is pump protons. That is their whole purpose. Without them aerobic respiration breaks down and you have no ATP to run anything. If they get blocked, all respiration breaks down because the buildup of metabolic intermediates shuts down anaerobic glycolysis as well. It's fine and dandy that they're sexy metalloproteins, and allow scientists with exotic equipment free license to study them, but if they didn't pump protons, what's the point? Can you point to any other useful function of these complexes? <BR><BR>Back to characterization: What I would suggest is a functional breakdown of the various pumps. Is this pump devoted to ionic balance? Does this pump dump acid into the gastrointestinal tract? Does this pump co-transport ions? Is this pump involved in electron transport in mitochondria? What do the proton pumps you are familar with do? I'll be happy to add my two cents about the proton pumps I'm most familar with, which are the electron transport complexes. Dwmyers 19:29 Feb 13, 2003 (UTC)
I think we're talking past each other here. I'll think about the function issue. Meanwhile, your response makes me think you thought I was challenging your credentials or opinion, when actually I was only offering information to help you or others assess my own. But I'm glad now to have the opinion of someone so in-the-know and to sense that it coincides with my own. You do sound like you don't consider metalloproteins _foremost_ pumps, in my terms. Anyway, since I think of these as "electron transport proteins" and vaguely recall that the electrons at least in some instances move as hydronium, I wonder if you wouldn't consider them hydronium pumps more than proton pumps. 168... 21:45 Feb 13, 2003 (UTC)
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At least so far as guys like Peter Mitchell and Marten Wikstrom (Marten may be the smartest man no one knows that I've ever run into. I had the pleasure of meeting him a couple times) go, no, they think of these complexes as proton pumps. To get a feel for this, there is a nice bio of Peter Mitchell whose url I stuck up on the chemiosmotic hypothesis entry that is hugely worth reading. The electrons that travel the electron transport chain, AFAIK, usually enter through NADH and FADH2, and then are either housed in the redox centers of the complexes (or cytochrome c) or in the oxidized and reduced quinones. They never are transferred laterally as hydronium. <BR><BR>I certainly do not think of a generic metalloprotein as a proton pump per se, but just about everyone that deals with electron transport complexes calls them proton pumps. The mechanism of proton pumping in the electron transport complexes was/is the Holy Grail of mechanistic understanding of these complexes. The person who explains it at the molecular level is going to be a really big fish in the field. With luck, they could end up a Nobel candidate (though Boyer may have gotten the last of those). Dwmyers 22:18 Feb 13, 2003 (UTC)
As a layman I didn't understand the article at first.  Then I researched the concept and added clarification.  Specialists may be annoyed by the loosy goosy analogies but specialists already  know what a proton pump is.Cayte 21:09, 14 June 2006 (UTC)
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message: This article could still use more references, and definitely more clarity. I agree with the previous point that the picture is very misleading - time to remove it?
Esotera (talk) 17:19, 8 February 2011 (UTC)
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