Talk:Oxidative phosphorylation

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	Oxidative phosphorylation is a featured article; it (or a previous version of it) has been identified as one of the best articles produced by the Wikipedia community. Even so, if you can update or improve it, please do.
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Contents 1 Things to consider 2 First paragraph 3 Reactive Oxygen Species 4 Edits to intro paragraph and ETC 5 References 6 GAN Comments for Oxidative phosphorylation 6.1 Overall assessment 6.2 Specific points 6.2.1 Complex III 6.2.2 Complex IV 6.3 ATP synthase 6.4 Alternative oxidase 6.5 Inhibitors 6.6 Major staff duties error 6.7 Overall organisation 6.8 History 6.9 Concluding remarks 6.10 Second pass 7 This article is now a GA 8 An alternative lead 8.1 Introduction 9 Some comments 10 Complex III picture

[edit] Things to consider

Things to consider adding to this article:

1) Diagram or illustration of transmembrane and free electron carrier molecules (Complexes I, II, III, IV, and V).

  a) Coenzyme Q (Ubiquinone)
  b) cytochromes; heme prosthetics groups
  c) Iron-Sulfur proteins (including Rieske iron-sulfur proteins)

2) Discuss the proton gradient in terms of chemiosmotic theory.

  a) Charge Seperation
  b) pH differences between the intermembrane spaces and the matrix.

3) Breif review of redox reactions and reduction potential (or link to article discussing redox reactions).
4) Discussion on the importance of respiration to the introduction of oxygen as a final electron acceptor.
5) Discuss the Q Cycle
6) Census of electrons versus protons. (ie. two electrons release versus four protons released)
7) Discussion on the rotational catalysis mechanism of ATP synthase.

  a) Currently the article makes it sound as though protons can flow in either direction across the ATP synthase complex.
  b) Discuss various subunits to protein.
  c) Discuss the Binding-Change model.

--Mike Filbin 23:53, 8 December 2005 (UTC)

• Is the role of aerobic conditions (ie oxygen) mentioned in this article? It is not clear from the article why this process is unable to continue in anaerobic conditions. Perhaps the article would benefit from reference to Electron transport chain, using that content in the context of oxidative phosphorylation.

• Inconsistency among articles. This article states that the equivalent production of ATP molecules along the glycolysis -> citric acid cycle -> oxidative phosphorylation is 30 ATP, whereas the article on the Citric acid cycle cites 36 ATP.

-- CoeurDeLion

The intro bio text I am looking at reports 30 ATP. I don't have a reason to doubt it. Citric acid cycle may be incorrect. --DrNixon 04:39, 10 February 2006 (UTC)

The total number of ATPs is 38. 2(glycoysis) + 30(NADH at the Krebs circle) + 4(FADH2 at the Krebs circle) + 2(GTP at the Krebs circle) = 38 ATP per glucose molecule. However, sometimes it can be 36, depending of the transport of the NADH to the mitochondrion. --62.57.165.71 21:34, 8 November 2006 (UTC)

It should always be 36 max. If you use 38 there is an assumption that the glycolytic NADH can suddenly be inside the mitochondira. This is always wrong. The text books are wrong. And of course since ATP, phosphate and pyruvate all require energy (using the proton gradient) to get in and out of the mitochondria 36 is wrong too. But if we just consider a snap shot of making ATP in the mitochondria 36 is the most correct for the theorectical maximum. David D. (Talk) 22:08, 8 November 2006 (UTC)

[edit] First paragraph

The first paragraph contains this sentence: "This generates a pH gradient and a transmembrane electrical potential across the membrane." Would it be less confusing (and perhaps more correct) to call it a H⁺ gradient instead? -- Jasabella 12:48, 18 September 2006 (UTC)

I believe that the change to proton gradient (or H+ gradient) would be appropriate. All are equivalent terms, but in this field, proton/H+ seems more commonly used.--Antelan ^talk 21:43, 23 March 2007 (UTC)

[edit] Reactive Oxygen Species

It seems like the chemical equation for "hydrogen peroxide into molecular oxygen and water" should have hydrogen peroxide on the left hand side, not water. Aaronatwpi 18:32, 2 March 2007 (UTC)

[edit] Edits to intro paragraph and ETC

1. Changed 'synthesized' to 'replenished' since ATP isn't "synthesized" per se (despite the name of ATP Synthase) but replenished from less-phosphorylated forms. This is more a stylistic edit, so feel free to edit without worrying about my input.
2. Noted the aerobicity requirement.
3. Changed the stated number of ATP produced during ox-phos to 26 from 23. Reference: p. 491 Biochemistry, Fifth Edition - Berg, Tymoczko, Stryer 2002.
4. Added reference to electrochemical potential. Normalized some links on the page so that the first instance of a term is linked.

I hope these are helpful, and please let me know if I do something that causes displeasure. --Antelan ^talk 21:46, 23 March 2007 (UTC)

[edit] References

I've added a reference to back up a specific claim that is the frequent subject of discussion (ATP yield). I also added the <references /> tag to allow inline references to be displayed. I created a section, "Further Reading", for the Lehninger reference, because it no longer fit the formatting of the references section. Furthermore, it wasn't used as a typical reference because it was not cited to support any specific claim in this article. I'm sure there's a better way to deal with it, but I'll leave the discovery of that to someone else. --Antelan ^talk 21:55, 23 March 2007 (UTC)

[edit] GAN Comments for Oxidative phosphorylation

Hi Tim,

Rather than giving all remarks at one time as I usually do, I'll keep feeding in things as I come across them. Since they may be mostly clarifications for my understanding, this will be a better model to follow. The remarks are given in the following paragraphs :

[edit] Overall assessment

Firstly, I must say that this is one of the good articles on cell biology in Wikipedia that I have come across. It is well developed, with references, seems quite complete in its coverage(AshLin 17:44, 23 July 2007 (UTC)) and well-organised. This is how the article fares with respect to the Good article criteria:

1. Well Written - I have carried out some analysis of the article for language and structure. There is definitely an overall requirement to make the english simple without dumbing down the text.
2. Factually accurate & verifiable - Yes.
3. Broad in its coverage - Yes. This is with reference to my note regarding 'phosphorylation' part.AshLin 17:44, 23 July 2007 (UTC)
4. Neutral - Yes.
5. Stable - Yes.
6. Images have acceptable copyright status - Are you kidding! You truly are a contributor for mankind. I hope someone has given a barnstar for just this alone. You come into a very select class of creative wikipedians. AshLin 17:44, 23 July 2007 (UTC)

[edit] Specific points

• This has incorrect grammar so it doesnt make sense : Y Done AshLin 18:53, 23 July 2007 (UTC)

During oxidative phosphorylation, the energy released as electrons flow through the electron transport chain is used to transport protons across the inner mitochondrial membrane from the mitochondrial matrix into the intermembrane space. AshLin 10:30, 23 July 2007 (UTC)

Reworded to The energy released as electrons flow through this electron transport chain is used to transport protons from the mitochondrial matrix into the intermembrane space, across the inner mitochondrial membrane.

• Wikilink 'substrate' appropriately in line 3 (introduction).AshLin 10:30, 23 July 2007 (UTC) Y Done AshLin 18:53, 23 July 2007 (UTC)

Reworded to During this process, electrons are transferred from electron donors to electron acceptors such as oxygen, in an redox reaction.

• Did not understand the term 'oxidation FMNH2' (in the sentence below) since in the previous sentence it is said that FMN is reduced to FMNH. It may be a grammar error. Y Done AshLin 18:53, 23 July 2007 (UTC)

The electrons formed from the oxidation FMNH2 are transferred through a series of iron-sulfur clusters; the second kind of prosthetic group present in the complex.[6]

Reworded to The electrons are then released by the oxidation of FMNH₂ and are transferred through a series of iron-sulfur clusters;

AshLin 10:30, 23 July 2007 (UTC)

• In the image on overall equation the text on energy release after the equation proper should be put in brackets or unitalicised to distinguish it. It would make for better comprehension.AshLin 16:41, 23 July 2007 (UTC) Desireable but not being considered for GA. AshLin 18:53, 23 July 2007 (UTC)

[edit] Complex III

• Hey, the image shows UQ molecules, the text Q...this causes confusion. Please have the image amended to refer to Q molecules. I checked Coenzyme_Q10 and there is no mention of ubiquinone being abbreviated as UQ. In the caption text of the image on the article page, it says the abbreviations are discussed in the text, but no mention of UQ in text. Now the problem here is that UQ in the image appears to be a non-standard implementation while Q in the text appears to be standard. You need to resolve this issue one way or the other. AshLin 14:16, 23 July 2007 (UTC)

Y Done AshLin 10:11, 24 July 2007 (UTC)

Different texts use UQ or Q, I've checked the most authoritative and Q seems most common. I've standardised to this. Tim Vickers 17:09, 23 July 2007 (UTC)

Will you be amending the images also? AshLin 18:53, 23 July 2007 (UTC)

I have, you might have to reload the page? Tim Vickers 20:13, 23 July 2007 (UTC)

[edit] Complex IV

You have references to bovine, mammalian etc. I got the impression the mechanism was a eukayotic one. So why mention of these terms? Is the example given here an example of how it proceeds in cows? Are the mechanisms different for other taxa of eukaryotes? Please clarify the terms? AshLin 15:07, 23 July 2007 (UTC) Y Done AshLin 18:53, 23 July 2007 (UTC)

At the moment the eukaryotic system is the only one discussed. I need to add a section on the bacterial system as well as a section on archaeal oxidative phosphorylation. These appear to be similar in principle but differ in details such as number of subunits in enzymes, which complexes are present, and the carriers involved. In prokaryotes, as noted in the introduction, Ox Phos occurs in the outer membrane of the cell, rather than in mitochondria. Adding this material is the big step that I need to complete before I consider the article as giving a complete treatment of the subject. Adding material on bacteria and archaea will also be the step that takes this article past the level of normal biochemistry textbooks, which ignore these organisms entirely and only deal with the eukaryotic system. Unfortunately, this means I can't write this from textbook sources and I've been working my way through the primary literature and some reviews, so this is going to be a difficult task. Tim Vickers 17:25, 23 July 2007 (UTC)

Well, we cant do original research in WP, but we can sure as hell do excellent encyclopedic writing! All the best in this endeavour! AshLin 18:53, 23 July 2007 (UTC)

[edit] ATP synthase

The image[1] needs to be included here albeit at smaller thumb size. The ATPSynthase is as much or more important than the ETC complex molecules which are given in such detail above, and you have given images there. Dont worry - you are very far from the state where adding more images would be superfluous. AshLin 16:45, 23 July 2007 (UTC)Y Done AshLin 10:22, 24 July 2007 (UTC)

Yes, this section needs considerable expansion. I've added the image and will get to work on the text. Tim Vickers 17:31, 23 July 2007 (UTC)

Tell me when you are done.AshLin 18:55, 23 July 2007 (UTC)

Done. Tim Vickers 23:43, 23 July 2007 (UTC)

[edit] Alternative oxidase

• Wikilink 'ubiquinol'.AshLin 16:56, 23 July 2007 (UTC)

Could you not find a suitable wikilink? AshLin 10:28, 24 July 2007 (UTC)

• From the text I could not make out whether alternative oxidase is a protein enzyme or a complete mechanism. The opening sentance of the main article on it also suffers from the same defect. Y Done AshLin 10:28, 24 July 2007 (UTC)
• The wiki on alternative oxidase needs serious development. You do need to have a concise but complete section on how the oxidative phosphorylation cycle works out in plants and bacteria. As compared to the state of development of this article alternative oxidase seems really underdeveloped, but I think both articles need to be on parallel development paths.AshLin 17:44, 23 July 2007 (UTC) Y Done AshLin 10:28, 24 July 2007 (UTC)

I've rewritten this section and added a better lead to try to make the role of this enzyme clearer. Tim Vickers 22:08, 23 July 2007 (UTC)

[edit] Inhibitors

• Could some mention be made of the likely effect of such inhibition by each particular inhibitor on the organism. I cant make out if all are lethal or effect is partial in some cases. AshLin 17:12, 23 July 2007 (UTC)Y Done AshLin 10:29, 24 July 2007 (UTC)

Difficult to say, the difference between a drug and a poison is only the dose! :) Tim Vickers 17:36, 23 July 2007 (UTC)

Even a guarded sentance would help how an organism is affected. Are there any clinical studies? AshLin 19:05, 23 July 2007 (UTC)

Not for compounds like cyanide and DNP, I've rewritten this a bit and tried to give either functions (antibiotics and pesticides) or just state that the compounds are poisonous. Tim Vickers 22:14, 23 July 2007 (UTC)

[edit] Major staff duties error

Oh my, Tim! Your article is titled 'Oxidative phosphorylation' but yet the key mechanism of phosphorylation has not been elaborated upon! Major flaw here! This is what is called a major SD flaw in military parlance. We have to, have to get this right. FA peer review will tear us apart! AshLin 16:54, 23 July 2007 (UTC)Y Done AshLin 10:31, 24 July 2007 (UTC)

Do you think an image showing the enzymatic mechanism of the ATP synthase would be useful. Something like this? Tim Vickers 17:33, 23 July 2007 (UTC)

Definitely, but what I had in mind was a good explanation of the phosphorylation mechanism as it occurs in this particular reaction. I got the impression that the issue was treated in ATP_synthase#Binding change mechanism in a better way than here and could be included here but with better english. AshLin 19:01, 23 July 2007 (UTC)

Added with Gif illustration of the mechanism. Tim Vickers 23:43, 23 July 2007 (UTC)

[edit] Overall organisation

You have an excellent introduction - but there's a problem! As per WP FA Criterion 2(a) and MOS Guide to layout, the introduction to an article needs to be a well structured summary which gives an overview of the article, sets the stage for the section and contains no facts which do not occur elsewhere. So you need to rewrite one from scratch!

Now what about the present introduction. It could form a good opening section giving the overview and setting up the other headings, with a title such as 'mechanism' or something like that. The section could carry a complete, reasonably concise and good overview of the complete mechanism, the subsequent sections giving details of ETC etc.

The text below needs to be moved out of ETC section as it refers to the overall process of oxidative phosphorylation:

Oxidative phosphorylation produces a great deal of energy. For example, the oxidation of the 10 NADH and 2 succinate molecules created during the complete oxidation of one molecule of glucose to carbon dioxide and water, produces 26 of the 30 total ATP molecules that come from this process.[1] This ATP yield is the theoretical maximum value, in practice there is some proton leakage across the membrane, resulting in somewhat lower ATP yields.

It also appears that the Chemiosmosis section is a logical part of the proposed initial section dealing with the overall mechanism of oxidative phosphorylation. AshLin 16:26, 23 July 2007 (UTC)

FA criterion so not considering it for GA. Your choice to do it now, later or not at all.AshLin 10:43, 24 July 2007 (UTC)

[edit] History

Could 'cellular fermentation' and 'sugar-phosphate esters' be wikilinked. AshLin 19:11, 23 July 2007 (UTC)

Done. Tim Vickers 22:16, 23 July 2007 (UTC) Y Done AshLin 02:31, 24 July 2007 (UTC)

[edit] Concluding remarks

Well, Tim. I'm done. I'm only a run-of-the-mill editor who can project as to how things should be and judge if existing work meets upto that expectation. For more serious development towards FA you will need a very competent editor who thinks very differently from me to do a first-class peer review. ( I know I'm quite weak on MOS issues). After such a review, FA should be a piece of cake. Could I also request you to deal with these issues early so that I can pass it before 12 Aug 2007 to meet my five article requirement for my my first barnstar? AshLin 17:44, 23 July 2007 (UTC)

[edit] Second pass

OK, there's one more point that I noticed which I give below. Besides that, the only things pending are the wikilinking of 'ubiquinol' and the rewrite of introduction. Rewrite of introduction is not required as per GA, You can do it later as per your convenience, or not at all. Remember that FA review can peel off the skin off an article and look below. They can be merciless nitpickers. Better not to give them quickfail criteria. Let them nitpick on minor style issues rather than important criteria. So you literally have to take up each coloured glass sheet (important MOS guideline or FA criterion) and look at the article through it. Finish these two points and I'm done. The article reads much better now!

• In the rotating diagram of ATP Synthase, the caption says ADP and Pi in pink. What is this Pi? Where is it referred to in the text? What is the small blue dot that approaches each sector when it is light pink in colour? Are the colours maroon, orange and pink directly correlated to each state? Would you like to explicitly link them in the text?

Regards, AshLin 10:41, 24 July 2007 (UTC) Y Done AshLin 16:33, 24 July 2007 (UTC)

Pi is short for phosphate, I might introduce this abbreviation later, but I'll keep with spelling it out for now. I've made a new version of the animation without the blue dot (which was meant to be the chemical step, but seemed distracting). Looking at this more closely, the colours of the subunits don't seen to quite correlate with the binding and release of substrates, so while I think this animation is OK for giving the general idea, I think I'll have to make a more accurate version before I can discuss it directly as specific steps in the mechanism. Tim Vickers 15:25, 24 July 2007 (UTC)

Did the wikilinking of ubiquinol myself.AshLin 16:33, 24 July 2007 (UTC)

[edit] This article is now a GA

Congratulations, Tim, Oxidative phosphorylation is now a GA. AshLin 16:33, 24 July 2007 (UTC)

[edit] An alternative lead

Hi Tim,

Its great to see you developing the wiki even more. However, I still find the lead difficult to follow and this hampers my understanding of the issue. I've taken the liberty of rewording of the lead to read more simply for me and other scientifically challenged as follows :

<-introductory lead sentance regarding OP - which tells what it is->

Oxidative phosphorylation is a metabolic pathway that uses the energy released by the oxidation of molecules such as NADH and succinate to drive the production of adenosine triphosphate (ATP). While organisms may obtain energy in different ways, such as photosynthesis or <oxidation of ...>, they all carry out oxidative phosphorylation in order to utilise this energy for producing ATP, the principal source of energy for cells in any organism.

<-this sentance tells that OP is carried out at different locations and in different ways in the eukaryotes and prokaryotes->

In eukaryotes the reactions involved in oxidative phosphorylation are carried out by a series of protein complexes located in the mitochondrion that are called the electron transport chain. In prokaryotes, the electron transport chain is located in the cell's inner membrane. In eukaryotes there are usually four complexes in this chain, while in prokaryotes many different enzymes are present, which use a wide variety of electron donors and acceptors.

<-summary of how OP works->

In eukaryotes, this process is carried out by a series of protein complexes in the electron transport chain which results in the transfer of electrons from the electron donors NADH and succinate to electron acceptors such as oxygen, in a redox reaction. As electrons flow through this electron transport chain, the energy released is used to transport protons from the mitochondrial matrix into the intermembrane space, across the inner mitochondrial membrane. This generates a pH gradient and a electrical potential across the membrane. The protons flow back down this gradient from the intermembrane space into the mitochondrial matrix through a large enzyme called ATP synthase. This enzyme uses the energy released to generate ATP from adenosine diphosphate (ADP), in a phosphorylation reaction. Unusually, the ATP synthase reaction involves the proton flow driving the rotation of part of the ATP synthase - the enzyme is a rotary mechanical motor.

<-about reactive oxygen & inhibitors->

Although oxidative phosphorylation is a vital part of metabolism, it is also a source of reactive oxygen species such as free radicals, which damage cells and may contribute to ageing and disease. The enzymes that carry out this metabolic pathway are also the target of many drugs and poisons that inhibit their activities.

I request you to consider this as an alternative to the present lead. Regards, AshLin 10:14, 26 July 2007 (UTC)

[edit] Introduction

I think the introductory paragraph of the article, as it currently exists, is suitable for a biochemistry textbook, not an encyclopedia. The legend of the first figure on the page links to Citric acid cycle, but the figure itself uses the term "TCA cycle". As far as I can tell, the term "TCA cycle" is never used anywhere on the page except in the figure. Maybe the introduction could use an illustration of a simplified oxidative phosphorylation system. The greater complexity of eukaryotic oxidative phosphorylation could be covered later in the article. Key concepts: protons moving across a membrane, proton-driven ATP synthesis (phosphorylation), proton-pumping electron transport protein (PPETP) and the overall goal of transforming chemical energy from what is available in various "food molecules" into a standard form (ATP) that can be used by many cell processes. Maybe there could be a table/diagram showing available chemical energy in the "food" and "waste" molecules compared to ADP and ATP.....some visual representation of energy in the reactants and products. --JWSchmidt 06:21, 26 August 2007 (UTC)

Fixed the TCA cycle thing. This article is not intended to stand on its own, but as a more in-depth and specific discussion of the ideas that are introduced in the article on metabolism. However, even this article seems a bit more complex that what you are envisioning - it might be an idea to follow the lead of other wikiprojects and produce an Introduction to biochemistry article, so there isn't such a steep learning-curve. Tim Vickers 15:08, 26 August 2007 (UTC)

I've made a proposal for an Introduction to biochemistry article at the MCB wikiproject. Tim Vickers 22:40, 26 August 2007 (UTC)

[edit] Some comments

1. Electrochemical potential. We need to include somewhere an equation that shows the difference of chemical potentials of protons exactly as sum of electric potential (delta-Psi) and delta-pH. Unfortunately, this is not clear at all from WP article Nernst equation. An equation for delta mu-H as sum of delta-Psi and delta-pH could be included in article electrochemical gradient,... but "electrochemical gradient" is actually wrong or misleading term. The only thing that matters here is difference of electrochemical potentials in media from different sides of the membrane. Gradient is not the difference of potentials in and out the cell. Gradient shows how fast a property (say potential) changes in the given point of space. Biophys 04:53, 26 August 2007 (UTC)

The article electrochemical potential was merged into electrochemical gradient in November 2005, perhaps it is time to re-expand it or move content back across? Tim Vickers 05:02, 26 August 2007 (UTC)

I think article electrochemical potential should definitely be improved, but with a focus on electrochemistry rather than biology. Electrochemical gradient across membrane is a different topic; so we should have both articles. I hate terminology "Electrochemical gradient" although it can be found in many books. One would expect that "Electrochemical gradient" is defined by partial derivatives of electrochemical potential in point (x,y,z) as described in article gradient. But this is actually a differences of electrochemical potentials across the membrane, exactly like the difference of electric potentials on a capacitor. Any way, this is more a problem of other articles rather than this article.

2. Inroduction of this article. May be it worth mentioning that Oxidative phosphorylation is a more efficient and evolutionary advanced mechanism, which has been developed instead of the more ancient glycolysis, and compare the number of ATP molecules produced in glycolysis and oxidative phosphorylation.

"Although the many forms of life on Earth use a range of different nutrients, almost all carry out oxidative phosphorylation to produce ATP". This seems to be an overstatement with regard to many bacteria and plants.

Although the ultimate goal of oxidative phosphorylation is to produce ATP, it only produces delta muH (which is also produced in photosynthesis, by bacteiorhodopsin, and so on.). The existence of electrochemical potential difference as a "common energetic currency" in very different biological systems is the essence of chemiosmotic theory. May be this should be mentioned in second rather than third paragraph. (but some bacteria use sodium gradient rather than H+ gradient - see I just said "gradient" because it is easier to say) Biophys 15:07, 27 August 2007 (UTC)

I've expanded the lead a little, to discuss comparative energy yield, which is then covered in detail in the fourth paragraph of the "Energy transfer by chemiosmosis" section. The near-universality of Ox Phos is I suppose debatable, but the only organisms lacking some form of this pathway are strictly fermemtative microorganisms. Plants, animals and even chemolithotrophs all carry out oxidation-driven ATP synthesis - which is the definition of oxidative phosphorylation used in this article. Tim Vickers 16:46, 27 August 2007 (UTC)

[edit] Complex III picture

Two things seem off with the picture illustrating the reaction meachanism of complex III:

• QH2 is converted to Q in the upper part, but the picture doesn't show that Q leaves.
• 2H+ are shows to enter from the matrix at the same time. Wouln't one H+ enter at the first step and form the radical, and another H+ at the second?

Narayanese 11:45, 10 November 2007 (UTC)

There are several steps missing from this picture, I omitted most of the internal electron transfer steps and several of the binding and release steps, I tried to get a picture with more of them in, but it became astoundingly complex - for example fig 1 is the electron transfers with no structural information, while fig 2 is the structural information with less information about electron transfers. On the second point, both protons do enter in the final step, as you can see in fig 1, since the radical intermediate doesn't bind a proton. However, I'm open to people making an improved version of this figure - as long as we keep it simple. Tim Vickers 18:27, 10 November 2007 (UTC)

Hmm, I guess I should have read the text closer, it does say Q^.-. I changed the picture to clarify that it is Q^.- and not QH (which the coenzyme Q page mentions) that is in the enzyme, and added to the caption to clarify that QH2 doesn't mysteriously disappear but is converted to Q - it took me quite a while when I first looked at the figure to the net reaction, at the first glance it looked like the reaction was Q->QH2:). Narayanese 22:54, 11 November 2007 (UTC)