Wikipedia:Featured article candidates/Oxidative phosphorylation

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The following is an archived discussion of a featured article nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article candidates. No further edits should be made to this page.

The article was promoted 21:28, 30 August 2007.

Oxidative phosphorylation‎[edit]

Self nomination. Article is currently a GA and is 65 kb in size. Tim Vickers 23:05, 24 August 2007 (UTC)[reply]

  • Support. Very impressive. One of the best technical scientific articles I've read here on Wikipedia. —Verrai 05:03, 25 August 2007 (UTC)[reply]
I'm the GA reviewer of this article but being non tech and having done it a month plus ago, I have regained my newbie POV. Para 3 of the lead needs modification.
  • - :The energy released as electrons flow through this ...electron transport chain is used to transport protons across the inner mitochondrial membrane. This generates a pH gradient and a electrical potential across this membrane. The energy is released as protons flow back across ...the membrane and down this gradient, through a large enzyme called ATP synthase.
Shouldnt release of energy be involved in only one of the flows? You have energy released first as electrons flow across then as protons flow across. Please clarify. AshLin 05:43, 26 August 2007 (UTC)[reply]
Reworded to try to make clearer that energy is transferred from one form to another as part of this process. Tim Vickers 14:41, 26 August 2007 (UTC)[reply]
  • Hi Tim, In this sentance,
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 about 26 ATP molecules.[4] In contrast glycolysis only produces 2 molecules of ATP. This ATP yield is the theoretical maximum value, in practice some protons leak across the membrane, lowering the yield of ATP.[5]
the ATP yield appears to point to that of glycolysis rather than P. Oxid. because of its juxtaposition. Could it be rewritten so that the glycolysis yield is mentioned first and high ATP yield of P. Oxid. is later, so that the statement This ATP yield is the theoretical... yield of ATP. now cannot be confused to mean something else. AshLin 16:29, 26 August 2007 (UTC)[reply]
Good point, rearranged. Tim Vickers 16:41, 26 August 2007 (UTC)[reply]
  • Support - Previous reviewer: please don't segment the page (see instructions). This is an excellent article at first look. Can you fix a few MOS things: some hyphens for page ranges remain in the bib. Minus signs (see MOS), not hyphens, in the table. Lead: "in eukaryotes" needs a matching comma. "An redox"? Tony 14:17, 26 August 2007 (UTC)[reply]
Hyphens fixed, "An redox" zapped, comma added, and a new type of dash added to the table. Tim Vickers 14:41, 26 August 2007 (UTC)[reply]
Ah, I never look at who the nominator is: no wonder it's excellent! Tony 13:30, 28 August 2007 (UTC)[reply]
  • Support, very nice article of a good size for the topic, with excellent referencing and clear, helpful images. --Cpt. Morgan (Reinoutr) 18:26, 27 August 2007 (UTC)[reply]
  • Support. Will serve as a good model for other articles. --Arcadian 20:46, 27 August 2007 (UTC)[reply]
  • Comment. An excellent article, generally as clear as an article on something so technical stands much chance of being, well referenced, up to date and well illustrated.
    • My main problem is with the history section, which seems rather terse, oddly placed at the end, and unlinked to the main text; for example, how does chemiosmotic theory link with the main text?
Argh, terrible omission. Added definition of chemiosmosis and link in first section and lead. Hopefully, that gives more context. It goes best at the end though, since it discusses the discovery of things that are defined and explained above.
    • The alternative reductases and oxidases section felt a little brief. Are these alternative reactions substitutive or additive? What proportion of oxidative phosphorylation do they handle, where used?
Expression levels are variable, as noted at end of section on what advantages they may confer. No single simple answer I'm afraid.
    • A glossary might help newbies to understand the terminology, especially the numerous different names for the complexes. Care should be taken to choose one main naming convention and stick with it, eg in complex III figure caption, a different name is used from the text.
Caption fixed, I get rather lost in all the alternative names myself. I'm worried that hyperlinks and a glossary would be redundant. As I've gone along I've created articles on anything needing defining, so if there are any terms remaining unlinked that need articles, I'll do these as well.
    • The article uses US spelling, and should therefore standardise on 'heme'. I've done a lot of this, but complex II figure needs changing.
Fixed. Damn colonials.
    • In section on complex II, I couldn't make sense of 'As this reaction releases less energy than the reduction of oxidation of NADH' -- seems to be either a typo or a bad phrasing.
Typo, fixed.
    • In section on complex III, could mention that ubisemiquinone (Q.-) is a free radical.
Added.
    • Organisation of complexes section -- 'Initially, the respiratory chain complexes were thought to diffuse freely and independently in the mitochondrial membrane' is little unclear. When does initially refer to? Can you provide a reference?
Reworded and ref added.
    • In the Prokaryotic section, it read a little oddly when the introduction stated that the section would concentrate on E. coli, but later introduced Nitrobacter. I'd suggest separating these into sub-sections. Can the repetitive sentences that book-end the table be amalgamated? The sentence that starts 'This flexibility is possible' reads as a little clumsy; could you just say 'use the same ubiquinone pool'?
Reworded as you suggest and added ref.
    • The headers in the table on E. coli need some definitions, eg redox pair, midpoint potential. Can you give some idea of how common usage of these different redox pairs are?
These terms are all linked, defining "Midpoint potential" in particular would need an entire section of its own, which I added to the article I linked to, rather than this one. I've added an explanation of what "midpoint potential" indicates in practice to the last sentence above the table.
    • ATP synthase section -- the aside on vacuolar H+ATPases was a little confusing; perhaps it could be moved? 'Rotation might be caused by changes in the ionization of amino acids in this ring' (paragraph 4) 'in this ring' needs clarifying. I'd suggest not referencing colours of the diagram in the text as the text should stand alone if the figure is removed or changed.
On the other hand, if the figures change, the text can be changed as well, I think the colours are particularly important to help readers follow the animation.
    • I wondered whether colour coding for oxidised and reduced in various of the figures might be helpful?
    • The minus in e- is rather small in the figures.
Either minus enlarged in complex I and IV, or figure enlarged in complex III.
    • Figure captions use dash to introduce text, which is rather confusing given the abundance of hyphens in the compound names. Perhaps change to a colon or full stop?
Switched to colons.
    • Can 1st diagram on ATP synthase be modified to show the path of the protons?

Espresso Addict 16:44, 29 August 2007 (UTC)[reply]

  • Support. This is FAC quality. I do have some comments and points were I (who never took Biochemistry) was confused.
    • Lead: I found the lead to be a little weak. I would like to see it introduce chemiosmosis (which is never mentioned in article text outside of the History section despite being used in subtitles and hatnotes). I would also like to see it clarify that "eletron transport chain" does not always mean the specific version used by mitochondria. I was confused by that point into thinking that the "Energy transfer by chemiosmosis" section was only talking of eukaryotes. Also the last two-sentance paragraph is very awkward.
Lead reworded to define chemiosmosis and electron transport chains.
    • Energy transfer by chemiosmosis: As I said above the term chemiosmosis is never mentioned in this section, which is confusing. I think it does give a nice overview, but when first reading it I couldn't understand that is was to be an overview and not the first step. I think it could be titled better.
Retitled "Overview of energy transfer by chemiosmosis".
    • Eukaryotic electron transport chains: This whole section is so good at times I forgot the article was meant to be about more than this. I understand the reasons, but it would be nice if the introductory paragraphs contained a disclaimer about why so much focus is given here.
Done, in second paragraph of this section's lead.
    • Electron transfer flavoprotein-Q oxidoreductase: This appears to me to be an "an alternative entry point to the electron transport chain." If I am correct, is there a reason it is not labeled as such like Complex II is. If I am wrong where does it fit in with the rest of the chain?
This is a quirk of the nomenclature for historical reasons that I'm not very clear about, I've reworded the first sentence of this and complex II to try to clarify their respective roles.
    • Prokaryotic electron transport chains: Can we have some illustrations here. Every illustration seems to involve a mitochondria. Also a short explanation of what midpoint potential would be useful, the link is not (unless of course you already understand it and expect the link to give you the detailed math).
Now defined in last sentence of text above table.
    • Reactive oxygen species: Molecular oxygen is . . . a strong oxidizing agent This sentence opens the section and seems a bit . . . circular. Can this be actually explained. "Oxidizing agent" to me means something that can not be shipped together with flammables. Also you mention the mitochondrial answer to this problem, what is the prokaryote answer?
Reworded to say "cells" rather than "mitochondria" as this is a universal problem in aerobic life.
    • Big picture: Maybe these thoughts have no place in this particular article, but I can't help wondering. This is obviously a key process, it seems to be the "raison d'être" of mitochondria. So I wonder is it? The sometimes-advantage of prokaryotes having a more flexible process is mentioned, but their also must be a disadvantage to that system. What advantage do mitochondria offer that explain their continued existence? I think it must have to do with this whole process. Does the evolution of this process and it varied forms deserve coverage in this article?--BirgitteSB 18:20, 29 August 2007 (UTC)[reply]
The "raison d'être" of mitochondria, as you put it, is increased surface area. That benefits oxidative phosphorylation, but it also benefits other metabolic functions that gain from having more membrane to work with. More membrane space allows more copies of the same enzymes, which allows those processes to occur in more places at once. At least, that's what high school biology taught me that I haven't since forgotten. —Verrai 05:50, 30 August 2007 (UTC)[reply]
  • Support. Some small cleanups here and there I'm fixing as I find them, but nothing show(i.e.,FA)-stopping. (forgot to mention: very nice, comprehensive article covering the material well for multiple target audiences). DMacks 22:22, 29 August 2007 (UTC)[reply]
Typography question: in the enzymes and substrates table, do enzyme names contain the formatting of the underlying chemical terms? That is, should the "D" in "D-amino acid dehydrogenase" be small-caps, given that it represents the D optical isomer configuration? Likewise, should the "N" in "Trimethylamine N-oxide reductase" be italicized per IUPAC rules for locants? DMacks 16:06, 30 August 2007 (UTC)[reply]
Yes, enzyme names should follow chemical nomenclature, fixed the ones you mentioned. Tim Vickers 16:37, 30 August 2007 (UTC)[reply]
The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article candidates. No further edits should be made to this page.
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