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Wikipedia:Featured article candidates/Enzyme/Archive 1

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Enzyme edit

My first self-nom. Please don't be too harsh, guys~ :-D By the way, this biological article is pretty informative. The diagrams were well drawn to give a much clearer picture of the mechanism of enzymes. -- Jerry Crimson Mann 15:12, 31 July 2005 (UTC)[reply]

  • Support - looks great --PopUpPirate 15:26, July 31, 2005 (UTC)
  • Support. Very comprehensive and well-explained. Easy to understand with even a very basic knowledge of chemistry. Phils 16:31, 31 July 2005 (UTC)[reply]
  • Support It took 2 minutes to load all the pictures on my computer. Very impressive Karmafist 17:53, 31 July 2005 (UTC)[reply]
  • Support, although I would recommend moving the list of enzymes to a separate page. Flcelloguy | A note? | Desk 18:52, 31 July 2005 (UTC)[reply]
  • Object, reluctantly. This article still needs some work, and I'm looking forward to seeing the results once these objections are addresssed:
    • Monomer discussion in "structure and function" is unclear
      • What do you mean by unclear? -- Jerry Crimson Mann 15:21, 1 August 2005 (UTC)[reply]
        • I mean that it doesn't define its terms. My (very limited) background in chemistry tells me that monomers are single elements that, strung together, make a polymer like plastic, DNA, or a polypeptide. The article seems to be referring to polypeptides as monomers, which I find confusing. Assuming I understand the first few lines of the paragraph, either changing the word "monomer" to "polypeptide" or saying "each monomer is actually produced as a long, linear chain of amino acids..." earlier in the paragraph would help
    • Applications table is hard to follow (add lines to separate rows and/or columns)
    • "protein folding" should be linked to from something less ambiguous than the words "general principles," as the reader has to move the mouse over the text or click it to find out what's being linked to.
    • The section on rate of reaction should probably be expanded. Saying it depends on "many factors" isn't really enough.
    • In-line references (footnotes or parenthetical citations) would go a long way towards making this article more authoritative. Right now, it's difficult to verify many claims the article makes.
      • Is that really necessary? I saw some FAs like evolution that are without in-line references... -- Jerry Crimson Mann 15:21, 1 August 2005 (UTC)[reply]
        • Editors are allowed to have their own guidelines/requirements for supporting articles, and this is one of mine, especially for scientific articles. I didn't support evolution. You could almost certainly get this featured even without addressing this objection, but only if you address everything else. Dave (talk) 13:54, August 2, 2005 (UTC)

**Long sentences like this one are hard to follow, even for a biology major like me:

Because the precise structure of each region tends to be fairly critical to correct function, and because the frequency of a mutation which would produce a nonfunctional active region is proportional to the length of the chain separating the amino acids involved, evolution works against having the amino acids from an active region widely dispersed, instead tending to keep the amino acids involved in each active region compacted fairly closely together in the chain and conserved against mutation, separating these regions by long stretches of 'spacer' amino acids where mutation is much less critical (although some mutations in these regions can also inactivate the product).
      • Corrected sooner or later.
        • There will still be other readability problems even after you fix that sentence. I'll try to help. Dave (talk) 13:54, August 2, 2005 (UTC)
    • The discussion of energy in the structure and function section could probably be streamlined. I like the analogies, but it's hard to follow.
    • Links to names should be fixed: Fischer is a disambig (including two nobel-prize winning chemists, among others) and Koshland is a blank page. First names should probably be included as well.
    • The article needs a copyedit. Three examples include "short0lived" (lock and key hypothesis section), "fromevidence" and "breakdown" (in the induced fit section)
    • Making the kinetics section more accessible to non-biochemists may not be possible, but I hope someone tries.
  • If all (or even most) of these are addressed, I'll support. Good luck! Dave (talk) 01:36, August 1, 2005 (UTC)
You know what, I could hardly find people knowing one or two about biology during the peer review. You are one of the guys who could give pretty clear and constructive feedback. :-) Btw, could you give us a hand in improving this article, please? -- Jerry Crimson Mann 14:18, 1 August 2005 (UTC)[reply]
Yeah, the process is sort of dumb. No one (including me, most of the time) pays attention to peer review. Maybe I should. I'll see what I can do with the article, but nixie is more knowledgeable than I am on the subject. I'm sure she'll give you a hand when she has time if you ask. Dave (talk) 13:54, August 2, 2005 (UTC)
  • Support-This is a very interesting and well done article. It is exceptionally informative and explains the concept of enzymes quite clearly, even to someone who isnt in the field. I also like the diagrams, they add a lot to the article in terms of clearity and make it much more readable. --Gpyoung talk 03:25, 1 August 2005 (UTC)[reply]
  • For now I have to object. As a biochemist I noticed that there are several things that could be improved, there is little discussion of coenzymes (vitamins and metals), multi-subunit enzymes and where enzymes are actually active within a cell eg. organelle specificity, enzyme inhibition/allosteric enzymes. Basically this article should cover everything in the chapter TOC for a textbook like Matthews, Van Holde and Ahern or Voet and Voet (two widely used undergraduate level biochem texts).
As an editor I think the specific enzymes section should be renamed and include some more examples, and that the list is unnecessary given the link to the list on another page. The tables should also be fixed so that they are outlined.
As a general reader, the order of text could be improved, for example, the reader is hit with The advantage of enzymes compared to most other catalysts is their sterio-, regio- and chemoselectivity and specificity before something like this Enzymes are essential to living organisms, and a malfunction of even a single enzyme out of approximately 2,000 types present in our bodies can lead to severe or lethal illness - which is much easier to understand and would interest a general reader. There are similar examples throughout where diffuicult concepts are explained before the easy ones.--nixie 03:29, 1 August 2005 (UTC)[reply]
1) I reconfigured two tables at the bottom and noticed there was a lot that could be improved in those tables. A lot of copy editing of the text in the table is required.
  • Any suggestion?
2) I then looked at the main article. I did not get past the structure function section. Why the emphasise on monomeric versus oligomeric (quaternary structure)? Surely the most important thing is the residues at the active site (tertiary structure).
  • This part would be deleted.
3) You cite the active site of the enzymes figure 2; I could not find firgure 2 (do you mean your first 5a-c figure?). Why is figure 2 cited in the text before figure 1? It looks like you have reaaranged everything without correcting the order of the figures. You have two figure 4's and two figure 5's. The second figure 4b has two panels a) and b. Worse your first figure 4b (i) ( as opposed to figure 4b (ii)) also has an a and b panel. Do you see how crazy this is? All the figures need to be relabelled since they are not consistent with the text or each other. If the figure has panels a) and b) you cannot label it 4 a) Label it 4 (a-b) and the second panel, 4c. For example, the succinate (is succinic correct?) dehydrogenase panel should be a 4c not a 4b.
  • An anonymous user rearranged the figures. Problems fixed sooner or later.
4) The next sentence after the incorrect figure citation is "Sometimes enzymes contain additionally other binding sites." This is poor grammar and I presume not up to featured article standards. As with the tables, it looks like this article needs some proof reading.
  • Any suggestion?
5) A quick scan through shows that you do not define EIS nomenclature.
  • Enzyme-inhibitor-substrate
6) Is this correct with respect to non competitive inhibitors? "they disable or enable the ability of the enzyme to turn over its substrate" I don't think they can enable. You may be thinking of allosteric enzyme with regard to this statement.
  • I don't write this. Let's see what we can do with it
7) Is metabolic feed back beyond the scope of this article? That is getting into the regulation of metabolism.
  • If you read any book about enzyme, this part is often mentioned for good reasons.
8) Modifications seems to be too early in the article. That would be better suited with regard to the feedback control and the regulation of metabolism.
  • Good advice.
9) Prosthetic groups seem to be an add on at the end. These should be discussed with respect to the active site right at the begining of the article.
  • I don't think so. It's a kinda cofactors, which in most cases are discussed in the later parts. It's not desirable to have it next to the active site.
10) One of the most important aspects of enzymes that is absent in this article is conformation changes that occur during catalysis. These conformation changes are critical for enzyme function. Hexokinase is a good example of an enzyme with a large conformation change, almost like a Pac-Man.
  • Induced-fit hypothesis? Did you see it?

:11) The thermodynamics section needs work and might not be appropriate for this article. The following is another example of a sentence in dire need of copy editing. "For instance, the high energy compound ATP is generated in the cell by coupling its synthesis to the oxidation of sugars, which releases more energy than the synthesis of ATP requires; then the ATP is broken down in turn by other enzymes coupled to other processes, releasing the energy stored in it to drive other, otherwise energetically unfavorable, chemical reactions."

Clearly this article has a lot of potential but it really needs to be cleaned up a lot before being a featured article. David D. (Talk) 01:22, 5 August 2005 (UTC)[reply]
Wow, you don't hang around with the editing. I'll read it over more thoroughly and do some copy editing. I have already made quite a few changes to the table, I'll edit that some more too. I think your solution of just removing the figure numbers is perfect. Wikipedia does not need to be like a review paper. David D. (Talk) 05:21, 5 August 2005 (UTC)[reply]
Oh, you're so good, man. Thanks a million dollars. :-D -- Jerry Crimson Mann 05:46, 5 August 2005 (UTC)[reply]
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