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Enzyme

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Self-nomination. A core article in biochemistry written as a complete introduction for both general and more specialised readers. Multiple revisions, clarifications and refinements have been added since the last draft of this page was submitted for Featured Article in 2005 Archive of previous discussion. TimVickers 18:43, 28 August 2006 (UTC)[reply]

  • Comment: My first impression is this looks great. I've fixed a few minor things and I'll need a chance to properly read it before supporting, but in the mean time I have two suggestions:
    • See if you can merge those one sentence paragraphs (or expand them if it makes more sense to do that) - especially the ones in the lead, and
    • See if you can find someone to convert the diagrams (obviously not the ribbon ones) into SVG format.
I'll be back later tonight to read through this. darkliight[πalk] 19:12, 28 August 2006 (UTC)[reply]

Thanks, good suggestion about the intro, I've merged some of the fragments. I don't know how to do vector graphics though, what is the advantage of this format over jpeg? TimVickers 01:28, 29 August 2006 (UTC)[reply]

SVG vector graphics now substituted for diagrams. TimVickers 20:13, 30 August 2006 (UTC)[reply]
  • Object for now. I would love to see this become an FA but it needs a copyedit and some tweaking first. I went through the first couple of paragraphs but don't have the time to do much more right now. Withdrawing objection; good work. See below. Opabinia regalis 02:25, 31 August 2006 (UTC)[reply]
    • There's a lot of two- or three-sentence paragraphs or subsections that need either fleshing out or merging. (Especially the "coenzymes" section and the out-of-place-sounding little paragraph in the lead about industrial applications.)
Sections expanded, figure added to Coenzymes section.
    • The statement that 10 amino acids on average come in contact with the substrate needs a citation (the standard deviation on that must be huge).
Changed to refer to catalytic residues with added citation. TimVickers 03:49, 29 August 2006 (UTC)[reply]
    • The sentence "The activities of enzymes are determined by their three-dimensional structure" is overstated - plenty of proteins have nonessential bits of tertiary structure. This would be clearer if the introduction of the active-site concept were moved up one paragraph. I'm not convinced you really even need a discussion of protein synthesis here; it's covered in protein, protein biosynthesis, gene expression, and elsewhere.
Moved section upwards as suggested, activities are solely determined by structure so that broad statement has to stay but there is probably too much on protein synthesis, I shrank this a little. TimVickers 04:07, 29 August 2006 (UTC)[reply]
I would dispute that "activities are solely determined by structure" unless you're using a very broad definition of "activity" or "structure". What about protonation states, solution conditions (low Mg concentration, high product concentration), etc? Maybe it would be clearer as "specificities are determined by structure"? Opabinia regalis 04:45, 29 August 2006 (UTC)[reply]
A difficult distinction to draw, since properties like pH optima or requirements for cations are also determined by the structure of an enzyme. Indeed, all physical properties of proteins are determined by their primary sequence and any subsequent post-translational modifications. This statement is true as a ultimate cause, but you are indeed correct that other, proximal causes exist. I'll make a note about this on the talk page and bring other minds to bear. TimVickers 13:53, 29 August 2006 (UTC)[reply]
    • The inhibition section is large but regulation in general isn't covered as thoroughly as you might expect. Titling this section "regulation" or something similar and including a section on post-translational modifications would be useful. Currently the function section contains some regulatory information but it would be clearer in one place.
Moved and merged.TimVickers 04:07, 29 August 2006 (UTC)[reply]
    • The applications table is a clever idea, but it's huge and clunkily formatted, and I'm not sure readers will really get much out of it. It's only useful to those looking for very general information, who would probably not get past the more technical kinetics section. I'd suggest moving it to subarticle.
Asked for suggestions/formatting on talk page. TimVickers 13:53, 29 August 2006 (UTC)[reply]
Shrank it a little by re-formatting, but also added another section (see below, responses to reviewer Steven Fruitsmaak) TimVickers 22:39, 2 September 2006 (UTC)[reply]
    • On the subject of technical levels, I think the early sections might be a bit too dumbed down. People who don't know what catalysis is won't understand enzymes no matter how many simplified or appositive explanations are included. Opabinia regalis 02:58, 29 August 2006 (UTC)[reply]
This page is intended as a general introduction to a larger set of more specialsed pages. We have therefore tended to try for the simplest langauge possible to convey the concepts with a minimum of jargon. TimVickers 04:07, 29 August 2006 (UTC)[reply]
  • Comments I didn't notice this before, but the sentence containing the Paracelsus quote in the inhibition section needs a citation (and possibly a rewrite). I still cringe at saying activity is "determined" by structure but for an article at this level it's a minor point. Pending other input I'd still also suggest moving or at least reformatting the table; it's by far the largest section in terms of screen real estate and it's also the least important. But the latter two are stylistic issues and, in terms of content, if the Paracelsus quote is cited I support this nomination. Opabinia regalis 02:25, 31 August 2006 (UTC)[reply]
Citation added. After I chased down an accurate quote I found the famous formulation is a shortened version of his actual words! TimVickers 03:42, 31 August 2006 (UTC)[reply]

Does anybody else have comments or responses to the alterations made above? TimVickers 15:21, 30 August 2006 (UTC)[reply]

  • Comments Your layout needs to correspond to WP:GTL. It would also be a good idea to include all PMIDs and ISBNs on your footnotes and references: PMIDs are easy to add, and provide a direct link to the studies. There are patches of text that don't have inline citations. This looks like a copyedit issue, not sure: "However, some cofactors known as prosthetic groups are covalently bound (e.g.'Italic text, thiamine pyrophosphate in the enzyme pyruvate dehydrogenase)." You should remove all external jumps, for example, on "The International Union of Biochemistry and Molecular Biology has developed ... " I won't be able to Support or Object, as I will have limited internet access for a few weeks, but just wanted to leave those notes of things to work on. Sandy 02:05, 1 September 2006 (UTC)[reply]
Sections re-ordered according to WP:GTL. ISBN, PMID and more wikilinks added. External ink removed. Thank you for your suggestions. TimVickers 04:21, 1 September 2006 (UTC)[reply]
  • Oppose for now. I've just looked at the first paragraphs. Judging from some changes I've made this article isn't comprehensive enough yet, but definitely a Good Article. In my opinion the introduction is still a little to technical for a general audience.--Steven Fruitsmaak (Reply) 11:24, 1 September 2006 (UTC)[reply]
I'd also cut down the See also-section, things like molecule have been linked in the article so don't need a See also in my opinion: if two concepts are truely linked, they should be wikilinked in the text itself, with See also used sparingly, I think. Same with external links: things that do not relate specifically to enzymes but to proteins in general I would move to the protein article.--Steven Fruitsmaak (Reply) 11:29, 1 September 2006 (UTC)[reply]
Thank you for your comments, but I'm puzzled. "Molecule" isn't linked in "See Also" and there are only 4 links in this section. I have moved the PDB "Molecule of the Month" external link to the proteins article, as I think this is what you were referring to. I have also tried to simplify the introduction a little, but as you can see above, some reviewers have suggested this is already oversimplified! If you had any specific suggestions on areas we have missed and need to be added in order for the article to be more comprehensive, then I would be happy to try to include them. However, the article can't get much bigger as it is already 37 kilobytes in size. TimVickers 15:32, 1 September 2006 (UTC)[reply]
  • I'm sure the biggest part of the readers still doesn't consider it to be oversimplified, and even then the body of the article is complicated enough to satisfied those hungry for knowledge.
Intro simplified a little.
  • I prefer a see also section to be as short as possible, omitting any articles that have already been linked in the text itself (e.g. protein), but I can imagine that's not everyone's preference.
See also secion only contained 4 links, but I removed Protein and now it is down to 3 links.
  • Those two last external links seem only remotely related to me: more to genes and CytP45O, they don't belong here in my opinion.
Removed.
  • The "paper industry" section should show a product (i.e. paper), not a factory. Also, enzymes are very important in bio-research.
I discovered that factory picture was actually of a paper mill, so I just added a caption. Section on Genetic engineering added.
  • The errors in metabolism-section should have a wikilink to genetic disease.
Done.
Section on enzyme induction added.
  • The Greek word is ενζυμον, énzymon.
Greek root added.
I think I covered everything. Any more suggestions? TimVickers 19:19, 1 September 2006 (UTC)[reply]
I still oppose and made some more major changes. This is mainly because the current article is biased to much towards enzymes involved in metabolism.--Steven Fruitsmaak (Reply) 00:59, 2 September 2006 (UTC)[reply]
I'm sorry, I'm not sure I understand, since metabolism is the sum of chemical reactions that occur in a living organism, I have always thought that enzymes sole function in biology is metabolism. The only non-metabolic roles of enzymes I can think of are their uses in industry. I agree that apart from the table of industrial uses, the commercial uses for enzymes are not covered in detail within this article, do you think this area should be expanded? TimVickers 01:24, 2 September 2006 (UTC)[reply]
  • Weak object:
Added, good point.
  • there is a maybe usable Michaelis-Menten image on german wiki: here
Taken one from Enzyme kinetics
  • in Etymology and history section: nothing happened after 1950 in enzymes' history?
Structure of Lysozyme is probably the most important recent example. I've added this.
Section expanded and figure added.
  • WP:MOS#Headings: headings generally should not repeat the title of the article
Fixed.

Anyway, great article, after the suggested changes, I'm surely support it. NCurse work 14:49, 2 September 2006 (UTC)[reply]

Section on inhibition shortened by replacement of second, semi-redundant figure. TimVickers 22:58, 2 September 2006 (UTC)[reply]

Comment:Overall, this is an excellent article, but my impression is that it's not quite FA level. Here are some suggestions for improvements:

  • The article seems a little too slanted towards protein enzymes; consider re-wording the first two sentences and the discussion of folding to treat RNA and proteins on a more equal footing. This article should be written so that it may be linked from, e.g., the ribozyme, ribosome and RNA world hypothesis pages.
Although the principles are the same, I'm sticking to the dictionary definition of Enzyme in this article.
  • Instead of the vague "millions of times faster" in the second paragraph, how about using the example of orotate decarboxylase, which if I recall correctly accelerates its reactions by kcat/KM/kuncatalyzed = 1023 M-1 under optimal conditions?
Superb example. Thank you. Added to introduction.
  • An example of extreme enzyme specificity would be good. A sentence or two about the trade-off between specificity and binding energy would be good.
Excellent point. Since a binding energy discussion risks becoming over-technical for general reader (and has a lot to do with turnover rate also), I added a section on proofreading enzymes as a more accessible example of extremely specific enzymes, with references to DNA polymerase, ribosomes and aaRS.
  • You might want to link to Lineweaver-Burk and Eadie-Hofstee in the kinetics section. Some description of how enzyme assays are carried out (or a few links) and how the kinetic parameters/MM parameters are determined experimentally might be good. The relation Vmax = kcat [Enzyme]tot might be helpful, since kcat seems to appear without explanation.
Link to Enzyme assays added. Definition of kcat added. I put links to those plots on the Enzyme kinetics page, since they are not for the casual reader!
  • I would mention uncompetitive and suicide inhibitors, and write the non-competitive inhibition section to be more plausible. A lay-person will undoubtedly ask, "If the inhibitor binds so far away, how does it affect the active site?"
This section was muddled. I've clarified non-competitve inhibitors and divided the section into reversible and non-reversible inhibitors.
  • The cofactor/coenzyme discussion seems split up into two places? A fuller description of what they're doing in catalysis would be good, e.g., electron sink. Some prosthetic groups cannot be removed to form the apoenzyme, e.g., the pyruvate cofactor in the pyruvoyl enzymes (e.g., amino-acid decarboxylases).
I really think these are some of the most annoying terms in enzymology! I split co-enzymes (substrates) from co-factors (bound components of enzyme structure) to try to emphasise that the two types of compounds are very different (in a strict usage of these decidedly loose terms!). Stryer divides cofactors (structural) from coenzymes (substrates) but adds that bound coenzymes are called prosthetic groups (what a muddle!). I'll merge these sections and disambiguate as much as possible. I've also added a bit on the role of co-factors, using heme and flavin as examples. Prosthetic groups are mentioned in the last paragraph of the co-factors section.
  • At the risk of being too technical, the article should allow the possibility of seeing an actual enzyme mechanism, to make the thermodynamics come to life and illustrate how the transition state is stabilized preferentially to the substrate and product. Perhaps chymotrypsin?
These animations are linked and explained on the Enzyme kinetics page.
  • A discussion of general acid-base catalysis versus other types of mechanisms seems appropriate. More generally, a sentence or two about how alternative mechanisms are discerned (e.g., pH dependence, mutagenesis, chemical modification, stable isotope labeling, transition-state analogs, spectroscopy, deuterium kinetic effects, etc.) would be excellent.
I think this is out of the scope of this introductory article written for the general reader. These concepts are touched on briefly in the Enzyme kinetics article, but even here no experimental details are given. Perhaps you could have a look at that page and add some comments at Wikipedia:Peer review/Enzyme kinetics/archive2?
  • Semantics question: does prolyl peptidyl cis-trans isomerase catalyze a chemical reaction? Some isomerases seem to catalyze quasi-chemical rearrangements that are not strictly speaking chemical reactions.
Any change in the electronic structure of a chemical is a chemical reaction. Cis-trans isomerases have the EC number EC 5.2.x.x
  • An external link to KEGG seems appropriate. The Enzyme Structures Database link is outdated.
Thanks, added link and updated link.
  • Perhaps include some discussion of enzyme design (a la Homme Hellinga and those ribozyme researchers), catalytic antibodies and artificial evolution?
Excellent point. I haved added a brief mention of this as part of a new intro to the Commercial uses section. TimVickers 20:43, 3 September 2006 (UTC)[reply]

I hope that this helps. If you'd like, I would be happy to help out, although I'm kind of busy with other articles and (gasp!) real life. ;) Good luck, and I look forward to reading your contributions! :) Willow 07:57, 3 September 2006 (UTC)[reply]

More comments ;) The improvements are excellent, particularly your handling of orotate DC. I think the header section needs more work on its writing and organization, though:

  • I would define substrate and product right after the ribozyme section, and follow them with the 4000 reactions/nomenclature sentences from the last paragraph of the header. We all know what they mean, but many readers will not. Then perhaps follow with your comment, "Unlike most catalysts, however, enzymes are extraordinarily specific for their substrate..." or some such.
Definition added and intro re-arranged and rephrased to improve flow.
  • At this point, you might want to highlight that the ability to adjust specific reaction rates independently of one another makes life possible and that some organisms (such as plants) often have several different enzymes for the same reaction, to give more possibilities for regulation of reaction rates.
This first idea is contained in the last sentence of the first paragraph of the intro. I have added the concept of parallel enzyme activities into the Metabolism section.
  • I would re-word "alternative pathway" since, to my understanding, the pathway itself is not changed significantly, merely the activation energy. This may be a semantics issue.
I've replaced "pathway" with "path" and added a disambiguation wikilink to Reaction coordinate here to show this term is being used in its sense in physics. I hadn't noticed how confusing it might have been use "pathway" with two meanings in the intro, good catch. TimVickers 17:39, 4 September 2006 (UTC)[reply]

Gotta run off to work — have fun and good luck! Thanks for your really nice comments on my talk page, too! :) Willow 13:01, 4 September 2006 (UTC)[reply]

Support. Great article! --WS 16:31, 3 September 2006 (UTC)[reply]

Support - Great work, this has come a long way! – ClockworkSoul 16:03, 5 September 2006 (UTC)[reply]

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