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Wikipedia:Featured article candidates/Enzyme kinetics

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Enzyme kinetics

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Self-nomination. An article on enzyme kinetics that tries to explain the basics, details and importance of this area. The article aims to be both comprehensive and reasonably approachable. This article is currently GA and has recently been peer-reviewed (Link) Thank you. TimVickers 20:24, 28 September 2006 (UTC)[reply]

  • Support : I was asked to be a reviewer of this more than once. I regret I did nothing on it.. But this page is superb. Enzyme Kinetics is SO boring but SO important. This a wonderful page Kudos to you! Adenosine | Talk 23:50, 28 September 2006 (UTC)[reply]
  • Weak oppose due to ongoing discussion at the article's ongoing peer review. In a nutshell: Wikipedia's best articles should be intelligible in a print medium, too; "(Gif)", "(Flash required)" and "(Link: Java required)" may be better placed as footnotes. Using Lupin's tools, there is no loss in convenience by doing so, and it's reasonable to assume that a browser capable of Flash and Java can do JavaScript, too (required for Lupin's tool). - Samsara (talk • contribs) 11:16, 29 September 2006 (UTC) Changed to support. - Samsara (talk • contribs) 09:47, 30 September 2006 (UTC)[reply]
I moved the links into references, but as a newbie, I haven't heard of Lupin. I found User:Lupin but there wasn't anything there that seemed relevant. Was I looking in the correct place and what are these tools? TimVickers 14:49, 29 September 2006 (UTC)[reply]
Wikipedia:Tools/Navigation popups. - Samsara (talk • contribs) 18:53, 29 September 2006 (UTC)[reply]
Are you happy with the new format showing the links as references? I saw this tool, but doesn't it require the reader to install software in their browser before the popups will work? Is that a practical or desirable requirement in an encyclopedia entry? TimVickers 19:14, 29 September 2006 (UTC)[reply]
Are you happy with the new format showing the links as footnotes? I still don't know how to apply this tool however, could you explain what it does? TimVickers 21:32, 29 September 2006 (UTC)[reply]
Although this is a clever solution, I don't think the links are prominent enough this way. As a reader I'd be unlikely to follow a footnote unless I specifically wanted a source for a statement, so I probably wouldn't follow these links. As I mentioned on the peer review page, I actually like external links properly integrated into the text where appropriate, but in this case I'd rather see them in an external links section than tucked away in another set of small-text footnotes. Opabinia regalis 00:38, 30 September 2006 (UTC)[reply]
Yes, that's the other possible solution. I've no preference between the two. - Samsara (talk • contribs) 09:47, 30 September 2006 (UTC)[reply]
I'll add the page with the two best examples to the external links section as well, to make it more obvious. TimVickers 01:14, 30 September 2006 (UTC)[reply]
  • Support: This is a readable article which feels to give an appropriate level introduction. Some nitpicky comments:
  • I like the first figure, but it doesn't seem a representative first figure to include. I wonder if it could be brought in lower down the article (eg where you discuss multi-substrate reactions) and some sort of colour graphic better representing enzyme kinetics used up front? (Anyone who doesn't know what an enzyme looks like is probably better served going to look at other articles first.)
This figure is mainly aesthetic, although it is referred to in the introduction. The start of the article was otherwise a bit dull. Did you have any suggestions for something better to accompany the introduction? TimVickers 17:08, 29 September 2006 (UTC)[reply]
You could try a simple colour diagrammatic depiction of E + S --> E-S --> E + P which I think would be valuable. Also, this might be a stupid suggestion, but is there any way you can visualise enzyme reactions macro-scale with colour changes/fluorescence -- a time-lapse shot might be interesting. Espresso Addict 17:48, 29 September 2006 (UTC)[reply]
I suppose I like this figure because it illustrates the point I try to make in the second paragraph of the intro, that a blend of structure and mechanism gives a complete picture of enzyme action. I'll have a go this evening, but I'm not sure I can produce something so striking from just a simple block diagram. I think moving images are discouraged, since they increase page size and download times a great deal. TimVickers 18:10, 29 September 2006 (UTC)[reply]
  • The figure "Enzymes become saturated at high concentrations of substrate" would benefit from some indication of rate of reaction (either a graph underneath the diagrams, or just some graphical interpretation, eg different-sized text).
Changed the legend to explain this. TimVickers 19:18, 29 September 2006 (UTC)[reply]
  • In Single-substrate mechanism/Michaelis-Menten kinetics, the two figures in this section are a bit blurry and text hard to read -- can they be improved? Perhaps increase preview size, if this won't make the text run strangely.
Figures resized. TimVickers 17:08, 29 September 2006 (UTC)[reply]
  • k & V in these figures need italicising. The left-hand figure should have v added.
Corrected, italics added. TimVickers 17:08, 29 September 2006 (UTC)[reply]
  • Standardise italic/not for E and S in the equations vs text.
Fixed. TimVickers 18:03, 29 September 2006 (UTC)[reply]
  • I found the use of 'you' a bit distracting.
Removed. TimVickers 17:08, 29 September 2006 (UTC)[reply]
  • The full stop for multiplication was hard to see -- a larger dot is available from the insert menu (•) and might improve
Larger dot substituted. TimVickers 19:20, 29 September 2006 (UTC)[reply]
  • Do you need full stops at the end of the equation 'sentences'?
I wasn't sure so I added them just in case somebody objected! TimVickers 17:08, 29 September 2006 (UTC)[reply]
  • y = mx -- define m (and possibly avoid, given all the subscript m's included)
"m" defined as slope. TimVickers 17:08, 29 September 2006 (UTC)[reply]
  • In Practical significance of kinetic constants, 'Oxaloacetate can then be consumed by' -- is this strictly accurate? A diagram might be helpful in explaining the concept in paragraph 2.
I have added links to the pathways concerned. TimVickers 19:32, 29 September 2006 (UTC)[reply]
  • 'Although this goal is far in the future for any eukaryote, attempts are now being made to achieve this in bacteria such as Escherichia coli.' -- fascinating! Would it be appropriate to explain in slightly more detail?
A bit more detail added. TimVickers 19:32, 29 September 2006 (UTC)[reply]
  • In Ternary-complex mechanisms, 'these two possibilities are therefore known as random or ordered mechanisms.' is this phrase necessary? It feels over-laboured, and the terms don't seem to be used later.
Reworded. TimVickers 18:13, 29 September 2006 (UTC)[reply]
  • In Non-Michaelis–Menten kinetics: I think you need to explain co-operative binding a little more clearly at first intro. Allosteric could be defined and figure a little blurry, axis legends need to be larger
Image resized, text reworded to define terms.
  • In Pre-steady-state kinetics, burst phase needs to be explained in text before it's used, or at least the figure needs to be referenced.
  • Should the graph y axis be labelled Amount of E* rather than Amount of product?
I've reworded this and tried to explain both burst phase and the link between product formation and [E] more clearly. TimVickers 17:08, 29 September 2006 (UTC)[reply]
  • In Irreversible inhibitors, the language in the second sentence needs simplifying.
Broken into 2 sentences. TimVickers 17:08, 29 September 2006 (UTC)[reply]
  • Mechanisms of catalysis: I wasn't sure why this section is needed here? If retained, a direct link to kinetics should be clarified.
Most of this removed and a new paragraph on relation between kinetic and mechanistic studies added. TimVickers 17:19, 29 September 2006 (UTC)[reply]
  • In the reference list, strictly number ranges should have n-rules, but it's a pain to add them in this referencing system.
I agree! TimVickers 17:19, 29 September 2006 (UTC)[reply]

Espresso Addict 14:58, 29 September 2006 (UTC)[reply]

I'm always in awe of your thoroughness and eye for detail Espresso Addict, you remind me strongly of my PhD supervisor - a brilliant scientist with a laser-like focus. Thank you for this excellent copy-edit I will get cracking on these. TimVickers 15:11, 29 September 2006 (UTC)[reply]
  • Support, concerns have been addressed Dr Zak 02:27, 1 October 2006 (UTC) Oppose. Sorry. Enzyme kinetics is a subset of chemical kinetics, and there are some assumptions that (almost) always hold true within the narrower field. I would start out with the Michaels-Menten equation and outline the assumptions that that is built on and also mention things like the Lineweaver-Burke plot early on. Then one can proceed to multisubstrate reactions. Dr Zak 19:17, 29 September 2006 (UTC)[reply]
I hope this is what I have done here. After the introduction for non-specialists (conforming to Wikipedia:Summary style) and how the data we analyse is gathered, I do introduce the MM equation, the assumptions behind this and when these assumptions break down. The article tries to produce a gradient of detail going from the least (general principles), then as you say to multi-substrate reactions and then finish with the most complicated (non-MM kinetics and pre-steady-state kinetics).
I only mention Lineweaver-Burke plots and do not show an example as they are rarely used in modern enzymology and when seen are only present for illustrative purposes, because they have a very misleading non-linear error distribution. TimVickers 19:42, 29 September 2006 (UTC)[reply]
The Michaelis-Menten equation is derived from the assumption that the equilibrium between free enzyme and substrate is established much faster than products are formed and that that [ES] remains constant. This is important. Of course the treatment of errors in the Lineweaver-Burke is not completely trivial, but the plot is very instructive.
I would then mention pre-steady-state kinetics and non-Michaelis kinetics next, because that's where the assumptions just made break down and finally talk about multisubstrate kinetics.
Real-life applications could go farther to the back - this is about the mathematics, not so much about applications of the maths.
Others may have a different viewpoint how things ought to be treated - having done physical-organic chemistry in the past I'm very friendly towards mathematics. Dr Zak 20:11, 29 September 2006 (UTC)[reply]
Thank you for your edits Dr Zak. Yes, the two different ways of deriving the MM equation (rapid-equilibrium and steady-state) are dealt with here, I hope you are happy with how this is done. I have also added more detail about L-B plots (rather than simply linking to the page where they are discussed in detail). I however disagree that this page is solely about the mathematics. This page does include the mathematics, but sets these in the broader context appropriate for an encyclopedia article. This is done by discussing the uses and meaning of the maths - as this article is not intended simply as a resource for specialists such as ourselves, but as a useful introduction for the general reader. TimVickers 21:10, 29 September 2006 (UTC)[reply]
There's always the usual option of forking off the detailed derivations to a separate article. Purely my bias, but I hate the way Lineweaver-Burk plots are taught as if they're in common use and would minimize their importance. Opabinia regalis 00:38, 30 September 2006 (UTC)[reply]
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