Talk:Enzyme kinetics

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Article Milestones Date Process Result August 29, 2006 Peer review Reviewed September 24, 2006 Good article nominee Listed September 29, 2006 Peer review Reviewed October 3, 2006 Featured article candidate Promoted Current Status: Featured article

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The following users are actively contributing to this topic and may be able to help with questions about verification and sources: TimVickers (talk • contribs • email)

As per discussion on the Enzyme page, I believe this article should be combined with the Rate of enzyme mediated reactions page and the inhibitor section of the Enzyme page. The actual text of this article should probably be replaced with the "new" article.

Hichris 15:44, 6 December 2005 (UTC)

I agree and will watch this page for further action and elp out if possible. David D. (Talk) 19:26, 9 December 2005 (UTC)

Yes, it is obvious that these pages give informations about the same subject : enzyme kinetics. Maybe we should first add what is on the other pages on this page, and then if it's okay, delete the content from the original pages. --Totophe64 13:13, 19 December 2005 (UTC)

Agree. Most of this material is common to the Enzyme article. -CoeurDeLion

Contents 1 suggested merge with Enzyme 2 Unanswered Questions 3 Good article nomination 4 biological significance 5 Briggs-Haldane modification to the M-M scheme 6 Sigmoidal curves with non-cooperative binding?

[edit] suggested merge with Enzyme

Disagree. Enzyme kinetics is on a deeper scientific level that the enzyme article, and the background given in this article is geared towards that purpose; a merge would make the enzyme article clunky. The internal link from enzymes to enzyme_kinetics is enough to show that this topic is covered. Vermiculus 16:16, 3 April 2006 (UTC)

Disagree. Enzyme kinetics is much more the theory and physics of enzymes. The article under Enzyme is much more the tangible material. Also the vastness and the usefullness of enzyme kinetics makes it essential to be separate, as a matter of fact it should be expanded. A merger with Michaelis-Menten kinetics would be more logical

Disagree. The enzymes page needs to be accessible to the non-specialist and this material would fit poorly. I am in the process of expanding the enzyme inhibitor page and moving some of the stuff from enzymes over to there. The section in this page on inhibition will be replicated and covered in more depth in this new version of enzyme inhibitors. I agree that merging this page with Michaelis-Menten kinetics and Rate of enzyme mediated reactions would be preferable.--TimVickers 23:40, 28 June 2006 (UTC)--TimVickers 23:40, 28 June 2006 (UTC)

Just a little background here. I think the original suggestion was to move things from enzyme to here, not vice versa. There used to be a horrendous enzyme kinetics section in the enzyme article. It contributed to the article being way too long and far too complex for the average reader. Obviously that has since disappeared from the current enzyme article. David D. (Talk) 21:41, 29 June 2006 (UTC)

In fact, there is nothing in the Rate of enzyme mediated reactions page that is not in the other enzyme pages. What about?

• Enzymes - General introduction
• Enzyme kinetics - Page divided into kinetics and mechanism. First section covering simple MM kinetics, then multi-substrate reactions and allosteric effects. Second section covering mechanisms of catalysis.
• Enzyme inhibition - Modes and examples. Mostly finished now.--TimVickers 21:43, 29 June 2006 (UTC)

Looks good to me. This is long overdue. David D. (Talk) 21:45, 29 June 2006 (UTC)

OK, over the next few weeks I will move stuff from MM kinetics to here and then when people are happy with this article the old MM page can be deleted. I suggest we put up the Rate of enzyme mediated reactions page up for deletion.--TimVickers 21:50, 29 June 2006 (UTC)

I'd suggest letting 'Rate of enzyme mediated reactions' lie dormant until the project is complete. Redirecting that page is always an option too. David D. (Talk) 21:59, 29 June 2006 (UTC)

OK, good plan. I'll redirect the links to that page to here.--TimVickers 22:20, 29 June 2006 (UTC)

Stuff moved until I can fit it in to main article--TimVickers 17:19, 1 July 2006 (UTC)

[edit] Unanswered Questions

This article, like the enzyme article and the DNA article, dodges all the fundamental questions in a fairly spectacular manner. I realize that Wiki articles are meant to be about what we know rather than what we don't, but I strongly believe that all science articles that beg fundamental questions so glaringly should post those questions as work for the future. How can nonliving bodies like enzymes, that have no DNA, no hardwiring, no brains, and no switches, perform all these complex tasks? They are used to explain almost everything, especially in the groundwork of DNA replication, and yet their motions are completely mysterious. How do they happen to be in the right place at the right time in the right form? How is it that extremely useful self propelled "blueprints" seem to be universally available? How are they manufactured, how are they read, how is their necessity known before they get there? I am not some crank from the far right, proposing inserting god here. I just think these obvious questions should not be swept under the rug. It looks bad, as science.81.164.252.74 00:50, 6 August 2006 (UTC)

How do they happen to be in the right place at the right time in the right form? How are they manufactured, how are they read, how is their necessity known before they get there?

See articles on the control of gene expression, transcription, protein synthesis and sub-cellular localisation of proteins.

How is it that extremely useful self propelled "blueprints" seem to be universally available?

All life involves enzymes, this question relates to the origin of life.

These are a mix of biochemical questions that are dealt with in other articles and interesting philosophical questions. Enzymes are just one class of proteins, so the mechanism and control of their synthesis and activity is not fundamentally different from that of structural proteins, channels or sensory proteins. Therefore these questions are best dealt with in general articles rather than repeated in each page on particular classes of protein.--TimVickers 10:17, 8 August 2006 (UTC)

[edit] Good article nomination

Is it a B-class article? My suggestions:

• links in the end of section Ternary complex mechanisms; Ping-pong mechanisms should be references.

I deliberately didn't make these references since I want people to look at these at the same time as reading the text and looking at the figure. I thought if I put them as references then most of the readers would miss them.

Ok then at least, it should be written in prose. NCurse _work 18:07, 23 September 2006 (UTC)

OK, done. TimVickers 21:58, 23 September 2006 (UTC)

• in section Enzyme inhibition: images are merged for me (Firefox, 1024*768)

I added more text and moved the image up, which should fix this.

• I think this one is a great picture

Hmm. Well it says the same amount as the one in the article at the moment, but takes far more space. I tried linking the table and figure more explicitly as an alternative.

• more external links.

Added some more.

Anyway well-referenced, well-written, you should consider FAC. NCurse _work 10:57, 23 September 2006 (UTC)

Thank you, I will - but this is still pretty arcane, needs a lot of work first! TimVickers 17:00, 23 September 2006 (UTC)

It's a good article now. Well done! :) NCurse _work 18:14, 24 September 2006 (UTC)

[edit] biological significance

Not really sure this is the right page for this but I wonder if we need a passage discussing the biological significance of K_m. I think this would help people relate more to these numbers. For example, physiological substrate concentrations are often quite close to the K_m. Different isozymes can have different K_m values, depending on the location in a cell or tissue. This type of thing. What do you think? David D. (Talk) 22:04, 26 September 2006 (UTC)

Yes, I suppose we do need a "What the hell do all these numbers mean?" section. Perhaps as a sub-section in Single substrate reactions, which is where they are first introduced. TimVickers 22:14, 26 September 2006 (UTC)

[edit] Briggs-Haldane modification to the M-M scheme

Would like to a see a little on that. Some material here http://www.bio.brandeis.edu/classes/biochem102/hndEnzKin.pdf and http://www.jbc.org/cgi/reprint/235/8/2440.pdf cheers Shyamal 01:52, 27 September 2006 (UTC)

Paragraph on this added to end of Michaelis-Mentan section. TimVickers 14:50, 29 September 2006 (UTC)

What about Adair & Monod equations? And Koshland's? (allosterism) And why don't you explain how do we reach the inhibition equations?

Since these equations relate to allostery in general, not just enzyme kinetics, they would be best added to the page on cooperativity. I think deriving all the inhibition equations would take several pages and not add much to an article for the general reader. TimVickers 20:41, 19 October 2006 (UTC)

[edit] Sigmoidal curves with non-cooperative binding?

The article says: "Some enzymes produce a sigmoid v by [S] plot, which often indicates cooperative binding of substrate to the active site." Could non-cooperative binding with multiple binding sites also produce sigmoidal curves? In other words, do sigmoidal curves always necessitate a ligand binding to one site to affect the affinity of other sites? Is there a counter-example? Can non-cooperative binding cause threshold effects via sigmoidal activation? (it seems so based on the following article, but I am not sure: http://arxiv.org/PS_cache/physics/pdf/0609/0609227.pdf) Suu 14:35, 26 January 2007 (UTC)

Substrate activation is a possibility in one active site, where ES₂ is more active than ES. However, these two molecules of substrate must bind in different places, even if these are adjacent. However, I can envisage a model where an enzyme has two slowly-interconverting conformations with the active conformation being stabilised by substrate. I'll try to find if this has been observed. TimVickers 16:55, 26 January 2007 (UTC)