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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)
In fact, there is nothing in the Rate of enzyme mediated reactions page that is not in the other enzyme pages. What about?
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)
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)
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?
How is it that extremely useful self propelled "blueprints" seem to be universally available?
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)
Is it a B-class article? My suggestions:
Anyway well-referenced, well-written, you should consider FAC. NCurse work 10:57, 23 September 2006 (UTC)
It's a good article now. Well done! :) NCurse work 18:14, 24 September 2006 (UTC)
Not really sure this is the right page for this but I wonder if we need a passage discussing the biological significance of Km. I think this would help people relate more to these numbers. For example, physiological substrate concentrations are often quite close to the Km. Different isozymes can have different Km 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)
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?
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/abs/physics/0609227) Suu 14:35, 26 January 2007 (UTC)
I haven't been able to read the whole article yet, but through skimming and searching I can't see any mention of the action of temperature on enzyme kinetics (e.g. exponential increase of activity then sudden denaturation, different optimums in coldblooded and warmblooded animals, thermophiles etc), and there also seem to be little on the effects of chemical factors (such as pH changes, different environments in various organs and organelles). The article is no doubt of a high quality, but these seem to be serious omissions for a featured article. They are mentioned briefly in the enzyme article, and I was expecting the main discussion of them to be here. Richard001 04:45, 31 July 2007 (UTC)
A surprisingly long and vigorous discussion on a small point of nomenclature |
---|
The following discussion has been closed. Please do not modify it. |
User:TimVickers said see talk, but went to my talk page instead and based his argument on a recent, disputed addition top the MoS by none other than User:TimVickers. See Wikipedia talk:Manual of Style#Units of measurement. Gene Nygaard 23:45, 22 October 2007 (UTC) Here is what NIST has to say about it:
NIST Special Publication 811, Guide for the Use of the International System of Units (SI), 1995, section 8.6.5 [1] Gene Nygaard 23:53, 22 October 2007 (UTC)
It's not evident on this web page abstract, but according to the text visible in my Google search, this one does (in the form mol/(l s), which is the same thing in case anyone is unfamiliar with the superscript notation which I merely continued as it existed before):
Gene Nygaard 00:22, 23 October 2007 (UTC) I'll just cite a web link for this abstract, http://www.maik.ru/abstract/polscia/98/polscia9_98p871abs.htm
Gene Nygaard 00:31, 23 October 2007 (UTC) Here's a .pdf file for use in a class at Rowan University: http://users.rowan.edu/~hesketh/0906-316/Handouts/Catalytic%20Rates&delP.pdf I would certainly hope that there are more and more teachers out there who follow the recommendations of the standards organizations. I remember how grateful I was ages ago when I had a college professor who insisted on using SI, relieving us of all the confusion of angstroms and ergs and the like. Too bad Wikipedia hasn't caught up to that yet, though it is pretty good in most areas. Gene Nygaard 00:41, 23 October 2007 (UTC)
The two are exactly the same and I think we should use the one that is more common. Searching on Google for "M s-1" enzyme returns 11,700 hits, while doing the same for "mol s-1" enzyme only returns 767. If we use a different set of units from everybody else this is just going to make things difficult for our readers. Let's just follow the literature. Tim Vickers 01:21, 23 October 2007 (UTC)
Could someone please fix the terminology in question? Currently it reads: mol-1 L-1 s-1. Regardless of whether you use M or mol L-1, mol-1 L-1 is incorrect. To input on the discussion, I do not consider Google the best place to look for scientific articles. Pull out a journal like Biochemistry and read through it. I have yet to find an article that does not use the more conventional M in place of mol L-1. Be forewarned that a significant proportion of the scientific community will favor the use of M, in which case it can hardly be considered obsolete. BobertWABC 19:58, 26 October 2007 (UTC)
Biochemistry
Journal of Biological Chemistry
Hey Gene, should we be woried that no one uses Pascals? I find it incomprehensible that wikipedia is still using atmospheres, bars, mmHg AND pounds per square inch! David D. (Talk) 03:16, 26 October 2007 (UTC)
FYI The most recent edition of the major international Biochemistry textbooks ((Voet, Lehninger, Garret & Grisham) all use M-1 s-1 format. All of my previous research articles have also used the same format. Not sure why there is a desire to change it, since it is the most prevalent and commonly used form. "We should be understandable to scientifically literate people, without them having to learn, especially when it comes to measurements, an arcane jargon peculiar to a specific field of endeavor." The concept of Molarity (M) is taught in high school Chemistry and once again in freshman level Chemistry, so calling it arcane jargon is specious. To me M-1 s-1 is more accessible of a unit that mol-1 L d-1, people that know what a mole is, remember what molarity is. If you expect them to think that mol-1 L is the same as M-1 on a first read through, I think you are mistaken. if this article is for the masses then lets go back to the unit that the majority use Hichris 21:18, 8 November 2007 (UTC) Straw pollM−1 s−1
mol−1 L s−1 Lack of foundation, object to relevance and phrasing and choices and much more
CommentsI would like to point out that in the current version of the International Union of Biochemistry and Molecular Biology's nomenclature recommendations ( http://www.iubmb.unibe.ch/ -> Publications -> Biochemical Nomenclature -> Nomenclature Website -> ( http://www.chem.qmul.ac.uk/iubmb/nomenclature/) -> Enzyme Kinetics -> 13. Summary of recommended symbols) allows for the use of M (molar):
That is to say, the recommendations of an international body writing on the specific point at hand differ from the recommendations of a standards body of a particular country, writing about the topic in generalities. -- 17:03, 6 December 2007 (UTC) |
I believe the arrows in the second half of the diagram are going the wrong direction - P and Q are leaving the complex, not being added, so the arrows should be pointing away from the hexagonal pathway. IMKatgrrl ( talk) 11:01, 23 October 2009 (UTC)
I sincerely apologize if I am being stupid, but this picture, which appears in the first section after the lead in the article, makes very little sense to me. If I understand correctly, whenever the article talks about the rate of reaction for a given concentration of substrate, it means the instantaneous or initial rate. So I take "at relatively high substrate concentrations, the reaction rate asymptotically approaches the theoretical maximum; the enzyme active sites are almost all occupied and the reaction rate is determined by the intrinsic turnover rate of the enzyme" to mean that if you've got very concentrated substrate then the enzyme will just eat away at the substrate, and the reaction will go at pretty much the same speed, since it was at the maximum already, but then after a while the rate will drop as the substrate is depleted. The figure, on the other hand, appears to bear no relevance to the caption, showing enzymes making ... more and more substrate over time? Please explain. Leonxlin ( talk) 04:14, 18 August 2011 (UTC)
Under "Linear plots of the Michaelis–Menten equation" the article seems to be too focused on Lineweaver-Burk, which is probably the worst of all the plots mentioned. Would it be worth changing this to Eadie-Hofstee or Hanes-Woolf, or just removing the focus on any one plot?
Esotera ( talk) 10:57, 4 January 2012 (UTC)
Agree it should be changed. Who ever maintains this page I would recommend you use Lineweaver-Burk as an example of how not to analyse kinetic data. Rhodydog ( talk) 00:29, 19 March 2013 (UTC)
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The use of the word "quickly" in the sentence "The two most important kinetic properties of an enzyme are how quickly the enzyme becomes saturated with a particular substrate, and the maximum rate it can achieve." ( Enzyme kinetics#General_principles) is very misleading because it seems to relate to time, whereas the MM model describes steady-state kinetics... What about "how easily it is saturated..." instead? Lewisiscrazy ( talk) 09:17, 21 January 2018 (UTC)
I think it would be useful to add a subsection entitled "Reversible catalysis and the Haldane equation" in the section about Single substrate reactions. I have worked on this draft https://fr.wikipedia.org/wiki/Utilisateur:Lewisiscrazy/Brouillon-2, what do you think? can somebody contribute? Lewisiscrazy ( talk) 15:41, 21 January 2018 (UTC)
This 2006 Featured article has not been maintained to WP:WIAFA standards. Unless someone can cite the considerable amount of uncited text, the article should be submitted to Featured article review. SandyGeorgia ( Talk) 21:03, 13 December 2020 (UTC)
![]() | This article is written in British English, which has its own spelling conventions (colour, travelled, centre, defence, artefact, analyse) and some terms that are used in it may be different or absent from other varieties of English. According to the relevant style guide, this should not be changed without broad consensus. |
![]() | Enzyme kinetics is a featured article; it (or a previous version of it) has been identified as one of the best articles produced by the Wikipedia community. Even so, if you can update or improve it, please do so. | |||||||||||||||||||||
![]() | This article appeared on Wikipedia's Main Page as Today's featured article on October 22, 2007. | |||||||||||||||||||||
|
![]() | This article is rated FA-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | ||||||||||||||||||||
|
Priority 3
|
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)
In fact, there is nothing in the Rate of enzyme mediated reactions page that is not in the other enzyme pages. What about?
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)
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)
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?
How is it that extremely useful self propelled "blueprints" seem to be universally available?
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)
Is it a B-class article? My suggestions:
Anyway well-referenced, well-written, you should consider FAC. NCurse work 10:57, 23 September 2006 (UTC)
It's a good article now. Well done! :) NCurse work 18:14, 24 September 2006 (UTC)
Not really sure this is the right page for this but I wonder if we need a passage discussing the biological significance of Km. I think this would help people relate more to these numbers. For example, physiological substrate concentrations are often quite close to the Km. Different isozymes can have different Km 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)
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?
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/abs/physics/0609227) Suu 14:35, 26 January 2007 (UTC)
I haven't been able to read the whole article yet, but through skimming and searching I can't see any mention of the action of temperature on enzyme kinetics (e.g. exponential increase of activity then sudden denaturation, different optimums in coldblooded and warmblooded animals, thermophiles etc), and there also seem to be little on the effects of chemical factors (such as pH changes, different environments in various organs and organelles). The article is no doubt of a high quality, but these seem to be serious omissions for a featured article. They are mentioned briefly in the enzyme article, and I was expecting the main discussion of them to be here. Richard001 04:45, 31 July 2007 (UTC)
A surprisingly long and vigorous discussion on a small point of nomenclature |
---|
The following discussion has been closed. Please do not modify it. |
User:TimVickers said see talk, but went to my talk page instead and based his argument on a recent, disputed addition top the MoS by none other than User:TimVickers. See Wikipedia talk:Manual of Style#Units of measurement. Gene Nygaard 23:45, 22 October 2007 (UTC) Here is what NIST has to say about it:
NIST Special Publication 811, Guide for the Use of the International System of Units (SI), 1995, section 8.6.5 [1] Gene Nygaard 23:53, 22 October 2007 (UTC)
It's not evident on this web page abstract, but according to the text visible in my Google search, this one does (in the form mol/(l s), which is the same thing in case anyone is unfamiliar with the superscript notation which I merely continued as it existed before):
Gene Nygaard 00:22, 23 October 2007 (UTC) I'll just cite a web link for this abstract, http://www.maik.ru/abstract/polscia/98/polscia9_98p871abs.htm
Gene Nygaard 00:31, 23 October 2007 (UTC) Here's a .pdf file for use in a class at Rowan University: http://users.rowan.edu/~hesketh/0906-316/Handouts/Catalytic%20Rates&delP.pdf I would certainly hope that there are more and more teachers out there who follow the recommendations of the standards organizations. I remember how grateful I was ages ago when I had a college professor who insisted on using SI, relieving us of all the confusion of angstroms and ergs and the like. Too bad Wikipedia hasn't caught up to that yet, though it is pretty good in most areas. Gene Nygaard 00:41, 23 October 2007 (UTC)
The two are exactly the same and I think we should use the one that is more common. Searching on Google for "M s-1" enzyme returns 11,700 hits, while doing the same for "mol s-1" enzyme only returns 767. If we use a different set of units from everybody else this is just going to make things difficult for our readers. Let's just follow the literature. Tim Vickers 01:21, 23 October 2007 (UTC)
Could someone please fix the terminology in question? Currently it reads: mol-1 L-1 s-1. Regardless of whether you use M or mol L-1, mol-1 L-1 is incorrect. To input on the discussion, I do not consider Google the best place to look for scientific articles. Pull out a journal like Biochemistry and read through it. I have yet to find an article that does not use the more conventional M in place of mol L-1. Be forewarned that a significant proportion of the scientific community will favor the use of M, in which case it can hardly be considered obsolete. BobertWABC 19:58, 26 October 2007 (UTC)
Biochemistry
Journal of Biological Chemistry
Hey Gene, should we be woried that no one uses Pascals? I find it incomprehensible that wikipedia is still using atmospheres, bars, mmHg AND pounds per square inch! David D. (Talk) 03:16, 26 October 2007 (UTC)
FYI The most recent edition of the major international Biochemistry textbooks ((Voet, Lehninger, Garret & Grisham) all use M-1 s-1 format. All of my previous research articles have also used the same format. Not sure why there is a desire to change it, since it is the most prevalent and commonly used form. "We should be understandable to scientifically literate people, without them having to learn, especially when it comes to measurements, an arcane jargon peculiar to a specific field of endeavor." The concept of Molarity (M) is taught in high school Chemistry and once again in freshman level Chemistry, so calling it arcane jargon is specious. To me M-1 s-1 is more accessible of a unit that mol-1 L d-1, people that know what a mole is, remember what molarity is. If you expect them to think that mol-1 L is the same as M-1 on a first read through, I think you are mistaken. if this article is for the masses then lets go back to the unit that the majority use Hichris 21:18, 8 November 2007 (UTC) Straw pollM−1 s−1
mol−1 L s−1 Lack of foundation, object to relevance and phrasing and choices and much more
CommentsI would like to point out that in the current version of the International Union of Biochemistry and Molecular Biology's nomenclature recommendations ( http://www.iubmb.unibe.ch/ -> Publications -> Biochemical Nomenclature -> Nomenclature Website -> ( http://www.chem.qmul.ac.uk/iubmb/nomenclature/) -> Enzyme Kinetics -> 13. Summary of recommended symbols) allows for the use of M (molar):
That is to say, the recommendations of an international body writing on the specific point at hand differ from the recommendations of a standards body of a particular country, writing about the topic in generalities. -- 17:03, 6 December 2007 (UTC) |
I believe the arrows in the second half of the diagram are going the wrong direction - P and Q are leaving the complex, not being added, so the arrows should be pointing away from the hexagonal pathway. IMKatgrrl ( talk) 11:01, 23 October 2009 (UTC)
I sincerely apologize if I am being stupid, but this picture, which appears in the first section after the lead in the article, makes very little sense to me. If I understand correctly, whenever the article talks about the rate of reaction for a given concentration of substrate, it means the instantaneous or initial rate. So I take "at relatively high substrate concentrations, the reaction rate asymptotically approaches the theoretical maximum; the enzyme active sites are almost all occupied and the reaction rate is determined by the intrinsic turnover rate of the enzyme" to mean that if you've got very concentrated substrate then the enzyme will just eat away at the substrate, and the reaction will go at pretty much the same speed, since it was at the maximum already, but then after a while the rate will drop as the substrate is depleted. The figure, on the other hand, appears to bear no relevance to the caption, showing enzymes making ... more and more substrate over time? Please explain. Leonxlin ( talk) 04:14, 18 August 2011 (UTC)
Under "Linear plots of the Michaelis–Menten equation" the article seems to be too focused on Lineweaver-Burk, which is probably the worst of all the plots mentioned. Would it be worth changing this to Eadie-Hofstee or Hanes-Woolf, or just removing the focus on any one plot?
Esotera ( talk) 10:57, 4 January 2012 (UTC)
Agree it should be changed. Who ever maintains this page I would recommend you use Lineweaver-Burk as an example of how not to analyse kinetic data. Rhodydog ( talk) 00:29, 19 March 2013 (UTC)
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Cheers.— cyberbot II Talk to my owner:Online 02:24, 23 June 2016 (UTC)
The use of the word "quickly" in the sentence "The two most important kinetic properties of an enzyme are how quickly the enzyme becomes saturated with a particular substrate, and the maximum rate it can achieve." ( Enzyme kinetics#General_principles) is very misleading because it seems to relate to time, whereas the MM model describes steady-state kinetics... What about "how easily it is saturated..." instead? Lewisiscrazy ( talk) 09:17, 21 January 2018 (UTC)
I think it would be useful to add a subsection entitled "Reversible catalysis and the Haldane equation" in the section about Single substrate reactions. I have worked on this draft https://fr.wikipedia.org/wiki/Utilisateur:Lewisiscrazy/Brouillon-2, what do you think? can somebody contribute? Lewisiscrazy ( talk) 15:41, 21 January 2018 (UTC)
This 2006 Featured article has not been maintained to WP:WIAFA standards. Unless someone can cite the considerable amount of uncited text, the article should be submitted to Featured article review. SandyGeorgia ( Talk) 21:03, 13 December 2020 (UTC)