Talk:Enzyme

As an enzymologist, a few notes:

I've read the discussion below and I really feel that the article must at least mention ribozymes and link to a more specific article.

The kinetics section needs some work. The Briggs-Haldane equation isn't even mentioned, and the use of double recipricol plots is not very common in research, except possibly as a quick test but it is so easy to fit the data properly now that I don't know anyone who uses them.

No mention of transient kinetics?

Any thoughts/objections? Hichris 21:57, 30 November 2005 (UTC)

• Welcome! Those sounds like excellent suggestions. Be bold and start editing. (An aside: the usual convention is to add things to the bottom of talk pages: it makes following along a little easier). Turnstep 03:27, 1 December 2005 (UTC)

competitive inhibition of succinic dehydrogenase by malonate

Somebody wrote: "The inhibitor may bind to the substrate binding site as shown in the figure below, thus preventing substrate binding. Alternatively, binding of substrate to a different binding site may change protein conformation in a way that prevents substrate binding, while substrate binding changes protein conformation to prevent inhibitor binding. These two possibilities can not be distinguished by enzyme kinetics (X-ray crystallography would be a suitable method), thus the frequently found statement that competitive kinetics proves inhibitor binding at the substrate site is "false". A well-known example is inhibition of enzyme succinic dehydrogenase by malonate."

I searched the primary literature as well as text books but could only find the statement that malonate is a competitive inhibitor of succinate dehydrogenase? Please give a reference to a primary literature that says that malonate acts as competitive inhibitor not by binding in the active site but by binding somewhere else. It is definitly not a "well-known example"! TimBarrel

New Diagram

It occurred to me that the diagram we had didn't emphasize that the lowered activation energy was reached more quickly and led to the reaction going to completion more quickly, so I attempted to edit it to show this. My drawing skill sucks, but anybody who wants to improve the diagram, feel free. Gzuckier 20:20, 25 Feb 2005 (UTC)

I have a question... Do enzymes exist in food? If so are they used by our body as they come?

Yes, enzymes are components of many foods, but the more processed the food, the more likely the enzymes have been permanently inactivated. I can't think of any case where a food enzyme is 'used' by the body. In general, the digestive system treats enzymes the same as it treats other, non-enzymatic proteins. They are digested and the smaller molecular pieces that made up enzyme are used in the body's metabolism. ike9898 19:06, Feb 25, 2005 (UTC)

There is a quack dietary fad which holds that cooking destroys the enzymes in foods which are needed by the body. Hence, you should eat raw foods. It's pretty much bogus. There are no examples as far as I know in which an enzyme from food is incorporated into the body. As a matter of fact, very few enzymes can survive the harsh environment of the stomach (which has very low pH and lots of proteases) other than those specifically adapted to be there. Unless you have a specific digestive disease, your body should be producing all the enzymes it needs. --Theyeti 20:26, 4 Apr 2005 (UTC)

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What factors affect enzyme action?

Try this page: Rate of enzyme mediated reactions Bensaccount 19:46, 30 Dec 2004 (UTC)

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Could you write example methabolic track for each inhibition method ? --Taw

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is the last figure too large on small screens?

It's not necessarily that the figure is too large, but the text on the side of it is squished down to a column width of one or two words, and so extends about a screen height above and below the image. It looks... quite wrong. --Brion

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Stupid point, but in the discussion of enzymatic inhibitors, the example of carbon monoxide binding to hemoglobin was used for competitive inhibition. Thing is, hemoglobin is not an enzyme, it is a transport protein. David M

A better example might be sulfonamide inhibition of folic acid synthesis in bacteria. Sulfonamides are competitive inhibitors of PABA. --David M

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This is a suggestion, but for each enzyme (or protein for that matter) that an article is written about, take a look at the Protein Data Bank and see if a structure for the enzyme exists. It will be recorded by a 4 alphanumeric character index symbol that should be placed in the article. As well, another number, the "E.C." number is used to characterize enzymes, and that should be recorded as well. Dmyers

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The section on 'enzymes and digestion' does not represent mainstream science. It seems to be written by an advocate of 'the living foods diet' mentioned in the article. I am trying to fix what I can, but need the help of nutritionist. Beyond this, I am wondering if this subject is even fits on this page. Digestion is only a very limited part of the role of enzymes in living systems. User:Ike9898

I agree, some of that stuff about 'food enzymes' seems highly questionable to me. The idea that 'foods' contain enzymes to facilitate their own destruction is somewhat comical and panglossian. Care to explain yourself, TonyClarke? Graft 20:58 25 Jun 2003 (UTC)

Hi guys: I agree that what I wrote is not as scientific in tone as the rest of the article, and so might be best placed elsewhere. However, if enzymes are as important in digestion as some people think then maybe it should stay. I also agree that it is not mainstream science, in the sense that the role of enzymes is not fully understood or agreed, as I tried to point out. Also I agree that a nutritionist would be helpful to contribute here.

Having said all that, there are a lot of pointers to the importance of enzymes in food digestion, particularly the enzymes present in food itself. My daughter at high school says she is taught that food has its own enzymes, but not that they are essential to good digestion. See also the Joel Fuhrman book on Wikipedia, particularly the paragraph on enzymes in raw food p 45 chap2, English edition, and the reference there to what seems like respectable research, quoted as Wright State University School of Medicine, Prochatska and Pickupatia, 1994 "On the synergistic effects of enzymes in food with enzymes in the human body..."Med Hypothesis 42(6),355-362.

There are other sources around if you search on Google, but some of them are non NPOV, ie commercial promotion masquerading as science. Thanks for your comments and I look forward to your further thoughts.

TonyClarke 00:12 27 Jun 2003 (UTC)

I am not a nutritionist, but I do have a degree in Biochemistry. I am going to try really hard not to make this a rant against the Living Foods Diet, or harp on some of the incorrect statements above. But let me stick to the point, which is that I see no need to single out digestion when talking about enzymes except to bring up the living foods diet. If you consider that all living things have enzymes but only a small branch of the phylogenetic tree has a digetive system, I am not even sure that digestion makes the top ten list of important enzymatic processes. Some more talk about metabolism would probably be more worth while. Or perhaps pick a digestive enzyme (of which there is a lot known about) and describes how it works and the reaction it catalyzes. Also I think I noticed one of the users above is a biochemical engineer, a part dicussing enzymes in industry would be cool. Maybe I will come and make some of this changes myself but I am fairly new to this and still feel a little strange deleting some else's work. But once agian, I vote delete the part on digestion.

DiJay

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OK,you're right, this stuff does look a bit out of place, I'll look at it again and probably delete it. Welcome to Wikipedia!

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Ribozyme debate

I reverted the edits that said "enzyme" could refer also to RNA. Unless things have changed in the last couple years, biochemists never use the word enzyme alone to refer to an RNA. You'll read or hear them say "RNA enzyme," but you'll hear people say "vegetarian lasagna" too, which doesn't mean that "lasagna" now means either a tomato-noodle casserole with meat or a tomato noodle casserole without meat. "Lasagna" implies meat unless modified by "vegetarian", and "enzyme" likewise implies protein unless modified by "RNA." If people want a one-word reference to a catalytic RNA, there's a perfectly good one available--it's "ribozyme." 168... 04:28, 27 Oct 2003 (UTC)

You are right in a narrow technical sense of protein biochemist, but biologists in general, sometimes speaking loosely, will still use the word "enzyme" to also mean a molecule, as you note, with "enzymatic" capability, i.e. a molecule that has catalytic ability. If not in the definition para of an enzyme, I would still suggest a para or two outlining this very fact, especially given that there is not a single link to ribozyme in the entire article, and the two things are not entirely unrelated, especially when it comes to certain theories of the origin of life. --Lexor 09:19, 27 Oct 2003 (UTC)

There was a big hoopla about discovering catalytic RNA (and later, DNA) -- and broadening the definition of "Enzyme". I think the scientific community has largely accepted the broadening (as opposed to the restriction of enzyme to proteins -- otherwise we wouldn't have a useful term to encompass all biological catalysis. While nonscientific sources (like merriam-webster online) have not caught up, there are many scientific sources which are very careful about being broad about the definition of enzyme:

[1] [2] [3]

If HHMI, PNAS, and nature do it, then so should wikipedia. Furthermore, if enzyme only means protein we get some problematic terms like "ribozyme enzymology" -- nobody says "ribozymology" to refer to the study of kinetics, thermodynamics, etc of ribozymes. As for lasagna, that is an incredibly poor example, because lasagne does not imply meat, as the wikipedia article will show, rather it implies layered pasta. Similarly, historically enzyme has implied "biological" more than "protein", it just so happens that for about 50 years or so the only known biological catalysis was performed by proteins, therefore the strong association.

a bit of clarification on the ribozyme debate. probably this comes from the 1982 article first reporting catalytic RNA - kruger, et. al cell (1980) "because the ... RNA is not an enzyme but has some enzyme-like characteristics, we call it a ribozyme". since then, as the dates on the more recent articles show, researchers have taken to calling them RNA enzymes. some feel that the term ribozyme is kludgy, and the general scientific community has seemed to have accepted the broader definition -- i personally have sat in on biology lectures where it has been said "most enzymes are proteins -- though there are some exceptions". of course, when one mentions "enzyme" the default thought is "protein", as it should be, but wikipedia should respect the difference between connotation and denotation and not conflate the two.

The section above was contributed by anon user 137.131.130.84. The use of biopolymer is obviously contentious and the anon user keeps refering to the discussion above in his/her edits. It took me a while to figure out the anon users contribution on this talk page since it was unsigned. Now the anon user is editing from a diferent IP (137.131.130.109). Could the anon user please use a login name and sign messages so we can follow the edits more easily? Personally I do not like the use of the word biopolymer and would prefer some compromise that recognises that the majority of enzymes are protein. David D. (Talk) 23:34, 29 August 2005 (UTC)

more references:

MIT article

Nobel prize lecture

I totally agree that the article should talk about ribozymes. I just didn't feel like taking the time to do it then myself. I was just correcting what I saw and still see as a mistake in the definition of the stand-alone word (I suspect that in the loose talk you're thinking about, the word "RNA" must crop up very near to the word "enzyme"--as in "that RNA there is an enzyme," ala "that lasagna there is vegetarian" --because it's hard for me to see how people could understand what was being said otherwise). 168... 16:41, 27 Oct 2003 (UTC)

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Moved this paragraph added by anon IP contributor to the article to Talk, which seems of dubious quality and accuracy:

Cooking food kills enzymes.

mostly true

Enzymes die at around 116 degrees.

way too generalized

Our pancreas produces enzymes,but it was meant only as a backup system,it can produce just so many enzymes and when it runs out we can no longer live.

Just plain wrong

Enzymes also kill cancer cells that occur in out body regularly.

Way too simplistic, and particularly in this context it's pretty much wrong

Great success has been reported using enzymes to turn maligment cancer cells into non-maligment,effectivly killing the cancer.

In the sense being used here, pretty much wrong.

The enzymes responsile for this are trypsin and chymotrypsin,but they were taken out of almost all digestive enzmes available to the public,except in small doses and are now used in sewage treatment plants to breakdown raw sewage.

Pretty confused

Enzymes are molecules, so they can't "die", but because they are proteins they can denature, perhaps it can be reworded. I don't know where the 116 degrees (C or F?) comes from, is that the temp. for the denaturation of all enzymes? The rest is somewhat poorly written, could somebody who knows more about enzymes, please review and clarify which claims are true and just badly expressed, and which are just way off? At the very least it needs some serious copyediting. --Lexor 10:19, 24 Nov 2003 (UTC)

OK, see above. My final verdict, don't put it back in. Gzuckier 19:22, 25 Feb 2005 (UTC)

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116 is Farenaith. In Celsius would be arouns 40 something.

Lost enzymes

These are a list of enzymes in the Wikipedia:Orphaned_Articles list they could certainly do with being properly catagorized and adopted on a page or two. I know absolutely nothing about the subject (perhaps I should read the article) that is why I am dumping them here in the hope that one of you clever bods know what to do.

Phosphoglucomutase, Protein disulfide isomerase, Uridine monophosphate synthetase, ATCase, DNase I, DnaB helicase, Enoyl CoA isomerase, Galactokinase, Glucose Oxidase Enzyme

Some of those are DNA enzymes which deserve to be in the DNA article. Or maybe an article describing the proteins involved in DNA replication. I haven't decided yet. I'll give it a look. --G3pro 13:30, 22 Sep 2004 (UTC)

Defaced

Somebody has defaced the enzyme page somewhat

• Thanks for bringing this to our attention. See also Wikipedia:Vandalism in progress. -Fennec (はさばくのきつね) 21:50, 18 Oct 2004 (UTC)

Some Suggestions

Why is there a section on protein purification here? It is basically content free and irrelevant IMO.

Secondly, why is there a section on the quantum mechanical model of enzymes? There is no actual explanation of the model. I don't know what people thought in 1972, but as things stand today, quantum mechanics is considered to be mostly irrelevant to enzymology, because the molecules involved are too large, with the possible exception of the hydride transfer.

It would make more sense to have an overview of the lock and key model, the induced fit model, and then a comparison to contemporary views. --Theyeti 04:40, 17 Nov 2004 (UTC)

Ready for FAC?

This looks like a great article overall, but I don't know enough about the topic to know if some of the criticisms of the article in above previous sections are correct and should be implimented or not. If so can someone that is qualified do so, and nominate this on Wikipedia:Featured article candidates? The nomination will only work if someone qualified is willing to fix the criticisms it recieves there. Thanks - Taxman 23:26, Feb 23, 2005 (UTC)

• Well the the list of enzymes at the end need to be double-checked and put in the list of enzymes article if they're missing (categorized and all). But, yes, I had the same feeling the moment I saw the article. I'll have to read thouroughly to see if it's ready though. - Mgm|^(talk) 11:32, Mar 28, 2005 (UTC)

Origin of the term

There are two different meanings for the greek root words listed. Someone more knowledgable than me, please address this. 128.61.70.49 06:06, 28 Apr 2005 (UTC)

"zyme" = "leaven" as per Merriam-Webster; I suspect there are a number of other reasonable translations for it, but ours ought to at least match. - Nunh-huh 06:12, 28 Apr 2005 (UTC)

wrong diagram

the diagram http://en.wikipedia.org/wiki/Image:Activation2.JPG is wrong the blue line is wrong, it does not join the red line at the start of the reaction, the peak should be in the middle.

Well, time is used as the independent variable. -- Jerry Crimson Mann 10:37, 29 July 2005 (UTC)

Removed section

A user removed the following, saying it was speculation. Could someone verify it before it gets put back in?

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). It is because the precise structure of each region tends to be fairly critical to correct function, and 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. This has the additional effect of making each region act, relative to mutation, somewhat like an independent subunit which can be duplicated, deleted, moved, or "mixed-and-matched" with other such regions, generating new proteins to be tested for evolutionary success. This would seem to be a more efficient process in terms of the likelihood of successfully generating functional new enzymes than would having the functionally related amino acids of the active site widely dispersed throughout the amino acid chain, with random mutation occurring anywhere.

Dave (talk) 17:46, August 2, 2005 (UTC)

The sequence of amino acids in a protein determines its three-dimensional shape, which in turn confers its function. Segments of the protein that are critical to its function resist evolutionary pressures because mutations of such segments are often lethal to the organism. These critical "active sites" tend to be conserved over time and so can be found in many organisms and proteins that have similar function. Analogously, functionally important segments of an organism's DNA tend to be conserved and to recur as common motifs. In this chapter, the author introduces algorithms for comparing DNA and protein sequences to reveal similar regions. Particular attention is given to the problem of searching a large database of catalogued sequences for regions similar to a newly determined sequence of unknown function. [4] Gzuckier 19:57, 2 August 2005 (UTC)

CO₂ concentration and balance

Shouldn't the comment at the lower equation at Enzyme#Thermodynamics say "in lungs - low CO₂ concentration"? Otherwise there would be no clear reason why the reaction should be reversed there. — Pt _(T) 08:35, 5 August 2005 (UTC)

Seems like it's been fixed by now. — Pt _(T) 07:56, 18 September 2005 (UTC)

Quantum mechanics

Someone keeps adding a section on quantum mechanics, with a reference of a Word doc on a geocities page, that starts out the second paragraph with "In 2004, in the Internet were published many articles about the works of above mentioned scholars". As I've written the person who keeps submitting this, we need a better reference than this. A paper in a peer-reviewed scientific journal would be a good start. I's also be willing to hear from our new enzymologist about the paragraph that was removed:

The lecture "Quantum Theory of some Biochemical Reactions", presented to the IV International Biophysical Congress (Moscow, 1972) by R.R. Dogonadze and Z.D. Urushadze, formulated the first quantum-mechanical (physical) model of the simplest form of enzyme catalysis. In 1972-1975, in the works of M.V. Volkenshtein, R.R. Dogonadze, Z.D. Urushadze, A.K. Madumarov, Yu.I. Kharkats and V.K. Khidureli were formulated the first Quantum-mechanical Theory of Enzyme Catalysis. These works demonstrated also the role of conformational transformations in catalytic reactions and supported a theory that enzyme catalysis use quantum-mechanical effects such as tunneling.

Does this belong on the page? Thanks. Turnstep 04:04, 1 December 2005 (UTC)

This specific paragraph doesn't really tell me much and as such I don't feel should be part of the article. However, any time individual electrons or protons are involved, quantum mechanics plays a role. In enzyme kinetics, tunneling plays a very important role and therefore needs to be mentioned. Hichris 22:37, 2 December 2005 (UTC)

But this article should not be about enzyme kinetics. I wonder if the enzyme kinetics should be consolidated on another page. Preferably on the page Enzyme kinetics, although i notice that this is currently a redirect. There are currently seperate pages for competitive, non-competitve etc. reactions. this realy should be together since they related to each other very closely. David D. (Talk) 07:42, 5 December 2005 (UTC)

Some basic kinetics should be covered in this page--nixie 07:44, 5 December 2005 (UTC)

I agree, but possibly laymans terms here, with a "main article:Enzyme kinetics" pointer to more detailed text at the start of each section. This article is overly long, in my opinion, and tries to cover too much depth with inhibitors. I know the inhibitors are not in the kinetics section, but that topic should be regarded as kinetics since it addresses all the changes to Km and Vmax. David D. (Talk) 07:55, 5 December 2005 (UTC)

The current 2 paragraph section still needs to be reworked a bit, however adding a third paragraph on Inhibition and moving the details and figures from the Inhibition section to an Enzyme kinetics article would be my vote. If someone wants to start on this I'm happy to help. Possibly a merge of the Rate of enzyme mediated reactions (which Enzyme kinetics currently redirects to) with the detailed Inhibition material would be best.

Hichris 15:25, 5 December 2005 (UTC)

To Urushadze or whoever continuosly puts info on quantum stuff in, please discuss here why it is relevant. Electron tunneling was established in the 1960s and Proton tunneling was proposed before your 1972 paper, HJ Gold has a 1971 paper about it. Please let us know why you think your work belongs here, because what the article says now doesn't rely on it. If there is something in the article that should be expanded, please explain, but perhaps it would be better suited in another article. Hichris 21:20, 15 December 2005 (UTC)

Dear friend, Electron tunneling was established in 1959-1960 and Proton tunneling in 1970 by Professor Revaz R. Dogonadze and his coworkers. The first Quantum-Mechanical Model of Enzyme Catalysis was formulated in 1971-1972. Please read my addings on the article and additional references carefully. Please, read also the Revaz Dogonadze Memorial Issue of the Journal Electroanal.Chem., Vol. 204, 1986. With kind regards, Prof. Dr. Zurab D. Urushadze, 16 December 2005

This article is a basic introduction to enzyme. This topic you are trying to introduce to this article is not appropirate for the target audience. If you want to start a new article on the topic go ahead but don't scare people off by adding it here. David D. (Talk) 04:29, 17 December 2005 (UTC)

Metabolic pathways and allosteric enzymes

Does this section add much to the article, I don't find it very informative. The Metabolic pathway article covers nearly all of this material. The allosteric effector info could be added to a more concise kinetics section. Any thoughts?

Hichris 19:03, 5 December 2005 (UTC)

I am with you in this analysis. In my mind this article should be briefer and more an introduction to the topic with links to the more complete articles in enzyme kinetics and metabolic pathways. It it a lot of work to consolidate the kinetics articles which is why i have been reluctant to start but it definitely needs attention in the future. David D. (Talk) 20:53, 5 December 2005 (UTC)

Vandalism

The user 81.139.75.141 will stop vandalising this page or the IP address will be permanently blocked from Wikipedia and all of its sister projects.

—gorgan_almighty 12:26, 8 December 2005 (UTC)

Clean Up

Quantum stuff, I believe that (Urushadze) one of the authors of the cited quantum mechanics articles is the one who continuosly put the info in. However, doing a simple search I found at least one reference from 1971 on tunneling in an enzyme, which is before the first article continuously cited. Perhaps a bit more history of tunneling, etc., prior to their work would be helpful in explaining this, so if you have something to add please do so.

I have begun streamling the article to remove redundant information beginning with the cofactor sections. If you think something should be added back, feel free, but please state why. I hope to begin tackling the kinetics section next week. Hichris 18:17, 9 December 2005 (UTC)

• Wow, this article is the envy of so many other science articles, but it is a tad messy! Towards the bottom the tables seemed cluttered. Perhaps some stricter boarders? I just don't know, coding tables has always hurt my head...

Adenosine | Talk 01:07, 10 December 2005 (UTC)

I have continued my clean up, however I'd like some opinions/help with a few things:

• The image of Factor D, really doesn't serve any purpose, so I plan on removing it but I don't want to leave the area "empty". I think perhaps a real enzyme reaction mechanism or the like might look good there, but it would need to be relatively simple and clear. Anyone know of an image or can make one? Trypsin might be a good one to try. If you other thoughts please share.

• The applications table at the bottom is a bit long and not very "pretty", but I don't see a good way to "fix" this. Hichris 20:26, 12 December 2005 (UTC)

I removed the Factor D image, and made the other one larger. I never liked the Factor D one anyway, and I don't think it needs replacing, as the other one is nicely detailed. I'll see what I can do about the table. All those diagrams are formatted pretty ugly too. They're next, if I get the time. Turnstep 23:10, 12 December 2005 (UTC)