Talk:Enzyme/Archive 2

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Enzymes and Heat

I removed the following section

"Enzymes are very vulnerable to heat. Rising the temperature of the substance that contains the enzyme can usually induce it to lose its tertiary structure. Once the substance is once again cooled off the enzyme will often fold back, but usually not in its previous folding. For this reason once they have been through this process of heating and cooling an enzyme is often not active anymore."

This section is very generalized, there are enzymes are not sensitive to heat (from thermophiles). There are also enzymes that can refold after being heated. The phrasing is also a bit awkward. Certainly many enzymes can be heat inactivated, but it does not warrent a section in itself, perhaps a sentence added towards the beginning of the 3-D structure, but it would be better if there was a paragraph describing what primary, secondary, and tertiary structure were before describing how it is disrupted. Any thoughts? Hichris 16:28, 23 January 2006 (UTC)

It surely can be improved, and please do help to fix it. But taking it off hardly seems the solution. Yes, there should be more information on what are primary, secondary and tertiary structure. I suppose there are also entries in wikipedia for them so we could refer to them in the meantime. I should try to put it back inserting your information inside. Please, don't just take it off. Adapt, modify, integrate. Thanks, Pietro--Pietrosperoni 16:51, 23 January 2006 (UTC)

I readded the information, as you said in the 3-D structure. I tried to integrate with the information you inserted. If it does not sound nice please don't delete it, but try to fix it. I totally agree that there should be a section on folding and this should be part of it. For now I added a link to tertiary structure and if you feel like starting the section on folding then we can add it to it.--Pietrosperoni 17:09, 23 January 2006 (UTC)

If I have time I'll work on it, the phrasing is very awkward in my opinion, so that the info was not very useful which is why I removed it. For example "Rising the temperature of the substrance that contains the enzyme" is overly wordy and somewhat confusing.Hichris 18:48, 23 January 2006 (UTC)

Most of the info that is relevant is already included in the protein article, I've reduced the information in this article to a sentence. Perhaps another line about structure would be good along with the appropriate links to other articles. Hichris 21:09, 23 January 2006 (UTC)

Seems fine. I just added an internal link to tertiary structure without changing the outer wording.--Pietrosperoni 23:09, 23 January 2006 (UTC)

Enzyme in Greek

On the opening sentence there is an error in the transliteration of Greek into English regarding the word "Enzyme". It should be rendered into English as "en" = in or at, and "zume or zumos" (alternatively zyme and zymos, where u and y are the same) = yeast, leavened and not given the pronunciation/transliteration of "ensimo". Sorry just thought it would help the reader. Other than that the Greek spelling is correct.

If this is correct then it should be changed--I'm not a greek scholar, but this does follow the german Enzyme article. Hichris 18:15, 7 February 2006 (UTC)

Lock and Key/Induced Fit

I changed back to the simplified figure, because the two small figures are over detailed and not clear at the size they need to be for this general article on enzymes. For a detailed article on substrate binding it may be better. Feel free to make a new figure, but I don't think the current one is ugly.

Also there were many errors reintroduced when the figure was changed. Hichris 18:15, 7 February 2006 (UTC)

What are the errors I'd like to ask? The image you made looks really weird and rather coarse. Just wonder what the wrong would it be if using my images, which shows clear descriptions, and perky illustrations. -- Jerry Crimson Mann

Hey your edits were great but I'm inclined to revert to the older diagrams, they are very well done, very informative and show how the Lock and key model can be used to understand enzymatic action on substrate(s). The new diagrams are too simple and are confusing in my humble opinion, ideas?! Adenosine | Talk 03:02, 8 February 2006 (UTC)

If you'd like to know the error just check the history, e.g., several competitives were changed to competive, several wiki links were removed, etc.

I'm not going to start reverting back and forth, but while the figures that are now there are more detailed, my point is that the detail is lost due to their size, since you call them yours, perhaps you can go back to the originals and make it clear the binding site is changing shape upon binding (it is too subtle) and make the text legible--my eyesight is normal and I can only read the figure text if I move closer to the screen. The reason I liked the simplified figure was that it was apparent what was going on and needed no text--maybe if you used just the first step it would allow you to increase the font size. Hichris 15:15, 8 February 2006 (UTC)

I really don't like the current 3 figures and for the reasons above. I may remove the third because while trying to show induced fit, just confuses the issue. What is shown in the 3rd figure appears to be 3 different bound substrates, which all seem to fit. For those who don't like the simplified figure, please come up with something you like better that resolves the problems Hichris 21:37, 14 February 2006 (UTC)

I haven't heard any responses, should I take that to mean no one wants to fix the figures? Hichris 16:09, 22 February 2006 (UTC)

Catalytically "Perfect" Enzyme"?

In reference to the opening figure of the ribbon diagram depicting the folding of Triosephosphateisomerase, it seems that the description of it as catalytically "perfect" is a misnomer. First of all it seems difficult to describe one enzyme as catalytically perfect considering that most enzymes are substrate specific. Secondly, I would argue that evolution does not create "perfection". Therefore, I believe a more descriptive, useful caption would be "Ribbon Diagram Depicting the Structure of the Enzyme Triose-phosphate isomerase".

Catalytically perfect describes any enzyme which is only limited in rate by diffusion and is commonly used terminology. So it doesn't need to be changed. Hichris 21:38, 14 February 2006 (UTC)

Hichris, what does is only limited in rate by diffusion tell you? That to increase the reaction speed the only thing left is to put the enzymes right next to each other - it's called substrate channeling. This can explain why the enzymes have so many isoforms, they just need to bind to different "substrate channeling" partners. When there is no need for that then we get multyfunctional enzymes like fatty acid synthase. -- Boris 20:02, 17 February 2006 (UTC)

Factual or not, still seems to be fairly strange caption for the first paragraph for the casual reader that has no knowledge of enzymes. Seems that if I was reading an introductory biology book about enzymes and in the first paragraph I saw an figure captioned "catalytically perfect" I would wonder the relevance to the accompanying text (which in this circumstance there is none). Seems like an introduction to jargon minus any explanation. -stuckonempty

I don't think the caption is necessarily bad, but there should be something added to the text about catalytically perfect. The TIM article is only a stub and doesn't really explain things well either. Hichris 15:38, 17 February 2006 (UTC)

The caption certainly attracts your attention. I've been working with that enzyme and never realised why we use it so much. Just about the abbreviation (TIM), in scientific articles one abbreviates TriosePhosphateIsomerase (TPI) since it is significant that is changes one triosephosphate to another. I'll correct it as soon as I have the chance. CBSB 07:38, 29 September 2006 (UTC)

Actually both abbreviations are used, I don't know which is preferred amongst people who study the enzyme. However among those who study protein folds, TIM is used almost exclusively ('e.g' TIM barrel). So I'll change it back to TIM in the article, if you think TPI is popular enough of an abbreviation put it back but keep TIM as well. Hichris 14:18, 29 September 2006 (UTC)

Enzyme Catalysis Models

This section keeps getting added back, in personal discussions it was thought best to remove it, since it was repititive. It may work as a seperate article, which could be linked to here.

If you think it belongs in the article, please discuss it here before adding it back. Hichris 23:22, 4 April 2006 (UTC)

Top disambiguation link

Is it really necessary? It only points to a stub for a Dutch Record label Enzyme Records, maybe if it were more popular or based in an English speaking country it would be worth keeping.

I move it gets deleted, anyone else? Hichris 23:22, 4 April 2006 (UTC)

I personally thought it was kind of odd when I saw it. I say delete it too. --Scienthomas 17:33, 13 April 2006 (UTC)

Enzyme inhibition

I've made a start at expanding the enzyme inhibitors page as a specialised section written for a less general audience. If people want to move any of the examples of more rare inhibition types from the main article into this page then this would be very welcome. I also have not touched on substrate or product inhibition or on multi-substrate inhibition patterns. --TimVickers 13:51, 27 June 2006 (UTC)

Plan of action

Over the next few months I'm going to be concentrating on this section. I hope to improve on the already excellent work here and bring this entry up to an even higher standard. I intend to make this page a general introduction for the interested reader with a large number of links and references for further reading at a more specialised level. Some material may be moved to other pages, but I will try not to lose anything! --TimVickers 18:13, 27 June 2006 (UTC)

contradiction with respect to the direction a reaction

There exists a contradiction in the page--at one point the article says that enzymes catalyze forward and reverse reactions equally while later when describing Michaelis-Menten the secondary reaction is described at irreversible. I know that the Michaelis-menten kinetic are correct but I'm not sure if it's true in general that forward and reverse reactions are catalyzed equally. —The preceding unsigned comment was added by 24.255.60.50 (talk • contribs) .

The contradiction is a confusion between the mechanism of the enzyme and the thermodynamic proterties of the reaction. In principle, it is true that an enzyme can catalyse both forward and reverse reactions. The direction of any reaction, however, is dependent on the thermodynamic properties of the reaction. If the physiological concentrations of the substrate and product have a large negative value for delta G (exergonic) then the reaction is effectively irreversible. Since the thermodynamic proterties of the reaction are independent of the enzyme both statements can be true. Does this make sense? What needs to be changed to make this more clear? David D. (Talk) 01:10, 7 July 2006 (UTC)

Is the new version more clear?--TimVickers 03:18, 7 July 2006 (UTC)

Unanswered Questions

This article, like the enzyme kinetics 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 00:53, 6 August 2006 (UTC)

Your questions are good ones. During the past 4,000,000,000 years or so there has been selection for genes that code for useful proteins. There has been selection for cellular control systems that make sure enzymes are produced and targeted to cellular locations at the "right time in the right form". The idea that "their motions are completely mysterious" is not true. At the level of single molecules biochemists have some understanding of the motions that are possible and that are involved in enzyme activity. At the level of cells, cell biologists study many mechanisms by which enzymes are produced and transported to the needed locations. These topics are covered in textbooks for biochemistry and cell biology....some good ones are online. --JWSchmidt 04:03, 6 August 2006 (UTC)

And don't forget they have self organising properties due to specific protein protein interactions. Tubulin and actin forming microtubules and microfilaments spring to mind (despite the fact they are not enzymes in the sense of this article) as a simple example. But clearly all protein complexes behave this way. i disagree that the article dodges the fundamental questions. It is just more specific, by neccesity, than 81.164.252.74 is it is about the actual enzymes not how their functions are coordinated at the cellular and developmental levels. Gene regulation and morphogenesis might be articles more suited to 81.164.252.74 interests. David D. (Talk) 13:33, 6 August 2006 (UTC)

A Thought on the Role of Enzymes in Cells

I am a retired professor of biology, new to Wikipedia and delighted to have found it. I have long felt that the role of enzymes in the cell is not well understood by many biologists. I believe that textbooks in general have done a disservice in describing the need for enzymes as being to speed up reactions so that the reactions are “fast enough to support life”. This sort of statement, without further clarification, is very common in college level textbooks. But how fast must reactions go to “support life”? It seems to me that it is not the absolute rate of enzyme-catalyzed reactions that is important. What is important is the catalyzed rate relative to the rates of uncatalyzed reactions. It is necessary only that enzyme-catalyzed reactions go a lot faster than uncatalyzed reactions (the faster the better). A molecule in a cell will enter into a myriad of thermodynamically favorable reactions, even in the absence of enzymes. Glucose, for example, will break apart in a number of ways; it will also interact with ATP to become phosphorylated at one or more of its carbons; and it will become similarly phosphorylated by encountering other high-energy P-donating substances. These reactions (and many more I can’t think of) progress so slowly in the absence of enzymes that they are virtually undetectable. But all of them occur whether enzymes are present or not. Out of all these reactions, enzymes choose, by their specificity, the ones useful to the cell and cause them to go at high speed. Unchosen ones (producing “junk”) go so slowly as to be nearly undetectable. In this way, enzymes direct the metabolism of the cell. I would like to put this notion into the article along with a clarifying graphic if I can figure out how to do it. I am hoping for some feedback. --Emhale 18:04, 9 August 2006 (UTC)

Sounds a good set of ideas to add. It might fit best in the "Function and control of enzymes in the cell" section and could be done by expanding the "Metabolic pathways" subheading. Good to have another scientist on board Emhale, have you seen the Molecular and Cellular biology wikiproject? TimVickers 12:17, 10 August 2006 (UTC)

My paragraph which describes the role of enzymes in the cell had been moved; I put it back to what I think its proper location is, at the introduction of the article. The function and purpose of enzymes should be described at the beginning of the article, as it makes discussion which follows easier to understand. As before, the paragraph replaces the one which was wrong or misleading but pleasantly short (beginning Enzymes are essential for life because . . . ) Mine explains the important point, often missed, that enzymes select or “choose” the useful reactions which are beneficial to the cell and accelerate them, while the useless reactions, which are also occurring but are producing “garbage”, are left alone.-Emhale 12:41, 16 August 2006 (UTC)

From the perspective of a scientific article the introduction in a wikipedia article is analgous to the abstract. The content you are adding would be more appropraite after this 'abstract'. David D. (Talk) 20:10, 16 August 2006 (UTC)

I have again replaced the sentence Enzymes are essential for life, because most chemical reactions in living cells would occur too slowly, or would lead to different products without enzymes. I’ve been able to keep the change short this time; there were objections to the length of my first try. The sentence above that I replaced is really quite bad and something had to be done to fix it. It makes two points:1. Most chemical reactions in living cells must go fast, or they would go too slowly. This is not helpful. 2. most chemical rections in living cells would lead to different products without enzymes. This doesn’t make sense to me. The writer may have meant that molecules would undergo different reactions without enzymes, thus leading to different products, but this is not true. A given molecule in a cell will undergo a great variety of thermodynamically favorable reactions whether enzymes are present or not. Adding an enzyme does not change this. If there are objections, I am hoping for some comments.-Emhale 21:59, 18 August 2006 (UTC)

No objections Emhale, this is an important and under-appreciated point. Tried to make this section less "science heavy" for non-specialist readers. TimVickers 23:24, 18 August 2006 (UTC)

Thank you Tim. And your re-statement is an improvement. It has not escaped me that you have done an extraordinary amount of work on the article and I appreciate your long effort.-Emhale 10:49, 19 August 2006 (UTC)

I agree with David D. Dear Emhale, What's the difference between "... reactions are extremely slow when not catalysed by enzymes."(by Emhale) and "... reactions would occur too slowly... without enzymes." (=original version) And Emhals "Any molecule in a cell could in principle undergo a vast number of possible chemical reactions." implies that this different chemical reactions lead to different products, isn't it? TimBarrel

By the way: Emhale acknowledges that the disputed statement is very common in textbooks, but he has a different few on it. If he could prove that he is right, and all the textbooks wrong, he should publish a scientific article in a peer reviewed journal. TimBarrel

I thought the point was that the enzymes present select the reactions that occur from the set of possible reactions. For example, glucose and ATP could react (given time) to produce multiple different products, but if hexokinase is present then only glucose-6-phosphate will be formed. TimVickers 01:12, 21 August 2006 (UTC)

Hi TimBarrel (I do like your screen name) The difference between “…reactions are extremely slow when not catalysed by enzymes” and “…reactions would occur too slowly… without enzymes.” Is that the former is a statement of fact that can be tested, and needs no further explanation. But what does it mean to say that reactions would occur too slowly without enzymes? Too slowly for what? How slow is too slow? How fast must reactions go in order to support life? One might say that uncatalyzed reactions go too slowly to support life. But the slowness of change in the absence of enzymes is actually crucial to life. How slow do uncatalyzed reactions go? A good answer would be “slow enough to support life”. Because the great stability of organic molecules, their resistance to change in the absence of enzymes is just as important as the high rate of cellular reactions that are enzyme catalyzed.

<<And Emhals "Any molecule in a cell could in principle undergo a vast number of possible chemical reactions." implies that these different chemical reactions lead to different products, isn't it?>>

I suggested that the original writer may have meant that in the absence of enzymes, different reactions would lead to different products and that the presence of enzymes would prevent this . But my point was that enzymes would not prevent it. A molecule enters different chemical reactions that do lead to different products. This is what would occur in a test tube in the absence of enzymes, as molecules enter into a vast number of possible reactions going so slowly you could hardly detect them. But in a cell, there are enzymes. An enzyme will choose one reaction among all this vast number of reactions (going so slow you can hardly detect them) and cause it to go extremely fast.

All the textbook aren’t wrong, just most of them. One of the worst examples was in a textbook we used for years, Biology. 7th ed. Solomon, E. P., et. al. Brooks/Cole-Thomson. 2005. Page 128 (this is a very widely used college textbook): “Cells cannot wait for centuries for glucose to break down, nor can they use extreme conditions to cleave glucose molecules. Cells regulate the rates of chemical rections with enzymes, which are biological catalysts that increase the speed of a chemical reaction without being consumed by the reaction.” (Cells can’t wait for centuries! It completely misses the point).

Contrast this with Biology. Raven, P.H. et al. McGraw Hill. 2005. Page 149 (this too is a very widely used college texbook): By facilitating particular chemical reactions, the enzymes in a cell determine the course of metabolism – the collection of all chemical reactions – in that cell. (Very good. No drivel about fast enough to support life. My problem is the text should take an additional page or two to explain further this profound idea. In my view, enzymes are the clearest link between DNA and life).

The best I ever saw was in an old text on biological thermodynamics: The Vital Force: A Study of Bioenergetics. Harold, F. M. W. H. Freeman & Co. 1986. Page 31. From the thermodynamic point of view, the conversion of nutrients into cell constituents can be regarded as a grand chemical reaction that proceeds with an overall decrease of free energy. This is the warp of the metabolic web. Its woof is the work of a multitude of enzymes that select the particular strands out of many that are thermodynamically possible in order to carry the flux of matter through the web.

And take a look at TimVickers comment immediately above. It hits the nail on the head.Emhale 13:38, 21 August 2006 (UTC)

Dear Emhale, You just remove one sentence and copy&paste your paragraph, again and again. I changed this one sentence to fit it to your taste: You didn't like "Enzyme are essential to life, because..." I changed it (not deleted your paragraph but moved it!) You didn't like "too slowly" I changed it to "very slow". I moved you paragraph to the appropriate space in the article ("Function and control of enzymes in the cell") You can change the title if you like, but do not delete. You completly miss the point (with your lengthy discussion here), I do not say you are wrong; I just say in the introduction/abstract, just after the definition, your paragraph, starting "Any molecule in a cell could in principle undergo a vast number of possible chemical reactions. However, most of these reactions are extremely slow..." is a discussion about metabolism, that would better fit to the article "metabolism" (as I told you before) or further down in the enzyme article! And take a look at David D.s comment! Thank you for your understanding. Tim Barrel

I'll reiterate my original point. "From the perspective of a scientific article the introduction in a wikipedia article is analgous to the abstract. The content you are adding would be more appropraite after this 'abstract'." Emhale, I think you are making a great point but the bulk of this point should be in the article itself. David D. (Talk) 15:26, 21 August 2006 (UTC)

I have replaced the sentence: “Enzymes direct the metabolism of living cells because most chemical reactions would occur very slow, or might lead to different main-products without enzymes,” which does not make sense to me. It makes two points: 1) Enzymes direct metabolism because without them most reactions would go very slowly. It is true that without enzymes reactions would go very slowly, but this doesn’t explain how or why enzymes direct metabolism. 2) Enzymes direct metabolism because without them different main-products might arise (Enzymes direct metabolism because without them metabolism wouldn't be directed). This doesn’t explain how enzymes prevent different main-products from arising. I have also placed an expanded discussion of the role of enzymes in the body of the article under the heading Function and Control of Enzymes in the cell. I think it might be good to consider separating the Function of Enzymes part of this subheading from the Control of Enzymes part but I have not made this separation in the article.-Emhale 11:42, 23 August 2006 (UTC)

You three guys have done a great job on what I think is the most important section of the article, and I was glad to be a part of it. I hope you will introduce the material of this section into your classes if you are teaching – it has important points that are often missed. Watch out for possible objections – you are not on firm ground David D. with “Enzymes . . . determine the pathways of metabolism . . . This is arguably a more significant role for enzymes than speeding up the reactions.” The two roles are inseparable. A crucial property of enzymes is that they are specific, but remember enzymes do no more, and no less, than speed up reactions.

I think that a lot of biologists imagine that in the absence of enzymes the reactions of, say, glycolysis, would flow along ok but not quite as fast as needed, and so enzymes are provided to speed things up. It is the fault of textbook writers, and of course is a misconception: without enzymes the reactions would not flow along ok, they would be so slow as to be virtually dead in the water. But that’s a big virtually. Thermodynamics is inexorable and you could get into trouble, formally, with your “it is a misconception that without enzymes metabolism would progress through the same steps, but would go too slow to serve the needs of the cell”. That’s not really a misconception. Because it is certainly true that any metabolic pathway passes through a series of reactions whose overall change in free energy must be negative. So even in the absence of enzymes some of the molecules, changing as slow as those in aging wine, will at least in theory still pass through the same steps but go too slow to serve the needs of the cell. I was wondering how to deal with this myself . But the important idea in the article is clear: without enzymes, reactions go so slow that they can be ignored. I say leave it alone.

Its been great messing around in Wikipedia. I’m going to stop for a while. TimVickers, thank you for your continuing hard work on the Enzyme article. Dave D., thanks for your encouragement. I have enjoyed reading the correspondence on your eclectic Talk page. TimBarrel, I still say you have a great screen name.-Emhale 10:24, 24 August 2006 (UTC)

I really have no idea what this guy meant TimBarrel, I value your input and effort very highly. Please ignore this comment and go and rest on your scientific laurels. TimVickers 15:14, 25 August 2006 (UTC)

I was just being an ass. It happens all the time.-Emhale 21:10, 25 August 2006 (UTC)

Ah, a common problem with me also. For us all to get irony you have to hit us over the head with emoticons. ;) TimVickers 21:24, 25 August 2006 (UTC)

Suggestions from FA review

As you can see above we are being reviewed for FA again. Some suggestions I have dealt with, others below may need more discussion or help from others. TimVickers 13:56, 29 August 2006 (UTC)

• "See if you can find someone to convert the diagrams (obviously not the ribbon ones) into SVG format." darkliight[πalk] 19:12, 28 August 2006 (UTC) Done. TimVickers 17:39, 1 September 2006 (UTC)

I don't think this is to be considered done. All diagrams in the article that have the .svg extension (except for Image:Amylose.svg) are just big PNG files embedded in SVGs. It would've been better to just keep them as PNGs instead of turning them into "fake" SVGs. To actually convert them to SVGs they would need to be vectorized. –Gustavb 07:18, 12 September 2006 (UTC)

• "The sentence The activities of enzymes are determined by their three-dimensional structure is overstated - plenty of proteins have nonessential bits of tertiary structure." Opabinia regalis 04:45, 29 Consensus reached TimVickers 17:39, 1 September 2006 (UTC)
• "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." Opabinia regalis 04:45, 29 Re-formatted to reduce size. TimVickers 17:39, 1 September 2006 (UTC):

Just passing through, but wanted to mention that I, as a reader, love this table and the info it provides. There's nothing like being able to connect theoretical concepts with everyday applications. --NoahElhardt 15:33, 2 September 2006 (UTC)

I too like seeing practical/real-world examples of scientific topics. But I agree the table is kinda ugly. The "Uses" column is the only one that contains extended prose text, yet it's the narrowest one! The widest is the "Notes and examples" column, which contains no notes and only a single example of each, as an image that gets visually lost vertically. Maybe the image should be moved into the first column, the same way most wiki articles have an image of a specific example at the very beginning? That would free up more horizontal space for the currently-squashed text column. For example:

Application	Enzymes used	Uses
Biological detergent File:Washingpowder.jpg	Primarily proteases, produced in an extracellular form from bacteria	Used for presoak conditions and direct liquid applications helping with removal of protein stains from clothes.
	Amylase enzymes	Detergents for machine dish washing to remove resistant starch residues.
	Lipase enzymes	Used to assist in the removal of fatty and oily stains.
	Cellulase enzymes	Used in biological fabric conditioners.

May as well get this hashed out on Talk before making the change because table formatting is such a pain:( DMacks 16:53, 3 October 2006 (UTC)

I'd suggest just give it a try. We can always retrieve the original if it looks out of balance. David D. (Talk) 17:04, 3 October 2006 (UTC)

I've added a bit more content to fill some of the white space. TimVickers 17:06, 3 October 2006 (UTC)

Just made some bold edits. See what you think and feel free to revert back. David D. (Talk) 17:14, 3 October 2006 (UTC)

Looks good to me. Thanks. TimVickers 17:24, 3 October 2006 (UTC)

Concurred! DMacks 17:26, 3 October 2006 (UTC)

References

Einfluss der configuration auf die wirkung derenzyme is written differentliy here:

• [1] 3. E. Fischer, Einfluss der Configuration auf die Wirkung der Enzyme, Ber. Deutschen Chem. Ges. 27 (no. 3), 2985-2993 (1809).

but like in the text:

• [[2]]

The Reference is morel likely written in the form of the first citation. Writing did not change so much from than to now. Configuration might be changed during the first german writing reform start of 20th century to Konfiguration. If nobody objects or has the literature at hand I will change it!--Stone 20:42, 29 August 2006 (UTC)

I'm a bit confused by what your saying Stone, the reference in the article does need to be altered slightly-which I will do in a minute.

The article is available online with a paid subsription, however the title and information can be found at: http://www3.interscience.wiley.com/cgi-bin/abstract/112380531/ABSTRACT

Unfortunately there is no abstract listed and it looks like it was just put online this year-I would think given the age of the article it would be public domain (at least in the US) the article is German so it may not be there.

In General the References need some clean up. They should all be numbered (or listed in order with all numbers removed, but most are already numbered). The also should all be in the same format, most are somwhat close, but not quite. Hichris 22:05, 29 August 2006 (UTC)

Looking through the refrences more closely, they need more work than I thought! There needs to be a consistent format for the references.

Science format is below (note 308 is the volume# and 405 is the page#):

9. C. Nilsson, C. A. Reidy, M. Dynesius, C. Revenga, Science 308, 405 (2005).

However the article name is not part of the reference, but this could be easily added-since I believe it is helpful to include. So it could simply be added after the author names or we could use Biochemistry format, which is slightly different.

Biochemistry format:

9. Nilsson C., Reidy C. A., Dynesius M., and Revenga C. (2005) Fragmentation and Flow Regulation of the World's Large River Systems, Science 308, 405.

My vote would be for Biochemistry format, but either way one needs to be decided on and used exclusively. Hichris 22:29, 29 August 2006 (UTC)

I'd vote for the biochem format as well, giving titles is pretty vital. TimVickers 23:00, 29 August 2006 (UTC)

Biochemistry. The references are worth much less without the title of the paper. David D. (Talk) 18:19, 22 September 2006 (UTC)

Carbonic anhydrase figure

The figure on the right of the page, illustrating carbonic anhydrase, is perhaps not the best choice. 1DDZ is, for one, a beta CA, whereas when the main article discusses carbonic anhydrase, it seems to be implicitly refering to an alpha CA (the tissue vs lung distinction). Also, 1DDZ represents a structural arrangement of beta CA which is now known to be catalytically inactive - see Cronk et al Biochemistry 2006 Apr 11;45(14):4351-61 for a full discussion of this. There are several structures for beta CA in the active form, including 1EKJ, if this is what's really wanted. There are however, also many many structures for alpha CA; maybe Duda et al's Homo sapiens structure at 1.05 A is a good choice, not only because it is human and the highest resolution one to date, but also because of the great RCSB i.d. "1MOO" !

New figure added. TimVickers 19:02, 11 October 2006 (UTC)

=Table of different uses in technology is distorted

Anyone wana fix it? Dreamm 22:08, 29 November 2006 (UTC)

Looks clean to me. What specifically is wrong? DMacks 22:16, 29 November 2006 (UTC)

Looks good to me as well. What is your browser and screen resolution Dreamm? TimVickers 22:25, 29 November 2006 (UTC)

Probably just my brower then. Its Internet Explorer 7, at 1152 by 864. I'll post a picture of it... not a big problem anyway. Dreamm 21:21, 30 November 2006 (UTC)

I suspect this is the first of many IE7 errors you will experience. Good luck with it, and there is always Firefox if you get tired of dealing with them! TimVickers 21:26, 30 November 2006 (UTC)

Yea... reverting to IE 6. :) Dreamm 02:27, 1 December 2006 (UTC)

'High energy' ATP?

ATP is a high-energy compound, is it? What nonsense! The cell keeps ATP concentrations at much higher levels relative to ADP than the equilibrium. When an unfavourable reaction is coupled to the ATP to ADP reaction, the high concentration of ATP drives the reaction forwards. It's the concentration of ATP that is crucial, not some magic bond attaching the third phosphate (usually drawn with a ~ as if it's some sort of special bond).

Also from the thermodynamics section: "However, the uncatalyzed, "spontaneous" reaction might lead to different products than the catalyzed reaction." This could be construed as meaning that the enzyme can change the products of the reaction. How about "Without catalysis, the reaction might be so slow that other reactions (leading to different products) might occur instead." Ewen 08:07, 11 October 2006 (UTC)

Certainly the high concentration of the ATP is can increase the energy charge and the available free energy from hydrolysis. Nevertheless, the fact that the hydrolysis has a large negative free energy would not be true except for the properties of the magic bond. Without the large difference in resonance stabilization before and after hydrolysis even a high concentration of ATP would be worthless for coupling unfavourable reactions. David D. (Talk) 08:41, 11 October 2006 (UTC)

Just checking the figures given in Stryer: The equilibrium for a coupled reaction is increased by a factor of about 10⁵ by the ATP/ADP+Pi reaction, but an additional factor of about 10³ is due to the high levels of ATP maintained in the cell. Ok, that means the standard free energy of reaction itself is about 100 times more important than the ATP levels in coupling. On the other hand, if ATP levels were allowed to fall then eventually the low ATP concentration would negate the favourable free energy of the hydrolysis. Also worth considering is that ATP is not particularly special. Phosphoenolpyruvate, for example, has a much larger free energy of hydrolysis. How 'magic' is that bond, then? If the standard free energy was all that was important, then ATP would be a poor choice of energy currency. I feel that refering to ATP as having some sort of high energy magic bond is misleading. Ewen 09:27, 11 October 2006 (UTC)

Clearly both are important. And it depends what kind of magic you are looking for in the bond. With respect to ATP, being an intermediate energy bond is the magic, ADP can easily be phosphorylated (PEP as a source of phosphate for one) as well as ATP being able to couple reactions. Both are required for the ATP to be so versatile as an energy carrier. See if Stryer discusses that idea or not. I agree that it is not the highest energy bond but it is high energy enough to drive endergonic reactions (combined with the high energy charge). David D. (Talk) 15:01, 11 October 2006 (UTC)

I agree that the term "high-energy bond" is misleading as it is displacement from equilibrium that provides useful energy, not really any property unique to ATP itself. I have reworded the section on spontaneous reactions. TimVickers 15:30, 11 October 2006 (UTC)

A.L.A SUCKS!!! —Preceding unsigned comment added by 206.81.147.225 (talk) 21:04, 31 March 2009 (UTC)

Promiscuous

In http://en.wikipedia.org/wiki/Enzyme#Specificity the word promiscuous is a wikilink but links to the word as it is generally used. I would recommend either creating a disambiguation page with a red link, eg. for Promiscuous (biology) or perhaps, consider not wikilinking it at all. It depends on whether it is a term that gets used, and hence, whether it will ever get a page of its own. 128.250.6.247 10:22, 11 October 2006 (UTC)

Removed link and reworded, since plant secondary metabolites are produced by quite specific enzymes. GSTs and P450s are the broad-specificity enzymes. TimVickers 15:33, 11 October 2006 (UTC)

Diagram captions

The text below the "Induced fit" diagram is slightly misleading - perhaps clearer might be "substrate entering active site on enzyme" and "product leaving active site on enzyme' Paul venter 10:31, 11 October 2006 (UTC)

I'm thinking it's supposed to be read as enzyme + substrate-entering-active-site. but i agree, it's very confusing. It's makes it sound like as if both the enzyme and the substrate were entering/leaving the active site. --`/aksha 12:19, 11 October 2006 (UTC)

It is confusing, will need new diagram. TimVickers 15:34, 11 October 2006 (UTC)

New diagram uploaded. TimVickers 18:26, 11 October 2006 (UTC)

Catalytically perfect enzymes

I really think that comment "TIM is catalytically perfect, meaning its conversion rate is limited, or nearly limited, to its substrate diffusion rate." should be removed from the caption of the TIM picture.

It's not a particularly important/significiant enzyme concept, putting it up in the caption for that picture basically means it will be one of the first things a reader reads when they reach the article.

For someone who doesn't already know about enzymes and hasn't already read the article, the comment is a bit out of place and confusing, even with the "meaning its conversion rate is limited, or nearly limited, to its substrate diffusion rate." explaination.

Can we remove the comment and/or replace it with something more general that would be fitting for an article introduction? Something like "Ribbon diagram of the enzyme TIM. TIM is an essential enzyme for efficient energy production, and is found in almost all organisms...etc"

Catalytically perfect enzymes are already mentioned in the article body anyway, in a place that's appropriate (i.e. under Kinetics, not at the really top of the article.) --`/aksha 12:18, 11 October 2006 (UTC)

I agree, reworded caption to be as simple as possible. TimVickers 15:37, 11 October 2006 (UTC)

Mass edits and vandalism

Why has this article become the target of vandals with too much time on their hands? --HashiriyaGDB 12:22, 11 October 2006 (UTC)

Why are you surprised? If you're wanting to vandalise wikipedia but you don't know which article to choose, why not start with the one which is on the front page? featured article = tons of attention = tons of attention from vandals as well. --`/aksha 12:27, 11 October 2006 (UTC)

Yep - perfectly normal syndrome - only time makes them go away. Paul venter 13:23, 11 October 2006 (UTC)

Catalase

Should we briefly mention the turnover rate of catalase or something to give people an idea of how effective enzymes can be? Nil Einne 14:32, 11 October 2006 (UTC)

This was in the lead but was removed. Now added back to second section of kinetics section. TimVickers 15:28, 11 October 2006 (UTC)

Vectorized diagram

I believe this has been discussed before, but here goes: I have created a vectorized version of Image:Competitive inhibition.png (properly vectorized, not embedded the .PNG in an .SVG file) and uploaded it to Commons as Image:Competitive inhibition.svg. I made no noteworthy changes whatsoever, it is practically a facsimile of the .PNG, and have replaced it in the article. If anyone wishes to change it back, go right ahead. I can also vectorize the remaining .PNG diagrams (induced fit and Inhibiteur competitif on Enzyme inhibitor) – would that be OK? Fvasconcellos 15:37, 11 October 2006 (UTC)

Looks great, thanks. Go right ahead, but I'd hold off on the Induced Fit diagram since this will be changing soon, as per above discussion. TimVickers 15:40, 11 October 2006 (UTC)

Agreed. Thanks, Fvasconcellos 15:41, 11 October 2006 (UTC)

Confusing Fig Refs or Missing Figures?

Several figure references have confused me:

In the "Cofactors" section, the reference "a cofactor is carbonic anhydrase, and is shown in the diagram above with four zinc cofactors bound in its active sites" was a little confusing because the referent image is two images above, and several screens (on this low-res display).

In the "Inhibition" section, what figures are meants by "(right, top)" and "(right, bottom)"? I believe I understand that the bottom figure shows an enzyme and an inhibitor, but not the act of inhibition, whereas the top diagram does show the act. It's be less confusing if the top diagram had a third section showing competitive inhibition.

Maybe a good fix is to label all figures and refer by label? It'd be nice if wikipedia automated this...

I have tried to reword this to be less confusing. TimVickers 19:44, 11 October 2006 (UTC)

I still find this confusing; also, there is a lot of overlap, but with different diagrams and text, with Enzyme Inhibition.

Contact Lens Cleaner

Probable error:

• "To remove proteins on contact lens to prevent inflections."

I would fix this myself but I'm not 100% and it is a featured article today. I assume it is suposed to be infections. Perhaps this is a technical term in this narrow area having to do with internal reflections?--Nick Y. 19:17, 11 October 2006 (UTC)

Typo indeed. Corrected. TimVickers 19:43, 11 October 2006 (UTC)

Enzymes that slow reactions?

Can anybody think of an example? TimVickers 16:30, 17 October 2006 (UTC)

I'm not sure I see where this is going. What made you think of this? To answer your question, I cannot think of one off the top of my head. David D. (Talk) 16:42, 17 October 2006 (UTC)

If I had to quess of a reaction, it would be an enzyme to slow down the release of free radicals. David D. (Talk) 16:46, 17 October 2006 (UTC)

See the edit histtory, somebody was saying some enzymes slow reactions. Antioxidant enzymes just remove the oxidants, so they speed removal reactions - reducing the steady-state concentration of things such as H2O2 or superoxide. TimVickers 18:24, 17 October 2006 (UTC)

Many enzymes will effectively slow down a reaction, by promoting a different reaction. However, I don't know an enzyme that actually slows a reaction - by default this would not be catalysis - so I don't think you could even call it an enzyme maybe an "anti-enzyme" :-) Hichris 18:30, 17 October 2006 (UTC)

What about chaperone proteins that prevent a protein from folding until it is fully translated? Ewen 20:25, 17 October 2006 (UTC)

Chaperones don't appear to be enzymes themselves. DMacks 20:29, 17 October 2006 (UTC)

Yes, if a chaperone just binds to the unfolded state then this is a simple ligand binding process, so not really a chemical reaction. Even inhibitory kinases or phosphatases accelerate their reaction and it's the effects of this accelerated reaction that slow a second, independent reaction. TimVickers 20:45, 17 October 2006 (UTC)

Enzymes are by definition biological catalysts. You can't catalyse something to not happen, or to happen more slowly. It would be a contradiction in itself. A protein that slowed down a reaction or stopped it would be an inhibitor of some kind. A enzyme could catalyse a reaction that results in the slowing down or prevention of some other reaction from occuring, but the primary purpose of the enzyme would still be to speed up a reaction. --`/aksha 04:19, 18 October 2006 (UTC)

Enzymes may slow reactions relative to their previous reaction rates. Enzymes accelerate reactions, but the rates of a particular enzyme's reactions may depend on inhibitors and substrate concentrations. Thus they are at times malleable catalysts which may control reactions based on substrates and inhibitors. This is a bit more than acceleration and a bit more than catalysis. These are enzymes. See the section on inhibition. Strictly speaking, "accelerate" is an inaccurate and misleading term in this context as catalysts increase the rate of a reaction, they do not cause a continuous rate change. "Accelerate" implies a constantly changing rate positive or negative. The rate increases in comparison to an uncatalyzed reaction but then the rate may stay steady or vary depending on activating or inhibiting factors and substrate concentrations. —Preceding unsigned comment added by Bcebul (talk • contribs) 22:47, 1 April 2008 (UTC)

That's a good point. "Accelerate" is a bit loose, however, if an enzyme is inhibited by an inhibitor, it is the inhibitor that is slowing the reaction, not the enzyme itself. This discussion originated when somebody changed the article to read something like "enzymes change the rates of reactions.", which is unnecessarily vague. Tim Vickers (talk) 04:26, 2 April 2008 (UTC)

New lead image

I'm not sure who added the new lead image but I personally prefer it to the older image with the black back ground. I have not seen that style of ribbon and space filling model before, it is quite effective. David D. (Talk) 00:26, 31 October 2006 (UTC)

It came in the blizzard of edits on our day in the sun. I like it too and am glad my namesake enzyme is still on top! TimVickers 00:30, 31 October 2006 (UTC)

Energy profile image

File:Activation2.svg

Image:Activation2.svg has an error in the time axis of the graph, as noted in the summary by the user who converted it to vector graphics format. Since this is a featured article, and the picture is featured prominently in the thermodynamics section, it would be best to correct the graph to reflect a more accurate description of the reaction. Besides this, explaining carefully why the graph should not look like this could also be helpful (or linking to a page explaining the phenomenon). It is quite counter intuitive at first to think the enzyme doesn't speed the reaction up, but this isn't what the graph is reflecting - rather it is showing the path of a single reacting molecule, not the species as a whole, creating the confusion. I can't offer to edit it myself as I have very limited experience with digital images, especially vector graphics. Richard001 08:08, 26 November 2006 (UTC)

Hi there, Fvasconcellos has kindly offered to fix this. Before we do so can I just check if there is only one problem? The error is that the two humps are different widths, (a difference in time). In fact the two humps should only differ in height (a difference in energy). Is this the problem? Thanks. TimVickers 16:39, 26 November 2006 (UTC)

No, no, the problem is that it should say reaction coordinate in the X axis; (that is more or less how far from the reactants and how close to the products the molecules are). The only important thing is that the energy barrier is lower for the catalysed reaction; the positions or widths are not really important. It's important to note that time is NOT the variable in X axis!! Knights who say ni 18:13, 26 November 2006 (UTC)

I gave myself a green light and did it. How's this? Fvasconcellos 19:01, 26 November 2006 (UTC)

Good Job!! It looks great now. Knights who say ni 20:02, 26 November 2006 (UTC)

Thank you Fvasconcellos. TimVickers 21:20, 26 November 2006 (UTC)

I like this updated figure a lot, thanks to all your efforts. I have a minor quibble that may be easily corrected. The e.g. cited under reactions (C6H12O6 + O2) and products (CO2 + H2O) are not the reactants and products of a SINGLE enzymatic reaction, but rather the summation of numerous enzymatic reactions occurring over three different metabolic pathways (namely, glycolysis, TCA cycle, and oxidative phosphorylation). However, activation energy diagram represents energy changes during a single enzymatic reaction. So I would suggest either removing the e.g. under both reactants and products or replacing the e.g. with a more realistic example for a single enzyme. --Kompala (talk) 17:29, 28 May 2008 (UTC)

Fvasconcellos has produced a new version. Tim Vickers (talk) 18:23, 28 May 2008 (UTC)

Removed a section

I removed the "Factors that control the rates of enzyme reactions" section as this was a list that duplicated some of the material in the structure and kinetics sections. I added the removed text to the Enzyme assay page. TimVickers 21:22, 29 November 2006 (UTC)

Activation energy and alternate pathways

As I recall, and I'll find a citation and add the necessary edit later, enzymes can act in several ways:

• Lowering the activation energy by creating an environment in which the transition state is stabilised (e.g. straining the shape of a substrate).

• Providing an alternative pathway (e.g. temporarily reacting with the substrate to form an intermediate which would be impossible in the absence of the enzyme).

• Reducing the reaction entropy change by bringing substrates together in the correct orientation to react. This lowers ΔG. Considering ΔH alone overlooks this effect.

Ewen 06:24, 19 December 2006 (UTC)

That's a pretty good summary. In all cases, they lower ΔG^‡ for "the net conversion of A to B", but whether it's by lowering it for the same pathway or by providing a different pathway entirely is specific to each case. DMacks 06:32, 19 December 2006 (UTC)

Just want to point out that the ΔG for a reaction does not change with the presense of an enzyme. It is the activation energy that is lowered. It sounds as if these are being confused here. David D. (Talk) 21:59, 22 February 2007 (UTC)

My statement is probably more properly

ΔΔG^‡ (SM→T-state) not the actual energy of the T-state. DMacks 22:51, 22 February 2007 (UTC)

Non-living?

In 1878 German physiologist Wilhelm Kühne (1837–1900) coined the term enzyme, which comes from Greek ενζυμον "in leaven", to describe this process. The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment used to refer to chemical activity produced by living organisms.

If proteins are built of amino-acids, which have COOH, how can they be non-living? -Chemistry Noob —The preceding unsigned comment was added by 86.87.66.216 (talk) 23:41, 28 December 2006 (UTC).

Have a look at the page Life for a discussion of how people usually define "living things". TimVickers 23:49, 28 December 2006 (UTC)

Alright, thanks. I went by the definition that it has to have C, O and H atoms. --86.87.66.216 00:09, 29 December 2006 (UTC)

Thankfully that definition doesn't really work, since whisky has all of these! TimVickers 01:47, 29 December 2006 (UTC)

That's what I learned from my schoolbook! --86.87.66.216 02:00, 29 December 2006 (UTC)

Might they be confusing Organic compounds with Organic matter? TimVickers 02:11, 29 December 2006 (UTC)

It sounds like you might be thinking about a definition of "organic compound". --JWSchmidt 02:16, 29 December 2006 (UTC)

Whoops! Yes, I confused living with organic compound. --86.87.66.216 14:50, 29 December 2006 (UTC)

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