Talk:Enzyme

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[edit] investigative methods section should be added

Perhaps there should be a section on how enzymes are investigated, such as how they are discovered, isolated, how their function, conformation, and necessary co-enzymes are determined, and with links to relevant other pages like folding at home, etc.

This is covered already in Enzyme assay, Protein purification and Protein folding. TimVickers 04:32, 13 June 2007 (UTC)

[edit] size info

There is no info on this page about the size of enzymes. There should be at least 1 sentence that says "enzymes are usually between x and y nannometers in diameter."

Size info added to Structure section. TimVickers 17:22, 5 May 2007 (UTC)

[edit] 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)

[edit] '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)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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.

[edit] 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)

[edit] 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)

[edit] 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)

[edit] Energy profile image

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)

Thanks, Fvasconcellos and TimVickers. This new figure addresses my quibble perfectly and looks great.--Kompala (talk) 15:40, 30 May 2008 (UTC)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] Suicide Inhibitors

Because there's been some ambiguity in edits to the section...

  • I think it's better to have a clear description of the method of action of suicide inhibitors. The earlier section deals with an allosteric effect ("binds to a site distinct from the active site") and does not mention the mechanism of something like the action of transpeptidase on a beta-lactam ring, which is quite different. Obviously there's more information on the enzyme inhibitor page, but a one sentence clarification might be useful here. Icelight 20:04, 19 February 2007 (UTC)
Wow, what on earth was non-competitive inhibition doing there? Thanks for pointing that out. TimVickers 20:19, 19 February 2007 (UTC)

[edit] Ribozymes

In the first sentence of this article it is unabashedly stated "Enzymes are proteins...". What about ribozymes? They're not proteins and yet manage to catalyze reactions. I feel this article should at least mention that nucleic acids may, in some circumstances, catalyze reactions. Werothegreat 17:52, 22 February 2007 (UTC)

The definition of a enzyme is a catalytic protein. Ribozymes are discussed in the second paragraph of the introduction "Not all biochemical catalysts are proteins, since some RNA molecules called ribozymes also catalyze reactions." TimVickers 18:01, 22 February 2007 (UTC)

Sorry for the bother. Must have slipped my notice. Werothegreat 21:09, 22 February 2007 (UTC)

No problem at all, the point about ribozymes is a good one since their coverage in Wikipedia is pretty minimal considering their importance. TimVickers 21:37, 22 February 2007 (UTC)
We just had another user making a similar edit, apparently missing the current reference to ribozymes. I left a message on the users talk page. Will wait a bit before reverting or rewriting in a way to stop people repeatedly 'correcting' this issue. David D. (Talk) 17:12, 6 April 2007 (UTC)
I've added a dictionary definition as a reference to the first sentence, hopefully this will do the trick. TimVickers 17:21, 6 April 2007 (UTC)
The Oxford Dictionary of Biochemistry and Molecular Biology defines enzymes thus: "Enzymes are naturally occurring or synthetic macromolecular substance composed wholly or largely of protein." Tim Bugg's book "An introduction to enzyme and coenzyme chemistry." states as the title of chapter 2 "All enzymes are proteins". Ribozymes are discussed in chapter 11 on "Non-enzymatic biological catalysis." There is the classification "Biological catalysts" and under this are two sub-classifications - enzymes, which are catalytic proteins and ribozymes, which are catalytic RNA.
I have looked at the Stryer textbook and this seems to be wrong on this point. More specialist reviews are better-written. For example the first sentence of David Lilley's review on ribozymes is "Ribozymes are catalytic RNA molecules – RNA species that behave like enzymes." TimVickers 17:48, 6 April 2007 (UTC)
Never trust a textbook for a definitive answer. Snustead defines exon as being ONLY the ORF of mRNA. The UTR sequences, according to them, is not part of any exon. They are not the only ones that do that, Lodish has it that way too. This is just wrong and very sloppy work from the reviewers/editors. Another example is that many text books say that the theoretical maximum number of ATP from the full oxidation of glucose is 38. This ignores the fact that the glycolytic NADH cannot donate electrons to complex I in the mitochondria. The real 'theoretical maximum' is 36 (2 ATP from cytoplasmic NADH not 3). Of course, the theoretical maximum is a pretty meaningless number anyway David D. (Talk) 18:54, 6 April 2007 (UTC)

The "Enzymes are proteins..." statement is overly emphatic. Sure, several leading researchers have adopted the usage that RNA enzymes are not enzymes, but are strictly ribozymes, however, "RNA enzymes" has been and continues to be in widespread usage in leading publications. See scholar.google.com "RNA enzyme" for examples. Agesworth 10:56, 5 November 2007 (UTC)

Any suggestions to improve it? David D. (Talk) 12:37, 5 November 2007 (UTC)
Well as 99.95% of enzymes are proteins and people are split on whether ribozymes are enzymes, I say we stick with the simple approach in the lead. We could add a paragraph at the end of the two introductory paragraphs in "Structures and mechanisms" discussing the ambiguity of the definition, if people think this needs more explanation. Tim Vickers 16:16, 5 November 2007 (UTC)
If the point is accepted, then I suggest altering the 2nd last sentence of the second paragraph. Given Tim’s 99.95% figure, the opening sentence is OK to be left as is. Note that Tim agrees that there are enzymes that are not proteins (0.05% of them). There is no need to get too excited here as this issue is covered in the article ribozyme. My suggestion would be to change:

“Although all enzymes are proteins, not all biochemical catalysts are enzymes, since some RNA molecules called ribozymes also catalyze reactions.[3]”

to

A closely related class of biochemical catalysts are RNA enzymes, or ribozymes. These molecules, which sometimes are, and other times are not, classified as “enzymes”, are far fewer in number, and are thought to be relics of very early versions of life on earth. (Add two or three references here, one using “ribozyme”, one “RNA enzyme”, one supporting “relic of early life”)

or something like that. Agesworth 21:10, 5 November 2007 (UTC)

[edit] Expert review

I've been bold and asked three eminent enzymologists to review this page, Christopher Walsh, Alan Fersht and Tim Bugg. They are all probably very busy people but hopefully they will find time to look this over and comment. TimVickers 23:10, 8 May 2007 (UTC)

Tim Bugg replied this morning:
Dear Tim,
I just took a quick look at the Enzymes & Enzyme Kinetics articles, and they both look really good! I thought the section on industrial applications was very useful, as that is generally not discussed in academic books & reviews. Figures looked clear and nicely prepared. Seems at the right level for Wikipedia, and referencing seemed good as well.
Tim Bugg
Very encouraging! TimVickers 14:45, 9 May 2007 (UTC)
Indeed. We should probably push more often for external reviews on such important topics, when possible; any more strings you can pull for any other articles? ;) Fvasconcellos (t·c) 14:59, 9 May 2007 (UTC)
See the MCB talk page. TimVickers 15:18, 9 May 2007 (UTC)

[edit] Nice Article!!!

Great job, guys!

WriterHound 17:55, 25 June 2007 (UTC)

[edit] Consistent spelling of catalyse/catalyze etc.

Can someone please ensure that ALL spellings of catalyse/catalyze/catalysis/catalysed etc. are all either spelt with a 'z' or an 's'. Personally I favour the English spelling (with an 's') but as long as it is consistent I don't mind. It is just irritating to come across different spellings within the same article. Not very reminiscent of an encyclopedia.

Fixed the three "ise" spellings I found. Tim Vickers (talk) 17:28, 21 February 2008 (UTC)

[edit] small add-on

"unfolded and inactivated—by heating or chemical denaturants" (10M urea is the most common one) --Redeemer079 18:21, 18 April 2008 (UTC)

Done. Tim Vickers (talk) 17:44, 28 May 2008 (UTC)