Talk:Enzyme/Archive 6

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Removed Enzyme Diagram.jpg

I've removed this diagram since it is quite inaccurate.

1. It shows the catalytic and binding areas of an enzyme only partially overlapping with its active site.
2. It shows a cofactor binding outside of the active site
3. It has three undefined blobs between the substrate and the "catalytic site".

The active site is defined as the part of the enzyme that binds to its substrates and carries out catalysis, and this is (almost always) the place where cofactors bind. Since we already have File:Induced fit diagram.svg as a schematic for enzyme action this diagram is also unnecessary. Tim Vickers (talk) 20:25, 27 January 2010 (UTC)

Naming Enzymes : the "-ase" suffix : origin

I tried to find the origin of the custom of naming an enzyme by adding the suffix “-ase” to the enzyme’s substrate. Sources trace the practice to French scientist Émile Duclaux (1840-1904), who suggested it.[1] However, I couldn’t find a source that cited the publication in which Duclaux’s suggestion first appeared. The year in which Duclaux made the suggestion is also ambiguous: some sources say 1882, others say 1883, but most say 1898.

My own investigation leads me to conclude that Duclaux made the suggestion -- and it wasn’t explicit -- in volume 2 of his Traité de Microbiologie (1899). On page 9, he says that French chemists Payen and Persoz made a major discovery in 1833 when they isolated, from barley, the first enzyme, which they called “diastase” but which is now called “amylase”. In their honor, Duclaux states that he intends to use the word “diastase” instead of the then current word “enzyme”. Subsequently, he names new enzymes by adding the suffix “-ase” to the enzyme’s substrate. Hence on page 10, “plasmase” acts on blood plasma, “pectase” acts on plant sap, “casease” acts on casein in milk ; on page 11, “sucrase” acts on sugar, “maltase” acts on malt ; etc. Chapter 2 of his book lists most of the enzymes that were known at the time, and in that chapter he continues to name new enzymes in the same fashion. Similarly, on page 688, “thrombase” acts on thrombi (clots in blood vessels). In 1899, Duclaux was director of the Pasteur Institute, so his ideas -- including a proposed nomenclature for enzymes -- would have been influential among his colleagues.

I therefore believe that I have found the origin of the nomenclature. However, if you can read French, you may want to examine Duclaux’s book Traité de Microbiologie, vol. 2, yourself. It’s available on-line at: http://books.google.com/books?id=Kp9EAAAAQAAJ&printsec=frontcover&ie=ISO-8859-1&output=html . Cwkmail (talk) 06:26, 28 April 2010 (UTC)

[1] See, for example, William Henry Howell, A Text-book of Physiology for Medical Students and Physicians (Philadelphia, Pennsylvania, U.S.: W.B. Saunders, 1905), page 662.

I will put this to a colleague who does the history of biochemistry, for evaluation. Note that whatever one arrives at, one has to explain the parallel running of the separate -ase (protease) and "-ese" (rhodanese) suffixes for enzymes catalyzing bond breaking and forming transformations, respectively, at least through to the 1970s. Cheers. Leprof 7272 (talk) 09:01, 8 October 2012 (UTC)

Hemagglutinin

Under Control of activity it mentions "hemagglutinin in the influenza virus is activated by a conformational change caused by the acidic conditions, these occur when it is taken up inside its host cell and enters the lysosome." I'm just wondering if Hemagglutinin is an enzyme? If I'm not wrong it's just a glycoprotein, although it changes its shape in the situation mentioned. Maybe another example for this would be better. 218.186.8.253 (talk) 17:22, 25 June 2010 (UTC)

I don't think the influenza HA is an enzyme. The influenza C HEF is an enzyme, but I am not sure does the catalytic activity of HEF depends on a change in pH. Rlmrace (talk) 15:51, 5 December 2010 (UTC)

Removed mention of hemagglutinin as it is not and enzyme and therefore not relevant to this article. Boghog (talk) 11:19, 15 February 2015 (UTC)

Quality

I think this article needs a revision if it is really worth a star, I am not so sure if the history section is complete, if it isn't it should be removed. At least I found the history section of this article to be insufficient and did not use it as a part of my high school essay, and because of that I decided not to use the article.

Otherwise I think it is a pretty well written article, but it is only worth a star if it is 100% complete and in my opinion the history section is not. —Preceding unsigned comment added by Sebbex (talk • contribs) 18:51, 13 October 2010 (UTC)

Creation of enzymes

Nowhere in this article is there any word about how enzymes are created. If someone wants to know where they come from, they have to know to click on protein and find out about protein production.

I realized this when looking to answer to whether animals can consume enzymes and use them, or whether they get broken down in the digestive system. For example, people advocate eating sprouted grains because of the enzymes that are created when the grains are sprouting, and I wanted to know whether this was nonsense. I didn't have high hopes of finding that information out in this article, but was surprised to see that there's nothing at all about how enzymes come to be found in living organisms. — Sam 63.138.152.135 (talk) 15:54, 9 November 2010 (UTC)

I understand eating raw fruits and vegetables, due to living enzymes present, is beneficial to humans because enzymes act like little automobiles carrying nutrients from food to our cells, and that cooked and pasteurized food are devoid of beneficial living enzymes. Ann 11/24/10 —Preceding unsigned comment added by 66.153.152.249 (talk) 18:20, 24 November 2010 (UTC)

Very few enzymes can go through the digestive system intact - so your automobile analogy is flawed. Cooked and Pasteurized food tend to lose some nutrients for various reasons (breakdown, loss in cooking liquids, etc.). Hichris (talk) —Preceding undated comment added 19:12, 24 November 2010 (UTC).

I agree that neither this article, nor the protein article, make clear that dietary protein is completely broken down into amino acids before being built into new proteins. Both articles should be edited for clarity, given that most people are mostly familiar with dietary protein. T. Shafee (Evo&Evo) (talk) 03:52, 14 October 2014 (UTC)

Definition of 'Enzyme'

The current article's first sentence states "Enzymes are proteins that catalyze (i.e., increase or decrease the rates of) chemical reactions.". What I am questioning is that all enzymes are proteins. The statement have two references, although I do not have access to any of them and can't verify. However, I found a reference stating that "nearly all known enzymes are proteins", see below.

Reference: Berg, Jeremy M.; et al. (2006). "8 - Enzymes: Basic Concepts and Kinetics". Biochemistry (6:th ed.). New York: W.H. Freeman and Company. p. 205. ISBN 9780716767664. Nearly all known enzymes are proteins. {{cite book}}: Explicit use of et al. in: |first= (help) 83.233.164.45 (talk) 12:07, 11 November 2010 (UTC)

It is debatable in biochemistry and biology whether or not all true enzymes are proteins. There are enzymatic RNAs (ribozymes) which some people consider enzymes proper and others do not. Hichris (talk) —Preceding undated comment added 19:15, 24 November 2010 (UTC).

Yes, this is also my interpretation. The article is however written in a manner that states that true enzymes can only be proteins. Do we have any ground for this, or should it be rewritten in a manner which states that the question is dabateble? 83.233.164.45 (talk) 13:56, 28 November 2010 (UTC)

There are a lot of examples of ribonucleoproteins, which act as enzymes. In some of them the catalytic function is performed by nucleic acid, e.g. ribosome or splisosome (in Eukarya domain), in others RNA acts as a guide, e.g. Ago and Piwi proteins, involved in RNAi. Furthermore, as far as I remember, the majority of enzymes are actually metalloproteins, what is not emphasised in the article. Furthermore, the part about the specificity of the enzymes is just ridiculous. 'Many, if not most, enzymes can promiscuously catalyze reactions, or act on substrates, other than those for which they evolved.' - says a prominent protein scientist, Dan Tawfik in his review called 'Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective'. Even a protein which is generally not considered as an enzyme can catalyze chemical reactions. An example could be Kemp elimination, catalyzed by albumin. Even a single amino acid can catalyze reactions, e.g. histidine. In general, I would conclude that this article needs a major update.Fermmyt (talk) 22:06, 8 March 2012 (UTC)

I disagree with the overall tone and conclusion of this commenter, based on the review/perspectives that follow. In my view (see user page as to why to care): [a] any further changes should be based on a preponderance of scientific opinion, and not a fleeting citation or two, and [b] controversies receiving significant attention in major relevant journals should appear as a sentence or two until there is resolution in the literature, after which the resolved matter can be summarized for the article.

As for the specific matters raised, about which I have some understanding, in part from my own published work:

(i) Re: "...as far as I remember, the majority of enzymes are actually metalloproteins, what is not emphasised [sic.] in the article." It has been estimated in a reptuable source, by an expert, that a quarter to a third of enzymes have required metal cofactors [e.g., see Nat Rev Microbiol 2009, 7(1), 25–35. doi:10.1038/nrmicro2057. PMID 19079350; i.e., not "the majority", as this editor remembers from an unnamed source]. Moreover, in the wikipedisa "Enzyme" article, the matter of required metals is correctly covered under "Cofactors", where the separate, extensive wiki article on metalloproteins is referenced. And speaking of a lack of specificity: If particular mentions of metal cofactor activities and cases are really being suggested, a list of these specific edits and their references should be offered, so there is an actual proposal for change on the table that can be reviewed by other knowledgable contributors.

(ii) Re: "...the part about the specificity of the enzymes is just ridiculous. 'Many, if not most, enzymes can promiscuously catalyze reactions, or act on substrates, other than those for which they evolved.' - says a prominent protein scientist, Dan Tawfik..." This foregoing wiki editor's point is naive and overstated, and poorly reflects the fine work of Prof Tawfik at Weizmann (or the pioneering Benner ETH work before him). While some enzymes display breadth of substrate specificity, scores are very proscribed in their substrate range, generally operating on no other to a few other very similar molecules. Here is a starting point to investigate enzyme specificity examples based on a standard, reliable training framework (see also point iii, folowing):

  A. Absolute/high, and/or stereochemical specificity (uricase, arginase, carbonic anhydrase, lactase, sucrase, and maltase in the first case; the distinct L- and D-amino acid oxidases, and α- and β- glycosidases in the second case).
  B. Dual specificity (e.g., xanthine oxidase, and sequential xanthine and hypoxanthine substrates)
  C. Moderate structural or group specific transformations (pepsin, trypsin, chymotrypsin, the various aminopeptidases, and carboxypeptidase).
  D. Relatively low but bond specific (e.g., amylase and lipase).

[Cf.

 http://www.worthington-biochem.com/introbiochem/specificity.html
 http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0000716.pub2/full   ]

Do your conclusions accurately reflect these and other examples? If so or if not, what are your actual edit ideas and sources? Is your original conclusion of the ridiculousness of the current article justified? If so, how would you summarize a more accurate representation of the preponderance of current literature opinion (not one passing citation). Bottom line, If there is a serious proposal here for a change to the article, it needs to be more than a sophomoric flail (no insult to sophomores intended): the editor must catalogue and present some cases contrary to the working paradigm, for consideration.

(iii) Re: "Even a protein which is generally not considered as an enzyme can catalyze chemical reactions. An example could be Kemp elimination, catalyzed by albumin." The point of this comment is not particularly clear, but again seems naive in its intended extrapolation from this reasonable observation to dire consequences for the article. As proteins as a class are an exquisitely variable set of stereo-electronic surfaces, how is it not surprising that when various proteins are arrayed against various organic moieties, some new abiologic transformations are discovered? The same has been known for any manner of synthetic and natural materials that are not enzymes, but that similarly present a unique varieties of surfaces (e.g., zeolites, montmorillonite clays, etc.). One discriminating point is, in part, that selective pressures operating in biological systems take the material they have to work with—a polypeptide chain that can reduce E-dagger for a transformation—and perform a multivariate optimization of the polypeptide's various functions so that a subset of the many possible permutations increase survival of the organism carrying the gene for the protein (i.e., so that it can create progeny). This means when we look at an enzyme, and say it doesn't do its job right (specificity too low, kcat/Km not right, etc.), we simply may not understand over what set of variables nature has optimized the catalyst—i.e., what it is actually meant to do (see Benner, SA Chem Rev 1989, 89(4), 789–806). So, what is the relevance the editor sees, for the pairing of BSA and the Kemp oxazole ring opening (J Am Chem Soc, 1996, 118 (34), 8184–8185), to any larger issue in enzyme chemistry? What in the article needs to be changed?

(iv) Re: "Even a single amino acid can catalyze reactions, e.g. histidine." Here, the naivete of the foregoing commentary crescendos. Why stop there, why not simply state that protons can catalyze reactions? Of course protons do, and therefore so does imidazole, and therefore so does the alpha-amino acid bearing this protic heterocycle (i.e., histidine). But as structure and complexity of the catalyst change, so do the range of reactions mediated, and the specific conditions required. Histidine doesn't catalyze Friedel-Crafts alkylations (!), and when it does catalyze chemical transformation, it is generally group and not molecule specific. But when one gets to an evolution-driven and exquisitely complex histidyl catalyst, e.g., dehydroquinate dehydratase, we see that a single "buried" histidine of the polypeptide catalyzes sequential imination, elimination beta to a carbonyl to form an enone, and then imine hydrolysis—but only, effectively, to date, on one molecule, dehydroquinic acid (J Biol Chem, 2011, 286(5), pp.3531–3539). Here it again seems that the editor/commenter's lack of broad understanding of the concepts of specificity and selectivity lead to the foregoing comments (see Hedstrom link/citation, above). And so, again, begged is the question, what is the relevance of the "single amino acid" statement, to any larger issue in the enzyme chemistry article? What in the article needs to be changed?

(v) Re: "There are a lot of examples of ribonucleoproteins, which act as enzymes. ... in others RNA acts as a guide... RNAi." The matter of how to present ribozymes and other RNA-containing catalysts should be addressed, but with sophistication and referencing beyond what appears in the foregoing comment. It may be that the field has settled on the definition of enzyme as the family of protein catalysts, with RNP-type catalysts belonging to a second, smaller family, and nearly pure or purely RNA catalysts in another family still. This is for relevant opinion leaders in the field to determine, not us; we are to report (and not attempt to create) a preponderance of opinion. What do good references in this area suggest as the widely held, scholarly opinion?

I am sorry of this sounds harsh, but it is intended to spur the foregoing commenter to actually do the hard work necessary to determine if changes are needed to an already high quality article. (And as a side-benefit, if he or she does so, they might have the material for a decent one-hour university lecture on specificity in enzymology.) Bottom line, from this editor's perspective: The article should continue to be reexamined periodically, and updated by active researchers and writers in enzymology disciplines. I do not concur that the Enzyme wiki "article needs a major update", and it certainly should not be subjected to the sort of low quality citation-mining updates that some other articles have been subjected to, to their near demise. Not all ideas, or citations, are created equal. Cheers Leprof 7272 (talk) 08:48, 8 October 2012 (UTC)

(V) If this is your point, I agree completely. Just please remove ribosome, DNA polymerase and other RNP-catalysts if there are any more, from the article, because they are confusing, and put them to RNP-catalyst section. I couldn't express any objection to any other of your points either, probably because the article or my attitude changed over time.Fermmyt (talk) 08:28, 6 November 2012 (UTC)