Talk:Enzyme/Archive 3

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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)

why protein are produced in active form? —Preceding unsigned comment added by 196.41.62.51 (talk) 09:24, 28 March 2010 (UTC)

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)

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)

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)

One would think that the Enzyme Commission would be a better authority than a textbook. For example, peptidyl transferase has an EC number. It is emphatically not a protein. This page is failing to address new advances. —Preceding unsigned comment added by 171.67.164.89 (talk) 20:28, 5 July 2010 (UTC)

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)

Nice Article!!!

Great job, guys!

WriterHound 17:55, 25 June 2007 (UTC)