Talk:Ribozyme

Untitled
Does anyone know the size of the smallest known ribozyme? Memenen 05:32, 13 Dec 2004 (UTC)


 * Don't know, perhaps ask at the reference desk. --Lexor|Talk 08:10, Dec 13, 2004 (UTC)


 * To the best of my knowledge the smallest ribozyme is the leadzyme. It is about 30 nucleotides in size. [Duane(browser)]

Wiki Education Foundation-supported course assignment
This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Xikun Liu.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 08:09, 17 January 2022 (UTC)

ATP requirement
Introns don't require ATP for their catalytic activity, but is this a general property of ribozymes? --EnSamulili 19:19, 25 July 2005 (UTC)

I don't know of any ribozyme that requires ATP for their catalytic function. All of the small naturally occuring ribozymes (HDV, Hammerhead, Hairpin and VS ribozymes) require divalent (or high concentrations of monovalent) cations for their reaction. There are DNAzymes and other ribozymes that have been constructed from in vitro selection (SELEX) experiments that contain aptamer binding domains. The aptamer (could be any particular small molecule) is required for forming the active structure of the DNA/RNA enzyme, but doesn't participate directly in catalysis. There may be a DNA/RNA enzyme containing an ATP binding domain, but I'm not 100% sure (without checking) (Duane - Browser)


 * To the contrary, ligase and polymerase ribozymes require a high-energy phosphate bond. Usually in these reactions, pyrophosphate is the leaving group when the alpha-phosphate of a triphosphate group is attacked by a hydroxyl group.

This is similar to the mechanism of DNA ligase (DNA ligase, however, uses an adenylate as the leaving group, instead of pyrophosphate. Polymerases, of course, use NTPs as the substrates, so their leaving group is pyrophosphate. Phosphodiester bond hydrolysis doesn't require ATP. It is energetically favored.

LinkinPark 20:19, 30 October 2006 (UTC)

Creationism
I'm probably opening a huge can of worms here, but the first reference "The RNA World: A Critque" has significant intelligent design undertones (and 'overtones' in the conclusion!). As an undergraduate, I don't know how accurate the information it contains is, but I'm skeptical of its impartiality (a cornerstone of science). As I read through it, I actually thought that it reminded me of irreversible complexity essays I've read. Does biased science belong in a scientific article such as this one - or is this the thin end of the wedge refered to in "The Wedge Document"?

Aaadddaaammm 04:59, 7 June 2006 (UTC)


 * You were quite right, I have replaced that one with the real reference to the original article. Cpt. Morgan (Reinoutr) 12:41, 8 August 2006 (UTC)

Merger proposal
merge done Anthony Appleyard (talk) 21:40, 24 January 2008 (UTC)


 * What do people think about merging the content from RNA Biocatalysis with this page? Tim Vickers 15:37, 30 October 2007 (UTC)
 * I agree. Alexbateman 04:05, 31 October 2007 (UTC)
 * I agree. Both articles germane to the same topic JMB-Universidad Complutense de Madrid
 * yes i agree sinharaja2002 —Preceding comment was added at 14:20, 24 November 2007 (UTC)

Round 18
I could swear I saw Round 18 somewhere. Incredibly, it is missing from this article. Anyone see it? Cheers --Squidonius (talk) 18:50, 11 March 2008 (UTC)

Found it. It was two lines in the intro. sorry --Squidonius (talk) 18:52, 11 March 2008 (UTC)

Discovery section needs editing
The text in the "Discovery" section has many typos that makes it very difficult to read. —Preceding unsigned comment added by 76.100.118.114 (talk) 23:29, 15 May 2008 (UTC)


 * Done. Tim Vickers (talk) 02:07, 16 May 2008 (UTC)

Quote
How about adding the phrase that first mentions the word 'ribozyme' from Kelly Krugers original article (Cell, 1982) to the discovery section? WKoets (talk) 16:00, 24 September 2009 (UTC)
 * The quote: "Because the IVS RNA is not an enzyme but has some enzyme-like characteristics, we call it a ribozyme, an RNA molecule that has the intrinsic ability to break and form covalent bonds."


 * Sounds a good idea. Tim Vickers (talk) 16:13, 24 September 2009 (UTC)

What's a primer template?
? —Preceding unsigned comment added by 155.97.15.211 (talk) 05:42, 16 September 2010 (UTC)

Does it have anything to do with this? http://en.wikipedia.org/wiki/Primer_(molecular_biology) —Preceding unsigned comment added by 155.97.15.211 (talk) 05:44, 16 September 2010 (UTC)

If.. then.. could be… (then no citation)
I am leaving in place the speculative sentence in the "Activity" section, about RNA world and origin of life (all good valid stuff in principle)—but only for now, because with such vagaries, it better be take the form of text-with-citation, better, via a quote or other strong attribution. Because for every three PhD's on one side of this, there are three PhD's on another. No one gives two pence for an anonymous WIkipedia editor's ""if… then… could be…" statements.

Le Prof (an Urbana graduate back in the day, and an early archaeworld green jacket wearer)     Leprof 7272 (talk) 02:10, 4 June 2014 (UTC)

Three invalid citations from Activities section moved here
…and tag placed. Here is what were inserted, to appear as three citations (lead brackets omitted for each): Please, ladies and gentlemen. This is neither sandbox nor class or text notepad. Please. Le Prof   Leprof 7272 (talk) 02:14, 4 June 2014 (UTC)
 * ref>
 * ref>
 * ref>invalid reference

Self-cleaving ribozymes are not catalytic
The definition of a catalyst is that it participates in a reaction but is not consumed by it, and can thus participate in multiple turnovers. Self-cleaving ribozymes break their own covalent bonds, and thus are destroyed by the reaction they perform, and cannot perform multiple turnovers. For this reason it is incorrect to say that all rybozymes are catalysts. Antony–22 (talk⁄contribs) 18:50, 22 April 2016 (UTC)
 * WP:LEAD summarizes the body. pls read last paragraph of 1st section and 1st paragraph of 2nd section.  if you disagree with what is there please change it, with sourcing, then change the LEAD.  Thanks. Jytdog (talk) 20:22, 22 April 2016 (UTC)
 * The first paragraph you mention refers to "self-cleaving RNA or catalytic RNA molecules", implying that they are separate categories. The second paragraph says "in self cleaving ribozyme RNAs, an in-line SN2 reaction is carried out...", not catalyzed.  Later, the article specifically refers to self-cleaving riboswitches as "not true catalysts".  Nowhere in the body of the article is it stated or implied that self-cleaving ribozymes are catalytic.  The revised text does reflect the article body; clearly the prior text does not.  Antony–22 (talk⁄contribs) 05:19, 23 April 2016 (UTC)

looking for consensus
Hello. I added an external link to a presentation at the NIH that is directly relevant to this article. undid it with the explanation "This is technical; not especially accessible for every day people". To my knowledge, wp does not require articles to be written for every day people. Wp articles should be able to be understood by college students. I have taught biology to a large number of college students. I would not expect my freshmen gen ed students to understand NIH seminars. I definitely would expect my upper division undergrad biology students to understand the presentation. Perhaps jytdog isn't as advanced as my upper division students, but that doesn't justify jytdog censoring content that some readers may benefit from. So, I have reinstated the link to the NIH seminar, and I ask for community consensus on whether to include it. Finally, BTW, if that seminar is viewed as too technical for wp, then every single gene and protein infobox I've seen should be deleted, since they are clearly much more technical. Thank you for your time and replies. JeanOhm (talk) 17:10, 24 June 2017 (UTC)
 * I've no real opinion about the added content (way beyond my understanding), but I'd like to note that the way the way WP:BRD works is not "you add it and then you seek consensus before it may be removed". If the content is challenged, you seek consensus before re-adding.  Otherwise you may be accused of edit warring.
 * If you want to add this external link, you'd be better explaining why it aids the reader in a way that cannot be done within the article itself. Thanks. -- Escape Orbit (Talk) 17:35, 24 June 2017 (UTC)
 * Since jytdog appears to be intent upon censoring this content, I have included it here. BTW, judging from jytdog's edit history {edits at 2:48, 2:52, two at 2:55 AND THEN at 2:57, in which jytdog judged that the video seminar is inappropriate for wp} there is no indication that jytdog actually viewed the video before censoring it. The video is a verbal review of many research papers, with many great images that cannot be posted on the commons.JeanOhm (talk) 17:45, 24 June 2017 (UTC)
 * External links, if included at all, belong in the external links section, not in the body of the article. This particular lecture is pretty dense. Boghog (talk) 17:48, 24 June 2017 (UTC)
 * Why then, does the wp external media template exist? I use my own image to make it MUCH less intrusive into the article.JeanOhm (talk) 17:57, 24 June 2017 (UTC)


 * External media is for material or media that cannot be reproduced within Wikipedia, for example, a link to song or movie clip. That is not the case with this lecture.  This Wikipedia article already summarizes the main points of the seminar.  If there is important material that is not covered in the Wikipedia article, then it should be added directly to this article. Finally you are hyping one particular researcher within the article.  This is strongly discouraged. Boghog (talk) 18:19, 24 June 2017 (UTC)

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deleted text (Oct 30, 2018)
I deleted the following text. It seems to refer to a specific ribozyme, e.g., talks about the "six coordinated Mg2+" -- is this a property of _all_ ribozymes? Also, it's generally not very clear what the text is referring to. There are multiple classes of ribozymes that perform different reactions. Do all of these classes fit into the description?
 * The RNA molecule has a strong preference towards alkali earth metal especially Mg2+, but the six coordinated Mg2+ has low affinity for nitrogen ligands and cannot bind to sulfur. Ca2+ instead is common for coordination number over 6, and Mn2+can bind to both nitrogen and sulfur. The cations can neutralize the negatively charged RNA, and bind to specific sites to stabilize the catalytic active forms of RNA.

Zashaw (talk) 10:37, 30 October 2018 (UTC)

"cleavage (or ligation)" Incredibly Mysterious Term(s)
"Cleavage (or ligation)" is used without definition of what it is as if it were some common term. Even when searching Google specifically for what cleavage (or ligation) means with respect to RNA or DNA and ribozymes, all I found were highly technical research papers and websites that also don't define its meaning in a way a layperson could understands. I'm assuming some source somewhere, like an introductory, academic textbook, could be used to bring in more information to help non-academic people glean information from the article rather than think, "Hmm, what?"

It would be fantastic if some biologist with sympathy could beef up this and other articles to attempt making an article useful both to people studying biology in college and those not studying biology outside of a popular science fashion. One boon for the uninitiated would be making some of the jargon hyperlinks that lead to articles that explain different processes way more in-depth, hopefully featuring some explanations for people who haven't studied biology for the last half decade.

My best guess as to the meaning after reading this Wikipedia article and Googling some is that it may mean the ribozyme breaks RNA or DNA at a point when cleaving. Now, even in the best case where I am correct in the interpretation, a few problems remain:


 * I have no way to know if it is right.
 * I have no idea of why biological processes would need a ribozyme to cleave (or ligate) RNA or DNA. Is it the only way to do it?
 * I have no idea if the RNA and DNA is just two examples of the process, or if cleaving (or ligating) have other times when they do something different without relating to the RNA or DNA situation.
 * I'm unclear during which biological processes cleaving (or ligation) play a role, and in doing that role, what the role even is.

While trying to use context clues, nearby sentences just use more jargon that even Google searches cannot clear up:

"The most common activities of natural or in vitro evolved ribozymes are the cleavage (or ligation) of RNA and DNA and peptide bond formation. For example, the smallest ribozyme known (GUGGC-3') can aminoacylate a GCCU-3' sequence in the presence of PheAMP."

So here, I have to know what aminoacylate means, and there is little chance for a person to know that word if they don't know the terms cleavage (or ligation). Same as my previous Google searches, this only pulls up highly specialized resources that I'd imagine only a collegiate student of biology would (maybe) understand. And again, there is no attempt to help a layperson gain any information at all. Is this part of cell reproduction? Is it a way to destroy some faulty DNA or RNA? What is it doing at a high level? Even after figuring that out, I'm left wondering if aminocylating is the primary example of cleavage (or ligation), is just an arbitrary example, or if it is basically the only thing a person does when doing cleavage (or ligation).

This type of issue seems to permeate the biology articles as if it's a competition among the editors to come off as super smart, intentionally leaving out information a layperson might find useful.

The only places I find this type of thing is in advanced mathematics and physics articles, but in these, there is often paragraphs and sections dedicated to simplifying the concepts to a high level for a person who isn't in school for these topics have some chance of understanding something new. 96.60.251.105 (talk) 07:36, 24 November 2023 (UTC)