tag:blogger.com,1999:blog-37148773.post3410011752973573568..comments2024-03-19T00:24:23.577-04:00Comments on <center>Sandwalk</center>: Head Growth and Tail GrowthLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger11125tag:blogger.com,1999:blog-37148773.post-7428412172333619302020-05-04T13:38:50.514-04:002020-05-04T13:38:50.514-04:00Such an interesting concept; something that I'...Such an interesting concept; something that I'd never heard of in my past four years as a molecular genetics undergrad at UofT, and especially while taking BCH242; primarily I presume, because of the way the course was taught (as you mentioned, complete separation of all the four sections from one another) as well as the supposed fear of the instructors that if they bring up anything remotely related to organic chemistry, it's going to offense the students (which brings up the question of "why do you guys then make the poor students suffer through two organic chemistry courses if they're not supposed to see their application in biochemistry and molecular biology?!"). I'm curious to read a more in detail your explanation of the two mechanisms, is your book out for us, the class of '20 people, yet?!Anonymoushttps://www.blogger.com/profile/15768382432412283986noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22186418191943256442009-05-08T09:44:00.000-04:002009-05-08T09:44:00.000-04:00When does the next edition of the textbook come ou...<I>When does the next edition of the textbook come out?</I><BR><BR>Hopefully in January 2011.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29312209611401027162009-05-08T09:24:00.000-04:002009-05-08T09:24:00.000-04:00When does the next edition of the textbook come ou...When does the next edition of the textbook come out?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23247779844084512022009-04-30T23:40:00.000-04:002009-04-30T23:40:00.000-04:00@ Lorax:
I am interested in your easily envisioned...@ Lorax:<br /><I>I am interested in your easily envisioned evolution of a mechanism for proofreading in translation similar to replication.</I>Well, I did not say "evolution". I just said alternatives are possible. Here is the first fantasy that comes to mind (there ought to be 100s more possible):<br /><br />Redundancy. Right after peptide bond formation and before translocation, check once again that the codon matches. If not, full stop, no translocation. The stalled state is subject to the competing peptidase and non-specific aminoacyl transferase activities - until the second check gives green light and translocation occurs.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47339019650473717632009-04-30T17:03:00.000-04:002009-04-30T17:03:00.000-04:00DK,
I didn't say translation proofreading occurre...DK,<br /><br />I didn't say translation proofreading occurred in the same way it does for replication. As you noted it does occur, but you dont except it and want to redefine decades old terminology to suit your perspective.<br /><br />I can level the same "redefining terms" accusation at Larry, but from his context I assumed he was specifically talking about an C-terminal to N-terminal exopeptidase activity analogous to DNA replication. Based on the "tail growth" model, it seems like proofreading must occur before synthesis (just like in translation).<br /><br />I am interested in your easily envisioned evolution of a mechanism for proofreading in translation similar to replication.The Loraxhttps://www.blogger.com/profile/13361004494346338824noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79799089670446180442009-04-30T01:11:00.000-04:002009-04-30T01:11:00.000-04:00lol wut shit has everything to do with biochemistr...lol wut shit has everything to do with biochemistryAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68792307994978547502009-04-29T23:47:00.000-04:002009-04-29T23:47:00.000-04:00@ The Lorax:
There is proofreading in translation...@ The Lorax:<br /><br /><I>There is proofreading in translation, a fair bit actually.</I> <br /><br />Larry disagrees: <br />[protein synthesis is a "head growth"] and "that's why there's no proofreading in protein synthesis".<br /><br />I tend to agree with Larry. The well-known kinetic proofreading is actually a misnomer because it's a quality control that ensures proper synthesis but does not *correct* mistakes in polymerization that have been made. Unless you are saying that there does exist a real proofreading in translation, with nimbling down and restarting (?). I am not aware of such (if that were to happen, won't the polypepthe chain fall off the ribosome and be lost?).<br /><br />To add my to my previous comment: isn't the basic polymerization chemistry is the same for all complex carbohydrates (say, chitin or agarose)? If so, it seems highly dubious to assign "the fundamental reason why tail growth <B>evolved</B> [emphasis mine - DK] in both nucleic acid synthesis and glycogen synthesis".DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22779050376978694532009-04-29T22:26:00.000-04:002009-04-29T22:26:00.000-04:00DK,
There is proofreading in translation, a fair ...DK,<br /><br />There is proofreading in translation, a fair bit actually. Its just not like DNA. But so what, who ever said DNA proofreading is the right way?The Loraxhttps://www.blogger.com/profile/13361004494346338824noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9707261254565435292009-04-29T21:41:00.000-04:002009-04-29T21:41:00.000-04:00There needs to be a better term than "head" and "t...There needs to be a better term than "head" and "tail" since it is not obvious that "head" does or does not contain energy and similarly for "tail".<br /><br />Maybe something like "polymer activated" or "monomer activated" to describe whether the energy driving polymerization is contained in the polymer or in the monomer.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58422681296794772462009-04-29T16:37:00.000-04:002009-04-29T16:37:00.000-04:00I feel that this is straight out of some adaptatio...I feel that this is straight out of some adaptationist bible. I.e. "if it exists, it must be super-important for [insert post hoc explanation]". <br /><br />As you mention yourself, there is basically nothing wrong with reactivating the end if the need be and continue to go with the synthesis/proofreading activity. Certainly there are much more arcane ways of accomplishing things in the cell. <br /><br />Moreover, DNA proofreading almost certainly evolved long time after the basic chemistry was set up in stone (i.e., RNA world; RNA, I'd surmise, is made the same 5'->3' way). This kind of leaves the whole head/tail thing and its improtance pretty moot. <br /><br />Finally, it is not too difficult to come up with a mechanism that would enable proofreading in translation. But evidently that did not happen - whih may, in fact, be a pure chance event.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41132062681899632902009-04-29T15:09:00.000-04:002009-04-29T15:09:00.000-04:00As a possessor of a degree in History, I found tha...As a possessor of a degree in History, I found that fascinating. (I have often been puzzled by "proofreading").<br /><br />Thanks for this, and your many other posts on such matters.paul01https://www.blogger.com/profile/06306440944379183875noreply@blogger.com