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Author Topic:   The Mystery of Stop-Codons....
semilanceata
Junior Member (Idle past 3393 days)
Posts: 12
Joined: 04-21-2008


Message 1 of 14 (463859)
04-21-2008 2:06 PM


Here's an interesting question that maybe someone here can answer. The question revolves around the fact that codons have associated anti-codons by way of charged tRNA (if my memory serves). I have been wondering about the 3 so-called stop codons, those codons that serve as a 'full stop' as it were. I understand that these 3 'stop codons' have no associated, or complimentary, anticodon/tRNA. Thus, when a ribosome encounters them (via mRNA), there are no more amino acids gathered and the amino acid chain breaks off etc. My question is: How come there is no anti-codon/tRNA complex for a stop codon? Are such potentially befitting tRNA's destroyed somehow, or is there some physiochemical reason why (just) these 3 particular anti-codons cannot form? Seems to me that, for life (as we know it), it is crucial to have a stop codon (like the importance of full stops in text). This means that it is either 'luck' that three codons do not have anti-codons or that there is some cellular mechanism to destroy them. The former might seem most plausible. But then again, why? Why shouldn't all codons have associated tRNA anti-codon complexes?

To further confuse the issue, there are apparently certain organisms in which the three stop-codons DO have anti-codons. Which supports the latter idea that there is a cellular mechanism to destroy any corresponding anti-codons for the stop codons. But then this begs the question as to how such a mechanism got started. Anyhow, I will be much obliged if anyone on this forum can shed light on this mystery. After all, I am assuming that the reason why stop codons do not have complimentary anti-codon tRNAs has been firmly established by geneticists.


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Message 2 of 14 (463862)
04-21-2008 2:59 PM


Thread moved here from the Proposed New Topics forum.
    
Blue Jay
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Message 3 of 14 (463870)
04-21-2008 3:33 PM
Reply to: Message 1 by semilanceata
04-21-2008 2:06 PM


Hi, semilanceata. Welcome to EvC!

semilanceata writes:

Why shouldn't all codons have associated tRNA anti-codon complexes?

I'm not a cellular biologist or geneticist, but it seems to me that the answer could very well be simple. tRNA has to encoded by DNA. Each different tRNA in an organism would have to be encoded by a different gene, each of which would either arise independently or as a variation of the first tRNA gene. Either way, they would have arisen one by one.

Seeing how an "end" to a coding region is advantageous for condensing the genome into just a few chromosomes or plasmids, I see no reason why this condition would be selected against, thus it would be preserved and amplified in the succeeding generations. On the other hand, an organism that continues to produce new genes encoding tRNAs with "unused" anticodons, would reduce its ability to end a polypeptide and condense its genome, creating a greater inefficiency in transcription/translation.

{AbE: I can't confirm to you that this is correct: maybe Wounded King or other geneticist/molecular biologist could shed some light on this?}

Edited by Bluejay, : Addition


I'm Thylacosmilus.

Darwin loves you.


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semilanceata
Junior Member (Idle past 3393 days)
Posts: 12
Joined: 04-21-2008


Message 4 of 14 (463871)
04-21-2008 3:43 PM
Reply to: Message 3 by Blue Jay
04-21-2008 3:33 PM


Are you saying that the reason there are not these 3 particular anti-codon/tRNAs is because there are no genes for making them? If so, I will have to dwell on this and get back to you if my mind still cannot settle on the issue.
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Dr Jack
Member (Idle past 210 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 5 of 14 (463887)
04-21-2008 5:45 PM
Reply to: Message 4 by semilanceata
04-21-2008 3:43 PM


Yes, that's exactly it. The system that copies DNA is itself encoded in DNA. The DNA produces the tRNA, that copies the DNA. There is no DNA coding for producing tRNA that attaches to a stop codon and any mutation that produced such a tRNA would almost certainly render the containing organism non-viable.
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molbiogirl
Member (Idle past 747 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 6 of 14 (463894)
04-21-2008 6:49 PM
Reply to: Message 3 by Blue Jay
04-21-2008 3:33 PM


Each different tRNA in an organism would have to be encoded by a different gene, each of which would either arise independently or as a variation of the first tRNA gene. Either way, they would have arisen one by one.

I certainly don't know anything about tRNA evolution, but here is what I found:

The transfer RNA (tRNA) multigene family comprises 20 amino acid-accepting groups, many of which contain isoacceptors. The addition of isoacceptors to the tRNA repertoire was critical to establishing the genetic code, yet the origin of isoacceptors remains largely unexplored. A model of tRNA evolution, termed tRNA gene recruitment, was formulated. It proposes that a tRNA gene can be recruited from one isoaccepting group to another by a point mutation that concurrently changes tRNA amino acid identity and messenger RNA coupling capacity.

http://cat.inist.fr/?aModele=afficheN&cpsidt=2178528

IOW, a single change in the genetic code of one tRNA = a different tRNA. Perhaps this was one of the evolutionary mechanisms.

And I found this on wiki:

In certain proteins, non-standard amino acids are substituted for standard stop codons, depending upon associated signal sequences in the messenger RNA: UGA can code for selenocysteine and UAG can code for pyrrolysine as discussed in the relevant articles. Selenocysteine is now viewed as the 21st amino acid, and pyrrolysine is viewed as the 22nd. A detailed description of variations in the genetic code can be found at the NCBI web site.

The fact that non-standard amino acids are inserted in proteins (rather than "stopping" these proteins) is intriguing. It means that a stop codon can "attract" a tRNA that is aminoacylated (i.e. carrying an amino acid).

Also. Some vertebrate codons act as invertebrate stop codons.

AGA and AGG (AGR) are arginine codons in the universal genetic code. These codons are read as serine or are used as stop codons in metazoan mitochondria.

http://www.springerlink.com/content/p3518139p478jt0j/

Again, as with the non-standard amino acids, this suggests that some stop codons act as ordinary codons.

Edited by molbiogirl, : sp


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Blue Jay
Member (Idle past 803 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 7 of 14 (463897)
04-21-2008 7:25 PM
Reply to: Message 6 by molbiogirl
04-21-2008 6:49 PM


Thank you, molbiogirl.

molbiogirl writes:

IOW...

I'm glad you do translations, too: my molecular biologyese isn't very good (but it's a lot better than my Teslaese).

molbiogirl writes:

The fact that non-standard amino acids are inserted in proteins (rather than "stopping" these proteins) is intriguing. It means that a stop codon can "attract" a tRNA that is aminoacylated (i.e. carrying an amino acid).

And, it would appear to pose a serious challenge to my hypothesis. Unless...

From your wiki quote:

quote:
In certain proteins, non-standard amino acids are substituted for standard stop codons, depending upon associated signal sequences in the messenger RNA...

The presence of an auxiliary signal here indicates to me that the initial function of the codon was "stopping," and that the non-standard aminoacylation is a derived function. So, perhaps my model is still intact.

I read up a bit on Wikipedia, and I found that the signal is a SECIS element, which is just a short sequence of non-naturally-pairing nucleotides right after the UGA that's supposed to code for selenocysteine. Somehow, that assists the selenocysteine-carrying tRNA in binding to the stop codon. This also implies that the UGA codon itself was originally a stop codon.


I'm Thylacosmilus.

Darwin loves you.


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Brad McFall
Member (Idle past 3138 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 8 of 14 (463899)
04-21-2008 8:06 PM
Reply to: Message 1 by semilanceata
04-21-2008 2:06 PM


pre-speculation
I might try to think about that some complicated INEQUALITY in the kinetic energy of electrons and potential energy of protons established coincidentally, over time, some similarity in the hydrophobicity of nucleotides and amino acids, resulting in the prohibitions to formation no matter the rates.

I tried to explain something like this to Randy Wayne at Cornell today but that failed. I would have to think of it some more and specify how I think this is the same notion as Shrodingers on the "a periodic crystal"

Randy thinks my idea would not work because where I tried to describe a dynamics he sees only a constancy.

P.S. This conversation was a side-effect of getting the final results on the ostracod hepatopancreas of mine.
www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=14&t=2024&m=19#19 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=14&t=2024&m=19#19">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=14&t=2024&m=19#19
IT IS NOT ENDOSYMBIOTIC!! We could not see chlrophyll flouresence in the liver but we did see it in the stomach.

Edited by Brad McFall, : link


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Dr Jack
Member (Idle past 210 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 9 of 14 (463935)
04-22-2008 6:40 AM
Reply to: Message 6 by molbiogirl
04-21-2008 6:49 PM


Also. Some vertebrate codons act as invertebrate stop codons.

I believe you are over-generalising here. While some groups of single-celled organisms & organelles do use a slightly different coding system to that used in most prokaryotes and (IIRC) all eukaryotes, it is not the case that veterbrate and invertebrate codings are different.


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kalimero
Member (Idle past 550 days)
Posts: 251
From: Israel
Joined: 04-08-2006


Message 10 of 14 (463951)
04-22-2008 9:37 AM
Reply to: Message 1 by semilanceata
04-21-2008 2:06 PM


some science (not from wiki)
Right from the start I remembered that it was a translation termination factor, which is a protein... :cool:
From Molecular Cell Biology 5th ed - Lodish et al pp. 125-131.

I googled eRF1 and found something interesting here which basically implies that eukariotic polypeptide chain release factors can also work in bacteria (which still amazes me).


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molbiogirl
Member (Idle past 747 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 11 of 14 (463990)
04-22-2008 1:42 PM
Reply to: Message 9 by Dr Jack
04-22-2008 6:40 AM


While some groups of single-celled organisms & organelles do use a slightly different coding system to that used in most prokaryotes and (IIRC) all eukaryotes, it is not the case that veterbrate and invertebrate codings are different.

Mind you. I did all of 30 minutes worth of scholar.googling.

The ARG vertebrate codon acts as a invertebrate stop codon or a SER codon (in the metazoan mitochondria) in the paper I cited.

I didn't mean to suggest that ALL stop codons are different in metazoans. Which is why I used the word "some".


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Ooook!
Member (Idle past 3920 days)
Posts: 340
From: London, UK
Joined: 09-29-2003


Message 12 of 14 (464515)
04-26-2008 8:39 AM
Reply to: Message 1 by semilanceata
04-21-2008 2:06 PM


What came first the tRNA or the Stop?
This is an interesting question because it raises a number of different issues concerning the evolution of the universal code and the protein synthesis machinery.

The main thing that I would highlight is that your question almost assumes that the universal code evolved fully formed and that all codons would automatically be present. Is it not more likely that "stop" would be the default situation and that the universal code (and the corresponding tRNAs) evolved gradually.

The second thing to consider is that the ‘mechanism’ for preventing “stop tRNAs” popping up does not need to be a cellular one. What is wrong with good old evolution? Stop codons are not a complete necessity, as the ribosome cannot go on forever and would drop off eventually, but losing them all would be a disadvantage. Conversley, losing a seldom used tRNA gene and gaining a useful “stop” could be an advantage.

I suspect that this all a gross simplification but it would be interesting to see whether anyone knows of any research that tackles these ideas. I did find a paper ages ago that discussed the gradual evolution of the universal code by looking at the sequences of tRNA transferases, but can’t unearth it at the moment.


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semilanceata
Junior Member (Idle past 3393 days)
Posts: 12
Joined: 04-21-2008


Message 13 of 14 (464684)
04-28-2008 8:49 AM
Reply to: Message 12 by Ooook!
04-26-2008 8:39 AM


Re: What came first the tRNA or the Stop?
I have to confess that since posting the question, I am still baffled - in fact, the more I dwell on these matters the more perplexing it becomes. However, it seems the main answer is that charged tRNA's are specified by genes - and that there is no gene specifying STOP anti-codons (or such a gene is suppressed). Which, I suppose, makes sense. But then can a genetic system work without stop codons? I don't see how it could - because proteins are, apparently, quite specific in terms of their constituent amino acid chains. I would have thought that an in-effect 'stop command' was vital in specific protein building. So maybe, as you say, the original default situation was that all codons were STOP ones since charged tRNA genes had yet to evolve..... I dunno. Nature's 'technology' is extremely baffling. And quite brilliant too of course.
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molbiogirl
Member (Idle past 747 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 14 of 14 (464746)
04-29-2008 12:05 AM
Reply to: Message 13 by semilanceata
04-28-2008 8:49 AM


Re: What came first the tRNA or the Stop?
It's important to understand that the "universal code" evolved from earlier, simpler codes.

The genetic code, understood as the specific assignment of amino acids to nucleotide triplets, might have preceded the existence of translation.

Amino acids were utilized as cofactors by ribozymes in a metabolically complex RNA world. Specific charging ribozymes linked amino acids to corresponding RNA handles, which could basepair with different ribozymes, via an anticodon hairpin, and so deliver the cofactor to the ribozyme.

Growing of the ‘handle’ into a presumptive tRNA was possible while function was retained and modified throughout.

A stereochemical relation between some amino acids and cognate anticodons/codons is likely to have been important in the earliest assignments.

Trends in Genetics
Volume 15, Issue 6, 1 June 1999, Pages 223-229

Here.

It has also been suggested that the code and the AA biosynthesis co-evolved.

A coherent pattern of evolution will be seen to emerge in which addition of a new amino acid to the code typically followed path extension, tRNA diversification to a new acceptor, expansion in synthetase specificity and selection for each synthesized protein.

The coevolution hypothesis (Wong, 1975, 1976) requires that precursors among coded amino acids entered the code before their products. In this section, the time of entry of each amino acid into the code has been estimated from the number of reactions in its biosynthetic pathway. A phased pattern of synthesis emerges, in the sense that physicochemically divergent amino acids appear at divergent stages of code evolution. This has significant implications for code evolution and the origin of life.

Evolution of the genetic code
Brian K. Davis
Progress in Biophysics & Molecular Biology 72 (1999) 157-243.

The evolution of a stop codon isn't quite so difficult to imagine if you keep in mind that the whole thing was kluged together.


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