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Topic: The arbitrariness of the genetic code
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Art
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Member # 179
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posted 16. March 2006 23:08
quote:
So far as I have read in this thread, there is some sort of assumption that 20 aminos is not arbitrary.
It's not an assumption, but a hypothesis that is supported by some direct experimental examination.
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Art
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posted 16. March 2006 23:16
Jules said: quote:
Thanks Art, for the update. I'll have to go look up "aptamer" so I can better understand the review. However, it seems to be saying that there is significant binding for 8 amino acids, two for their codons, 6 for their anticodons. And that since these were the only amino acids tested for, it reasonable to assume the other 14 amino acids would show similar results. Is that about right?
I think there are some amino acids for which negative results have been obtained - Yarus mentions glutamine and histidine in the quoted passage.
This raises interesting questions - are there correspondences between different groups of amino acids as defined by these studies and amino acids that result from different OOL chemistry experiments? Is there a different chemical basis for the heirarchies that the aptamer studies suggest? Were the subsequent covalent associations uni- or bi (or multi)-molecular in nature?
Fun stuff, to be sure.
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Allen Lints
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posted 17. March 2006 00:23
http://bayes.colorado.edu/thesisreprint.pdf
Dr. Knight has a interesting review thesis on this topic. As for twenty aminos acids this is experimemtally determine for the vast majority of life forms with two notable exceptions. Methagen bacteria use pyrrolsine in a stop codon and seleccysteine is used in some creatures. However no life forms are know to use only 12 amino acids. So a number of mass extinctions must have occur evertime a new amino acid was added to some creatures code or twenty was in the LUCA assuming there was a LUCA.
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Jules
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posted 17. March 2006 10:24
14 amino acids...no,wait, let me take off my shoes....12! That's 12 amino acids we need information on....no wait, we have negative results for glutamine and histidine. So now we need to know about the other 10.
Let's assume that the other 10 bind to their anticodons. So now we have a total of 16 (gosh, I hope I got that number right) amino acids that bind to their anticodons. Let's assume that 16 is enough to make proteins. If I understand it, though, this means that the original proteins were made by the amino acids binding not the mRNA, but to tRNA. And not to the current binding sites of tRNA (what I would call the "stem"), but to the "middle leaf" of tRNA, where the anticodons are. And then somehow, the tRNAs have to line up and allow the amino acids to bind to each other. Presently, tRNA anticodons line up on the template of the mRNA codons. But if the amino acids are already bound to the tRNA anticodons, how are the tRNA anticodons also able to bind to the mRNA codons?
I imagine some Darwinian pathway may be conceivable. What I'm wondering is, should there be two threads: One for trying to figure out how a non-intelligent (Darwinian or other) pathway could have lead to the current translation system. The other thread would assume an intelligent pathway to the current translation system, and then try to figure out why it was designed this way. In other words, instead of arguing which is the "true" history, let each choose the story he/she prefers, and work on the problems it presents.
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Art
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Member # 179
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posted 18. March 2006 09:19
Hi Jules,
The relationship between amino acid-binding, codon/anticodon-containing RNA aptamers and tRNAs is an interesting question. It may help to think about tRNAs in ways different from those we usually see in genetic textbooks.
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Proc Natl Acad Sci U S A. 1987 Nov;84(21):7383-7.
tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: implications for the origin of protein synthesis.
Weiner AM, Maizels N.
Department of Molecular Biophysics and Biochemistry, Yale Medical School, New Haven, CT 06510.
Single-stranded RNA viruses often have 3'-terminal tRNA-like structures that serve as substrates for the enzymes of tRNA metabolism, including the tRNA synthases and the CCA-adding enzyme. We propose that such 3'-terminal tRNA-like structures are in fact molecular fossils of the original RNA world, where they tagged genomic RNA molecules for replication and also functioned as primitive telomeres to ensure that 3'-terminal nucleotides were not lost during replication. This picture suggests that the CCA-adding activity was originally an RNA enzyme, that modern DNA telomeres with the repetitive structure CmAn are the direct descendants of the CCA terminus of tRNA, and that the precursor of the modern enzyme RNase P evolved to convert genomic into functional RNA molecules by removing this 3'-terminal tRNA-like tag. Because early RNA replicases would have been catalytic RNA molecules that used the 3'-terminal tRNA-like tag as a template for the initiation of RNA synthesis, these tRNA-like structures could have been specifically aminoacylated with an amino acid by an aberrant activity of the replicase. We show that it is mechanistically reasonable to suppose that this aminoacylation occurred by the same sequence of reactions found in protein synthesis today. The advent of such tRNA synthases would thus have provided a pathway for the evolution of modern protein synthesis.
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Allen Lints
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posted 20. March 2006 21:44
Jules said:
quote:
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I imagine some Darwinian pathway may be conceivable. What I'm wondering is, should there be two threads: One for trying to figure out how a non-intelligent (Darwinian or other) pathway could have lead to the current translation system. The other thread would assume an intelligent pathway to the current translation system, and then try to figure out why it was designed this way. In other words, instead of arguing which is the "true" history, let each choose the story he/she prefers, and work on the problems it presents.
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Jules, this is what I find so insidious about Darwinian Theory. It always forces questions to be framed in a hypothetical paleontological perspective, than perfectly good questions go begging or not even ask. May I suggest we reframed the question to be: How can we design an experiment to created life? What features of the genetic codes may direct us to discover this experiment? These are more reasonable because the put the conclusions in the present or near future. Much more likely to be observe by us (intelligent beings).
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Jules
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Member # 181
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posted 23. March 2006 12:23
Allen, I don't find Darwinian theory to be insidious. Though I find non-intelligent design explanations for the origin of life to be implausible, I can understand why people would find an intelligent design explanation the origin of life to be implausible. So I think asking for mutual understanding and respect ("Can't we all just get along?") is not a bad thing. And according to Art, apparently scientists are conducting experiments to find a way to arrive at a non-intelligent origin of the genetic code. Are ID researchers trying to understand why the genetic code was designed the way it was?
Meanwhile, I'm still trying to figure out what "aptamer" means. And then I'll try to figure out Art's last post.
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Art
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posted 23. March 2006 13:11
A nice definition of aptamer: this site
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Jules
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posted 26. March 2006 15:40
Thanks for the link, Art. I finally know what aptamer means. Now how about a little help with, "CCA-adding enzyme, telomeres, CmAn, and aminoacylated"?
Meanwhile, I think the article you quoted is suggesting that tRNA served as a template for proteins, is that correct? But does it address the problem I raised of how, if the amino acids are binding to the anticodons, how and why would it come about that proteins are made that bind the amino acids not to the anticodons, but to the stem of the tRNAs, and how and why mRNA is ever needed or originates?
Or do I just need to read more carefully?
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Art
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posted 31. March 2006 18:48
Hi Jules,
recently, you said:
quote:
Thanks for the link, Art. I finally know what aptamer means. Now how about a little help with, "CCA-adding enzyme, telomeres, CmAn, and aminoacylated"?
CCA-adding enzymes are the enzymes that add the sequence "CCA" to the 3'-end of almost-mature tRNAs. (Recall that tRNAs have this distinctive sequence at their 3' ends, and that it is not encoded in the genome.)
Telomeres are the ends of linear DNA chromosomes (and, as Maizels and Weiner would suggest, perhaps of linear RNA genomes as well). This site has a nice picture and an explanation.
"CmAn" stands for a repeating polymer that consists of alternating stretches of C and then A - CCCAACCCAACCCAA would be "C3A2". Etc.
Aminoacylated is what we call a tRNA that has an amino acid covalently attached to its 3' end. (That's the end with the "CCA".)
quote:
Meanwhile, I think the article you quoted is suggesting that tRNA served as a template for proteins, is that correct?
No. Maizels and Weiner were suggesting that, before tRNAs were used for protein synthesis, they were sort of like telomeres for RNA chromosomes. The reason I posted the abstract was to try and get readers to think outside of the BIO101 box, and see that there is more to tRNA than just decoding on the ribosome.
quote:
But does it address the problem I raised of how, if the amino acids are binding to the anticodons, how and why would it come about that proteins are made that bind the amino acids not to the anticodons, but to the stem of the tRNAs, and how and why mRNA is ever needed or originates?
All good questions. Briefly, people hypothesize that the tRNA-amino acid "connection" arose because amino acids might make useful cofactors for some RNA biochemistry.
quote:
Or do I just need to read more carefully?
Don't we all?
Art
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