Didn't find yours? Ask a new question Get plagiarism-free solution within 48 hours. Review Please. Next Previous. Related Questions. Choose one of the following Which of the following is the primary site of protein assembly within eukaryotic cells? A the peroxisome B the Golgi apparatus C the ribosome D the smooth endoplasmic reticulum E the vesicles In order for translation Proteins synthesis Homework Name 1.
In DNA, adenine binds with 2. In RNA, adenine binds with 3. Transcription takes place in the and guanine binds with and guanine binds with translation takes place in the 4. The building blocks of nucleic acids are Complete a concept map of translation, indicate where it takes place, and describe what will happen if the anticodon is not attached to transfer RNA.
Together with data of other amino acids in [ 12 ] and also recent evidence in [ 31 , 33 ], it is also reasonable to conclude that anticodons, not codons, are more often significantly over-represented in aa-binding sites, and that in some cases, "codons might simply follow anticodons like hitch hikers " This conclusion is "welcome" by the stereochemical theory on the origin of the genetic code, considering the previous statement, "both anticodons and codons are over-represented in aa-binding sites", is ambiguous and hard to explain [ 7 ].
Indeed, the situation could be interpreted as the nucleotides of the codon contribute more to the specificity of interaction, or the nucleotides of the anticodon contribute more to the specificity of interaction. Then, the latter interpretation could be accepted considering the above conclusion that it might be anticodons that actually associated with cognate amino acids.
Thus, a new, interesting assertion, stronger than that in the CCH hypothesis, could be phrased as "the degeneracy of 1st position in anticodons 3rd position in 'future' codons also appears to have originated before translation". In this context, it is also attractive to attribute "the fact that codon's 3rd nt is more degenerated than the anticodon's 1st nt" to the cause that anticodons should have emerged before codons, which would be used only in the "future" translation system.
I think that this description has some problems. Now that aptamers have nothing to do with translation, how comes the ambiguity for coding? The logic is hard to understand. If so, a directly contrary motif should be 5'-GCGC-3' as I mentioned above , which should be abundant. However, the analysis or comment on 5'-GCGC-3' does not appear in the manuscript.
We found the reviewer's comments and critique particularly incisive; the two major issues are discussed below. Importantly, it is the CG at positions of codon positions of anticodon that actually specifies Arg, whereas the GC at positions of codon positions of anticodon is irrelevant specifying Ala.
The result - absence of this motif in Arg-binding sites - speaks for itself. Remarkably, in independently selexed Ile-binding sites we also do not see and probably exactly for the same reason the 5'-AUAU-3' tetraplet in which anticodon UAU supposedly drives codon AUA as a hitch-hiker but via the central Ile-irrelevant UA palindrome in the manuscript, we stress this fact just after describing the arginine case.
Needless to say, from the very beginning we have checked all possible Arg-related tetraplets including those, in which anticodon GCG was supposed to be a driver. Comparison of overrepresented and absent coding tetraplets in Arg-, Ile- and Tyr-binding sites of "selexed" RNA aptamers. Anticodons are underlined.
Complementary "yellow" and "green" tetraplets cannot be confused in contrast to self-complementary "blue" ones. However, the latter is not significantly overrepresented in Tyr-specific sites of RNA aptamers. Symmetrically, AUA is a significantly overrepresented triplet, as an anticodon, in Tyr-binding sites but not, as a codon, in Ile-binding ones. Thus, it appears that coding triplets in Ile-binding sites preclude confusion with Tyr and vice versa as if the RNAs selected for direct affinity to a specific amino acid have already been protected from confusion with its complementarily encoded partner.
This is surprising, because the RNA aptamers have not been specifically selected to avoid non-cognate amino acids. This fact is consistent with our hypothesis of two earliest r-aaRS precursors that have been complementary to each other [ 18 — 20 ]. In contrast, coding tetraplets in putative r-aaRSs formed by complementary anticodon and codon, are indeed confusion-prone simply because any such tetraplet is a perfect self-complementary palindrome. Same holds for tyrosine as well as complementarily encoded arginine and alanine.
In such cases, the two complementary r-aaRSs might have had virtually the same aa-coding sites, leading to the high risk of wrong aminoacylation accordingly, they would have been selected against. Obviously, the correct logical flow should be in reverse: selection for stereo-affinity of a given amino acid for example, Ile to the oligonucleotides containing this aa-cognate anticodon UAU within the 5'-UAUU-3' tetramer automatically entails selection for the presence of AUA within 5'-AAUA-3' in the complementary sequence which happens to be preferred by Tyr - the Ile's complementary partner in the real genetic code.
Of course, it is unlikely that the actual shaping of the genetic code had much in common with this in vitro multi-step selection of RNA aptamers each time beginning with a random sequence see our response to reviewer 1.
At this time, we do not suggest any mechanistic explanation for this somewhat surprising result but it shows us that there might have been, indeed, certain structural prerequisites for two complementary modes of tRNA recognition by aaRSs, firstly ribozymes then enzymes.
Moreover, this result indirectly supports, in our opinion, two basic hypotheses: 1 that primary stereo-affinity did play an essential role in the origin of the genetic code, and 2 that even before translation amino acids might have been engaged in coding by complementary pairs rather than one by one. The above immediately suggests a relatively simple idea for the selex experiment control - to use both plus and minus RNA sequences in selection of aa-binding RNA aptamers, so that selection for one aa-binding site would facilitate starting conditions for selection of its complementary partners.
To our knowledge, there were no reports of successful selection of RNA aptamers for Ala, the complementary partner of Arg for possible reasons see [ 20 ], the main text and our response to Reviewer 1 , whereas the available data on Ile- and Tyr-binding sites are consistent with this hypothesis.
The same result can be obtained by moving from Ile to Arg, i. We believe that this striking parallelism between coding motifs of such different amino acids as Arg and Ile sends us an important message about the origins of the genetic code. In particular, if at some point in the future the Yarus-type experiments "selexed" for alanine prove to be successful, we would not be particularly surprised by finding the 5'-CCGC-3' motif with anticodon CGC in Ala-binding sites of RNA aptamers.
Finally, we must confess that, in turn, we do not quite understand the reviewer's perplexity expressed in "Now that aptamers have nothing to do with translation, how comes the ambiguity for coding? Furthermore, as coding preceded translation, we do not need and thus avoid being caught in the implicit trap of the foresight evolution. And, the risk of ambiguous anticodon-to-aa assignment, while originally of crucial importance for primordial coding in the RNA world, was of less, if any, relevance for translation which most likely evolved later.
In conclusion, this remains a high priority task on our agenda - to find out which component of the genetic coding ambiguity has been minimized before and outside of , and which after and in co-evolution with the development of translation machinery. The Fibonacci-like iterative process in the model of tRNA growth Figure 5 is not based on an explanation of structure-function relationship.
For example, why tRNAs should grow in such a way? Without a detailed explanation on these intermediate steps, the model is not presented in a way consistent with the Darwinian Continuity principle. Actually, there are quite a lot other interpretations based on the authors' previous work that seems to be problematic because there is not a consideration on those intermediates steps involve in the origin of translation system, for example, those concerning r-aaRSs and the operational code.
If they should have existed, what is the original source of these RNA molecules before they were recruited into the translation system? In addition, what should their structure be like to implement their function? Similarly, those interpretations concerning the operational code are also obscure. If the operational code should indeed have worked in the RNA world, and have occurred before the emergence of the anticodon loop, what advantage would drive the later emergence of the anticodon loop?
On these points, I do not mean that the events involved is impossible, instead, I tend to agree the view of Koonin and Novozhilov "Origin and evolution of the genetic code: the univeral enigma" Iubmb Life , , namely, "a real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system".
The extended discussion in the present manuscript on these events seems to give readers an impression that there are too many assumptions without a detailed interpretation solidly based on a scenario according to the Darwinian Continuity principle. Perhaps a better choice of the manuscript is to focus its discussion on its formal schemes mentioned above, and extend the discussion only a little to the issues concerning the authors' previously work on r-aaRSs, the operational code and others.
We are certainly aware of the translation problem, and we are not at this time, anyway staking a claim to the full, comprehensive solution rather, we suggest a number of clues to that effect. As far as possible intermediate advantages in evolution of the operational code, putative r-aaRSs, and tRNAs are concerned, we feel that the reviewer might, figuratively speaking, be asking too much and not just from the proposed scenario, but from the field of the genetic code origin research in general.
Moving on to the specifics of the Fibonacci-like iteration coincidence, we would like to touch briefly on the following two aspects:. First, the internal periodicity of tRNA sequences and certain other considerations suggest to many investigators that tRNA precursors were at first much shorter why would they be longer?
If so, the following important questions arise: 1 how is it possible to achieve the same structure in the simultaneously growing molecules?
For 1 , we show how this could be perfectly possible, and for 2 we demonstrate that the process of Fibonacci-like iterative growth fits the continuity principle at least outwardly.
To tell the truth, it was not the yet another example of the golden ratio implementation in Nature that held particular appeal to us, but rather the idea of the regularized and coordinated growth of the initial coding tri- and tetra-nucleotides "towards" one and the same final cloverleaf, a process appealingly consistent with the continuity principle. Second, when studying evolution ab simplecioribus ad complexiora , it goes without saying that, in order to make any stepwise evolutionary scenario workable, one should think about "Darwinian" motivation for each step.
Gradual shaping of code adaptors into the final tRNA cloverleaf is no exception; however, we can only guess which specific agents in the "late" RNA world with translation already emerging could drive this process. This said, the tRNA molecule is truly a molecule "for all seasons" [ 91 ] it could have had many opportunities to do so.
This paper is a wonderful piece of detective work that at the same time synthesizes many separate observations and theories on the origin of the genetic code and tRNAs. I really found nothing in here that requires substantial comment or clarification, other than to say it is a thoroughly interesting read - real food for thought. The analysis of results of amino acid binding sites in vitro selected RNA aptamers is thorough, and the Fibonacci process-inspired model for the evolution of tRNAs is truly insightful and thought-provoking.
Perhaps one of the most interesting points of this process is that it yields a very precise stepwise model wherein tRNAs can converge independently from unrelated short RNA aptamers that bind amino acids upon a common length and structure , ultimately containing both operational and genetic codes. We are very grateful to Reviewer 3 for this encouraging, succinct and yet precise formulation of what we have actually set out to achieve when writing the manuscript.
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Press, Annu Rev Biochem. Download references. You can also search for this author in PubMed Google Scholar. Correspondence to Sergei N Rodin.
ASR contributed to the conception of the study, carried out the analyses, and drafted the manuscript. ES contributed to the conception of the study and helped to draft the manuscript. SNR conceived the study, contributed to the conception of the study, developed the model, and helped to draft the manuscript. All authors read and approved the final manuscript. This article is published under license to BioMed Central Ltd. Reprints and Permissions. Rodin, A.
On origin of genetic code and tRNA before translation. Biol Direct 6, 14 Download citation. Received : 14 September Accepted : 22 February Published : 22 February Anyone you share the following link with will be able to read this content:.
Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative. Skip to main content. Search all BMC articles Search. Download PDF. Abstract Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids aas.
Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. Conclusion Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and later the translation machinery in general have been co-evolving to ''fit'' the likely already defined genetic code, rather than the opposite way around.
Reviewers This article was reviewed by Eugene V. Background Genetic Code refers to a nearly universal assignment of triplets codons of nucleotides nts to amino acids aas , linking hereditary entities to the functional blocks of life Figure 1A.
Figure 1. Full size image. Results and discussion Origin of the genetic code: the major question Even before the final deciphering of the genetic code, the two general ideas were already aboard with respect to the code's possible origin s. RNA-amino acid binding sites: Asymmetry in frequency of anticodons and codons suggests pre-translational origin of the genetic code By now, aa-binding RNA aptamers have been successfully "selexed" for eight amino acids.
According to [ 12 ], their aa-binding sites are of the three types: Sites in which cognate codon and anticodon are both significantly over-represented, this group including arginine, isoleucine and borderline significant tyrosine.
Figure 2. Figure 3. The Atlantic Crossword. Sign In Subscribe. But despite knowing what the molecule looked like a double helix and what it did encode for proteins , nobody knew how, exactly, that translating and encoding happened. There had to be, Crick had postulated, some sort "bilingual" molecule , an intermediary that could talk both to DNA and to the ribosome that created the proteins.
Ultimately he was right—that's exactly the job that transfer RNA does. But it took decades before anyone actually knew what tRNA looked like. In , Paul Zamecnik, a scientist working at Harvard , and his group of researchers made what one of them, Mahlon Hoagland, would later call "a fortuitous discovery.
What he's talking about here is how, in cells, the information from DNA gets transformed into the proteins, with amino acids as the building blocks and RNA doing the shuttling in between.
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