Abstract
The following is the theoretical and experimental analysis of the role of the third nucleotide in codons during protein biosynthesis. Its role is largely enhanced compared to the existing understanding. Third nucleotide functionally and symmetrically divides codon families in 32 synonyms and 32 SYnonymous-HOMonymous hybrid codons—SYHOMs. Wherein, the syhoms function is to initiate nonlocal ribosome analysis of mRNA, representing real context in DNA language. Such analysis is a natural necessity for selection of one amino acid from two different amino acids, and between amino acids or a stop position, in situations when a ribosome interacts with syhom codons which have dual coding. This was theoretically substantiated earlier [1] [2] [3]. Experimental work [4] confirmed this theory: It was demonstrated that two different amino acids, selenocysteine and cysteine, are coded by a single UGA-syhom-codon for Euplotes crassus infusoria. This result does not call into question the dogma of unambiguity of amino acids and stop position coding by the cells genome, but it requires amendments to the existing model of genetic coding. These amendments are based on an enhanced understanding of the special linguistic/semantic role of the third nucleotide in codons and on the acceptance of the idea of real, rather than metaphorical, textuality of protein genes (mRNA). Such comprehension of the speech-similarity of genes (mRNA) and the role that third nucleotide in codons plays in this, leads to a simple statement about the quasi-consciousness (biocomputing) of the protein-synthesizing-system and its ability to recognize the context (meaning) of mRNA to make the correct choice of amino acids and stops in a syhom situation, based on the meanings of gene texts (mRNA).
Highlights
A lot has been written about the hypothesis of F
The syhoms function is to initiate nonlocal ribosome analysis of mRNA, representing real context in DNA language. Such analysis is a natural necessity for selection of one amino acid from two different amino acids, and between amino acids or a stop position, in situations when a ribosome interacts with syhom codons which have dual coding
The deciphered amino acids or stop positions in this case may not correspond to the table of the standard code, since they are recognized and selected by the ribosome according to codons-homonyms DYNAMICALLY while the ribosome is reading and logically analyzing the context of mRNA
Summary
GAT Asp GAC Asp GAA Glu GAG Glu syhoms (in red). Table adapted from article [3]. 3. The Choice of Amino Acids and Stop Positions in the Case of Ribosome Interaction with the Codon-Homonyms on mRNA. The standard genetic code table of the E. coli protein code, adopted by the scientific community, is STATIC and does not reflect the most important factor of dynamics in the process of protein biosynthesis in vivo This a reason why the majority has an incomplete understanding of the key linguistic function of the third nucleotide in the syhom-codons, the codons which take the genome to the level of real, non-metaphorical, textual constructions of DNA and RNA. At the level of mRNA translation into proteins in cases of reading frame shifts, the substitutions of 3rd nucleotides may lead to anomaly context dependent choices of amino acid coding and/or stop positions.
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