The Syhomy of the Genetic Code Is the Path to the Real Speech Characteristics of the Encoded Proteins

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 pro-tein-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).


The Wobble Hypothesis by F. Crick
A lot has been written about the hypothesis of F. Crick, including the works of the author himself, but most of the judgments are based on a formulation from F. Crick's book "What a Mad Pursuit" 1988. [5]. Here are the key words: "An important point to notice is that although the genetic code has certain regularities-in several cases it is the first two bases that encode one amino acid, the nature of the third being irrelevant-its structure otherwise makes no obvious sense." However, there are some significant additional issues that stem from this brief message. This is what this article is about. "The standard" genetic protein code

Unambiguity and Degeneracy Factor of the E. coli Protein Code
The

The Choice of Amino Acids and Stop Positions in the Case of Ribosome Interaction with the Codon-Homonyms on mRNA
Such a CHOICE is made by the ribosome due to the fact that it (and/or the whole cell) takes into account the context of the given mRNA. This choice automatically implies quasi-consciousness of the protein synthesizing system, more precisely, its biocomputer functions [7]. Quasi-consciousness is present because mRNA (gene copy) is a text in a literal, non-metaphorical sense [1] [2] acids and stops. This was believed until the work of Turanov et al. [4], where they demonstrated the same simultaneity of coding for selenocysteine and cysteine, which similarly had long ago been detected by Crick      In turn, this choice determines which "amino acid-tRNA-anticodon:codon-syhom" complex will be involved for the inclusion of the selected amino acid in the growing peptide chain.

Why Stop Codons Are in Syhom Families
Termination-the end of protein synthesis, is carried out when one of the stop codons-UAG, UAA, UGA-appears in the A-site of the ribosome. Due to absence of tRNAs, corresponding to these codons, peptidyl-tRNA remains bound to the P-site of the ribosome. Here, specific RF1 or RF2 proteins are involved that catalyze the separation of the polypeptide chain from mRNA, as well as RF3, which causes dissociation of mRNA from the ribosome. RF1 recognizes in the A-site UAA or UAG; RF-2 -UAA or UGA. This is preceded by an important event-the decision to stop protein synthesis with three stop codons (syhoms). The "solution" in this case is not an empty metaphor, but the result of the work of a nanobiocomputer, which probably a protein synthesizing system is [7]. It is the nanobiocomputer that analyzes the CONTEXT of mRNA sequences, and then, and only then, one of the three ambiguous syhom triplets (either stop, or amino acid) acquires the value of either stop or amino acid.
Why so? Imagine that stop functions belong to some codons-synonyms. Then the strategic function of analysis of the textual, semantic component of genes Open Journal of Genetics (mRNA) is lost. After all, synonyms strictly, unambiguously and redundantly encode amino acids, which follows from the invariance of natural native gene texts (mRNA). In contrast to the strict unambiguity of codons-synonyms, the stop-syhoms exist in mRNA in a 'standby mode' of meaning of mRNA (gene) context. Depending on context, a decision is made on the exact meaning of the ambiguous codon-syhom: to be the amino acid code and continue protein synthesis, or to stop, as it is meant to be a stop codon.

Discussion
The study presents a logically non-contradictory idea that ribosomes (or the en- Why are the additional characteristics of the protein code proposed here more pragmatic than M. Nirenberg's and F. Crick's code model [8] that is tactically correct, but strategically incomplete? And why were the attempts to see more within the code than its creators unsuccessful? These attempts were made in the works of Lagerkvist [6] and Rumer [10]. Lagerkvist was mistaken, believing that The term "mixed" was introduced by Lagerkvist. Open Journal of Genetics authors write: "In every case, the sequence of the reverted HTH allele matched the Ler wild-type sequence exactly" (In each case, the sequence of the returned HTH allele corresponded exactly to the sequence of the wild type Ler). This means that Lolle and Pruitt found the effect of a return to part of the ancestral genetics of Arabidopsis. This fact is fantastic because the returned "wild" gene and the mutant gene are identical in sequences, which is inexplicable in Mendelian genetics. But this can be explained from the standpoint of linguistic-wave genetics. Why does the same gene manifest in different phenotypes?
To obtain an answer within the framework of the considered amendments of the protein code model, it is necessary to check the collinearity of mRNAs and their protein products in wild and mutant genes. It can be predicted that the amino acid sequences of the products of these genes will be different. Amino acid sequences will differ in amino acid composition, since adjacent DNA se- This allows to predict different amino acid sequences of the protein products of both "pseudo identical" genes and, naturally, the different morphogenesis of the plant regions encoded by these genes.
A detailed analysis of the work by Lolle et al. [11], together with the study of Turanov et al. [4], are interesting, since their main results encourage geneticists to research genetic protein coding strategies further. As you can see, much more needs to be clarified. This new understanding in genetics facilitates the anticipation of possible faults in recombinant technologies of artificial hybridization of various genes. Such artificial hybridization may lead to semantic uncertainty at the level of mRNA meanings, which determine the choice and accuracy of amino acid and stop position coding by syhom-codons. The paradox of the situation in genetics is that over the 50 years of existence of the protein code model, it has never been checked on a large-scale: on hundreds of proteins, with all the statistics, and "proteins -mRNA codons" collinearity. If within the standard code table, any inconsistences for E. coli proteins are found, then, this would not deny the code model of M. Nirenberg and F. Crick. This would mean that the principles of genetic coding of proteins, especially in a linguistic, quasi-speech direction, are unlimited.