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 nucleoti...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).展开更多
This paper introduces the hypothesis that during the biosynthesis of prion proteins, the ribosome works in the opposite direction and thus, it is a “prion-poly-anticodon-dependent mRNA polymerase”. And accordingly, ...This paper introduces the hypothesis that during the biosynthesis of prion proteins, the ribosome works in the opposite direction and thus, it is a “prion-poly-anticodon-dependent mRNA polymerase”. And accordingly, in violation of the Central Dogma, information flows from protein to RNA. This requires dogma formula to be re-written as follows: DNARNA Protein. The idea of contextual orientations of the ribosome on mRNA during protein biosynthesis is introduced. This ensures the selection of the correct amino acid or stop position due to the strategic role of the “wobbling” off the 3’-codon nucleotide in non-synonymous codons. This leads to the transition of the genetic code from purely a physico-chemical level of its operation to mental-textual one. This is a representation of the fact of one of the levels of non-locality (continuity) of the genome. There are six such levels of nonlocality. Level 1—Organizational. Here, non-locality is expressed with the ability to regenerate, for example, in planarians. Level 2—Cellular. From every cell, and not just from zygotes, you can grow a whole organism. Level 3—Cellular-nuclear. Enucleation of nuclei from somatic and germinal cells with the subsequent introduction of other nuclei into them does not prevent the development of a normal organism. Level 4—Molecular: the ribosome “reads” the informational RNA not only for individual codons, but for the whole RNA, taking into account the context, that is, non-locally, continually. Level 5— Chromosome-holographic. The genome has a holographic memory, and this is a typically distributed (non-local) associative memory. At this and subsequent levels, non-locality acquires a new quality, a dualistic, material-wave character, since holograms as a substance are “read” by electromagnetic and/or acoustic fields that carry genome-wave information beyond the substance of chromosomes. Level 6—Quantum non-locality of the genome. Up to level 6, the non-locality of genetic information is realized in the space of the organism. Level 6 has a special character and a new quality. It manifests itself in one of the forms of quantum non-locality, namely, permissive, postulated in this work. In this case, the non-locality is realized both in the space of the biosystem and in its own, “compressible” to zero, time. Gene-wave programs that are instantly distributed in such ways, isomorphic to material ones, work in the body “here and there at the same time”, therefore, the semantic construction “first and then” loses its meaning. And this is a strategic factor, an extraordinary achievement for multicellular biosystems. We have obtained theoretical and experimental results confirming our ideas.展开更多
文摘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).
文摘This paper introduces the hypothesis that during the biosynthesis of prion proteins, the ribosome works in the opposite direction and thus, it is a “prion-poly-anticodon-dependent mRNA polymerase”. And accordingly, in violation of the Central Dogma, information flows from protein to RNA. This requires dogma formula to be re-written as follows: DNARNA Protein. The idea of contextual orientations of the ribosome on mRNA during protein biosynthesis is introduced. This ensures the selection of the correct amino acid or stop position due to the strategic role of the “wobbling” off the 3’-codon nucleotide in non-synonymous codons. This leads to the transition of the genetic code from purely a physico-chemical level of its operation to mental-textual one. This is a representation of the fact of one of the levels of non-locality (continuity) of the genome. There are six such levels of nonlocality. Level 1—Organizational. Here, non-locality is expressed with the ability to regenerate, for example, in planarians. Level 2—Cellular. From every cell, and not just from zygotes, you can grow a whole organism. Level 3—Cellular-nuclear. Enucleation of nuclei from somatic and germinal cells with the subsequent introduction of other nuclei into them does not prevent the development of a normal organism. Level 4—Molecular: the ribosome “reads” the informational RNA not only for individual codons, but for the whole RNA, taking into account the context, that is, non-locally, continually. Level 5— Chromosome-holographic. The genome has a holographic memory, and this is a typically distributed (non-local) associative memory. At this and subsequent levels, non-locality acquires a new quality, a dualistic, material-wave character, since holograms as a substance are “read” by electromagnetic and/or acoustic fields that carry genome-wave information beyond the substance of chromosomes. Level 6—Quantum non-locality of the genome. Up to level 6, the non-locality of genetic information is realized in the space of the organism. Level 6 has a special character and a new quality. It manifests itself in one of the forms of quantum non-locality, namely, permissive, postulated in this work. In this case, the non-locality is realized both in the space of the biosystem and in its own, “compressible” to zero, time. Gene-wave programs that are instantly distributed in such ways, isomorphic to material ones, work in the body “here and there at the same time”, therefore, the semantic construction “first and then” loses its meaning. And this is a strategic factor, an extraordinary achievement for multicellular biosystems. We have obtained theoretical and experimental results confirming our ideas.
