Another Understanding of the Model of Genetic Code Theoretical Analysis

Abstract

At present the model of the genetic code (the code of protein biosynthesis) proposed almost 50 years ago by M. Nirenberg and F. Crick has undergone severe erosion. Tactically, it is true that triplicity and the synonymous degeneracy are unmistakable. But the Nirenberg-Crick postulate about unambiguous coding of amino acids, i.e., the strategy raises reasonable doubt. The reasons to doubt showed up very early: it turned out that the triplet UUU codes both phenylalanine and leucine, which was inconsistent with the declaration of the unambiguity of the DNA-RNA encoding of amino acids in proteins. On the other hand, the ambiguity automatically stems from the Wobble Hypothesis by F. Crick relating to the wobbling of the third nucleotide in codons, (random, undetermined behavior), which means the 3’-5’ codon-anticodon pair is not involved in the encoding, and represents a “steric crutch”. In fact, amino acids are coded not by triplet, but by doublet of nucleotides in a triplet, according to “Two-out-of-Three” rule by Ulf Lagerkvist. From this perspective, the codon families split into two classes: 32 codon-synonym triplets and 32 codon triplets with undetermined coding functions, that is inherent to one of the 32 codons UUU. These “undetermined” codons have called homonyms. They are ambiguous as they potentially and simultaneously encode two different amino acids, or amino acid and the stop function. However, the ambiguity is overcome in real protein biosynthesis. This is due to the sign orientations of ribosomes within mRNA contexts. This is the way the semantics of the codon-homonyms occur, as an exact analogy of the consciousness work in the human languages, abounding with homonyms. This turn in the understanding of the protein code, as actual text formation, leads to a strong idea of the genome as a quasi-intelligent biocomputer structure of living cells.