Amino acid contribution to the genetic code structure: end-atom chemical rules of doublet composition

Up-to-date knowledge is not yet enough to prove or reject completely one of the leading alternative hypotheses considering external or internal origin of the genetic code organization (term "internal" means a peculiarity of amino acids and nucleotides which can propose some logical basis for explanation why definite codons are assigned to particular and not to other amino acids; term "external" in this context implies tRNAs and aminoacyl-tRNA synthetases which provide accuracy of translation but are not presented in the code table in the evident from). New data in favour of the internal approach have been proposed. A close correlation exists between chemical nature of single, the most remote from C alpha, end atoms of amino acid side chains and types of bases in appropriate codon doublets. There are two main rules reflecting this correspondence: (1) all O- or N-ended amino acids (i.e. with O, OO, N, NN, ON, OC and NC end patterns) possess the A-containing codon doublets; (2) all solely C-ended (excluding Ala) and S-ended amino acids (i.e. residues with C, CC and S ends) have the U-containing codon doublets. The discovered asymmetry is characterized by the following high reliable differences of A and U distribution among 21 patterns of individual doublets belonging to 18 amino acids (Pro and Gly are discarded): (a) proportion of A plus U bases corresponding to the two rules, 22/26 is much more than proportion of such bases in violating cases, 4/26; (b) A and U are dominant bases over each of other base types in the doublets of O/N- and C/S-ending amino acids, respectively; (c) the numbers of doublets bearing (18) and not bearing (3) dominant A or U bases are also significantly different. The concept of indicative amino acid end atoms (O/N and non-O/non-N) and doublet A/U bases has been proposed and discussed as so far unknown regulative system of submolecular level of heredity which, additionally to possible key role in the process of the genetic code arising, provides now control of its universality, stability and fidelity.