The Cipher of the Genetic Code.

A new approach to understanding of the genetic code is developed. In order to overcome the key paradox (and Darwinian selection problem) that the highly complex amino acid Phe is encoded by the simplest codons (UUY), and the simplest Gly encoded by the most complex codons (GGN); as well as the paradox of the duplication of some amino acids in the encoding process (Leu, Ser, Arg), we proposed an extension of the notion (and concept) of genetic code. For a better (and lighter) understanding of genetic coding, we proposed a hypothesis after that (under the conditions of allowed metaphoricity and modeling in biology) genetic code has to be understood, analogously in cryptology, as the unity of three entities: the code, the cipher of the code and the key of the cipher. In this hierarchy the term (and notion) "genetic code" remains what has been from the beginning: a connection between four-letter alphabet (four Py-Pu nucleotides, in form of codons) and a twenty-letter alphabet (twenty amino acids); the cipher is a specific chemical complementarity in chemical properties of molecules in the form: similarity in dissimilarity versus dissimilarity in similarity ("Sim in Diss vs Diss in Sim") and the key of cipher: the complementarity on the binary tree of the genetic code in the form: 0-15, 1-14, 2-13, …, 6-9, 7-8. These concepts improve understanding that within the two main Genetic Code Tables (of the nucleotide doublets and nucleotide Triplets) exists a sophisticated nuancing and balancing in the properties of the constituents of GC, including the balance of the number of molecules, atoms, and nucleons.

Genetic code: an alternative model of translation.

Our earlier studies of translation have led us to a specific numeric coding of nucleotides (A = 0, C = 1, G = 2, and U = 3)--that is, a quaternary numeric system; to ordering of digrams and codons (read right to left: .yx and Z.yx) as ordinal numbers from 000 to 111; and to seek hypothetic transformation of mRNA to 20 canonic amino acids. In this work, we show that amino acids match the ordinal number--that is, follow as transforms of their respective digrams and/or mRNA-codons. Sixteen digrams and their respective amino acids appear as a parallel (discrete) array. A first approximation of translation in this view is demonstrated by a "twisted" spiral on the side of "phantom" codons and by ordering amino acids in the form of a cross on the other side, whereby the transformation of digrams and/or phantom codons to amino acids appears to be one-to-one! Classification of canonical amino acids derived from our dynamic model clarifies physicochemical criteria, such as purinity, pyrimidinity, and particularly codon rules. The system implies both the rules of Siemion and Siemion and of Davidov, as well as balances of atomic and nucleon numbers within groups of amino acids. Formalization in this system offers the possibility of extrapolating backward to the initial organization of heredity.

A harmonic structure of the genetic code.

In this paper is presented a new, very harmonic structure of the genetic code (GC) within a system of "4 x 5" (and/or of "5 x 4") of amino acids (AAs) in two variants. In first variant, the five rows within the system start with one polar charged amino acid (AA) each, making first column, consisting from five polar charged AAs (D, R, K, H, E). Five polar non-charged AAs (N, P, Y, W, Q) follow, then five non-polar AAs as last column (A, L, F, V, I) and, finally, five polar or non-polar AAs, in a combination, as first to last column (A as non-polar; S, T as polar, and G, P as ambivalent AAs). A second variant is subsequent to this one-"4 x 5" system with five nitrogen AAs (K, R, P, H, W), five oxygen (D, E, Y, S, T), five solely carbon (A, L, F, V, I) and five "combined" AAs (G with hydrogen as side chain; C and M with carbon and sulfur; N and Q with carbon, oxygen and nitrogen). A strict balance of atom and nucleon number as well as molecule mass follows the classification in both system variants.