Most Used Codons per Amino Acid and per Genome in the Code of Man Compared to Other Organisms According to the Rotating Circular Genetic Code

Abstract

My previous theoretical research shows that the rotating circular genetic code is a viable tool to make easier to distinguish the rules of variation applied to the amino acid exchange; it presents a precise and positional bio-mathematical balance of codons, according to the amino acids they codify. Here, I demonstrate that when using the conventional or classic circular genetic code, a clearer pattern for the human codon usage per amino acid and per genome emerges. The most used human codons per amino acid were the ones ending with the three hydrogen bond nucleotides: C for 12 amino acids and G for the remaining 8, plus one codon for arginine ending in A that was used approximately with the same frequency than the one ending in G for this same amino acid. The most used codons in man fall almost all the time at the rightmost position, clockwise, ending either in C or in G within the circular genetic code. The human codon usage per genome is compared to other organisms such as fruit flies (Drosophila melanogaster), squid (Loligo pealei), and many others. The biosemiotic codon usage of each genomic population or 'Theme' is equated to a 'molecular language'. The C/U choice or difference, and the G/A difference in the third nucleotide of the most used codons per amino acid are illustrated by comparing the most used codons per genome in humans and squids. The human distribution in the third position of most used codons is a 12-8-2, C-G-A, nucleotide ending signature, while the squid distribution in the third position of most used codons was an odd, or uneven, distribution in the third position of its most used codons: 13-6-3, U-A-G, as its nucleotide ending signature. These findings may help to design computational tools to compare human genomes, to determine the exchangeability between compatible codons and amino acids, and for the early detection of incompatible changes leading to hereditary diseases.

The Quantum Workings of the Rotating 64-Grid Genetic Code

“…The analysis presented in this figure may be an example to help as a shortcut, for the study of multiple closely compatible genomes between organisms, which is a possible way to demonstrate my fourth rule of variation on compatible genomics (Castro-Chavez, 2011). The comparison of the human genome to the squid genome (squid pattern for its 3 rd nucleotide: _ _U/A, 13-6-3 U-A-G), will be presented elsewhere in this number (Castro-Chavez, 2011b), where it will be shown visually why is it that I prefer the circular genetic code representation for this kind of most used codons per genomic population comparisons.…”

Defragged Binary I Ching Genetic Code Chromosomes Compared to Nirenberg's and Transformed into Rotating 2D Circles and Squares and into a 3D 100% Symmetrical Tetrahedron Coupled to a Functional One to Discern Start From Non-Start Methionines through a Stella Octangula

“…The quasi-identical patterns seen in these four pairs of synthetic genetic code chromosomes remind us of the protective strategy of enzymes with a same function through nature, with the pair of synthetic genetic code chromosomes M (upper right pair of (Figure 6) mimicking the bias reported elsewhere in humans and mammals having a three H-bond preference for the third nucleotide of most used codons per amino acid (chromosome M2, where Met is located in its upper left arm), while on the other hand, invertebrates and plants have a two H-bond preference for their third nucleotide of most used codons per amino acid (chromosome M1, where the TGA stop codon, the most used in man [17], is located, in the lower right arm), a phenomenon also seen in the pair of genetic code chromosomes i1 and i2 shown in the lower left side of Figure 6.…”

“…An interesting feature seen both in the I Ching derived genetic code chromosomes and in Nirenberg's (Figure 24), is that the mammal/invertebrate exchange of most used third-nucleotides per amino acid in real life follows in general a similar pattern such as the one shown in these figures, having a G/A or a C/U exchange [17]. …”

“…So, we now have a start at the center of the table, in the first uneven spot, ATG, but also a specific end, or stop codon of choice, in the second uneven spot, being this, the stop TGA, the most used stop codon in man [17]; so here, if we start in Met (ATG), we will end in TGA.…”

“…Our initial studies of the genetic code were done independently of binary systems or of vectors, being rather aligned by periodicity, by functionality, and/or according to their compatible variation [1,2,16,17,49]; here however, I am exploring the novelty of the quantum logic as applied to the genetic code in order to pursue the reverse engineering of these two, apparently independent sets of representations: 1) the binaries derived from the I Ching , successfully transferred in this article into 2D and 3D genetic codes, and 2) the genetic codes based in the functional associations of amino acids and their codons, being these last ones independent of binary arrangements and/or pairings. It seems to me at this point that the informational flow from binaries to geometries is easier than the opposite.…”