DOI: 10.14704/nq.2011.9.4.499

The Quantum Workings of the Rotating 64-Grid Genetic Code

Fernando Castro-Chavez

Abstract


In this article, the pattern learned from the classic or conventional rotating circular genetic code is transferred to a 64-grid model. In this non-static representation, the codons for the same amino acid within each quadrant could be exchanged, wobbling or rotating in a quantic way similar to the electrons within an atomic orbit. Represented in this 64-grid format are the three rules of variation encompassing 4, 2, or 1 quadrant, respectively: 1) same position in four quadrants for the essential hydrophobic amino acids that have U at the center, 2) same or contiguous position for the same or related amino acids in two quadrants, and 3) equivalent amino acids within one quadrant. Also represented is the mathematical balance of the odd and even codons, and the most used codons per amino acid in humans compared to one diametrically opposed organism: the plant Arabidopsis thaliana, a comparison that depicts the difference in third nucleotide preferences: a C/U exchange for 11 amino acids, a G/A exchange for 2 amino acids, and G/U or C/A exchanges for one amino acid, respectively; by studying these codon usage preferences per amino acid we present our two hypotheses: 1) A slower translation in vertebrates and 2) a faster translation in invertebrates, possibly due to the aqueous environments where they live. These codon usage preferences may also be able to determine genomic compatibility by comparing individual mRNAs and their functional third dimensional structure, transport and translation within cells and organisms. These observations are aimed to the design of bioinformatics computational tools to compare human genomes and to determine the exchange between compatible codons and amino acids, to preserve and/or to bring back extinct biodiversity, and for the early detection of incompatible changes that lead to genetic diseases.

Erratum
1) Abstract, page 728, the statement: "a G/A exchange for 2 amino acids, and G/U or C/A exchanges for one amino acid" should be "a G/A and a G/U exchange for 2 amino acids, respectively, and a C/A exchange for one amino acid".

2) Page 736, first paragraph of right column, after Figure 7, it says: "two times the replacement has been G/A, while one time C/A and one time G/U, while five amino acids, as described in the image" It should say: "two times the replacement has been G/U and also two times G/A, and one time the replacement has been C/A, while four amino acids, and the stop codon, as described in the image".

3) Figure 8, in page 737, should be replaced with the next one: http://www.webcitation.org/66G6Cbuz6 , as it appears at PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271378/figure/F8

Keywords


compatible genomics, compatibility, genome, adaptability, adaptation, variation, biomathematics, bioinformatics, computational biology

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