p-Adic Structure of the Genetic Code

@article{Dragovich2011pAdicSO,
  title={p-Adic Structure of the Genetic Code},
  author={Branko Dragovich},
  journal={Neuroquantology},
  year={2011},
  volume={9}
}
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end of genes, i.e. it terminates process of protein synthesis. This article is a review of simple modelling of the genetic code and related subjects by concept of p-adic distance. It also contains some new results. In particular, the article presents appropriate… 

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References

SHOWING 1-10 OF 46 REFERENCES
p-Adic Modelling of the Genome and the Genetic Code
TLDR
It is shown that degeneration of the genetic code is a p-adic phenomenon and a hypothesis on the evolution of the Genetic Code assuming that primitive code was based on single nucleotides and chronologically first four amino acids is put forward.
p-Adic Degeneracy of the Genetic Code
TLDR
It is shown that genetic code multiplets are made of the p-adic nearest codons, which are building blocks of proteins, or code termination of protein synthesis.
A unifying concept for the amino acid code.
  • R. Swanson
  • Biology
    Bulletin of mathematical biology
  • 1984
Genetic Code and Number Theory
TLDR
An introductory brief review of genetic information, its coding and translation of genes to proteins through the genetic code and the role of $p$-adic numbers is underlined.
Crystalizing the Genetic Code
TLDR
A first attempt to represent the mutations relative to the deletion of apyrimidine by action of a suitable crystal spinor operator is proposed and a universal behaviour in the ratios of codon usage frequencies is put in evidence and is shown to fit nicely in the model.
Lie superalgebras and the multiplet structure of the genetic code. I. Codon representations
TLDR
The complete list of all typical codon representations (typical 64-dimensional irreducible representations) is given and the corresponding branching rules are presented, to discuss which of them reproduce the multiplet structure of the genetic code.
Origin of the Genetic Code
Rewiring the keyboard: evolvability of the genetic code
TLDR
The distribution and causes of secondary deviations from the canonical genetic code are examined, with the majority of non-standard codes arise from alterations in the tRNA, with most occurring by post-transcriptional modifications, such as base modification or RNA editing, rather than by substitutions within tRNA anticodons.
...
...