Literature DB >> 22997604

A Tetrahedral Representation of the Genetic Code Emphasizing Aspects of Symmetry.

Fernando Castro-Chavez1.   

Abstract

The genetic code is a mapping of 64 codons to 22 actions, including polypeptide chain initiation, termination, and incorporation of the twenty amino acids. The standard tabular representation is useful for looking up which amino acid is encoded by a particular codon, but says little about functional relationships in the code. The possibility of making sense of the code rather than simply enumerating its codon-to-action pairings therefore is appealing, and many have attempted to find geometric representations of the code that illuminate its functional organization. Here, I show that a regular tetrahedron with each of its four faces divided into sixteen equilateral triangles (for a total of 64 triangular 'cells') is a particularly apt geometry for representing the code. I apply five principles of symmetry and balance in order to assign codons to the triangular cells of the tetrahedral faces. These principles draw on various aspects of the genetic code and the twenty amino acids, making the final construct a positional balance of the amino acids and their functions rather than a re-analysis of them. The potential significance of this exercise, and others like it, is that this way of organizing the biological facts may provide new insights into them.

Entities:  

Year:  2012        PMID: 22997604      PMCID: PMC3445437          DOI: 10.5048/BIO-C.2012.2

Source DB:  PubMed          Journal:  BIOcomplexity


  6 in total

1.  Conversion of nucleotides sequences into genomic signals.

Authors:  P D Cristea
Journal:  J Cell Mol Med       Date:  2002 Apr-Jun       Impact factor: 5.310

2.  The rules of variation: amino acid exchange according to the rotating circular genetic code.

Authors:  Fernando Castro-Chavez
Journal:  J Theor Biol       Date:  2010-04-03       Impact factor: 2.691

3.  The Quantum Workings of the Rotating 64-Grid Genetic Code.

Authors:  Fernando Castro-Chavez
Journal:  Neuroquantology       Date:  2011-12

4.  The Rules of Variation Expanded, Implications for the Research on Compatible Genomics.

Authors:  Fernando Castro-Chavez
Journal:  Biosemiotics       Date:  2011-05-12       Impact factor: 0.711

Review 5.  Forces contributing to the conformational stability of proteins.

Authors:  C N Pace; B A Shirley; M McNutt; K Gajiwala
Journal:  FASEB J       Date:  1996-01       Impact factor: 5.191

6.  A tetrahedral representation of poly-codon sequences and a possible origin of codon degeneracy.

Authors:  L E Trainor; G W Rowe; V L Szabo
Journal:  J Theor Biol       Date:  1984-06-07       Impact factor: 2.691

  6 in total
  7 in total

1.  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.

Authors:  Fernando Castro-Chavez
Journal:  J Proteome Sci Comput Biol       Date:  2012

2.  File Compression and Expansion of the Genetic Code by the use of the Yin/Yang Directions to find its Sphered Cube.

Authors:  Fernando Castro-Chavez
Journal:  J Biodivers Bioprospect Dev       Date:  2014-07

3.  The "periodic table" of the genetic code: A new way to look at the code and the decoding process.

Authors:  Anton A Komar
Journal:  Translation (Austin)       Date:  2016-09-09

4.  ANATOMICAL MNEMONICS OF THE GENETIC CODE: A FUNCTIONAL ICOSAHEDRON AND THE VIGESIMAL SYSTEM OF THE MAYA TO REPRESENT THE TWENTY PROTEINOGENIC AMINO ACIDS.

Authors:  Fernando Castro-Chavez
Journal:  J Biol Nat       Date:  2016

5.  Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.

Authors:  Gregory A Babbitt; Mohammed A Alawad; Katharina V Schulze; André O Hudson
Journal:  Nucleic Acids Res       Date:  2014-09-08       Impact factor: 16.971

6.  Effective Encoding for DNA Sequence Visualization Based on Nucleotide's Ring Structure.

Authors:  A T M Golam Bari; Mst Rokeya Reaz; A K M Tauhidul Islam; Ho-Jin Choi; Byeong-Soo Jeong
Journal:  Evol Bioinform Online       Date:  2013-07-07       Impact factor: 1.625

7.  Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.

Authors:  Hervé Seligmann; Ganesh Warthi
Journal:  Comput Struct Biotechnol J       Date:  2017-08-12       Impact factor: 7.271

  7 in total

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