References


References, referred to in the text within brackets [ ]:

1. Chou KC: "Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid     Composition." PROTEINS: Structure, Function and Genetics, 43, 246-255 (2001).
2. shCherbak VI, "Arithmetic inside the universal genetic code," [Abstract],
    Biosystems 70 (3), 187-209 (2003).
3, Rakocevic MM, "A harmonic structure of the genetic code." J theor. Biol. 229, 221-234     (2004).
4.Downes AM, Richardson J, "Relationships Between Genomic Base Content and    Distribution of Mass in Coded Proteins." J Mol Evol 55, 476-490 (2002).
5. Perez JC, "Codon populations in single-stranded whole human genome DNA are fractal     and fine-tuned by the Golden Ratio 1.618." Interdiscip Sci 2(3), 228-240 (2010).
6. Wong TF, "The evolution of a universal genetic code." Department of Biochemistry,     University of Toronto, Canada. Communicated by J. Tuzo Wilson. (1976)
7. Wong JT, "Coevolution theory of the genetic code at age thirty." [Abstract], Bioessays,     27, 416-425 (2005).

Since this research started in the beginning of 1980's, the main source used was:
   Karlson P., 1974. Biokemi (Biochemisttry). Liber Läromedel, Lund, Swedish version of
   Karlson, P. Introduction to Modern Biochemistry, forth edition, 1975, Academic Press Inc. with later, new editions.

A few data taken from
a. Lindahl P E, Kihlström J E, Kiesling K-H, Sundell L-E: Zoofysiology (Zoophysiology) 1967, Almqvist & Wiksell, Uppsala.
b. Nicholson D. F 1976. Metabolic Pathways. Koch-Light Laboratories, UK.[A map over main processes in biochemistry.]
c. Wikipedia, the free encyclopedia, i.e. http://en.wikipedia.org/wiki/Histone#Classes.

A selection of other articles dealing with the same topic:

Arquès DG, Michel CJ: A Circular Code in the Protein Coding Genes of Mitochondria. J. theor. Biol. 1997, 189:273-290.
Arquès DG, Michel CJ: A Complementary Circular Code in the Protein Coding Genes. J. theor Biol. 1996, 182:45-58.
Balázs A: Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: A general physical framework theory. BioSystems 2006, 85:114-125.
Bedian V: Self-description and the origin of the genetic code. BioSystems 2001, 60:39-47.
Berger G: Deterministic hypotheses on the origin of life and of its reproduction. Med Hypotheses 2003, 61(5-6):586-592.
Biro J C, Benyó B, Sansom C, Szlávecs A, Fördös G, Micsik T, Benyò Z: A common periodic table of codons and amino acids. BBRC 2003, 306:408-415.
Chechetkin V R: Block structure and stability of the genetic code. J theor Biol. 2003, 222:177-188.
Chou, K-C: Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 2005, 21.1:10-19.
Copley S D, Smith E, Morowitz H J: A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc. Natl. Acad. Sci. 2005, 102:4442-4447.
Damjanovic Z M, Rakocevic M M: Genetic Code. An Alternative Model of Translation. Ann. N. Y. Acad. Sci. 2005, 1048:517-523.
Delarue M: An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 2007, 13:161-169.
Di Giulio M: The origin of the genetic code: theories and their relationships, a review. BioSystems 2005, 80:175-184.
Hartman H: Speculations on the Evolution of the Genetic Code. KIV. The Evolution of the Aminoacyl-tRNA Synthetases. Orig Life Evol Biosph. 1995, 25:265-269.
Heal J R, Roberts G W, Raynes J G, Bhakoo A, Miller A D: Specific Interactions Between Sense and Complementary Peptides: The Bases for the Proteomic Code. ChemBioChem. 2002, 3:136-151.
Hobish M K, Wickramasinghe N S M D, Ponnamperuma C: Direct Interaction between Amino Acids and Nucleotides as a possible physicochemical Basis for the Origin of the Genetic Code. Adv Space Res. 1995, 15:(3)365-(3)382.
Hoffmeyer J: Life and reference. BioSystems 2001, 60:123-130.
Hornos J E M, Braggion L, Magini M, Forger M: Symmetry Preservation in the Evolution of the Genetic Code. (Hypothesis Paper). IUBMB Life 2004, 56(3):125-130.
Ikehara K: Origins of gene, genetic code, protein and life: comprehensive view of life systems from GNC-SNS primitive genetic code hypothesis. J. Biosci. 2002, 27:165-186.
Jiménez-Montaño M A: Protein evolution drives the evolution of the genetic code and vice versa. BioSystems 1990, 54:47-64.
Johnson F Yan, Alexander K Yan, Benjamin C Yan: Prime Numbers and the Amino Acid Code: Analogy in Coding Properties. J. theor. Biol. 1991, 151:333-341.
Judson O P, Haydon D: The Genetic Code: What Is It Good For? An Analysis of the Effects of Selection Pressures on Genetic Codes. J Mol Evol. 1999, 49:539-550.
Karasev V A, Stefanov V E: Topological Nature of the Genetic Code. J theor Biol. 2001, 209:303-317.
Knight R D, Landweber L F: Rhyme or reason: RNA-arginine interactions and the genetic code. Chem Biol. 1998, 5:R215-R220.
Kohler H, Murali R, Kieber-Emmons T: The hidden code in genomics: a tool for gene discovery. Review. J. Mol. Recognit. 2001, 14:269-272.
Lu Y, Freeland S: On the evolution of the standard amino-acid alphabet. Genome Biol. 2006, 7:102:102.1-102.6.
Michel C J: An Analytical Model of Gene Evolution with 9 Mutation Parameters: An Application to the Amino Acids Coded by the Common Circular Code. Bull Math Biol. 2007, 69:677-698.
Mussat M, Bégin M E, Bureau J P: A constructionist model predicting the emergence, complementarity and classification of the nucleotide bases. Med Hypotheses 1998, 51:511-523.
Osawa S, Jukes TH: Codon reassignment (codon capture) in evolution [abstract.
J Mol Evol. 1989, Apr; 28(4):271-8.
Patel A: The triplet genetic code had a doublet predecessor. J. theor. Biol. 2005, 233:527-532.
Ronneberg T A, Landweber L F, Freeland S J: Testing a biosynthetic theory of the genetic code: Fact or artifact? Proc. Nat. Acad. Sci. 2000, 97:13690-13695.
Sanchez R, Grau R: A genetic code Boolean structure. II. The genetic information system as a Boolean information system. Bull Math Biol. 2005, 67:1017-1029.
Schimmel P, Giegé R, Moras D, Yokoyama S: An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci. 1993, 90:8763-8768.
Sciarrino A: A mathematical model accounting for the organization in multiplets of the genetic code. BioSystems 2003, 69:1-13.
Seligmann H, Amzallag G N: Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code. Naturwissenschaften 2002, 89:542-551.
shCherbak V I: Twenty Canonical Amino Acids of the Genetic Code: The Arithmetical Regularities. Part I. J. theor. Biol. 1993, 162:399-401.
shCherbak V I: Arithmetic inside the universal genetic code. BioSystems 2003, 70:187-209.
Shen N, Guo L, Yang B, Jin Y, Ding J: Structure of human tryptophanyl-tRNA synthetase in complex with tRNATrp reveals the molecular basis of tRNA recognition and specificity. Nucleic Acid Res. 2006, 34:3246-3258.
Sitaramam V: Genetic code preferentially conserves long-range interactions among the amino acids. FEBS Lett. 1989, 247:46-50.
Sowerby S J, Petersen G B, Holm N G: Primordial Coding of Amino Acids by Adsorbed Purine Bases. Orig Life Evol Biosph 2002, 32:35-46.
Sukhodolets V. V: The Genetic Code as a Clue to Understanding of Molecular Evolution. J. theor. Biol. 1989, 141:379-389.
Sungchul J: The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics. Ann N Y Acad Sci 1999, 870:411-417.
Trevors J T, Abel D L: Chance and necessity do not explain the origin of life. Cell Biol Int. 2004, 28:729-739.
Wilhelm T, Nikolajewa S: A New Classification Scheme of the Genetic Code. J Mol Evol 2004, 59:598-605.Woese C R: A Proposal Concerning the Origin of Life on the Planet Earth. J Mol Evol. 1979, 13:95-101.
Wong J T-F: Question 6: Coevolution Theory of the Genetic Code: A Proven Theory. Orig life Evol Biosph 2007, 37:403-408.
Wu H-L, Bagby S, van den Elsen J M H: Evolution of the Genetic Triplet Code via Two Types of Doublet Codons. J Mol Evol. 2005, 61:54-64.
Yarus M: Amino Acids as RNA Ligands: A DirectRNA-Template Theory for the Code's Origin. J Mol Evol. 1998, 47:109-117.
Yarus M, Caporaso J G, Knight R: Origins of the Genetic Code: The Escaped Triplet Theory. Annu. Rev. Biochem. 2005, 74:179-198.
Yu J: A Content-Centric Organization of the Genetic Code. Geno. Prot. Bioinfo. 2007, 5:No. 1 (1-6).


 

 

© Åsa Wohlin
Individual research
E-mail: a.wohlin@u5d.net


 

Links and Notes

Table 24 amino acids (ams)
R-chsins, A, Z, N

Abbreviations
- ways of writing -

Background model

Files here:

0. Amino acids and codon bases.
Why this coding system?





All these files in one document,
pdf, 118 pages

To 17 short files.
- partly other material -

The 17 files as one document,
pdf

 

An earlier version (2007)
with more material
on the same subject, 73 pages
:

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2017-01-16

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