Abstract
The problem of understanding genetic information coding is discussed from the position of the influence of amino acids and proline physical and structural properties is discussed in the chapter. The DNA molecule is considered as a polymer type of a one-dimensional molecular crystal with a complex elementary cell, containing two nucleotides, the sequence and orientation of which allows us to offer the model of a two-positional codon with a skip, directed on the understanding of amino acids and proline coding principle in the DNA molecule. The work also focuses on some evidence confirming the possibility of realization of a two-positional codon with a skip for DNA.
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Notes
- 1.
Actually the sequence of 19 amino acids and 1 imino acid proline.
- 2.
DNA contains thymine (T) instead of uracil (U).
- 3.
Such a code compliance is sometimes also called the standard.
- 4.
Only from the viewpoint of nucleic acids considering all the amino acids and the imino acid proline as equal.
- 5.
Can be either neutral or charged. Sometimes they are referred to as a polar group.
- 6.
Appearance in the “wrong” place or even its absence.
- 7.
Proline(0) has a special place here. Its deficit charge is large enough, but the order of its magnitude is almost identical to the average deficit for all 17 “negative” amino acids.
- 8.
For instance, the typical statistician leucine for some reason also has six codes.
- 9.
Such selectivity might suggest that the formation of these pairs could be the primary polarizing process on the whole.
- 10.
The maximum number of groups—4: polar, electrically neutral and two charge-neutral.
- 11.
The minimal number of significant acids is also four: proline(0), glycine(0), cysteine(\( \to \)) and any of the three amino acids accompanying glycine(0). They are: aspartic acid (−), arginine (+), or serine (\( \to \)).
- 12.
Isoleucine is an exception, which could be considered as some misunderstanding rather than the rule exception. A similar misunderstanding seems to take place also for one code for tryptophan and a "spare" code UGA for the end of the synthesis of arginine.
- 13.
According to the standard canonical genetic code superfluity (degeneracy) this is the opposite: not less than 1 code corresponds to the one amino acid.
- 14.
Two-positional codon with skipping (instead of a three-positional one without skipping) has been confirmed with the latest experimental evidence that reflect significant violation of currently accepted principle of three-positional code degeneracy.
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Shmeleva, L.V., Suprun, A.D. (2016). Coding of Amino Acids by Nucleotides: Consideration of the Problem from the Viewpoint of Physics of Proteins. In: Fesenko, O., Yatsenko, L. (eds) Nanophysics, Nanophotonics, Surface Studies, and Applications. Springer Proceedings in Physics, vol 183. Springer, Cham. https://doi.org/10.1007/978-3-319-30737-4_34
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