Editing Genetic code (section)

===Degeneracy===
{{Main|Codon degeneracy}}
[[File:Genetic Code Simple Corrected.pdf|thumb|Grouping of codons by amino acid residue molar volume and [[hydropathicity]].  A [[:File:ELLIPTICAL GENETIC CODE Ian.png|more detailed version]] is available.]]
[[File:3D Genetic Code.jpg|thumb|Axes 1, 2, 3 are the first, second, and third positions in the codon. The 20 amino acids and stop codons (X) are shown in [[Amino acid#Table of standard amino acid abbreviations and properties|single letter code]].]]
Degeneracy is the redundancy of the genetic code. This term was given by Bernfield and Nirenberg. The genetic code has redundancy but no ambiguity (see the [[DNA and RNA codon tables|codon tables]] below for the full correlation). For example, although codons GAA and GAG both specify [[glutamic acid]] (redundancy), neither specifies another amino acid (no ambiguity). The codons encoding one amino acid may differ in any of their three positions. For example, the amino acid leucine is specified by '''Y'''U'''R''' or CU'''N''' (UUA, UUG, CUU, CUC, CUA, or CUG) codons (difference in the first or third position indicated using [[Nucleic acid notation|IUPAC notation]]), while the amino acid [[serine]] is specified by UC'''N''' or AG'''Y''' (UCA, UCG, UCC, UCU, AGU, or AGC) codons (difference in the first, second, or third position).<ref name="MBG">{{cite book|first=James D. |last=Watson|title=Molecular Biology of the Gene|url={{google books |plainurl=y |id=MByWPwAACAAJ}}|year=2008|publisher=Pearson/Benjamin Cummings|isbn=978-0-8053-9592-1}} {{rp|[{{google books |plainurl=y |id=MByWPwAACAAJ|page=102}} 102–117]}} {{rp|[{{google books |plainurl=y |id=MByWPwAACAAJ|page=521}} 521–522]}}</ref> A practical consequence of redundancy is that errors in the third position of the triplet codon cause only a silent mutation or an error that would not affect the protein because the [[hydrophilicity]] or [[hydrophobicity]] is maintained by equivalent substitution of amino acids; for example, a codon of NUN (where N = any nucleotide) tends to code for hydrophobic amino acids. NCN yields amino acid residues that are small in size and moderate in [[hydropathicity]]; NAN encodes average size hydrophilic residues. The genetic code is so well-structured for hydropathicity that a mathematical analysis ([[Singular value decomposition|Singular Value Decomposition]]) of 12 variables (4 nucleotides x 3 positions) yields a remarkable correlation (C = 0.95) for predicting the hydropathicity of the encoded amino acid directly from the triplet nucleotide sequence, ''without translation.''<ref name="Michel-Beyerle1990">{{cite book|first=Maria Elisabeth |last=Michel-Beyerle|title=Reaction centers of photosynthetic bacteria: Feldafing-II-Meeting|url={{google books |plainurl=y |id=xD5OAQAAIAAJ}}|year=1990|publisher=Springer-Verlag|isbn=978-3-540-53420-4}}</ref><ref>Füllen G, Youvan DC (1994). "Genetic Algorithms and Recursive Ensemble Mutagenesis in Protein Engineering". Complexity International 1.</ref>  Note in the table, below, eight amino acids are not affected at all by mutations at the third position of the codon, whereas in the figure above, a mutation at the second position is likely to cause a radical change in the physicochemical properties of the encoded amino acid.
Nevertheless, changes in the first position of the codons are more important than changes in the second position on a global scale.<ref name=Fricke>{{Cite journal|last=Fricke|first=Markus|s2cid=51968530|title=Global importance of RNA secondary structures in protein coding sequences|journal=Bioinformatics|volume=35|issue=4|pages=579–583|doi=10.1093/bioinformatics/bty678|pmid=30101307|year=2019|pmc=7109657}}</ref>  The reason may be that charge reversal (from a positive to a negative charge or vice versa) can only occur upon mutations in the first position of certain codons, but not upon changes in the second position of any codon. Such charge reversal may have dramatic consequences for the structure or function of a protein. This aspect may have been largely underestimated by previous studies.<ref name=Fricke/>