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Degeneracy or redundancy [1] of codons is the redundancy of the genetic code, exhibited as the multiplicity of three-base pair codon combinations that specify an amino acid. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations . [ 2 ] :
For each codon (square brackets), the amino acid is given by the vertebrate mitochondrial code, either in the +1 frame for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue). The MT-ATP8 genes terminates with the TAG stop codon (red dot) in the +1 frame. The MT-ATP6 gene starts with the ATG codon (blue circle for the M amino acid) in the ...
Codon usage bias in Physcomitrella patens. Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).
Saturation mutagenesis is commonly achieved by site-directed mutagenesis PCR with a randomised codon in the primers (e.g. SeSaM) [2] or by artificial gene synthesis, with a mixture of synthesis nucleotides used at the codons to be randomised. [3] Different degenerate codons can be used to encode sets of amino acids. [1]
This is possible because the genetic code is "degenerate", meaning that some amino acids are coded for by more than one three-base-pair codon; since some of the codons for a given amino acid differ by just one base pair from others coding for the same amino acid, a mutation that replaces the "normal" base by one of the alternatives will result ...
Examples of degeneracy are found in the genetic code, when many different nucleotide sequences encode the same polypeptide; in protein folding, when different polypeptides fold to be structurally and functionally equivalent; in protein functions, when overlapping binding functions and similar catalytic specificities are observed; in metabolism, when multiple, parallel biosynthetic and ...
Four novel alternative genetic codes were discovered in bacterial genomes by Shulgina and Eddy using their codon assignment software Codetta, and validated by analysis of tRNA anticodons and identity elements; [3] these codes are not currently adopted at NCBI, but are numbered here 34-37, and specified in the table below. The standard code
However, in a protein-coding sequence, the DNA sequence is made up of a string of codons which correspond to amino acids. Because the genetic code is degenerate (more than one codon map to a single amino acid) and samples from the amino acids rather than the codons, the codons are not sampled uniformly thus leading to differences in the PCFs.