Of course, not all nucleotide sequence substitutions lead to amino acid substitutions in protein-coding genes. There is redundancy in the genetic code. Table 1 is a list of the codons in the universal genetic code.2 Notice that there are only two amino acids, methionine and tryptophan, that have a single codon. All the rest have at least two. Serine, arginine, and leucine have six.
Moreover, most of the redundancy is in the third position, where we can distinguish 2-fold from 4-fold redundant sites (Table 2). 2-fold redundant sites in which either one of two nucleotides can be present in a codon for a single amino acid. 4-fold redundant sites are ones in which any of the four nucleotides can be present in a codon for a single amino acid. In some cases there is redundancy in the first codon position, e.g, both AGA and CGA are codons for arginine. Thus, many nucleotide substitutions at third positions do not lead to amino acid substitutions, and some nucleotide substitutions at first positions do not lead to amino acid substitutions. But every nucleotide substitution at a second codon position leads to an amino acid substitution. Nucleotide substitutions that do not lead to amino acid substitutions are referred to as synonymous substitutions, because the codons involved are synonymous, i.e., code for the same amino acid. Nucleotide substitutions that do lead to amino acid substituions are non-synonymous substitutions.
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