|MoBio||Order in the Genetic Code||Chapter 3|
The genetic code is not randomly assigned. If an amino acid is coded by several codons, they often share the same sequence in the first two positions and differ in the third position. Such assignment is accomplished by the design of wobble position, but "the evolutionary dynamic that shaped the code remains a mystery" (Woese et al., 2000).
From the above figure, we see that the amino acids with close physical properties have similar codons. For example, both Asp and Glu are negatively charged. Their codons all contain "GA" in the first two positions. The physical properties of Ser and Thr are also very close. They are coded by UCN and ACN (N = any), respectively.
One advantage for this assignment is to reduce the damage caused by replication errors or other mutations. For instance, if the third nucleotide of Ser codon is mutated, the produced amino acid remains Ser. If the first nucleotide of Ser codon is mutated to A, it will produce Thr, which is similar to Ser. Such mutation will not have significant effect on the protein's structure and function. Let us consider a hypothetical case that codons are randomly assigned. Suppose Ser were coded by GAG, GUA, GCU and UGG; Thr were coded by AAA, AGU, UUU and CCC. Then, any mutation would produce an amino acid different from Ser and Thr.