The genetic code is degenerate. Amino acids are encoded by either 1, 2, 3, 4, or 6 triplet codons (see Figure 13.7). An interesting question is whether the number of triplet codes for a given amino acid is in any way correlated with the frequency with which that amino acid appears in proteins. That is, is the genetic code optimized for its intended use? Some approximations of the frequency of appearance of nine amino acids in proteins in E. coli are given in the following:

Amino Acid       Percentage
  Met                        2
  Cys                        2
  Gln                         5
  Pro                         5
  Arg                         5
  Ile                           6
  Glu                         7
  Ala                         8
  Leu                        10

How would you proceed with your analysis if you wanted to pursue this problem further?

Key Concepts

Degeneracy of the Genetic Code

The genetic code is described as degenerate because multiple codons can encode the same amino acid. This redundancy allows for a certain level of error tolerance during protein synthesis, as changes in the DNA sequence may not always result in a change in the protein produced. Understanding this concept is crucial for analyzing the correlation between codon usage and amino acid frequency.

Codon Usage Bias

Codon usage bias refers to the phenomenon where certain codons are used more frequently than others to encode the same amino acid in a given organism. This bias can be influenced by factors such as the organism's evolutionary history, the efficiency of translation, and the availability of tRNA molecules. Analyzing codon usage can provide insights into the optimization of the genetic code for specific amino acid frequencies in proteins.

Amino Acid Frequency in Proteins

Amino acid frequency in proteins refers to how often specific amino acids appear in the protein sequences of an organism. This frequency can be influenced by the organism's metabolic needs, environmental adaptations, and evolutionary pressures. By examining the relationship between amino acid frequency and the number of codons that encode them, researchers can assess whether the genetic code is optimized for the organism's protein synthesis requirements.