Question

It has been suggested that the present-day triplet genetic code evolved from a doublet code when there were fewer amino acids available for primitive protein synthesis. (a) Can you find any support for the doublet code notion in the existing coding dictionary? (b) The amino acids Ala, Val, Gly, Asp, and Glu are all early members of biosynthetic pathways (Taylor and Coates, 1989 ) and are more evolutionarily conserved than other amino acids (Brooks and Fresco, 2003 ). They therefore probably represent "early" amino acids. Of what significance is this information in terms of the evolution of the genetic code? Also, which base, of the first two, would likely have been the more significant in originally specifying these amino acids? (c) As determined by comparisons of ancient and recently evolved proteins, cysteine, tyrosine, and phenylalanine appear to be late-arriving amino acids. In addition, they are considered to have been absent in the abiotic earth (Miller, 1987 ). All three of these amino acids have only two codons each, while many others, earlier in origin, have more. Is this mere coincidence, or might there be some underlying explanation?

Short answer

Answer: The evidence supporting the doublet code notion is that certain pairs of amino acids share the same first two bases in their codons, suggesting that the first two bases were more significant in determining the amino acids, and the third base may have evolved later to provide more specificity. The significance of early amino acids in terms of base usage is that they all start with a G nucleotide, suggesting that during the early stages of genetic code evolution, the first base played a more significant role in specifying these early amino acids.

Step-by-step solution

(a) Support for the doublet code notion

To find support for the doublet code notion in the existing coding dictionary, let's first understand what the doublet code is. The doublet code is a hypothetical genetic code where each codon consists of only two bases, as opposed to the triplet code, which consists of three. In the modern genetic code, certain pairs of amino acids share the same first two bases in their codons, such as Glycine (GGX) and Glutamic acid (GAX), where X can be any of the four bases (U, C, A, or G). This pattern suggests that the first two bases were more significant in determining the amino acids, and the third base may have evolved later to provide more specificity. This observation provides support for the doublet code notion.

(b) Significance of early amino acids

The information about the early amino acids (Ala, Val, Gly, Asp, and Glu) is crucial for understanding the evolution of the genetic code. If these amino acids are more conserved and thus evolved earlier, it will help us in finding the patterns in their codon usage. All these amino acids share a common feature in their codon usage - the first base of the codon appears to be more significant in determining the amino acid identity. For example, Glycine (GGX), Alanine (GCX), Valine (GUX), Aspartic Acid (GAX), and Glutamic Acid (GAG) all start with a G nucleotide. This observation suggests that during the early stages of genetic code evolution, the first base probably played a more significant role in specifying these early amino acids.

(c) Codon abundance in late-arriving amino acids

Cysteine, tyrosine, and phenylalanine are considered to be late-arriving amino acids and are found to have only two codons each, while the early amino acids have more codons specifying them. This difference may not be a mere coincidence and could indicate an underlying explanation. One possible explanation could be that during the early stages of genetic code evolution, the doublet code provided limited specificity, with only 16 (4^2) possible codons. As more amino acids evolved, there was a need for a more specific code, leading to the evolution of the triplet code, with 64 (4^3) possible codons. The late-arriving amino acids, like cysteine, tyrosine, and phenylalanine, might have evolved during a time when the triplet code was already in place, and as a result, they have fewer codons specifying them, since they didn't evolve gradually with the code, but rather, joined the system when more specific codes were available. In summary, this exercise allowed us to explore the genetic code evolution and its implications on the codon usage for amino acids, providing insights into the early amino acids and the significance of their base usage, and possible explanations behind the codon usage variations in late-arriving amino acids.