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After looking at this question, some other questions poped in my mind.

The DNA code is redundant, there are 20 amino acids for 64 possible nucleotide combinations. Therefore some amino acid are coded by several different nucleotide combinations. While Leucine is coded by 6 codons, Tryptophan is coded only by 1 codon. It is worth saying the set of codons that code for one given amino acid tend to look alike each other more than random. Usually it is only the last nucleic acid that does not modify the coded amino-acid (third-position wobble).

Therefore, I would expect that the genetic code cannot not entirely be explained by "it happened to occur this way the first time (at the origin of life or in the last universal common ancestor [LUCA]) and it never changed".

So, my questions are:

  • Why some amino acids are coded by a big set of codons while others are coded only by one codon?

  • And more specifically, why methionine is coded by only one codon (start codon = AUG) where all other amino-acids (except Tryptophan, Selenocysteine and Pyrrolysine) are coded for by more than one codon?

  • Or more broadly: Why (by which mechanisms, which selective pressure if any, ...) has the genetic code evolved the redundancies?

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This is an area of ongoing research, and I don't think you'll get a great answer. There are some ideas about the early evolution of the code, and there is some variation among extant life, but it is hard to say how it evolves because it evolves so rarely. – adam.r Nov 27 '13 at 0:19
up vote 8 down vote accepted

This question is closely related, and the fascinating link posted by @JohnSmith is a good read.

In short, with a four-base system, and a codon size of 1, you get four possible amino acids. Silly system. A codon size of 2 gives 16. Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids. Codons of size 3 gives 64 - plenty of room to work with and it covers all your forseeable amino acids, and then some, without being too wasteful.

The redundancy, known as degeneracy, is pretty straightforward. There's room to expand, and any redundancy/degeneracy will only reduce the likelihood of errors. That's a huge benefit. For some amino acids, the first two bases are enough. That third position can be quite tolerant to mutation, which is very beneficial to organisms. It appears to be even more fine-tuned, to the degree that redundancy often not only reduces the likelihood of mutation but also reduces the damage caused when a base does mutate. Swapping a hydrophobic AA for another hydrophobic one is less likely to cause aberrant protein function, and anything with a U in the middle is probably hydrophobic. Convenient! I'll also note that, while it's not perfect or even a significant correlation, the more popular amino acids tend to get more redundancy; tryptophan is traditionally the least common AA.

Finally, there are a few non-proteinogenic amino acids, so, as the linked question/answer above points out, maybe in the future there will be more amino acids.

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Some elements of response to your question.

First, something about tRNA frequency. Even if there are six codons for a given amino acid, they are not equivalent because some will correspond to abundant tRNA, while others correspond to very minor tRNA. This has significant influence on the traduction speed, as the traduction will dramatically slow down on minor tRNA (while the ribosome waits for the proper tRNA). This may have very important impact on the folding of proteins (see for instance this paper: Having several codons for common amino-acids may actually be a powerful fine-tuning too for the folding of proteins.

Second, as in some cases (splicing, selenocysteine insertion, what else ?), the secondary structure of the mRNA produced is extremely important, the organisms must be able to tweak the sequence of RNA to leave room for that to happen, and that can only happen if there are lots of amino acids for which there is latitude to tweak the produced mRNA sequence.

Third, it is false that the genetic code is universal. There are some evolutions of the genetic code, see for instance the specific case of methionine in mitochondria:

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