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We all know why there are 3-base codons, and why there aren't any 2-base codons. But why is there not a 4-base a 5-base codon?

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marked as duplicate by MattDMo, jarlemag, Chris, GriffinEvo, biogirl Apr 14 at 8:38

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The more bases there are per codon the more information you can code for. There are only 22 different amino acids, in consequence we need minimum 3 bases per codon.

  • 1 base-codon --> 4^1 = 4 possible codes which are:
    • A / T / C / G
  • 2 base-codon --> 4^2 = 16 possible codes which are:
    • AA / AT / AC / AG / TT / TA / TC / TG / CC / CA / CG / CT / GG / GC / GT / GA
  • 3 base-codon --> 4^3 = 64 possible codes which are:
    • AAA / AAT / AAC / AAG / ACA / ACT / ACG / ACC / AGA / AGT / etc...
  • 4 base-codon --> 4^4 = 256 possible codes which are:
    • AAAA / AAAT / AAAC / AAAG / AATA / AATC / AATG / etc..
  • 5 base codon --> 4^5 = 1024 possible codes

If we had only 2 bases per codon we couldn't code for all of the possible different amino-acids.

On the other hand there are several costs associated with carrying lots of DNA. It takes space, it takes energy and matter to get copied, it takes time to copy it (generation time might be limited by copying time), … I have just asked this question hoping to make things clear about the possible costs. If there is a cost associated with having a 4-base codon system compare to a 3-base codon system but there is no associated benefit. Such trait (that has a cost with no benefit) are not expected to evolve (counter-selected).

You'll notice that there are 64-22=42 extra possibilities. In consequence the genetic code is redundant. Meaning that several codon codes for the exact same amino-acid. And interestingly, it is often a the last of the three bases of the codon the does no yield to any change in the coding sequence as you can see here.

enter image description here

This post about the evolution of genetic code might interest you.

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You really helped me, thank you. But could you please clarify your statement: "that would sounds stupid to have 5-base codon if there is no gain."? –  user6318 Apr 12 at 15:16
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@user6318 I already changed this sentence! I meant that there is a cost associated with having a 4-base codon system compare to a 3-base codon system but there is no associated benefit. In consequence, such trait are not expected to evolve. Hope that makes sense to you. –  Remi.b Apr 12 at 15:19
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I'm always bemused by arguments based upon the metabolic cost of maintaining DNA. I estimate that for E. coli less than 0.06% of ATP is used in replicating DNA, so for a 4 base codon system this would rise but would still be well below 0.1 %. This doesn't strike me as the basis of a strong selective pressure. –  Alan Boyd Apr 12 at 18:10
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What about physiological issues? Space taking up by DNA and the machinery having to deal with these big sequences in bacteria? And what about timing issue? I've heard (but have no reference, I should make sure of this claim) that in some species the generation time is limited by the DNA copying time –  Remi.b Apr 12 at 18:19
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@Remi.b great! let's see what answers you get. In E coli it takes 40 min to replicate the genome, but they can grow with a doubling time < 20 min by reinitiating before the previous round of replication has ended. I was once told that the limit to growth is the exponential increase needed in ribosome number as more and more ribosomes are tied up just making ribosomes. –  Alan Boyd Apr 12 at 19:36
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