3 ms·

There are actually 84 possible combinations with 4 base pairs if you accept sequences of length < 3. However, if you assume all sequences are length 3, you sti

There are actually 84 possible combinations with 4 base pairs if you accept sequences of length < 3. However, if you assume all sequences are length 3, you still get 64 combinations. We only use 20 out of that space. And if you look at how base pairs encode to amino acids, for half of them, only the first two base pairs even matter - since it's prefix-free you can guess the amino acid if you see those two and even ignore the third. Given how underutilized this space is, I'm not convinced that increasing the domain to 216 will lead to much more than the ability to express our current amino acid space with only two base pairs.

Terribledactyl 11y ago
Minor >> Underutilized may not be the best way to think about it. There is a lot of redundancy that affords protection against mutations.
- veddox 11y ago
  And actually, even the redundancy is not complete. A recent paper showed that seemingly "redundant" variations of triplets led to a slightly different 3D folding structure of the DNA, with effects on the physiology of the cell.
  - sciencerobot 11y ago
    did the have an effect on the translated amino acid sequence or translation? Do you have a reference?
    - veddox 11y ago
      http://journal.frontiersin.org/article/10.3389/fgene.2014.00140/abstract http://journal.frontiersin.org/article/10.3389/fgene.2014.00... Sorry, made a mistake in the comment above. It's not the DNA's structure that is changed, it's the resulting protein's. (Different codons slightly alter the rate of translation, leading to a different folding of the protein.)
      - sciencerobot 11y ago
        Thanks for replying with the reference. That is very interesting
- dibujante 11y ago
  You're absolutely right. The likelihood that any particular amino acid-generating codon will mutate to another amino acid-generating codon is non-uniform and the analysis of what impact these particular redundancies has on that is very complex - sometimes, certain amino acids can even stand in for each other. Certain mutations from one acid to another are more desirable than others, so it's quite possible that the existing structure biases the amino acids towards certain least harmful mutation tendencies. The whole thing is pretty fascinating.

Terribledactyl 11y ago

Minor >> Underutilized may not be the best way to think about it. There is a lot of redundancy that affords protection against mutations.

veddox 11y ago
And actually, even the redundancy is not complete. A recent paper showed that seemingly "redundant" variations of triplets led to a slightly different 3D folding structure of the DNA, with effects on the physiology of the cell.
- sciencerobot 11y ago
  did the have an effect on the translated amino acid sequence or translation? Do you have a reference?
  - veddox 11y ago
    http://journal.frontiersin.org/article/10.3389/fgene.2014.00140/abstract http://journal.frontiersin.org/article/10.3389/fgene.2014.00... Sorry, made a mistake in the comment above. It's not the DNA's structure that is changed, it's the resulting protein's. (Different codons slightly alter the rate of translation, leading to a different folding of the protein.)
    - sciencerobot 11y ago
      Thanks for replying with the reference. That is very interesting
dibujante 11y ago
You're absolutely right. The likelihood that any particular amino acid-generating codon will mutate to another amino acid-generating codon is non-uniform and the analysis of what impact these particular redundancies has on that is very complex - sometimes, certain amino acids can even stand in for each other. Certain mutations from one acid to another are more desirable than others, so it's quite possible that the existing structure biases the amino acids towards certain least harmful mutation tendencies. The whole thing is pretty fascinating.