Question

Problems 1) Look at the structure of the natural amino acids (look them up). What do the 8 primordial amino acids have in common (generally)? What do you notice about the ones with 2 or fewer codons? 2) Calculate the actual information content per amino acid of protein translation by using the genetic code and the fact that in nature, the frequency of U and C is 22%, A is 30% and G is 26%. Finally, since 3 of 64 codons are stop codons or "nonsense" codons, you should multiply by a correction factor of 1.05 at the end. As an example, tyrosine is encoded by UAU and UAC, so the expectation for tyrosine is: (.22)"(.3)"(.22)-{.22)(3)[26)-.03168 or 3.168%, and the correction for the stop codons (*1.05) gives you about 3.3%, and Plog2(Pi) for tyrosine is therefore .033"log2(.033). Do the same for the other 19 amino acids and then calculate-Σ Pi log2 Pi-How different is the answer from just using log2(20) (i.e. assuming all 20 amino acids are equally likely to occur)? 3) Once you have the real information content of translation from question 2, repeat the calculation with the observed frequencies found in the table, and take the difference between I(expected) and l(observed), i.e. subtract the two information calculations (doesn't matter which from which, the absolute value of the difference is all that's significant). This is a measure, in bits, of the work per amino acid natural selection had to do in order to evolve functional proteins. Does it seem like it was a hard job? Why or why not?

Answer 1

mRNA - Genetic information- codons containing 3 nucleotide- translation - aminoacids combine to form proteins

Aminoacids composition at site is may be random permutation of genetic code and use probabilities to aminoacids evolution.

Calculate expected frequencies of aminoacids with the observed frequencies. I.e multiply the frequency of each DNA base in a codon.

Ex. Tyr codes for UAU, UAC

(0.22)(0.303)(0.22)+(0.22)(0.303)(0.217)=0.0292

As 3 codons are stop codons multiply with correction factor 1.057

Conclusion: composition of aminoacids reflect random permutation of genetic code.