Below you have the sequence of 33 nucleotides(part of a coding region of gene TT

Question

Below you have the sequence of 33 nucleotides(part of a coding region of gene TTr34) from two different species of birds (Species A and Species B). For simplicity, the amino acids encoded by the codons of Species A is also indicated, and “.” indicates the same nucleotide as the one observed in the first sequence.

Use these two sequences to estimate the molecular distances.   

a. How many nucleotide changes produce a change in amino acid (nonsynonymous changes)(use the genetic code)?

b. How many nucleotide changes are synonymous (do not cause a change in amino acid)(use the genetic code)?

c. Calculate the molecular distance for synonymous (Ds) and Nonsynonymous (Da) for this gene region without correction. To estimate the total number of synonymous and nonsynonymous sites, assume that 25% of the sites are synonymous and 75% of sites are nonsynonymous.

* Please show all work and explain. *

Pro Gly Asn Thr His Glu Ala Gln Lys Ala Val Species A CCT GGG AAT ACT CAT GAA GCA CAA AAA GCC GTC Species B . . G . . T . . C . . . . . . . C . . . . . C . . . T A . . . . T

Explanation / Answer

a.
It has been observed in the triplet codon system. If there are changes in the first two nucleotides there is a possibility that the triplet codon will code for another amino acid. In this case four nucleotide changes in species B codes for different amino acids.

Therefore four changes are non-synonumous changes

b.
Four changes in the nucleotide position in species B are synonymous, do not cause a change in amino acid.

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