Question

1. What do you notice about the divergence of the amino acid (protein) sequences when compared to the nucleotide (DNA) sequences?
2. Given a large section of a gene, say a complete exon, how could you determine reading frame?

Answer 1

a. Amino acid sequences divergence would be more conserved than Nucleotide sequence divergence

example:

Nucleotide sequence: ATG AGG AGC AGT Mutated Nucleotide sequence: ATG CGG AGC AGT

Aminoacid sequence : Met Arg Ser Ser Mutated Aminoacid sequence : Met Arg Ser Ser

The examples shows a silent mutation which the aminoacid sequence cannot capture while the nucleotide sequence can capture. Divergence in the Nucleotide cannot be observed in Amino acid sequence due to degeneracy of codons (except for tryptophan and methionine all other 18 aminoacids more than one codon).

b. Exon is the part of mature-RNA after splicing and removing of introns from pre-mRNA from the transcription of a gene.

Reading Frame starts with a start codon (ATG) and ends with a stop codon (TGA,TAG,TAA). If exon does not contain start codon, stop codon or both of them , the exonic sequence can be aligned with the DNA sequence and the start codon before the exon to stop codon after the exon would be Reading Frame