Question

Below are the DNA sequences that encode the first eight amino acids for five alleles of the Adh protein in Drosphila pseudoobscura. Nucleotides that differ from the first sequence are shown by a lowercase letter.

ATGTCTCTCACCAACAAGAACGTC

ATGgCTCTCACCAACAAGAACGTC

ATGTCgCTCACCAACAAGAACGTC

ATGTCTtTgACCAACAAGAACGTC

ATGTCTCTCACCAACAAGAACGTg

a. What are the first eight amino acids for each of these five DNA sequences?

b. For each of the five polymorphic sites, indicate whether the site represents a synonymous or nonsynonymous polymorphism.

c. The fourth sequence shown above has two mutational differences from the first sequence. Specifically, the third codon is TTG versus CTC in the first sequence. These two codons are two mutational steps away from each other. Supposing that the CTC sequence gave rise to the TTG sequence, do you think it is more likely that the one-difference intermediate was TTC or CTG?

d. In general, synonymous polymorphisms tend to be more common than nonsynonymous polymorphisms. Why might that be?

d.

to the TTG sequence, do you think it is more

Answer 1

a. 1st sequence - ATG TCT CTC ACC AAC AAG AAC GTC  

  Amino acid sequence of 1st sequence: met ser leu thr asn lys asn val

2nd Sequence : ATG gCT CTC ACC AAC AAG AAC GTC

Amino acid sequence of 2nd sequence: met ala leu thr asn lys asn val

3rd Sequence : ATG TCg CTC ACC AAC AAG AAC GTC

Amino acid sequence of 3rd sequence: met ser leu thr asn lys asn val

4th Sequence : ATG TCT tTg ACC AAC AAG AAC GTC

Amino acid sequence of 4th sequence: met ser leu thr asn lys asn val

5th Sequence : ATGTCTCTCACCAACAAGAACGTg

Amino acid sequence of 5th sequence: met ser leu thr asn lys asn val

b. In sequence 2, serine at position 2 has been changed to ala , so this is nonsynonymous mutation. because for this SNP, the amino acid sequence is altered. Rest of the SNPs do not cause change in amino acid sequence, so they are synonymous mutation.

c. Cytosine to Thymine (C to T) and Cytosine to Guanine (C to G) are both transversion. So probability is same for both to occur. So the first step intermediate may be any one of them.There is equal probability for both

d. nonsynonymous mutation change the amino acid sequence in the protein which may alter the function of the normal protein and effect may be deletorius to cell. On the other hand synonymous mutation does not change in amino acid sequence in the protein, so the function of the protein is not altered. So synonymous mutation is more common rather than nonsynonymous mutation.