Expert: Dana Krempels, Ph.D. - 10/3/2008

Question
Hi, I have a question on peptide sequence and translation .
How many possible peptide sequences can be potentially translated during the standard genetic code from the following short DNA sequence?   

5' ATGAGTATCGAAGCTA 3'   
3' TACGCATAGCTTCGAT 5'       

The answer is 4. But why is that so? When we see the sequence to be translated, should we take note the upper sequence or lower sequence? I can't find any stop codon corresponding nucleotide (TAA, TAG and TGA). How can I determine how many peptide sequence can be translated?

Answer
Dear Jiaming,

To know how many amino acids could be encoded in the segment you show in your post, you must know several things about the strand first:

1.  which is the coding strand?

2.  which is the non-coding strand?

3.  are we to assume that the codons here start from the end of the     
strand?  (We know the code is non-overlapping, but since the number of nucleotides here is not a multiple of three, you'd have to know where to start, or figure out if there is a start codon mixed in there somewhere in what would be the 5' end of the translated mRNA.)

 Only one strand is going to be transcribed into RNA, and that will be the non-coding strand (the coding strand has the same sequence, 5' to 3' as the mRNA transcribed).

If we consider the top strand to be the non-coding strand, then the mRNA sequence transcribed from it, in the 5' to 3' direction will be:

5' UAG CUU CGU UAC UCA (U) 3'

This would translate as:

(stop) leu arg tyr ser

If the bottom strand is the non-coding strand, then the mRNA transcribed from it would be:

5' AUG CGU AUC GAA GCU 3'

which would translate as

start (methionine) arg ileu glu ala

I'm guessing that whoever wrote the question is considering the bottom strand to be the non-coding strand, and is NOT including the starting methionine as one of the amino acids in the finished strand, since it is often removed during post-translational processing.

But to tell you the truth, I don't think the question is worded clearly or with enough information to let you get the right answer very easily.

Hope that helps!

Dana