A small amount of a rare protein has been isolated and treated with proteases to
ID: 91521 • Letter: A
Question
A small amount of a rare protein has been isolated and treated with proteases to cleave the protein into peptide fragments, which were separated by chromatography and subjected to mass spectrometry to determine their amino acid sequence. Unfortunately, as is often the case when only small amounts of protein are available, only the following three short stretches of amino acid sequence from the protein were obtained:
Peptide #1: Ala-Gln-His-Leu-Met-Lys Peptide
#2: Arg-Arg-Asn-Ile-Val-Ala Peptide
#3: Val-Asn-Ser-Thr-Ala-Pro A.
Using the genetic code (see Figure 7.24), design a collection of DNA probes specific for each peptide that could be used to detect the gene in a cDNA library by hybridization. (2 points) B. Which of the three collections of oligonucleotide probes would be preferable to use first. Explain your answer. (Hint, since the genetic code is redundant, each peptide has multiple potential coding sequences).
Explanation / Answer
Hi,
The protein sequence can be back-translated to corresponding nucleotide sequence either manually from the genetic code table or using any tools online. I have carried out the work using EMBL online tool.
Protein 1: The nucleotide sequence is = GCNCARCAYYTNATGAAR
Protein 2: The nucleotide sequence is = MGNMGNAAYATHGTNGCN
Protein 3: The nucleotide sequence is = GTNAAYWSNACNGCNCCN
The Letters W, ambiguiousN,S..etcambiguous bases.
As we can see there is a lot of ambiguity in the sequences, due to the redundancy of genetic code. The ambiguity is more in the protein 3 as compared to protein 1 and 2. Protein 1 has ATG which is a start codon.Hence it is useful to use the protein 1 DNA sequence for hybridization.