This exercise comprises 4 parts, and can be performed after Practical training tutorials held in the first part of Semester 1.
Prac 1, Exercise 2. Bioinformatics (4 marks)
Scenario 1:
A proteomic analysis involving 2D gel electrophoresis reveals that a protein is overproduced in cancer tissue biopsies. The “protein spot” is excised, digested with a protease and one of the peptides obtained is subjected to N-terminal sequence analysis, revealing the sequence PATTARGGPGKAGSRGRFAG.
1. Identify the overproduced protein in the spot. Provide the first four parts of its name in full using the format s/tpk.
You will want to search all known sequences of human (Homo sapiens) proteins. A place that houses this information and provides the search tools is the National Center for Biotechnology Information. It advances science and health by providing access to biomedical and genomic information. [When you have time explore their website and try the tools they provide]. Now you are going to the following website to search the protein database. This is a BLASTP search.
http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PAGE=Proteins
It should be straightforward to paste in the sequence and then at the bottom of the page select “BLAST”. You don’t need to select any other options unless you want a more specialised search. You will get a lot of hits but they are mostly the same. They represent each time someone has contributed data about this protein. Choose the second example.
3. Does this protein have counterpart(s) in yeast?
This requires another BLASTP search but this time we aren’t looking for an exact match, but we are looking for significant sequence similarity.
The best database for this search is the one for the main yeast used in research Saccharomyces cerevisiae. To reach this database go to www.yeastgenome.org [Welcome to another exciting information rich website – gaze at it for a while].
Now copy the human sequence in full – don’t worry about the numbers and the spaces between groups of 10 amino acids. Now click on BLAST and paste the human protein sequence into the search box. Next you need to “choose the appropriate BLAST program”. You should know now which one! You also need to select which database. Clue it has to be a protein database. Which strain? It could be any but lets make it BY4741. Now without choosing any defaults choose WU-BLAST.
Is there a hit? Express your answer as one of the following
None, One; About 10; About 50
4. Whatever you observe explain what the number of matches signify.
If you can, please add a literature reference that supports your observation.
Prac 1, Exercise 3. Biomarkers (3 marks)
Scenario 2:
Samples of blood taken from athletes in the 1980s are examined by your Protein Technologies laboratory. In the blood you find an unexpected peptide. Some amino acid sequencing yields a partial peptide sequence:
Glu Lys Leu Lys Asp Leu Glu Glu Gly Ile Leu Ala Leu
Is this a normal human protein? What is the likely source of this peptide?
Normal
0
false
false
false
EN-US
JA
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What is the likely explanation for the observations?