Bioinformatics - Assignment Example

Tasks 1-7 are related to the material in Section B. Task 8 is to be found in Section C and uses the peptide sequence that was allocated to you. Marks are shown in parentheses. Task 1 (no marks) Write down the peptide sequence (near the start of section B) in single letter format (put a space between each letter): C G L V P V L A E N Y N K S Task 2 (8 marks) What do you conclude about the top seven matches for the peptide sequence? The results show that the matches are all peptide sequences which code for transferrin protein, except for one match, ICA, which codes for an inhibitor of carbonic anhydrase in pigs.

The sequence matches code for different forms of transferrin proteins in various species. For example the 14 amino acid sequence is codes for serotransferrin in humans while it forms part of the protein code for lactotransferrin in horse. This shows that the same peptide sequence codes for the same protein in different species. Task 3 (1 + 1 marks) Write down: a) The number of amino acid residues: 698 b) The relative molecular mass (Mr): 77,064 Task 4 (2 marks) What are the details against TITLE?

Protein Chain A: 329 residues Ligands: CO3 338(A) Metal: FE 339(A) Water: ?138 Task 5 (1 + 2 + 1 + 4 marks) a) What is the number of cleavages for pepsin (at pH 1.3)? 214 b) Why is the pH quoted? The pH can affect the catalyst activity of an enzyme. Extreme pH can denature the active site of the enzyme. pH also gives an idea of the optimum temperature at which the enzyme is able to work. Changes in pH affect the actions of the enzyme. Therefore, at different pH, the hydrolytic action of the pepsin differs.

Therefore, it is important to quote the pH. c) What is the number of cleavages for trypsin? 79 d) By reference to average peptide fragment lengths, which of the above two enzymes would be better for producing peptides for amino acid sequencing (and why)? Pepsin can cleave at a greater number of sites than trypsin. This means that cleavage by pepsin can produce much shorter peptide fragments compared to cleavage by trypsin. For amino acid sequencing, usually if the peptide is less than 50 amino acid residues, there is no need to further cleave the peptide.

The peptides which are 50 AA residues or less can be sequenced by a cyclic procedure, where the AA is first labelled, cleaved and indentified; the process is then repeated on the shortened fragment. However if the peptide is longer than 50 residues, there is a need to first shorten the protein chain before the cyclic procedure is carried out. This means that the enzyme which makes smaller fragments is suitable for sequencing in this case. Calculating the length of the peptide fragments: Pepsin: 698/214?

3 AA Trypsin: 698/79?8 AA In this case, pepsin makes a fragment which is equal to a single AA. This means that pepsin is more suitable. Task 6 (1 + 1 + 4 marks) a) What is the name of the amino acid residue to which carbohydrate is attached? Asparagine b) What is the position number of this amino acid in the protein’s amino acid sequence? 432 c) How are sugars attached to proteins? Via glycosidic bonds Task 7 (1 + 1 + 1 + 4 marks) a) Number of disulphide bridges: 8 b) Number of strands: 13 c) Number of helices: 15 d) Why are disulphide bridges important for those proteins that have them?

Disulphide bonds have an important role in the stability of proteins. They also help to bring about folding in the proteins. The disulphide bond lowers the entropy of the unfolded form of the protein, thus lowering its