Q1. Basic knowledge of DNA, RNA and protein is important for better understanding of the subject. The following questions will help you get an overall idea of the basic biological molecules and databases. (8 Marks) a) What is central dogma? Explain the process briefly and the importance of DNA, RNA and

protein in protein synthesis. b) List 3 primary sequence databases along with their respective URL's for obtaining DNA and Protein sequence. c) List 3 protein structure databases with their respective URL's.

d) What is Genome? List three genome databases with their respective URL's.

Q2. Bioinformatics is an intelligent method for obtaining biological knowledge using computational techniques. In this question you will execute a workflow to produce a biological outcome. (12 Marks)

We will investigate Breast cancer in humans with reference to the Heat Shock Protein (HSP). a) Using the NCBI Gene Database, investigate HSPB1: search ID 3315. This display has a lot of information, list the information you infer about the particular gene.  Brief Summary of the gene (In your own words).  What are the major pathways involved.

b) Scroll to the (NCBI Reference Sequences) section and click the protein sequence (NP_001531). You will be taken to the entry in NCBI Protein. Select "FASTA", Click 'Send

to File' to save the protein sequence.  Paste your sequence into the structure model server http://swissmodel.expasy.org/interactive. 3D structure of your protein will be

generated. Provide the screenshot of your result page.

 Download the PDB file of the model generated and provide the .PDB file. c) Analyse the report provided in the results page and provide the following information.

 What is the template used in building the model and state the identity of the target with the template.  Provide the sequence alignment of the target and the template. (Check the model

report provided in the results page).  Open the protein structure using RasMol, save the image as GIF and paste it in your

report. d) Go to NCBI BLAST www.ncbi.nlm.nih.gov/blast. Select 'protein blast' and paste the protein

sequence saved from Q2b. Execute the search with the 'swissprot' database.

 Pastes the results obtained into your report and provide a brief analysis of the result.  The coloured lines indicate the coverage and quality of alignments of other proteins

in the database to your query. Translate the scientific name of five matching sequences organisms into common names e.g. Homo sapiens  human.

e) Scroll down your BLAST result page to find the match to Gallus gallus (Chicken). Click the accession link corresponding to Gallus gallus.

 Download the protein sequence as before, generate a 3D model using Swiss Model.

Provide the screenshot of your result page.  Load the PDB file in RasMol, save the image as GIF and paste it in your report.

 Compare it with the human protein structure generated in Q2b, what do you observe by comparing two structures?