there are six questions in for the lab report
Provide the followings with appropriate figure title. Please title each figure separately. Each descriptive title should include the following information: ● 4 digit PDB, (picture is attached) ● MMDB ID number (picture is attached) ● Common name: cattle. Scientific name: Bos taurus. Protein name: Trypsin Figure 1. One image of your protein’s 3D picture from CN3D website (3 marks) Include properly titled (see above) 3D picture of the protein: ● Secondary structures in two different colour. ● If the 3D structure contains multiple chains, you may print out the entire structure, or just a single chain. ● Point out noteworthy areas of the protein such as active site. ● Identify any cofactors or ligands present. If you do not have any, mention this too.( the pictures are attached from ncbi) ● Legend must include: Ion (if any), Ligand (if any), and secondary structure (helix & sheet) Figure 2. Protparam Output (1 mark) Provide a screenshot of your output and include the following: ● Descriptive title (see above ) ● Highlight the number of amino acids ● Highlight the pI Figure 3. PSIPRED Output (1 mark) Provide a picture of the image produced in PSIPREDView (showing alpha helices and beta strands) and include the following: ● Descriptive title (see above ) ● Highlight the regions discussed in Q2. Figure 4. Clustal Omega Output (5 marks) Provide a screenshot of your output and include the following: ● Descriptive title (see above ) ● Detailed legend for the color, symbols, and sequence names ● Table of common name, and title. For sequence names clearly indicate the name and species of origin of each protein in your alignment (*Note that your name of protein might be different if you choose distantly related organism!). Keep this info in the form of table as a legend. Figure 5. Clustal W - Phylogenetic Tree (3 marks) Provide a screenshot of your output and include the following: ● Descriptive title (see above ) ● Highlight orthologs, paralogs, and outgroup on your tree. ● Detailed legend which contains the following: Indicate, which sequences are paralogs, orthologs, and which make an outgroup ● Highlight areas referred to in Q6. Lab Questions (must be typed – do not scan typed answer) Question 1: Primary Structure (2 marks) • Assuming amino acids are used randomly, what would be the expected frequency of each amino acid in your protein? • How does the expected frequency compare to the actual frequency? • Is your protein rich or poor in certain amino acids? If so, provide examples for each to explain your answer. ★ Question 2: Secondary Structure (3 marks) This question will be marked. You do not need scientific papers as references. ● Compare the secondary structure prediction made by PSIPRED to the actual 3D structure of your protein (from Cn3D). • In general, was PSIPRED able to accurately predict the locations of alpha helices and beta strands? Explain, using 3 different secondary structures. • For each secondary structure, provide highlighted secondary structure that you are comparing in CN3D image, provide highlighted amino acid sequence (that will generate the highlighted secondary structure in CN3D image) from CN3D webpage, and provide highlighted amino acid sequence from PRIPRED. • Please include your figures and sequences in your answer. ★ Question 3: Quarternary Structure (3 marks) This question will be marked. You will need reference(s). (scientific paper) • Define a cofactor. Make sure to distinguish between organic cofactors (coenzymes) and inorganic cofactors (essential ions or metals) • Does your protein have a cofactor? • If yes, state what it is and which category it belongs to. Describe how cofactor is required for your protein’s function. • If no, give an example of two proteins with cofactors (organic and inorganic) Describe how cofactor is required for function of those two proteins. Do not use catalase when you answer this question (0 mark if catalase is used) • You may need to consult a biochemistry textbook to answer this question. Remember to reference! Sometimes the MMDB Structure Summary page will also have relevant information. Question 4: Sequence Choice for the Alignment (2 marks) • Explain which sequences you chose to include in the alignment and why. • Be sure to indicate whether the sequences were orthologs or paralogs. • Was there any outgroup? 22/23 ★ Question 5: Clustal Omega alignment (5 marks) This question will be marked. You will need scientific paper reference(s). • Part 1: Give examples of conserved sequence from your alignment. Can you find conserved sequence from other organisms? • Part 2: Correlate any information known about the structure and function of your protein with the pattern of conserved regions in the alignment. • You should use information from research papers, textbooks, and also from the 3D structure of your protein. • For example, if your protein is an enzyme, can you determine which residues make up the active site? Does your protein bind to anything? If so, are these residues conserved? Perhaps one domain (or cleft, or protrusion) is more or less conserved than in other areas. Why might this be? Question 6: Phylogenetic Tree (2 marks) • Are there any indels (insertion & deletion) in the alignment that are congruent with the phylogenetic tree? • Choose 2 specific areas of your alignment to discuss. Highlight 2 areas. • At what point in the phylogenetic tree did the indel most likely occur? Explain. References CANNOT INCLUDE Wikipedia and Lab manual. figure-5-rimodvce.png figure-3-dqaaa3mn.png figure-4-33r4xbz5.png figure-1-2sefgdsq.png figure-2-mbhoerir.png