BIOL 337 Online Module 3

BIOL337 Module 3 Worksheet Part 1 (30 pts.) Name: Watch the video https://youtu.be/OSKwuOccAak Important: Write all responses in complete sentences. The final worksheet should not exceed four total pages single-spaced (including the appendix of sequences), 1-inch margins, 12pt text size. Section 1 Bioinformatics Part 1: Find TASR238 (10 pts) 1. In your own words, what information from the ‘Summary’ pane is relevant to our experiment? 2. On what chromosome is TAS2R38 located? 3. Based on the diagram in the ‘Genomic context’ pane, what genes are located near TAS2R38? 4. Click on the nearby genes; what are their functions (briefly)? 5. Do any of the nearby genes share a similar function to TASR238? If so, should we expect nearby genes to have similar functions? Part 2: Determine Amplicon Size (1 pt) 6. What is the expected PCR amplicon size resulting from these primers? Part 3: Find PAV and AVI Alleles (4 pts) 7. Have you found records for the human TAS2R38 gene? What are the synonyms for TAS2R38 that you see? 8. Do any sequences listed have less than 100% similarity to the queried sequence? If so, what does this mean? Is there something wrong with our search parameters? Part 4: Explore TAS2R38 Gene Sequences (10 pts) Compare the Human taster sequence with the human non-taster sequence, and the predicted amplicons. 9. What is indicated by the initial stretch of highlighted sequence? Where does the amplicon align with the sequences of the two alleles? 10. List the nucleotide position(s) and nucleotide differences (called single nucleotide polymorphisms [SNPs]) between the two amplicon sequences. Compare the Human PTC taster sequence with the human PTC non-taster sequence and the other primates in the database (chimpanzee, bonobo, and gorilla). 11. What is the ancestral (original) state of this gene at the variable nucleotide position(s) that differentiate the human alleles? 12. Are non-human primates tasters or non-tasters, and what does this suggest about the functional evolutionary history of bitter taste receptors? ****Append your text document with the sequences you collected along the way**** (5 pts)