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Student Handout Virtual Lab Bacterial Identification Virtual Lab PART 5: DNA SEQUENCING 34. What is the ﬁnal PCR product, the stuﬀ contained in your 12 tubes? The mix of DNA pieces of variable lengths tagged with ﬂuorescent markers. 35. What is the purpose of gel electrophoresis? Separate individual DNA pieces and idenfy the end nucleode. 36. How do DNA molecules move in relaon to charge? Why? They move towards posive items because they are negavely charged. 37. What is the purpose of the laser beam in determining a DNA sequence? It excites the ﬂuorescents markers making the colors easier to see. Be sure to watch the virtual lab animaon before proceeding to Part 6. PART 6: DNA SEQUENCE ANALYSIS Click on "Learn about the science behind sequence matching." 38. What is the ulmate goal of the sequence matching analysis? Automacally ﬂushes out the buﬀer from the tube. 39. What is "homology"? Homology is the state of having the same or similar structure or relaon. 40. What is BLAST and how is it used? (Basic Local alignment search tool) matching sequences using an algorithm. www.BioInteractive.org Published January 2015 Page 8 Student Handout Virtual Lab Bacterial Identification Virtual Lab 41. What’s a major assumpon when drawing evoluonary relaonships between organisms based on DNA sequences? Number of posions that diﬀer I the nucleodes sequences is proporonal to the me elapsed since the two species formed their own lines of descent form a common predecessor Click to go back to Part 6 and click on "Learn more about BLAST search results." 42. Explain what the "Score (bits)" means on an actual BLAST search result. An indicaon of how good the alignment is, the higher the score the beer the alignment. 43. What does an E-value of 3 or less represent? It refers to the expected number of random hits for a given alignment score. It represents a more reliable match. Click to go back to Part 6 and proceed through the instrucons in the right-hand notebook window. • Hints: "Ctrl A" will select all the data in the pop-up window, "Ctrl C" will copy it, and "Ctrl V" will paste it into the NCBI website (large yellow box at the top of the BLAST search page). • Follow the steps listed on the page and be paent. BLAST data can take a while to search. • When the BLAST results appear, scroll down below the color key to the signiﬁcant alignments, and then go back to the virtual lab window (leﬅ) and follow the instrucons. 44. What is the scienﬁc name of the bacterium you sequenced? Bartonella sp 45. Write a brief descripon of this bacterium in the space provided. It is a genus of Gram negave bacteria. Only genus in the family of bartonellaceae. It can infect healthy people, but they are considered important as opportunisc pathogens. Aﬅer compleng Sample A, perform DNA sequence analysis on three of the other ﬁve samples . www.BioInteractive.org Published January 2015 Page 8

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