Bacterial identification virtual lab answers

Virtual Lab: Bacterial Identification Virtual Lab
Adapted from HHMI BioInteractive Student Handout
Go to https://www.hhmi.org/biointeractive/explore-virtual-labs. Scroll down and click on “The Bacterial Identification Virtual Lab.” Maximize the screen if you wish. Answer the following questions in the spaces provided.
Click to Enter the Lab. (Click the window on the left-hand side of the screen to enter the lab.) As you enter the lab, follow the instructions in the lab (left-hand window). Using the information in the Notebook window on the right, answer the questions

Now run the PCR. Be sure to watch the virtual lab animation before proceed
11. After 8 cycles, how many copies of the desired DNA have been synthesized?
Part 3: PCR Purification
12. Approximately how long is the 16s rDNA (number of base pairs)?
13. Why would it be useful to run an electrophoresis gel at this point?
The gel in not run in this virtual lab. In order to purify the PCR product, you use a microconcentrator column. (Proceed through the virutual lab steps for this.)
14. What should the final collection tube contain?
Part 4: Sequencing Preparation
Click on “Learn about cycle sequencing before proceeding” to learn more about how DNA sequencing works.
Click “go back to Part 4”
15. The purpose of the second PCR is not to create identical copies like the first PCR you ran. What is the purpose of this PCR?
16. What region do the primers used in the PCR and in this technique bind to?
Watch the virtual lab animation before proceeding to Part 5
Part 5: DNA sequencing
17. What is the final PCR product, the stuff contained in your 12 tubes?
18. What is the purpose of the laser beam in determining a DNA sequence?
Be sure to watch the virtual lab animation before proceeding to Part 6
Part 6: DNA Sequence Analysis
Click on “Learn about the science behind sequence matching”
19. What is the ultimate goal of the sequence matching analysis?
20. What is “homology”?
21. What is BLAST and how is it used?
Click to go back to Part 6 and proceed through the instructions 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” willpaste 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 patient. 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 (left) and follow the instructions.
22. What is the scientific name of the bacterium you sequenced?
23. After completing Sample A, perform DNA sequence analysis on TWO of the other five samples. Write the letter of the sample you chose and the scientific name of the bacterium below after doing a BLAST search.

Answer

Please find the answers of first four questions as per the norms. 11. After 8 cycles, how many copies of the desired DNA have been synthesized? Answer: The number of copies of synthesized DNA = 2n where n is number of cycles The number of copies ofdesired DNA = 28 = 2x2x2x2x2x2x2x2=256 copies. 12. Approximately how long is the 16s rDNA (number of base pairs)? Answer: The approximate size of 16S rDNA is 1,500bp-long. 13. Why would it be useful to run an electrophoresis gel at this point? Answer: The electrophoresis gel can be used to purify the PCR product, this separates both the strand of DNA as well as the contaminate DNA strand if present. 14. What should the final collection tube contain?

Answer: The final collection tube should contains the many copies of 1,500bp-long 16S rDNA, with a very small amount of longer DNA strands (which are contaminants).

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