Virtual Lab
Bacterial Identification Virtual Lab Student Handout
BACTERIAL IDENTIFICATION LAB HANDOUT
INTRODUCTION
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.
1. What is the overall purpose of this virtual lab?
2. What are the four basic steps involved in this bacterial identification lab?
3. What is "16S rDNA," and how is it used to identify species of bacteria?
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 following questions.
PART 1: SAMPLE PREPARATION
4. As the pathology lab technician, what is your task in this virtual lab?
5. Extracting DNA involves which initial step?
6. What is the wire ring used for?
7. Why are the proteolytic enzymes necessary?
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Virtual Lab
Bacterial Identification Virtual Lab Student Handout
8. Why do you then need to inactivate the proteolytic enzymes and how do you do it?
. After removing the enzymes, why do you spin the sample in the centrifuge?
1 . a. What is the pellet?
. What is the supernatant?
. Where is the DNA?
PART 2: PCR AMPLIFICATION
Go on to Part 2 and work through the PCR steps. Be sure to read the information in the notebook,
including “What is PCR?”
11. What does “PCR” stand for and what is the purpose of PCR?
12. Summarize the process of PCR in a diagram. Include all the steps, labeled and in the right order.
(If you are completing this handout online, draw the diagram on a piece of paper, take a photo,
save the image as a PDF, and upload it in the space below.)
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Virtual Lab
Bacterial Identification Virtual Lab Student Handout
Add the Master Mix and answer the following questions:
13. What does the Master Mix contain?
14. What are primers? Why is a primer added?
15. Once the primers bind, what occurs next?
16. What does "highly conserved" mean?
17. Why are highly conserved regions important in this lab?
18. What does "highly variable" mean?
19. Why are highly variable regions important in this lab?
20. What is missing in the negative control tube?
21. What is present in the positive control tube that is not in the negative control tube?
Now run the PCR. Be sure to watch the virtual lab animation before proceeding to the questions.
22. List each step of a PCR cycle, the temperature, and the duration (time).
a.
b.
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Virtual Lab
Bacterial Identification Virtual Lab Student Handout
c.
23. Describe what happens during each of the steps in one or two sentences.
a.
b.
c.
24. After eight cycles, how many copies of the desired DNA have been synthesized?
25. After 30 cycles?
PART 3: PCR PURIFICATION
26. Approximately how long is the 16s rDNA (bp)?
27. Why would it be useful to run an electrophoresis gel at this point?
28. If you were to run a gel, it would have three lanes. What would each lane contain, and what would
you see in each lane after running the gel?
a.
b.
c.
29. The gel is not run in this virtual lab. In order to purify the PCR product, you use a microconcentrator
column. (Proceed through the virtual lab steps.) What should the final collection tube contain?
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