Lab Assignment_Bacterial ID with PCR(1)
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Dec 6, 2023
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Lab Assignment – Bacterial Identification
Virtual Lab
HHMI BioInteractive
Copy and pasting text is not allowed, because doing so will not help you learn. There are ways to
detect copying/pasting in documents. Spacing is minimal here. Type your text in the space
provided and allow it to expand the space.
Click here
to access the virtual lab. Then click “Launch Interactive.”
Progress through the click and learn virtual lab, reading ALL of the text as you progress.
You
should also make sure to go over the powerpoint provided with this lab.
For each section of the virtual lab, you will find a section with questions below. Answer the
questions as you progress, and save your work often.
You will also be directed to take snips/screenshots at critical points and paste them in this
document.
Introduction
1. What are the 4 basic steps you will be performing in this lab?
a. Isolate DNA,
b. PCR amplify DNA,
c. sequence the DNA using Sanger Sequencing, and
d. analyzes sequences using BLAST against the GenBank Database in NCBI.
2. What is the purpose of doing each of these 4 steps?
You may have to go through the whole
lab to answer this.
The overall purpose of the virtual lab was to examine and understand the
science and methods behind the identification of bacteria based on their DNA sequences.
3. What is the 16s rRNA, and why is 16 s rRNA suitable for helping us identify bacterial species?
In your answer, make sure to state what organelle the 16s rRNA is a part of.
Because of the
complexity of DNA, DNA hybridization, 16S rRNA gene sequencing is used as a tool to identify
bacteria at the species level and assist with differentiating between closely related bacterial
species. Many clinical laboratories rely on this method to identify unknown pathogenic strains.
4. How will we know what species of bacteria is present based on the RNA?
The RNA present in
bacteria is In the bacteria, RNAP is a multiunit protein complex and contains both a catalytic
core enzyme and a specificity subunit known as σ. The core enzyme containing the β, β , two α,
′
and the ω polypeptide chains is able to catalyze the synthesis of RNA directed by a DNA
template.
Hit “Click to Enter the Lab.”
Part 1 – Sample Preparation
5. After putting on gloves, what is the first step?
6. What is the purpose of the digestive buffer?
Follow the steps in the window on the left to do the sample prep. You will be using Sample A.
7. Why did you heat the sample?
8. Why did you centrifuge the sample?
Part 2 – PCR Amplification
9. What is in the PCR Master Mix, and what is the purpose of each component (please use the
powerpoint in this folder to help you).?
10. Why do you think we are using a positive control? *if you do not know, you can return here during
Part 3: Purify PCR Product. The answers are there.
11. Why do you think we are using a negative control?
13. What do the green and yellow rectangles represent?
14. What do the blue rectangles represent?
Part 3 – Purify PCR Product
15. What is the purpose of spinning the column in the centrifuge?
16. At the end of step 3, what do you have in your microcentrifuge tube?
17. What have you discarded?
Part 4 – Prepare for Sequencing
18. What are the ingredients in our sequencing brew?
19. What do the different colors at the end of each DNA segment represent?
Part 5 – DNA Sequencing
20. What is the purpose of applying an electrical current?
21. Explain IN YOUR OWN WORDS how the sequencer determines the sequence of the DNA. You may
need to watch the animation and read the text in the window a couple times and possibly draw out what
is happening on a piece of scratch paper to help get a clear understanding.
Your preview ends here
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- Image 1 shows raw data of gel electrophoresis. Label/annotate image 1 (lanes, ladder sizes, etc). Explain what your seeing in the gel. Use the following information and picture 2 to assist in labelling. The purpose of this gel electrophorsis is to ensure that your GOI, FAP257, is in each BAC. Protocol that was done for Gel electrophoresis: -Place tray with gel into gel box -Fill gel box with IX TAE until the gel is completely submerged -Remove the comb for wells -Load 10ul of the 1kb Gene Ruler ladder (well 1) -Contains DNA ladder, 6X TriTrack DNA, Loading Dye, and Deionized water -Load other wells -Well 2: Control -Well 3: BAC- 15M5 -Well 4: BAC-39K10 -Well 5: BAC-27N17 -Run the gel at 100V for 30 minutes or until the dye front has migrated 2/3 down the gelarrow_forwardDiscussion for lab report of isolation, purification and quantification of bacterial DNA.arrow_forwardGive typed full explanationarrow_forward
- The gel below shows the results for five samples. Using the gel, determine the genotype of samples.arrow_forwardhelp?arrow_forwardIs Table Window Help 1 Exam_2_problem_set_new- Saved to my Mac Design Layout References Mailings Review View AaBbCcDdF AaBbCcDdF AaBbCcDd AaB Normal No Spacing Heading 1 Не s, fixes, and improvements, choose Check for Updates. 2. Calculate the effective dilution. You were given a sample which contained 5.5mL of bacterial culture. You added 10uL of phage solution to the culture. What was the effective dilution produced by the addition of the phage solution?arrow_forward
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SEE MORE QUESTIONS
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Recommended textbooks for you
- Case Studies In Health Information ManagementBiologyISBN:9781337676908Author:SCHNERINGPublisher:Cengage
Case Studies In Health Information Management
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Publisher:Cengage