Biotechnology Chapter 3 Day 1 Questions

Biotechnology Chapter 3 Day 1 Questions

1. Create a table with three columns (cell type, cell surface, and disruption method). Fill in information for at least four types of cells.
2. In phenol-based DNA purification techniques, would DNA be found in the aqueous layer or the phenol layer? Which layer would protein be found?  RNA?
3. For DNA precipitation, your textbook describes mixing your DNA solution (in water) with an equal part alcohol. Why would adding a salt such as sodium chloride increase the efficiency of DNA precipitation?  (Hint: Think about the property of DNA that makes it “move” during electrophoresis.)
4. Draw a picture of a gel that was loaded with the following in 3 consecutive lanes:
   1. A DNA ladder/”molecular weight standards” with bands at 5kb, 4kb, 3kb, 2kb, and 1kb
   2. Sample A with bands at 2.8kb and 900bp
   3. Sample B with bands at 1.2kb and 1.3kb
5. Why are UV light boxes important for analyzing DNA gels?
6. Agarose gel electrophoresis is recommended for DNA fragments that are 200-10,000bp in size. What types of electrophoresis could be used for analyzing DNA fragments outside of this range?
7. The restriction enzymes HpaI and EcoRI result in blunt and stick ends, respectively. What does this mean?
8. What is the difference between type I and type II restriction enzymes? What is a type IIS restriction enzyme?  (Hint: Ask Google.)
9. Make a figure of an EcoRII recognition sequence before and after getting cut. (Do not use a “W” in your sequence…use A, C, G, and T as appropriate.)
10. Where does the T4 DNA ligase come from?
11. After looking at the second lane of the faux DNA gels shown on page 69, explain the band labeled “cd”.
12. If plasmid DNA is cut once by a restriction enzyme and then treated with calf intestinal alkaline phosphatase (CIP), why wouldn’t it be able to be ligated back together with T4 DNA ligase?
13. The easiest way to measure the concentration of purified DNA is by measuring the absorbance of the sample using a UV light source.
14. How do you visualize radioactively-labeled DNA? (Draw a picture)
15. If you have some 32-P-labeled dNTPs and some 35-S-labeled dNTPs in your freezer and it is 100 days after the “assay date” for each, what percentage of radioactivity would be left in each sample?
16. How do you detect fluorescent tags? (Part of your answer should explain how fluorescence works.)
17. Biotin and streptavidin are commonly used together in experiments. Why? How is this similar to the use of antibodies to digoxigenin?
18. Describe an example of a reporter enzyme that produce a product with a color change.