Biotechnology Chapter 3 Day 2 Questions

Biotechnology Chapter 3 Day 2 (pages 73-85)

1. Genome browsers, such as the USCS Genome Browser, provide GC% content information. In other words, it shows information about whether guanines and cytosines are enriched in different stretches of genomic DNA.  One reason is related to genetic features called CpG islands.  Another reason for this information is related to interaction strength between the two strands in a given genomic region.  Discuss this second reason.
2. Figure 3.9 shows that the “melted” strands can “anneal” back together. Why does the reannealing step say “cool slowly”?
3. Sketch figure 3.10 and include information about the purpose of the different materials needed for this Southern blotting (and Northern blotting) technique.
4. Draw a picture of how a DNA probe would interact with its target sequence. Is the target sequence identical to or complementary to the probe sequence?
5. How does a dot blot differ from the set up shown in figure 3.10?
6. How does the technique called “FISH” work? Why is the result shown as a few green and red dots on a blue-ish background in this technique?
7. How can a double nuclease mutant of Cas9 be used in a similar fashion to the (more expensive) fluorescently-labeled probe?
8. List/discuss the seven useful traits of cloning vectors described in bullets on page 77.
9. What is the purpose of a polylinker (aka a multiple cloning site)?
10. How does blue-white screening work? If you are cloning a gene into the plasmid, would you be interested in screening the blue or the white colonies?
11. Discuss the genetic features you would expect in a shuttle vector.
12. Make and fill out a table with two columns labeled “vector type” and “insert size maximum”.
13. Compare/contrast heat shock transformation with electroporation.
14. Summarize how Herbert Boyer and Stanley Cohen put their research interests together to create a scientific breakthrough that revolutionized genetic engineering.
15. The gene library technique could perhaps be more accurately described as a genomic library. Would the technique work well for making human gene libraries?
16. Explain how hybridization-based gene library screening works. Can you think of why this system is often supplanted by “in silico” techniques to answer the same types of questions?