Genetics 371B Practice problems--Autumn 2000 week 4

 

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1. Assuming that a particular chromosome has equal numbers of the four bases, what would be the average size of the pieces formed by cutting the chromosome with the following restriction enzymes:
(a) SalI (recognition sequence: GTCGAC)
(b) NotI (recognition sequence: GCGGCCGC)
Would this average size change if the chromosome had 60% A-T base pairs and 40% G-C base pairs? Explain.

2. A researcher has a purified sample of a linear DNA. The sample is divided into three portions:
  • one portion is cut with the enzyme XbaI, giving three fragments with lengths of 5 kb, 7 kb, and 13 kb
  • one portion is cut with the enzyme PstI, giving two fragments with lengths of 8 kb and 17 kb
  • one portion is cut with both enzymes, giving four fragments with lengths of 3 kb, 5 kb, 7 kb, and 10 kb.
(a) How might the researcher have figured out the sizes of the fragments?
(b) How many cut sites are there on the DNA molecule for each of these two restriction enzyme?
(c) Draw a restriction map of the molecule with respect to the two enzymes. Can you find an alternative map that fits the data?
If you have not encountered restriction mapping in the past, don't panic--your TA will go over the logic of it in quiz section.

3. You heard in lecture that restriction fragment length polymorphisms can be used just as alleles for mapping purposes. Would you consider the two alleles of an RFLP to be (a) dominant/recessive (b) incompletely dominant, or (c) co-dominant? Explain.

4. The circular DNA shown below was cut in separate reactions with the restriction enzymes AvaI, ClaI, EcoRV, or ScaI (i.e., each sample of DNA was cut with only one enzyme). The number in parentheses besides each restriction enzyme cut site in the map refers is the location of that site in bp along the circle, going clockwise from position 1.

In the outline of the gel (left panel), draw the bands you would expect to see for each digest. (Ethidium bromide is a dye that fluoresces when bound to DNA. By soaking a gel with ethidium bromide and then taking a picture of the gel in UV light, one can detect all the DNA bands in the gel. See page 49 of your lecture notes for an example.)

In the panel on the right ("Southern blot") draw the bands you would expect to see if the gel was hybridized in a Southern blot experiment to the "Probe" fragment indicated in the DNA map. (The DNA sequence of the "Probe" fragment is identical to that of coordinates 6000 - 8000 of the circular DNA shown in the map.)

5. When mouse-rodent somatic cell hybrids are made, a standard practice is to do the cell fusions in the presence of aminopterin, as described in class. Once the hybrid cells have started to grow and multiply, the cells are usually transferred to growth medium lacking aminopterin. Why might it be desirable to leave the aminopterin out at this stage?