Sample questions for exam 2 -- from 1997

This is NOT a sample exam. The questions come from various sources and may not comprise one hour's worth; they are not fully representative of the material you should know for Exam 2.

1.	A certain X-linked dominant disease in humans occurs when there are more than 40 repeats of a CGG trinucleotide in a particular gene. The unique sequence outside the repeat region is as follows: 5' CAGTATGCA------(CGG)n-------ATGCGTAAT 3' 3' GTCATACGT------(GCC)n-------TACGCATTA 5'
	(a)	In the lab freezer, you find 5 primers of different sequences (listed below). If you wanted to use PCR to amplify the trinculeotide repeat region, which of these primers would you use? Primer: #1) 5'-GTCATACGT-3' #2) 5'-ATTACGCAT-3' #3) 5'-ATGCGTAAT-3' #4) 5'-CAGTATGCA-3' #5) 5'-TGCATACTG-3'
	(b)	Shown below are the outline of a pedigree for the disease described above, and a representation of a gel showing PCR-amplified fragments detecting the number of CGG repeats. The DNA corresponding to each individual is directly below his or her place in the pedigree. Based on the information you have been given, fill in the pedigree to show the sex of the individual as well as the phenotype (affected vs. unaffected).

2.	Males of the worm C. elegans are XO -- they have one X chromosome and no Y chromosome, and their sperm have either one X or no X chromosome. You have identified recessive mutations nd-1 and nd-2 that cause X chromosome non-disjunction in every cell undergoing meiosis I and meiosis II, respectively. For all three questions below, assume that the eggs came from normal XX animals; also assume that XX sperm produce viable, non-male offspring.
	(a)	What fraction of a +/nd-1 male worm's progeny do you expect will be male (XO)?
	(b)	What fraction of an nd-1/nd-1 male worm's progeny will be male (XO)?
	(c)	What fraction of an nd-2/nd-2 male worm's progeny will be male (XO)?

3.

The pedigree below shows the inheritance of an autosomal recessive disorder in humans. Shown below the pedigree (and lined up by individual) are the Southern blot data for two RFLP loci. One RFLP has alleles of either 7 kb or 5 kb and is revealed by digestion with the restriction enzyme BamHI; the other gives either a 4 kb or 3 kb EcoRI fragment. Is there evidence for linkage between the disease gene and either of the RFLPs? If so, which one(s)? Explain in ONE or TWO sentences. For the loci that you think are linked, which individuals are likely to be recombinants?

4.

Linkage analysis was done for a certain human disease gene with respect to polymorphic loci PL1, PL2, PL3, and PL4. Some of the resulting Lod scores are plotted. Each curve represents the lod score vs. recombination frequency distribution for a polymorphic site with respect to either the disease locus (D) or with respect to one of the other polymorphic sites. For example, Curve #1 shows the lod score vs. recombination frequency between the disease locus D and polymorphic site PL1. Construct the most likely linkage map that is consistent with the data shown. Your map should include all five loci, but they need not all be on the same linkage group.

5.	Five recessive mutations on the right arm of the X chromosome of Drosophila cause stringy bristle (sg), lazy eyes (ly), tin body (tn), zillion eye (ze), and miniature wing (m) phenotypes. Two wildtype male flies were exposed to X-rays and then mated separately with (non-irradiated) females showing all five recessive traits (Mating 1 and Mating 2).
	(a)	Mating 1 produced normal females and sg ly tn ze m males in equal proportions. One of these phenotypically normal females, when mated to a male sibling, produced F2 progeny that consisted solely of normal and fully mutant phenotypes. Why was this result unexpected, and how do you explain it? (ONE or TWO sentences.)
	(b)	Mating 2 produced sg ly tn ze m males and ly tn females in equal proportions. Explain the result. (ONE sentence.)

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