Genetics 371B, Autumn 2000

Problem set 4 -- based on lectures 20-27

Due Wed Nov. 29 at the start of class

1. Explain BRIEFLY whether each of the following conditions will increase the chance of cancer:

(a)

 a mutation in the promoter region of a tumor suppressor gene that results in that gene being overexpressed (assume that the cell is heterozygous for the mutation)
(b) a mutation in the promoter region of a protooncogene that results in that gene being overexpressed (assume that the cell is heterozygous for the mutation)
(c) a homozygous mutation that completely eliminates the coding region of a protooncogene
(d) a homozygous mutation that completely eliminates the coding region of a tumor suppressor gene

(e)

 a heterozygote where one allele is the mutant allele described in (c), the other allele being wild type

(f)

 a heterozygote where one allele is the mutant allele described in (d), the other allele being wild type

2. Great Northwestern pygmy mice are normally white with brown patches. A research lab in Bellingham, working on the genetics of coat color in this mythical rodent, does a mutagenesis screen and obtains a set of eight mutants (r1-r8) that show altered coat color.
(a) Pairwise crosses between strains each homozygous for one of the mutations gave the following results ('+' = wild type coat, '-' = mutant coat color):

  r1 r2 r3 r4 r5 r6 r7 r8
r1 - + - + + + + +
r2 - + + - - + +
r3 - + + + + +
r4 - + + - -
r5 - - + +
r6 - + +
r7 - -
r8 -

The researchers (correctly) conclude that they have identified three complementation groups involved in determination of coat color. BRIEFLY explain how they may have arrived at this conclusion, also indicating which mutations belong to the same complementation group, and whether any of the mutations had a dominant phenotype.
(b) The three complementation groups identified above were named B, D, and E; null alleles (i.e., alleles that make no product) of the three genes are called b, d, and e, respectively. Phenotypes of various strains are as follows:

Strain Genotype Phenotype
i bb fully white
ii dd fully black
iii ee fully brown
iv bbdd fully black
v bbee fully brown
vi ddee fully black

Strain (ii) was crossed to strain (iii), and the resulting F1 progeny were crossed to each other. The F2 progeny consisted of wild type, fully black, and fully brown progeny in 9:4:3 proportions, respectively.

Propose a genetic pathway for coat color in these mice, briefly outlining how you arrived at your pathway. Your model should explain all of the phenotypes described above, including the (ii) x (iii) cross.

3. E, F, G, and H are four complementation groups required for synthesis of the amino acid tryptophan in a certain mold. Strains lacking any of these genes cannot grow in minimal culture medium, but in some strains, growth can be rescued by the addition of supplements as indicated below ('+' = growth, '-' = no growth):

Mutant lacking:
Supplement E F G H
#1 + - + -
#2 - - + -
#3 + - + +
Tryptophan + + + +

Assuming that supplements #1, #2, and #3 represent normal intermediates in the synthesis of tryptophan, what is the pathway of tryptophan synthesis in this mold? Explain BRIEFLY. Your pathway should indicate the order of synthesis of the intermediates as well as the gene(s) required for each step.

4. A certain species of bacterium, when starved for nitrogen, synthesizes a thick wall and forms a long-lived spore. A cluster of three closely linked protein-coding genes (A, B, and D) was found to be required for spore wall synthesis: the ABD operon is not transcribed (or is transcribed at very low levels) when the cells are in rich culture medium, but is transcribed at a high rate in nitrogen-poor medium.
(a) Mutational analysis of these three genes revealed that:
  • a nonsense mutation (i.e., a mutation introducing a stop codon) in gene A resulted in cells that lacked functional protein A (mutant allele = a)
  • a nonsense mutation in gene B resulted in cells lacking functional proteins A, B, and D (mutant allele = b)
  • a nonsense mutation in gene D resulted in cells lacking functional proteins A and D (mutant allele = d)

Explain these observations, giving the map order of the three genes, also indicating the location of the promoter for this operon.
(b) A fourth mutation r (wild type = R ) results in failure to upregulate transcription of genes A, B, and D in response to nitrogen starvation. Furthermore, a partial diploid of the genotype

r ABD / R ABD

behaves like wild type cells (i.e., low levels of A, B, and D transcription in rich medium, induction of transcription upon nitrogen starvation). State whether each of the following hypotheses is consistent or inconsistent with the above data, BRIEFLY explaining your thinking in each case:

  1. r represents a mutation in the promoter of genes A, B, and D, that prevents their transcription
  2. r is a null (complete loss of function) allele of an activator of ABD transcription
  3. r is a null allele of a repressor of ABD transcription
  4. r is a gain-of-function allele of a repressor of ABD transcription
  5. r is a gain-of-function allele of an activator of ABD transcription

(If you are accepting a hypothesis as being consistent with the data, you should say how the data are explained by the hypothesis; if you are rejecting a hypothesis, you should specify the data that are in conflict with the hypothesis.)
(c) Suppose you receive authoritative word that the correct explanation has to be either (i) or (ii) above. Assuming that you could construct any partial diploid (using these 4 mutant and 4 wild type alleles), suggest a partial diploid genotype that you would construct to distinguish between hypotheses (i) and (ii). Explain how your custom-built strain would help you, giving the expected phenotype for each hypothesis.

5. Prof. Charles Xavier is deeply interested in the genetics behind the super-powers of his X-folk. In particular, he want to understand how his friend Cyclops can shoot killing-strength laser beams out of his eyes. Being a righteous individual, he does not want to experiment on Cyclops; instead, he wants to identify mutant X-mice that have the same properties. Suggest a selection scheme to identify such X-mice (i.e., mice that can shoot lethal laser beams out of their eyes when aggravated).