BIMM 110 Molecular Basis of Human Disease

TA: George Chen gtchen@ucsd.edu

OH: Tu 12:30-1:30 Sierra Summit or by appointment (See below)
Section: W 4:00-4:50 Center 203

Problem Set 4
Announcements:
•Office hours this week: 12:45-1:45 UCSD Guardian office - 2nd floor, Old
Student Center, above Groundworks Books
•No answers for problem sets will be posted, we will go over the problems in
section
•The following problems cover lectures 7 & 8
•Section on May 6th (day after midterm) is canceled.
•Please check WebCT for an announcement regarding midterm room
assignments
•Good luck on the midterm!

1. You know that Chronic Mylenogenous Leukemia is the result of the fusion
protein BCR-ABL. You wish to examine the expression level of the promoter
that encodes for this fusion protein. Design an experiment that could be used
to determine the promoter's expression level.

2. You believe that you have found a gene BIMM which may be a proto-
oncogene, that is, a gene that when mutated, becomes an oncogene (cancer
cell). You aim to test this theory by knocking in the mutant gene in a mouse.
Explain the steps to accomplish this at a molecular level.

3. What is the importance of using two drugs in selecting for knocked

out/knocked in genes in recombinant embryos?
4. A researcher wants to test her genotype for X-inactivation skewing using
GFP. How may she accomplish this?

5. Some scientists consider cell lines not a truly valid way for studying true
cancer cell responses in vivo. Why not?

6. What is the advantage of using the LoxP-Cre protocol to knock out a gene
in mice?

7. Scientists discover a new protein FISH which apparently causes a

hydration-related disease when overexpressed. It appears to be an inherited
disease. You are looking to find where FISH is coded in the human genome.
How would you do this? What kind of protocol is this?

8. You want to create a genetic map for two populations of mice that you
have bred. Assume that fur color and tail length are controlled by single
genes. They show autosomal dominant inheritance. Observe the following
data:

P 10 black fur, long tail mice x 10 white fur, short tail mice
F1 25 black fur, long tail mice x 25 white fur, short tail
mice
F2 37 black fur, long tail mice
11 black fur, short tail mice
13 white fur, long tail mice
29 white fur, short tail mice
100 total mice

Calculate the LOD score for the linkage between the fur color gene and the
tail length gene at a distance of 20 cM. Show your work.

(Note: for the exam, you will not be asked to calculate an LOD score, but you
may be asked to interpret LOD-related information. Being able to understand
the formula should help you out)

Is this LOD score significant evidence for the linkage between the two genes?
Justify your answer.

9. A researcher discovers a single nucleotide polymorphism associated with

Hemophilia that limits the amount of mutant factor VIII that is produced.
What type of SNP is this? Why are SNPs useful for marking human genomes?

10. Create a genetic map given the following information:

Luke is 50 cM away from Leia
Han is 34 cM away from Luke
Chewie is 15 cM away from Han
Chewie is 31 cM away from Leia