Download Take-Home Exam 1

Biology 311 Human Genetics
Take-Home Exam I (80 pts.)
Due in class Friday Oct. 27, 2006
 On separate pages, briefly TYPE DOUBLE-SPACED your answers to the
following questions.
 Copies of the papers for question 5 will be available as downloadable PDF
files on Blackboard.
 Feel free to consult the instructor if you need clarification on the
questions. It is highly likely that she is the only one on the planet that has
any idea where some of these questions are coming from.
 I expect this take-home exam to be your own work. You are allowed to
use student presentations on methods for information (some are posted on
Blackboard), but make sure the information is correct and cite the
particular presentation you used as a reference.
 If you use any other references besides your textbook, be sure to cite them
by author, year, title of book or journal, volume, and pages or provide the
URL address for web sources. Exams that do not reference sources will be
penalized.
1. (8 pts.) a. What is the most likely mode of inheritance of the trait shown in the
pedigree below (autosomal dominant or recessive, X-linked dominant or recessive, or Ylinked)?
b. What is the genotype of individual III-1 in the pedigree? Define the allele symbols
you use.
c. What evidence can you provide against other modes of inheritance? Hint: You may
want to duplicate the pedigree and work through all the possibilities to identify
individuals inconsistent with that particular hypothesis.
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2. (6 pts.) a. What is a dot blot?
b. Under what conditions would a short (20 nt) oligonucleotide bind to a specific DNA
sequence in a dot blot? What would you change in the hybridization conditions to enable
a similar oligonucleotide containing a single base pair mismatch to bind?
c. A dot blot DNA test involving allele-specific oligonucleotides (ASOs) was developed
for a human autosomal recessive disorder.
+ASO oligo to normal allele
mASO oligo to mutant allele
You perform a dot-blot hybridization on DNA isolated from a patient who wants to learn
if they are a carrier for the disorder. The test results as compared to those from
individuals with various genotypes are shown below. The test results as compared to
individuals with various genotypes are shown below; filled circles=hybridization, open
circles=no hybridization.
Patient
+/+
+/m
m/m
Dot blot probed
with +ASO
Dot blot probed
with mASO
Is the patient a carrier for this recessive disorder? Explain based on the hybridization
patterns shown above.
3.
a.
b.
c.
d.
e.
f.
g.
h.
(24 pts.) For any three of the following, outline a sequence of experiments to
produce a human protein in bacteria
separate large chromosomal regions
identify a gene that is expressed in particular cancer cells, but not in normal cells.
map the transcription start site of a human gene
locate the position of a gene or marker on a particular human chromosome
determine the subcellular localization of a human protein
identify proteins that interact with each other
isolate the 5’ end of a human cDNA
Be sure to include necessary steps and controls; detailed procedures can be abbreviated or
referenced.
4. (12 pts.) Define six of the following seven terms and indicate how they are relevant to
a particular molecular genetics method.
a. yeast artificial chromosome (YAC)
b. DNA chip
c. DNA polymerase I Klenow subunit
d. oligo dT cellulose column
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e. fluorophore
f. biotin-streptavidin
g. M13 phage
5. (30 pts.) Before he was selected to head up the Human Genome Project, Francis
Collins (along with Lap-Chee Tsui) developed new methods that led to the discovery of
the gene responsible for cystic fibrosis. Their general strategy of isolating a gene first,
then figuring out what it does is called "reverse genetics". Further studies in other labs
have helped explain why a deleterious allele for CF is maintained in the gene pool. You
may wish to consult any or all of the following papers to answer the questions below--be
sure to cite which ones you use. These papers can be downloaded from Blackboard or
from the Milne library web site (although this can be tricky and requires patience). There
also many more general references on the web for CF you may wish to consult.



Rommens, J. M. et al. 1989. Identification of the Cystic Fibrosis Gene:
Chromosome Walking and Jumping. Science 245, 1059-1065.
Riordan, J. R. et al. 1989. Identification of the Cystic Fibrosis Gene: Cloning and
Characterization of Complementary DNA. Science 245, 1066-1073.
Pier, G. B. et al. 1998. Salmonella typhi uses CFTR to enter intestinal epithelial
cells. Nature 393, 79-82.
a. Describe the nature of cystic fibrosis, its mode of inheritance, and illustrate its
transmission in a typical pedigree.
b. What chromosome is the CF gene located on? Describe two different approaches that
could be used to map a gene to a particular chromosome.
c. What is a genomic library? Why were genomic libraries essential to isolation of the
CF gene? Describe how a lambda phage or cosmid genomic library, such as those used
in these studies might be constructed.
d. What is chromosome walking? How does it differ from the new method Collins
developed, called chromosome jumping?
e. The regions of the CF gene that code for protein were identified by comparing a series
of overlapping cDNAs with the genomic region. What are cDNAs and how are they
synthesized? How was the amino acid sequence of the CF protein (CFTR) deduced?
f. Describe the method used to identify the most commonly observed mutation seen for
CF (ΔF508; shown in Fig. 4 of Riordan et al. 2004).
g. Heterozygote superiority is a possible hypothesis for the maintenance of the mutant CF
allele in the population. Devise an explanation of how the typhoid bacterium might
contribute to maintenance of CF heterozygotes. Describe some of the experiments used
by Pier et al. to test this hypothesis and the results they obtained.
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