Name__________________
ChE355/599 Autumn 2004
Exam 1
DUE: November 1, 2:30 pm
Work on this on your own, do not discuss it with other members of the class. You
can use any web or printed resources to help, and you can ask any of the course instructors or
the TA for clarification help. Please answer the questions on a separate sheet of paper.
1. DNA Forensics
Background:
DNA forensics is an offshoot of our understanding of sequences in the human genome that vary
significantly between individuals. One part of DNA forensics is determining the origin of human
remains. Bones retain DNA in the marrow and bones as old as 50-100 years will yield sufficient
DNA to PCR out specific diagnostic regions for sequence. Family groups can be determined this
way. Since they are closely related, their DNA sequences should be identical compared to DNA
sequences from non-related individuals. Standard targets for DNA forensics include the same
region of mitochondrial DNA you sequenced in lab, as well as regions of the X and Y
chromosome. A general resource on DNA forensics is:
http://www.ornl.gov/hgmis/elsi/forensics.html
Important facts:
 mitochondrial DNA is inherited only from the mother; therefore, the genes are the same
as the mother and can be used to match mothers and children (both sons and
daughters) through many generations
 genes on the Y chromosome are inherited only from the father; therefore, the genes are
the same as the father and can be used to match fathers and sons through many
generations
 family relationships can be determined back many generations, if a direct descendant is
willing to donate a sample to determine the appropriate sequences
Scenario:
A famous (true) DNA forensics case involves Nicholas Romanov, the last Tsar of Russia, and his
family including the Tsarina Alexandra, who was a granddaughter of Queen Victoria of England.
They were killed in 1918, during the Russian Revolution and their bodies were buried outside
Ekaterinburg, Russia. In 1991, a grave was exhumed that was claimed to contain their bodies.
Were the bones found there the remains of the Romanovs? Find out about this case and how it
was solved here:
http://history1900s.about.com/gi/dynamic/offsite.htm?site=http%3A%2F%2Fusers.rcn.com%2
Fweb-czar%2Fdna.htm
http://www.geneticorigins.org/geneticorigins/mito/media3.html
http://www.romanov-memorial.com/Final_Chapter.htm#Top
Answer the following about this famous forensics case:
1. Were all of the Romanovs identified? If not, who was missing?
2. What was the physical evidence that these bodies were the Romanovs?
Name__________________
3. What was the genetic evidence that
a. There was a family group in the grave?
and
b. That these were the members of the Romanov family?
(Note that there is ongoing controversy about this subject, but the bottom line still supports the
data from 10 years ago).
For this exam, you will consider a fictional addendum to this story, as follows:
A skeleton has been unearthed near Ekaterinburg, Russia during an excavation for a new
hospital that has created great excitement because circumstantial evidence suggests it may be
the long sought-after remains of Grand Duke Alexei Romanov. The skeleton appears to be that
of a young boy, gold and porcelain dental work is similar to that found for the other Romanovs,
and the body has been badly damaged. However, a son of Tsar Nicholas’ sister is also missing
and this might be his remains. One distinction between them was that Alexei was known to
have hemophilia, which is a genetic disease in which the gene for a human blood clotting factor
(a protein) is defective. This gene is known, it is present on the X chromosome, the sequence
is available, and the mutations that cause hemophilia are well-documented. You are the head
of a DNA forensics laboratory, and the Russian government has hired your firm to investigate
these remains.
1) Your task is to generate a plan for how to determine whether these remains are
those of Alexei Romanov. There are two issues: was this person related to the Romanovs,
and was this person Alexei Romanov? Here are some questions to guide you, but DO NOT
simply answer the questions, use the questions to help you write the plan.
a) What are your clues? To what hypotheses do these lead you?
b) What target DNA region would be most useful (e.g. mitochondrial, Y chromosomal,
hemophilia gene, etc)?
c) What kinds of samples would you hope to obtain and from whom?
d) What results would allow definite conclusions? Why?
e) What results would be inconclusive? Why?
f) What kinds of quality control would you need to be concerned about, for instance,
with sample contamination, etc.?
Use this format for your plan:
I. Determination of whether this person was related to the Romanovs
A. Samples needed
B. DNA region to be sequenced
C. Results expected if subject IS or IS NOT a Romanov
II. Determination of whether this person was Alexei Romanov
A. Samples needed
B. DNA region to be sequenced
C. Results expected if subject IS or IS NOT Alexei Romanov
III. Quality Control Plan
IV. Conclusions Based on the Results
Name__________________
2. Genetic Diseases
Go to the OMIM database: http://www.ncbi.nlm.nih.gov/omim/, type in Marfan Syndrome, click
on the first entry, and use information there to answer the following questions regarding this
genetic disease. Here is another possible source of information:
http://www.bsped.org.uk/NN/MARFAN.htm
And you can always type in key words to Google…
Answer the following questions:
1. What is the protein defective in patients with Marfan syndrome?
2. Explain (in general terms) why the defect in this protein results in the
symptoms observed in patients. In other words, what is the role of this
protein and how does that affect function in the body?
3. Within which human chromosome is this gene found?
4. The gene defective in Marfan syndrome is a dominant gene. What is the
probability of a parent with Marfan passing on the gene to a child, if the other
parent does not have Marfan?
5. Discuss the possibility of using gene therapy to cure Marfan syndrome. Do
you think this would be feasible? Why or why not?
6. Compare the sequence of this protein from humans to the homologs from
mouse and rat:
First, get the protein sequences:
a. Click on the Gene map locus link (in the OMIM section for Marfan
Syndrome, this button is underneath the list of titles and identifiers),
then click on the 1st entry under Location. You should now be in
“Homo sapiens Map Viewer”.
b. The correct gene, FBN1, should be highlighted. Click on hm, which will
take you to the homolog database (genes that are related).
c. Click on the HomoloGene link
d. In the blue box entitled "Regenerate Alignments", select H. sapiens
(human) and M. musculus (mouse), then click on BLAST. This will
automatically give you an alignment.
e. "Identities" (at the top of the alignment) tells you how many are
identical out of the total. How many amino acids are different between
the human and mouse sequence? (if you can, print out the alignment
to save you having to go back to it)
f. Now do the same for the human and rat sequence. How many amino
acids are different for these sequences? (if you can, print out the
alignment to save you having to go back to it)
7. Map the Marfan Syndrome mutations against your alignments. Go back to OMIM,
search for fibrillin, and click on the link. Scroll down to Molecular Genetics
Name__________________
a.
From the first paragraph, list the 2 amino acid mutations that are
known, (they are designated as, for instance, Xxx123 to Yyy).
b.
Find those mutations in your alignments (the amino acid number in
the mutation [123, in the example above] will be the amino acid number in
your alignment). Are these amino acids the same (conserved) in the mouse
and rat as in the human?
c.
Do you think if these same amino acids were mutated in the mouse or
rat, they would cause defective fibrillin? Why or why not?
d.
Why do you think the amino acids that differ between human and rat
or mouse do not affect fibrillin function (why are all 3 of these proteins
functional)?