Name ______________________________________ Bioinformatics
1.
What is bioinformatics?
2. What is BLAST (Basic Local Alignment Search Tool) used for?
3. What can we learn by BLASTing the primer sequences we used in the mtDNA lab?
4. Why does the mitchondrial control region mutate at 10 times the rate of nuclear DNA?
5. The high mutability of the mt genome means that it evolves more quickly than the nuclear
genome. This makes the mt control region a laboratory for the study of DNA evolution.
However, can you think of any drawbacks to this high mutation rate?
6. There are numerous insertions of mt DNA into nuclear chromosomes. Most of these are very
ancient. However, a 540-bp insertion of the mt control region on chromosome 11 is an example
of a relatively recent event that occurred about 350,000 years ago. Would you expect any
difference in the mutation rates of the control region sequence in the mt genome versus the
chromosome 11 insertion?
7. When we compare the control regions of the mitochondrial genome of all modern humans we
find that there are, on average, seven SNPs (mutations) within a 375 nucleotide sequence.
Anthropological data suggest that modern humans arose 140,000 years ago. If this is so, what is
the approximate mutation rate for the mt control region?
8. Why is this calculation only approximate?
9. “Otzi” the Iceman is a 5,300 year-old human discovered in the Otzal Alps between Austria and
Italy. He had tools and the weapons of a hunter and carried domesticated wheat. How does
your mtDNA sample compare to Otzi?
What does this mean?
10. What is the average number of differences between Neandertals and modern humans?
11. Using the mutation rate calculated in #7 above, when did humans and Neandertal share a
common mt ancestor?
12. What does this tell us about the relationship between Neandertals and modern humans?
13. How many differences did you have when compared to a chimp sample?
14. Using the calculated mutation rate from above, when did humans and chimps share a common
mt ancestor?
15. If we were to compare two different Africans samples to a European or an Asian sample, would
you expect…
a. The two African samples to have greater similarity (homology ) to each other than they
do to the European sample
b. The European sample will have greater homology to one of the African samples than the
two African samples have with each other.
16. Test your hypothesis from # 10 above. What did you discover?
17. Explain how DNA is sequenced. Review the tutorial at
http://www.geneticorigins.org/mito/mitoframeset.htm
What does this mean?