FINAL EXAM - MB409
May 8, 2000
1. What are the 3 primary evolutionary branches of life? (5 points)
2. What are the two primary phylogenetic groups of Archaea? (5 points)
3. What are the three phenotypic groups of Archaea? (5 points)
- Extreme halophiles
- Sulfur-metabolizers (usually thermophilic)
4. What are the three general explanations for the origin of viruses ? (5 points)
- Degenerate cellular parasites
- Remnants of the RNA World
- Genetic satellites of their hosts
5. Match the following forms of sulfur metabolism with the correct equation? (5 points - write appropriate letter in space)
Questions: Answers: __B_ Sulfur respiration A. Sulfur + H2 ---> H2 S + protons __C_ Sulfur oxidation B. Sulfur + organics ---> CO2 + H2 S __A_ Sulfur reduction C. Sulfur + O2 ---> H2 SO4
6. List 5 traits of the last common ancestor(s). (5 points)
- DNA genetic material
- same set of RNAs as modern organisms
- lipoprotein envelop
- mRNA/ribosome/tRNA-mediated translation
7. For each of these traits, which are true for Archaea, Bacteria, and Eukarya? (20 points - check as many as apply)
Archaea Bacteria Eukarya linked transcription and translation ___X__ ___X__ ______ genes in operons ___X__ ___X__ ______ ether-linked membrane lipids ___X__ ______ ______ fatty-acid containing lipids ______ ___X__ ___X__ promoters bound by transcription factors ___X__ ______ ___X__ RNA polymerase II ___X__ ______ ___X__ translation initiated by formyl-Met ______ ___X__ ______
8. Corals are symbiotic organisms composed of an animal and an alga. In most cases, the algae are typical eukaryotic green algae (chlorophytes). How many different small subunit ribosomal RNA sequences could you clone from such a coral, and where would they come from? (5 points)
5 : 2 from the animal (1 nuclear, 1 mitochondrial) + 3 from the alga (nuclear, mitochondria, chloroplast)
9. Whole microbial genomes are sequencing using a 'shotgun' random sequencing approach. Why are randomly-determined sequences not enough to assemble the complete genome? (5 points)
- First, the physical gaps that result from randomly-sampling the sequence. These could mostly be filled by continued random sequencing, but would require enormous numbers of sequences of fill small gaps.
- Secondly, repeated sequences that have to be 'ordered' to link regions flanking them properly.
10. Describe the phenotype, habitat, and metabolism of any particular Archaeal species, genus, or group you find interesting. (10 points)
e.g: Pyrodictium occultum
Pyrodictium is a marine organism that is apparently common in deep sea hydrothermal vents. It is a flat coccus w/ long cytoplasmic fibriles that connect cells together. The optimal growth temperature is 105C, and cultures grow well at temperatures up to 115C, a tie with Methanopyrus for the World Record! They are also tied, with Thermococcus, for the most primative organisms known. Related species are Desulfurococcus, Staphylothermus, and Thermodiscus.
11. Going through the collection shelves in the basement of the North Carolina Natural Science museum one night, you discover the 200 year-old remains of a herring. It appears to have hemorrhagic lesions that look to you like those caused by the now-infamous Pfisteria piscicida. The fish is preserved in formaldehyde, and so you know that any infectious agent will no longer be alive - and in any case, you do not have the facilities or expertise to cultivate this dangerous organism. How would you go about determining if these fish harbored Pfisteria piscicida in their previous life? (10 points)
The first step would be to amplify parasite rRNA from tissue samples of the pickled fish. The trick will be to design primers to amplify the parasite and not from the fish. The next step would be to create a specific fluorescently-labeled oligonucleotide primer to do in situ hybridization to make sure the sequence you amplified really comes from the fish parasite, and show you exactly where the parasites are and how many there are.
12. Compare conjugative transfer of the F plasmid with the infective transfer of bacteriophage M13. How are these processes similar? How are they different? (10 points)
The F plasmid carries a series of genes that direct replication & conjugative transfer of the plasmid. The donor and recipient come into direct contact, and one strand of the plasmid is transfered via a vplasmid-encoded protein pore. M13 is very similar in that transfer is directed by a series of virus-encoded proteins, but transfer of the DNA is via a protein-encapsulated form rather than by direct contact.
13. Here is a phylogenetic tree of a set of organisms based on ssu-rRNA molecular phylogenetic analysis. There is a fossil record for these organisms, and the time scale on the left of the tree is based on data from these fossils. Draw a related tree that would result from analysis of a gene that had transferred 100Mya (million years ago) from the common ancestry of organisms A and B to the ancestor of organism D (10 points).