MICRB 413/411 (S04)

MICRB 413/411 Mid-Term Exam (20% final grade out of 100 pts.)

Good news: This is a take home and open “book” exam. The points and questions answer type and expectations are given for each question. Type your answers if your hand writing is sloppy (be honest).

Warning: You are expected to work independently, unless a question indicates otherwise. Any evidence of answer sharing will result in the grade being divided by the number of students involved (e.g. 8/10 on a question shared by two will give each student 4/10). Please, resist the temptation to share information, as it will create a very embarrassing situation. Write in your own words!

1. (20 pts; write an essay that cites the Woese handout in addition to other resources; use illustrations; define keywords.)

Why is the 16SrRNA gene (16SrDNA) most commonly used as a “molecular chronometer” in phylogenetic studies? Start with Carl Woese’s perspective on some of the historical limitations to the taxonomy and phylogeny of prokaryotes. Include why many genes won’t be good choices as molecular chronometers. End by explaining how the process of determining the phylogeny of a bacterium works. Explain step-by-step from an unknown bacterium in pure culture to a completed phylogenetic tree comparing the unknown to other related and distant bacteria.

2. (10 pts; choose one method)

For either TRFLP or DGGE, define the acronym and describe the method’s general application(s). Then describe the general steps you would take to apply your chosen technique to study the diversity of microbes in a soil sample. Don’t go into too much detail, but rather focus more on what is accomplished at each step. Use diagrams, such as one to illustrate the final result and what it means.

3. (20 pts)

Thoroughly define the following terms in no more than three clear sentences. Give an example of prokaryote taxa that matches or exemplifies the term and the habitat in which it can be found.

Chemolithoautotroph Fermentation

Photoheterotroph Sulfate Reduction

Methanogenesis Hyperthermophile

Anoxygenic Photosynthesis Acidophilic Iron Oxidizing Archaea (IOA)

Anaerobic Respiration Green Sulfur Bacteria

4. (10 pts; short essay or detailed point-form)

Describe biochemical (physiological or structural) features of a photoautotrophic archaea that are different from a photoautotrophic bacterium. Make sure the differences are well defined.

5. (10 pts; effectively repeat the assignment due February 16th, 2004)

Define your proposal topic and give a list of eight critical references. Give a brief description of how information in each article will be used in your proposal.

6. (10 pts; 2pts each for five papers you did not present)

For each paper, tell me about two specific aspects of microbiology presented in the paper that interested you. This could be a new subject area, method used, or means of presenting the data.
7. (20 pt; clearly label the diagram)

What is a hypereutrophic lake and why do we see the profiles given in the diagram below? Include which organisms are responsible for the given parameter’s profile; don’t ignore the role of consumption in addition to production of a given compound.