Diversity of Bioenergetic Mechanisms

CH464/564; BSC474/574 (3 credit hours)
Time: T/Th 2:00-4:30
Place: 231 Shelby Hall
Instructor: Kevin Redding
(Office: 343B Shelby Hall; e-mail: Kevin.Redding@ua.edu)

Prerequisites: CH461/561 or BSC450

Topics covered:

This is a new course on diversity of bioenergetics, available to graduate and senior undergraduate students. It will also draw graduate students from biology and chemical engineering. The course would be a survey of how organisms on this planet make a living, in terms of obtaining energy, fixing carbon, etc. As most standard biochemistry courses deal with fermentation and aerobic organotrophic metabolism, this course would focus on the more ≥exotic≤ bacteria, including the following (with potential exemplary organisms noted):

∑ Oxygenic photosynthetic bacteria (Synechocystis, Anabaena)

∑ Anoxygenic phototrophs: purple sulfur bacteria (e.g. Rhodobacter), green nonsulfur bacteria (Chloroflexus), and green sulfur bacteria (Chlorobium)

∑ Fe²⁺- and sulfide-oxidizing bacteria (Acidithiobacillus, Geobacter)

∑ Sulfate-reducing bacteria (Desulfobacter, Archeoglobus)

∑ Nitrifying bacteria (Nitrosomonas, Nitrobacter)

∑ Methanotrophs & methylotrophs (Methylococcus, Methylosarcina)

∑ Methanogenic archaebacteria (Methanothermobacter, Methylosarcina)

∑ Bacteriorhodopsin-based photosynthetic archaebacteria (Halobacterium)

Goals:

1. Learn as much as possible about these topics. In the process, gain an appreciation of the huge differences in the way organisms make a living on this plant, as well as the underlying similarities between them.

2. Research a specific bacterium and make a presentation to the class on it. You will learn how to research a topic and how to give a lecture.

3. Work with these bacteria in the lab and perform both set experiments and new ones that the class will come up with as we go.

4. Write a proposal and review other studentsπ proposals, in the process learning how to write a concise research proposal.

5. By the end of the semester, the entire course (instructor + students) will co-author a research paper from the results of some of the experiments perfomed on one or more of the bacteria.

Note that there 2 over-arching goals in this course:

1. Learn about how life on this planet extracts energy from the environment.

2. Gain valuable life skills that will serve you well in your future career, whether it will be in a teaching, research, medical, administrative, or other context.

Text: There is no textbook for this topic. However, as a reference, I strongly suggest you buy Brockπs Biology of Microorganisms. This will provide you with the biological background for the organisms that we will discuss.

Attendance: This course depends heavily upon participation and interaction. Unless excused for serious illness or a family emergency, you must attend each session.

Process & grading: The class will meet twice a week for a combination of lecture and discussion on what is known about how these organisms extract energy from their environment, with some in-class experiments. While we are discussing a particular organism, we will be growing it in the lab at the same time. With the use of a fermentation chamber and gas-analysis system, we will be able to monitor any physiological activities involving release/uptake of O₂, CO₂, H₂, and CH₄. Students will prepare mini-lectures on aspects of several organisms and give several short (informal) presentations to the class throughout the semester. Assuming that there are enough students, they will be divided into teams, each of which will focus on a specific enzyme or pathway; each participant would be in 2-3 different teams. Midway in the course, each will write a short research proposal, and the class will be divided into 2 study sections. Each section will assess the proposals of the other students. Finally, experiments doable by our class will be selected from the best proposals and we will spend the last month trying to perform them. The ultimate goal will be for the entire class to co-author and submit a paper on results from experiments done during the semester. There will be no exams in this course. Students will be assessed based upon their participation in discussions, experiments, presentations, proposal, and their involvement in the paper.

Office Hours: There are no set hours. There will be plenty of time during class hours to ask questions. If more is required, please make an appointment. (And if you make one, keep it – or, at the very least, cancel in advance).

Web site: I will maintain a web site for the course (found at http://www.bama.ua.edu/~kredding). It will contain useful information for the class, including the schedule, notes, etc. Your feedback on ways to improve the site is welcome.

Academic misconduct: All acts of dishonesty in any work in this course will constitute academic misconduct. The Academic Conduct Disciplinary Policy will be followed in the event of academic misconduct.

Disability accommodation: To request disability accommodations, please contact the Office of Disability Services at 348-4285. After initial arrangements are made with that office, contact your professor.