MICROBIOLOGY 401
MICROBIAL PHYSIOLOGY AND
STRUCTURE
FALL SEMESTER, 2007
102 Chemistry Building
INSTRUCTOR: Dr. Don Bryant OFFICE HOURS BY
S-235 Frear Building APPOINTMENT ONLY
Telephone: 865-1992
e-mail: dab14@psu.edu
TEXT: The Physiology and Biochemistry of Prokaryotes. David White. Oxford University Press, New York, 2007. (3rd edition).
ON RESERVE: Physiology of the Bacterial Cell. F. C. Neidhardt, J. L. Ingraham & M. Schaechter. Sinauer Associates, Inc., Sunderland, MA, 1990
The Physiology and Biochemistry of Prokaryotes. David White. Oxford University Press, New York, 2007. (3rd edition).
RECOMMENDED: Biology of Microorganisms.
Michael T. Madigan, John M. Martinko, and Jack Parker. Prentice Hall, New York,
2002 (Any recent edition).
CLASS NOTES: Class notes and other materials for this course are available on the World Wide Web. To access these materials, open a link using your Web browser (e.g., Netscape) to: http://www.bmb.psu.edu/courses/micro401/default.htm You may find it convenient to establish a bookmark for this link. Materials may be added to the site at any time, but I will attempt to have materials available to you prior to lectures. Please note: these materials are supplemental and will not serve as a substitute for attending lectures. A critical element that is missing in the notes is emphasis, and there is much too much material to sift through if you don't have some idea of what is most important. There will also be quite a significant number of handout materials throughout the semester.
The primary textbook is the best available in this area that is presently in print, and this textbook is not as expensive as many. I have used it extensively as a background resource in recent years but do not intend to cover the material in the order presented there. However, I prefer the philosophical approach to the subject taken by Neidhardt et al., which is on reserve. Unfortunately, this textbook is no longer available nor has it been updated.
ADDITIONAL GENERAL REFERENCES
1. Annual Review of Microbiology and Microbiology and Molecular Biology Reviews
2. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. American Society for Microbiology, Washington, D. C. 1996
3. Methods of General and Molecular Bacteriology. P. Gerhardt, American Society for Microbiology, Washington, D. C. 1993.
4. Bacillus subtilis and Its Closest Relatives. A. L. Sonenshein, J. A. Hoch, and R. Losick. American Society for Microbiology, Washington, D. C. 2002.
5. Microbial Physiology, 3rd Edition. Albert G. Moat and J. W. Foster. Wiley-Liss, New York, 1995.
6. Biology of the Prokaryotes, J. Lengeler, G. Drews, and H. Schlegel. Blackwell Science Publishers, Blackwell Science Ltd., 1998.
7. Journal of Bacteriology, Molecular Microbiology, Microbiology, and other specialty journals
EVENING EXAMS
Examinations will NOT be multiple-choice and will consist of a variety of essay and short-answer questions (e.g., List the major components of an E. coli cell). No sample examinations will be provided. You WILL have to explain things to me in sufficient detail that I can see that you understand major concepts. You may be asked to draw general diagrams, cellular structures, etc. but you will NOT be asked to draw chemical structures (e.g., draw the structure of tryptophan) or identify a chemical structure. Likewise, you will not be asked to regurgitate all steps in the glycolytic pathway or the TCA cycle or the enzymes involved. I will sometimes specifically tell you things that you WILL have to know. If you are in lecture, you will hear this. If you are notÑitÕs not my fault.
The first two examinations will
be given in the evening, and the 3rd examination will be given in the period
scheduled by the University as the final exam. Conflict exams will be given the
same day as the evening exam by pre-determined appointment (usually the
conflict exam will be at 4:00-4:30 on the same day of the evening exam). Only
in extraordinary circumstances will make-up exams be given, although
accommodation for course scheduling conflicts in the evenings will be made.
Exams that are missed will be scored as a zero and considered the ÒdropÓ score.
In those cases for which make-up examinations are given, the exam will be an
oral examination.
Exam 1 October
04, 2007 6:30
to 7:45 P. M. 073
Willard Building
Exam 2 November
06, 2007 6:30
to 7:45 P. M. 073
Willard Building
Exam 3 As
scheduled by the University in Final Exam Period.
TERM PAPER
A paper (minimum length for text, 10 pages, double spaced, 1-inch margins; maximum length for text, 15 pages) is required and will count for approximately 33% of your final grade (and may NOT be dropped; see below). The paper should be formatted to have margins of one inch on the top, bottom and sides, and should be printed in 12-point font (Times or Times New Roman). Headings should be printed in bold font, and a title page should be included (not included as part of the 10-pages for text required!). I must approve the subject of the paper by e-mail no later than October 10, 2007; the subject and a very brief outline of the paper should be provided and approved by e-mail. Examples of some suitable topics are provided below, and the paper may be focused on a particular aspect of one of these subjects. The effect of bacterial products on eucaryotic cells/plants/animals is NOT a suitable subject. Figures and tables may be used and are encouraged, but these are not to be included in the body of the paper and will not count against the page limits. The paper must cite at least 10 references; 8 of these must be primary research articles (for example an article taken from the Journal of Bacteriology) while the remaining 2 references may be reviews, books, book chapters, or other reference materials). Textbooks are NOT suitable as references. Citations in the paper MUST follow the form used by the Journal of Bacteriology (see journal for style). The references should be listed alphabetically and then numbered per ASM/Journal of Bacteriology style; cite the references in the text by number. Failure to follow these very simple instructions will reduce the total possible points for the paper. All references should be listed at the end of the paper, and the references will not count as part of the 10-page minimum page limit for the paper. Papers may be submitted to me for grading at any time until 5:00 P. M. on Monday, November 16, 2005. You will submit an electronic file by e-mail as well as a hardcopy for evaluation and comments. For each 24-h period (or part thereof) that the paper is late, the maximum possible score will be reduced by 10%.
Suitable examples of topics for paper:
1. flagellar structure/assembly
2. chemotaxis
3. bacterial photosynthesis
4. electron transport chains/complexes
5. protein secretion mechanisms
6. nitrogen fixation
7. methanogenesis
8. specific aspects of gene regulation
9. cell division
10. quorum sensing
11. signal transduction
Example of a topic that is NOT suitable for term paper:
1. Mechanism of action of diptheria toxin
Example of a topic that is suitable for term paper:
1. Iron regulation of diptheria toxin expression.
GRADING
Your final letter grade will be determined by your performance on two mid-term examinations, the final examination, and the term paper (see above). Each examination will be worth approximately about 120 points, and the term paper will be worth 100 points. You may drop your lowest exam score, and thus the total points available for the course will be approximately 300-340 points. You may NOT take the three exams and drop the term paper--i. e., the paper is mandatory. Attendance is not formally considered, but attendance and class participation can be used at the discretion of the instructor to adjust scores at grade borders. The anticipated grade point average for the class will be approximately 2.7 to 3.0 based upon past experience.
POLICY ON ACADEMIC INTEGRITY
All Penn State policies regarding ethics and honorable behavior apply to this course (see links below for policy statements). Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this institution. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students. For any material or ideas obtained from other sources, such as text or things you find on the web, in the library, etc., a source/reference must be given. Plagiarism is one of the most serious forms of cheating/academic dishonesty! Direct quotes from any source must be identified as such. Plagiarism on the term paper led to failing grades for 2 students in 2003. Each student in this course is expected to work entirely on her/his own while taking any exam, to complete assignments on her/his own effort without the assistance of others unless directed otherwise by the instructor, and to abide by University and Eberly College of Science policies about academic integrity and academic dishonesty. Academic dishonesty can result in assignment of "F" by the course instructors or "XF" by Judicial Affairs as the final grade for the student.
Any instances of academic dishonesty WILL be pursued under the University and Eberly College of Science regulations concerning academic integrity. Refer to the following URL for further details on the
academic integrity policies of the Eberly College of Science: http://www.science.psu.edu/academic/Integrity/Index.html
COURSE CONTENT
Some of the writings, lectures,
or presentations in this course might include material that some students could
find offensive or that they do not personally believe to be trueÑwhich is fine.
However, because the course content fulfills legitimate pedagogical goals, the
instructor does not grant content accommodation requests.
MICROBIOLOGY 401 FALL
SEMESTER 2007 102 Chemistry Building: 9:00-9:55 AM
Approximate order of topics
and relevant chapters in textbook; changes from year to year
1. August 27 Chapter 1, Web notes
2. August 29
3. August 31
September
3 Labor
Day HolidayÑNO CLASS
4. September 5 Chapter 10
5. September 7
6. September 10
7. September 12
September 14 NO CLASSÑLibrary Day for term paper topic
8. September 17 Chapters 11 and 17
9. September 19
10. September 21
11. September 24
12. September 26
13. September 28
14. October 1
15. October 3 Chapters 7 and 12
16. October 4 First Evening Exam 6:30-7:45 PM 073 Willard Bldg.
17. October 5
18. October 8 Chapter 8
19. October 10 Term Paper Topics Must Be Approved by This Date!!
20. October 12
21. October 15
22. October 17 Chapter 3
23. October 19
24. October 22
25. October 24 Chapter 4
26. October 26
27. October 29
28. October 31
November 2 NO CLASS Chapter 5 and 13
29. November
5
30. November 6 Second Evening Exam 6:30-7:45 PM 073 Willard Bldg.
31. November 7
32. November 9
33. November 12 Chapter 14
34. November
14
35. November
16 (Late
Drop Deadline) TERM PAPERS DUE AT 5:00 P. M.
November
19-23 Thanksgiving
HolidayÑNO CLASS
36. November 26 Chapter 16
37. November 28
38. November 30 Chapter 2
39. December 3 Chapter 15
40. December 5
41. December 7
42. December 10 Chapter 6
43. December 12
44. December 14 (Last Day of Classes)
45. December
17-December 21, 2007 Exam
3 (Scheduled as Final Exam by the University)