FALL SEMESTER 2001
This syllabus contains lots of information. Please
read it carefully and refer to it during the semester.
|About Dr. White||Teaching Philosophy||Selecting Topics and Seminar Dates|
|Time and Place||Groups and Group Function||Oral Presentation|
|Prerequisites||Case Study Problem Assignments||Final Interview|
|Recommended Texts||Writing a Case Study PBL Problem||"Appa"|
|General Comments and Grading|
Harold B. White
Office: 123 Brown Lab
Phone: 831-2908 (w), 737-7988 (h)
Office Hours: Normally, the hour after class will be available for office hours; however, you should feel free to contact me by phone or e-mail or to stop by my office at other times. If I do not have pressing business, I will be happy to meet on the spur of the moment.
Meeting Time and Place: 8:00 - 9:15 AM, Tuesdays and Thursdays in 109 Memorial Hall. Normally, important announcements are made at the beginning of class. Similarly, homework is due at the beginning of class. The tentative course schedule is available on line.
Prerequisite: CHEM-527 or CHEM-642, or equivalent
Text: There is no required text; however, any general text such as that by Voet and Voet; Lehninger; Zubay; Stryer; or Abeles, Frey, and Jencks will be helpful. Garrett & Grisham, Saunders College Publishing, the text for CHEM-641 & 642, can be used as a reference book in CHEM-643. The money you save by not buying a text can be used to photocopy articles that create personal resource files on case study problems and your case study topic.
General Comments and Grading: Because CHEM-643 is a graduate-level course with a small enrollment, personal initiative in the form of outside reading and class participation is expected. A fundamental general background in biochemistry at the level of CHEM-642 is assumed. Classes will be structured around interactive lectures, class and group discussion of problems, and student presentations. There will be no formal examinations per se. Evaluation of each student's performance will be based on homework assignments (40%), writing a case study problem (25%), presenting your case study (15%), and a follow up interview based on your presentation topic (10%). "Appa" (attendance, preparation, participation, and attitude) constitute the remaining 10%.
Intermediary metabolism is such a vast subject within biochemistry that there is only enough time in a general course to present a few fundamental pathways, and few students get a "feel" for the subject. Even in a full semester course like CHEM-643, many interesting and important topics go unmentioned. The first two months of this course (see schedule) will deal mostly with general principles and with pathways discussed in general textbooks but not covered in depth in CHEM-641/642. Classes from mid-November into December will be devoted to student presentations on pathways that may be presented in general textbooks but are not usually covered in prerequisite courses.
Teaching Philosophy: Courses in intermediary metabolism share with organic chemistry the reputation for presenting enormous amounts of tedious information that has to be regurgitated on impossible examinations. This course is not about memorization of structures and obscure pathways. You will have a lifetime to do that, if you want. This course is about understanding, thinking, pursuing knowledge, identifying resources, and communicating. It is about making metabolism understandable, hopefully interesting, and possibly exciting enough that you will want to continue learning about it for the rest of your life.
People learn best and almost effortlessly when they want to know something. Why else is it that many students (and some faculty) can recite for hours the details of soap operas, the personal lives of celebrities, or baseball statistics without expecting to be examined on the information? Intermediary metabolism will never have a comparable appeal; however, learning about it will come easier when there is a need to know, a focus for your learning. This is the essence of the problem-based approach to learning. Rather than lecture, I will conduct interactive discussions, ask questions, and have you work in groups during class time on case study problems. Hopefully you will find these problems interesting and they will stimulate you to ask questions - learning issues - in your pursuit of knowledge about intermediary metabolism.
Groups and Group Function:
Each student will be assigned to a group of about 4 students. These groups will function independently during class and outside of class for the whole semester. The collective resources and efforts of the group will be used to deal with the case-study assignments. For example, several learning issues may be identified in group discussion during class and group members will be assigned or volunteer to investigate particular issues and report back to the group. The goal is to have everyone learn more than they would have working alone. Nevertheless, individual work (often 8 - 12 hours/week) provide the foundation for productive and synergistic group work.
In order to promote effective group function, each group will discuss and agree upon a list of ground rules at the beginning of the semester. All students will evaluate themselves and their fellow group members with respect to contributions to group function at least twice during the semester. This evaluation will contribute to the "appa" (attendance, participation, preparation, and attitude) portion of the course grade and will be used primarily in deciding borderline grades.
Problem and Case Studies (40%):
There will be about five case study problems during the first part of the course. All are based on information gleaned from the biochemical literature. The purpose of these exercises is to promote understanding of metabolism by thinking about and analyzing real metabolic problems. The case studies will be introduced on Tuesdays starting September 4 and assignments based on the case study problems normally will be due at the beginning of class two weeks later. Classes from September into early November will be devoted to the analysis and discussion of these problems in group of 3 or 4 students. In the past, students reported that it took 5 to 10 or more hours per week to complete these case study problems. Because my objective is your understanding, I encourage you to use the library, the Internet, and discuss these problems with other students in and outside of class. Consider diverse resources including faculty here and elsewhere (via e-mail) after you have spent some time analyzing the problems on your own. Working with other students does not include plagiarizing their answers. Write up your own answers in your own words. I look for well-thought-out answers that are clearly and neatly presented. I also appreciate acknowledgment of the resources you use (books, articles, web sites, and people).
Writing a Case Study PBL Problem (25%):
This course is built around case study problems. This assignment asks you to research a significant topic in intermediary metabolism and write a problem based on your study. It should have an informative title, reflect substantive independent study, and present a thoughtful synthesis of the primary and secondary literature. A case study problem provides a pedagogical context for presenting and learning information. Because it requires a different presentation format, it necessitates an original synthesis. Creating an original synthesis presents formidable challenges for most students.
What is an original synthesis? Original syntheses often play with ideas, provide an overview of the subject, critique and evaluate research results, and generally display personal input. In other words, the voice of the author is evident throughout. Case studies can take many forms but good ones have intrinsic general interest, tell a story, and often involve a current controversy or dilemma that requires a decision based on incomplete information. Pedagogically, they should involve higher order thinking skills (analysis, evaluation, and judgement), stimulate group discussion, and require collaborative effort. Perhaps the best way to construct a case study problem is to consider what you have learned about your topic, decide what are the most important and interesting concepts to know, and then think about ways you could get your peers to discover, experience, and learn that information without being told. Creative approaches may include chemical demonstrations, illustrative objects, or in class activities as part of the presentation.
A case study should be well-organized, clearly written, and about five stages long (~1 page each) with a case summary ("teaching notes") of about 5 pages that provides and explains the kind of response expected including references. Relevant compounds, pathways, and mechanisms need to be illustrated. References should be cited in the format of Biochemistry or the Journal of Biological Chemistry. Your case study problem will be due on the day of your presentation to the class. You are responsible for having it typed, duplicated, and distributed to all the students in the class on or before the day of your seminar. It is important that this timing be observed. Late papers will preclude an "A" in the course!
You should select a topic from those listed on the next page and hand it in on the "Request for Case Study Topic" form by Tuesday, September 11. Other topics are acceptable but must be approved by the instructor. Remember, CHEM-643 is a chemistry course so do not neglect the chemistry. A check list of things I consider in grading case study problems may help in organizing and writing your paper.
Familiarize yourself with the meaning of plagiarism and the University's policies on academic dishonesty. Your Case study problem should be your synthesis. Don't rely heavily on one or two secondary sources. Read the original sources.
Selection of Case Study/Seminar Topics and Presentation Dates:
Case-study topics and presentation dates must be selected
and approved by me by Tuesday, September 11. While you may want to
schedule your presentation for as late as possible, consider that an early
presentation will give you more time to spend on other courses at the end
of the semester and will give you priority on topics. Your case study problem
and its class presentation are essentially your final examination. Because
you will become an expert on your topic by the end of the semester and
because a considerable part of your grade will be related to how well you
develop your topic, pick something of interest to you. Some subjects
you might consider are listed below; however, please feel free to request
other topics. A good places to start your search are the Web
of Science or Medline via PubMed,
a search engine provided by NIH. The links to article abstracts in the
table below were obtain easily in one afternoon using Medline.
|Vitamins & Coenzymes||Antibiotics
|folic acid||gramicidin||Other Pathways||BioPolymers|
|Vitamin B12||cyclosporin||phospholipid anchors||chondroitin sulfate|
|NAD(P)||cyanogenic glycosides||N or S assimilation||peptidoglycans|
|Vitamin K||hypoglycin||selenium metabolism||Asn-linked oligosaccharides|
Case Study Presentation (15%):
Student presentations will be limited to half a class period, i.e. ~40 minutes including class discussion, and will be presented during November and December. The class format will be different form a seminar and may involve demonstrations, leading the class in discussion, or long periods of observation and supervision. In order to emphasize the tremendous value of effective communication, part of the grade for the presentation (and the term paper) will be based on effective communication. There is no way you can present your whole case study so you need to decide what parts to show case for the class. You may discuss your topic and its presentation with me at any time. You are encouraged to rehearse your presentation with a friend so that you know how long it will be and so that the presentation of difficult points can be polished. Suggested reading: "The Art of Talking about Science," Science 154, 1613-1616 (1966) by Sir Lawrence Bragg.
Each of your classmates will fill out a questionnaire about your presentation. These will be handed to me after your presentation and given to you during the following week when we meet to discuss your case study and your class presentation. The philosophy of these evaluations and a sample questionnaire are available.
Each student must schedule a one-hour meeting with me to be held during the week following his or her seminar presentation. At that meeting, your case study problem will be returned and we will discuss issues related to your topic and your presentation. You will be expected to be able to discuss your topic in chemical terms and know the structures of common metabolites such as amino acids, TCA and glycolytic intermediates, common fatty acids and sugars, and common cofactors and how they work.
Each person has distinctive knowledge, experiences, learning styles, and communication skills. The person who knows the most may not be the person who explains things best. Success in life often depends on the ability to work together and tap the different strengths of coworkers. In order to contribute to the learning of your classmates and to learn from them, you need to attend class regularly and be on time, arrive prepared, participate in discussions, and generally have a constructive attitude. To encourage these traits, 10% of your grade will depend on them.
While your grade will be based on your performance, there
is no grading curve in this course. If everyone does "A" work, everyone
will get an "A." It is in your best interest to help your classmates; however,
do it as a teacher. If you know something, don't just give the information.
Explain it. Practice effective communication. If you don't know something,
seek understanding rather than "the answer." Develop the skill to recognize
and define what you don't know and learn not to be satisfied with superficial