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INTERMEDIARY METABOLISM SYLLABUS FALL SEMESTER 2007 |
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INTERMEDIARY METABOLISM SYLLABUS FALL SEMESTER 2007 |
This syllabus contains lots of information.
Please read it carefully and refer to it during the semester.
Instructor: Prof. Harold B. White
Office:
203
Brown Lab
Phone: 831-2908 (w), 737-7988 (h)
E-mail:
halwhite
at udel.edu
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: 9:05 - 9:55 AM, Monday, Wednesday, and Friday in 110 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; or Stryer will be helpful. Garrett & Grisham, Saunders College Publishing, the text for CHEM-641 & 642, can be used as a reference book in CHEM-643. A variety of textbooks will be available in the classroom for borrowing. 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 relatvely 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-527or 641 is assumed. Classes will be structured around interactive lectures (first half) and class and group discussion of problems (second half). Evaluation of each student's performance will be based on homework assignments (45%), midterm examination (15%), writing a case study problem (15%), and a follow up final exam (20%) based on your presentation topic during the final examination week. "Appa" (attendance, preparation, participation, and attitude) constitute the remaining 5%.
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 half of this course (see tentative 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 late October into December will be devoted to group work on Case Study/PBL (Problem-Based Learning) Problems.
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 prime time TV shows, the personal lives of celebrities, or football 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, and a social component. This is the essence of the problem-based approach to learning. Thus, in addition to interactive lectures, I will ask questions to encourage interactive classroom discussions, assign homework problems where collaboration is acceptable, and have you work in groups during class time on case study/PBL problems. Hopefully you will find these problems interesting and stimulate you to ask questions - learning issues - in your pursuit of knowledge about intermediary metabolism.
Early in the semester, each student will be assigned to a group of 4 or 5 students. These groups will function independently during class and outside of class. The collective resources and efforts of the group will be used to deal with the case-study/PBL 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 outside of class) provide the foundation for productive and synergistic group work. If you have questions or reservations about working in groups, please discuss them.
In order to promote effective group function, each group needs to discuss and agree upon a list of ground rules. All students will evaluate themselves and their fellow group members with respect to contributions to group function at the end of 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.
Problems and Case Studies (30%):
Tell me, and I will forget.
Show me, and I may remember.
Involve me, and I will understand."
This perceptive Chinese proverb, recognizes the limited effectiveness of lectures. Involvement is the key to learning. The process is as important as "the answer." While reading and studying help learning, solving problems focuses learning on knowledge gaps and requires one to review and integrate knowledge. I wish to promote this conceptual understanding through involvement. Thus, I assign homework problems. These often challenging problems, posted on the course web-site, are intended to stimulate understanding by thinking about and analyzing material from the research literature. They may require 5 to 10 hours or more per week to complete. There will be seven homework problem sets during the first part of the course. They are due at the beginning of class on successive Wednesdays. Homework assignments will not be accepted after the day they are due without explanation. 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. You may consider diverse resources including faculty here and elsewhere (via e-mail) after you have spent some time analyzing the problems on your own.
While only individuals learn, interactions with others can enhance the learning process. Thus, students may work together on solving these problems. I encourage such interactions and do not consider it cheating. However, "working together" here does not imply a divide-and-conquer approach in which students pool their individual work, but do not discuss it. Plagiarism or paraphrasing the work of others does not demonstrate understanding. Write-up your answers in your own words on your own to show what you understand. I look for well-thought-out answers that are clearly and neatly presented. I also expect your acknowledgment of the resources you use (books, articles, web sites, and people), i.e., if you work with others, please list their names at the top of your assignments. If you are uncertain about what constitutes plagiarism or how the university deals with cases of academic dishonesty such as plagiarism, check out the student handbook web-site devoted to these issues.
The Case Study/PBL problems assigned in the second
half of the course are more open-ended and complex. Assignments related
to the 2 or 3 of the 4 case study/PBL problems will be due about two
weeks after each problem is introduced. Both the homework problems and
the case study/PBL problems are based on information gleaned from the
biochemical literature. As with the homework problems in the first half
of the course, the purpose of these exercises is to promote
understanding of metabolism by thinking about and analyzing real
metabolic problems.
Midterm
and Final Examination (20% + 25%):
In the past there have been no formal examinations in this course.
However, as the enrollment has grown and the course has becomes phased
in as a required course in the undergraduate biochemistry curriculum,
it has become more difficult for me to assess each student solely on
class
assignments and a final interview. Therefore, there will be
midterm
and final examinations based on conceptual understanding and
interpretation
of data. Last year's Midterm
and Final
Examinations linked here.
Writing a Case Study/PBL Problem (20%):
This course is built in part around Case Study/PBL 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 could include chemical demonstrations, illustrative objects, or in class activities.
A case study should be well-organized, clearly written, and about three or four stages long (~1 page each) with a case summary ("teaching notes") of 5 to 10 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 at the beginning of class Friday, November 30. Late papers will be assigned lower grades and may preclude an "A" in the course!
You may select a topic from those listed on the next page and hand it in on the "Request for Case Study Topic" form by Friday, September 21. 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 and my rubrics for an A performance may help in organizing and writing your paper. See a rubric used for evaluating PBL problems as well.
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 and reference the original sources in your
teaching notes.
Selection of Case Study Topics:
Case-study topics must be selected and
approved by
me by Friday, September 21. 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 that interests 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. Topics which have been
approved as of 5:30 p.m. 24 September are highlighted in red
with the student's initials
following. Several topics have been developed exceptionally well by
students in past years. Those topics are listed as "retired" below,
because the case studies are available for examination or topics used
in class.
| Vitamins & Coenzymes |
Antibiotics & Toxins |
Pigments |
Hormones |
| biotin |
cardiac
glycosides (retired) |
carotinoids | gibberellins |
| ascorbic acid |
actinomycin LR |
anthocyanins | ethylene NB |
| Coenzyme A | cholchicine | indigo | prostaglandins EL
|
| biopterin | erythromycin
(retired) |
heme | steroid
hormones SSu |
| molybdopterin GR |
hypoglycin
(retired) |
chlorophyll |
serotonin AT |
| folic
acid (retired) |
gramicidin RT |
flavinoids |
thyroxine AA |
| riboflavin |
capsaicin ME |
Other Pathways | epinephrine SD, KB |
| pyridoxol
|
caffeine
MGi |
phospholipid anchors | BioPolymers |
| thiamin
|
penicillin MGr |
methanogenesis | cellulose
|
| Vitamin
B12 JH |
cyclosporin JW |
terpenes | chitin
|
| NAD(P) | cyanogenic glycosides JN |
carnitine SP |
chondroitin sulfate |
| Vitamin
K SSh |
Amino
Acids |
sphingolipids KC |
peptidoglycans |
| Vitamin A SH |
aromatic amino acids |
iron metabolism SL |
Asn-linked oligosaccharides |
| Histamines RH |
histidine |
sulfur metabolism | melanin CS |
| Quinine
(retired) |
aliphatic
amino acids |
selenium metabolism | triglycerides
|
| creatine
(retired) |
sulfur-containing amino acids PK |
copper
metabolism |
Cytochrome
P450 (retired) |
| Rifampicin LZ |
arginine
metabolism |
omega-3
fatty acids DK |
|
| purine biosynthesis
JC |
diabetes KK |
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, 5% 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 answers.