Medical Biochemistry

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Tentative Schedule Spring 2009

Instructor:   James Zimmerman
Office:   Keyes 314
Phone:   (207) 859-5762
Campus e-mail:   jkzimmer@colby.edu
Office Hours:   open, or by appointment
Course website: http://www.colby.edu/chemistry/BC362-2009_files/BC362-2009.htm
Additional website: http://www.clemson.edu/~jkzmm
Required Text: "Biochemistry: The Molecular Basis of Life" 4th edn.  McKee and McKee, Oxford Press, 2009.
Location:  Tue/Thur, 9:30--10:45  Olin Science Center 001 and Friday 12:00 -- 12:50 Lovejoy 205

Course Goals: This is an intensive course, covering many aspects of biochemistry, including:  biomolecules, enzymology, and metabolism. This course is designed for students who are more likely to go on to health professional school (M.D., D.O., D.D.S., D.V.M., N.P., etc.) than to a biochemistry Ph.D. program. Therefore, we won’t focus as much on the experimental nature of biochemistry. However, we cannot cede the chemical nature of the discipline. It is also important to recognize that biochemistry is essential to the study and practice of medicine – and this course will be valuable preparation for entrance exams and for advanced coursework in health professional school.

Lecture Topics (Tue/Thu, 9:30 - 10:45, Olin 001):

Tentative Schedule of Lectures

Water and pH                                                                   Chapter 3
Chemical Equilibria and Thermodynamics                           Chapter 4
Amino Acids, Peptides and Proteins                                    Chapter 5
Enzymes                                                                           Chapter 6
Carbohydrates                                                                   Chapter 7
Lipids                                                                               Chapter 11
Membranes and Transport                                                  Chapter 11
Overview of Metabolism                                                       
Glycolysis/Gluconeogenesis                                                Chapter 8
Pentose Phosphate Pathway                                               Chapter 9
Citric Acid Cycle                                                               Chapter 9
Lipid Metabolism--Ketone Bodies                                       Chapter 12
Protein Catabolism and the Urea Cycle                                Chapter 15
Oxidative Phosphorylation/Electron Transport                      Chapter 10


Discussion sessions (Fri, 12:00 - 12:50, Lovejoy 205)

During discussion sessions we will delve a bit deeper into medical biochemistry topics. We might discuss clinical case studies, current relevant biomedical issues, or practical applications of lecture material. We will occasionally share these discussions with local health professionals. There may be reading assignments or other preparation assigned specifically for discussion sessions. You are required to attend and participate in all discussion sessions.

There will be six, one page, papers concerning some aspect of biochemistry that you have read in a lay publication (newspapers, magazines, etc.)  in the last three months.  You must include the relevant points of the article and discuss its importance.  A copy of the article must be included.  These papers will constitute 5% of the final grade.

There will also be two longer papers to be done as a group project.  One will involve an enzyme of your choice and the other will be on the metabolic aspects of a diet plan of your choice.  The groups will be assigned using a random number generator.  These papers will be double spaced in 12  point type and will contain properly cited references.  The group will give an oral presentation in one of the Friday discussion sessions.  Each member of the group will receive the same grade for the project.  Also each member of the group will evaluate the contributions of the other members of the group using a zero sum method. 

There will be two hour exams tentatively set for March 19 and May 5.  Exam questions will come from all reading assignments and lecture material, but not from material discussed only during discussion sessions.  There will be no make-up exams. In the event of an excused absence, you will be given a grade commensurate with your performance relative to the class on the subsequent exam. (each exam = 17.5% of final grade)

The final exam will be given at a time and place to be assigned by the registrar. The final exam will be comprehensive (30% of final grade).

Attendance and class participation will be part of your grade in the course. During class time you will be expected to have completed the assigned reading and be otherwise prepared to participate in class discussions. This portion of your grade will be assigned at the Professor’s discretion (5% of final grade).

Grading / Exams / Quizzes:


          Two exams @ 17.5%  =  35%
          Long Papers               =  20%

          Short Papers               =    5%
          Class Participation       =    5%
          Peer Evaluation           =    5%
          Final Exam                  =  30%

Final Grade – I do not give final grades based on a strict 90-100 is an A basis. Rather the grades will be determined by the distribution at the end of the semester. You will be kept up-to-date on the distribution curve after each examination. Regardless of the distribution, if a student has a 90 or better for the semester, the student will receive at least an A-. If the student has a score of more than 80, but less than 90, the minimum grade will be a B-. Likewise >=70 but <80 the minimum grade would be a C- and for scores >=60 but < 70, the minimum grade would be a D-.

Academic dishonesty will not be tolerated. Please refer to the Student Handbook as well as the Chemistry Department policy (www.colby.edu/chemistry/Attend_Exam.html).

For students who have approval from the Dean of Students Office for time extensions on exams, it is departmental policy that these students must establish with the Dean of Students and the Chair of Chemistry an appropriate time extension. This must be accomplished at least two days before the first exam.

Your final exam will be in a room and at a date to be determined by the Registrar. The format will be very similar to the hour exams, but the final will be comprehensive, though favoring metabolism. It will be a two hour exam. For metabolism, you will be more responsible for glycolysis/gluconeogenesis, citric acid cycle, electron transport, and ATP synthesis than you will be for lipid and amino acid metabolism, which will be covered with broader questions.

Metabolic Pathways

There are many good websites for metabolic maps.  A few connections are given below

MiniMaps.  Housed by the IUBMB and done by Dr. Don Nicholson

AniMaps.   Housed by the IUBMB and done by Dr. Don Nicholson.  Requires Flash.

A general overview of metabolism by Dr. Pedro Silva

Glycolytic Pathway From the University of Texas. Has information on reactions, enzymes, structures, kinetics, and a quiz.

A site from Karl J. Miller labeled the Metabolic Pathways of Biochemistry. Fantastic site. Great pathways. Has Chime structures on substrates, coenzymes, etc. Really nice.

A site from Dr. Jim Hardy who is in the chemistry department of the University of Akron

ExPASy.  Run by the Swiss Institute of Bioinformatics

A very interesting site run by Dr. Mathijs Doets at Erasmus University, Rotterdam.  It has animation of the metabolic interplay between various organs and the metabolic cycles from the newly fed state to starvation.  This is done at several different levels starting with an overall view, going to individual organs, and then to individual organelles.  Requires Shockwave.


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