CHEMISTRY 370.  BIOCHEMISTRY
BAKER UNIVERSITY   Spring 2013
MWF  1:30 PM

Instructor:   M. Barbush
Office:  Mulvane 301  Phone:  594-8310
e-mail:  michael.barbush@bakeru.edu
Web Address:  http://www.bakeru.edu/faculty/barbush/
Office Hours: MW  2:30-4:00 PM; T 1:30-3:30 PM
               Many other times by appointment


TEXT:     Tymoczko, J. L.; Berg, J. M.; Stryer, L. Biochemistry A Short
          Course, W. H. Freeman and Company:  New York, 2010.

          A calculator with log(x) and 10x functions will be needed.

COURSE DESCRIPTION:  An introduction to the chemistry of biological compounds,
including proteins, nucleic acids, lipids, and carbohydrates

REQUIREMENTS:  Class attendance and participation are expected and will be
reflected in test and quiz grades.  There will be NO make-up quizzes.  Test
and quiz material will be drawn from class notes and assignments, including
textbook problems.

HOMEWORK:  The instructor will provide a list of minimum assignments.  As
assignments my be collected in lieu of quizzes, homework is to accompany its
author to class.

PRESENTATIONS: 

An informal, five-minute presentation will be given on a protein topic,
approved by the instructor, selected from specified chapters or current
events.  The presentation shall include both exposition relating structure and
function and computer graphics, using data obtained via the Internet from the
Protein Data Bank (www.rcsb.org).

A formal seminar will be given during the last weeks of class on a current
literature topic of your choice that is approved by the instructor.  It is
advisable to start looking through Biochemistry, Science, Nature, Scientific
American, and other locally available journals early to begin getting ideas. 
The topic with three references is due on April 19.  This may be revised as
necessary, based on consultation with the instructor.  Copies of a detailed
outline with bibliography (2 pages total), suitable for distribution to the
class, are due immediately prior to the presentation.  The seminar should be
clearly presented and well-organized and demonstrate a good understanding of
the subject chosen.  The presentation should last twelve to fifteen minutes,
with an additional five minutes for questions.
 
GRADING:  The course grade will be determined by three tests (300 points),
twenty quizzes (200 points), the protein presentation (20 points), the formal
seminar (100 points), a comprehensive final examination (200 points), and
class participation (5 points).  There will be at least twenty-three quizzes,
with the scores for the best twenty counted in the final grade.  That is,
there will be a quiz almost every day.


CH370.  TENTATIVE LECTURE AND EXAM SCHEDULE.  SPRING 2013.

Unless otherwise indicated, assignments from the chapters listed will be
announced in class.

Dates               Material

1/23 - 2/15    Ch. 1  Biochemistry and the Unity of Life
               Ch. 2  Water, Weak Bonds, and the Generation of Order...
               Ch. 3  Amino Acids
               Ch. 4  Protein Three Dimensional Structure
               Ch. 5  Basic Concepts of Enzyme Action
               Ch. 6  Kinetics and Regulation
               Ch. 7  Mechanisms and Inhibitors
               Ch. 8  Hemoglobin, an Allosteric Protein
               Protein Reports
               Ch. 9  Carbohydrates               

Mon. 2/18      TEST ONE

2/21 - 3/22    Ch. 10  Lipids
               Ch. 11  Membrane Structure and Function (parts)
               Ch. 13  Digestion:  Turning a Meal into ... Biochemicals
               Ch. 14  Metabolism:  Basic Concepts and Design
               Ch. 15  Glycolysis
               Ch. 16  Gluconeogenesis
               Ch. 17  Citric Acid Cycle -- preparation
               Ch. 18  Citric Acid Cycle -- harvesting electrons
               Ch. 19  Electron Transport Chain
               Ch. 20  Oxidative Phosphorylation -- proton-motive force

Mon. 3/25      TEST TWO

3/27 - 4/22    Ch. 23  Glycogen Degradation  
               Ch. 24  Glycogen Synthesis
               Ch. 25  Pentose Phosphate Pathway
               Ch. 26  Fatty Acid Degradation
               Ch. 27  Fatty Acid Synthesis
               Ch. 32  Structure of DNA and RNA
               Ch. 33  DNA Replication
               Ch. 38  Genetic Code
               Ch. 39  Protein Synthesis

Wed. 4/24      TEST THREE

4/26 - 5/6     Student Seminars
               Review for Final

Mon. 5/13      COMPREHENSIVE FINAL EXAMINATION  8:30 AM