BiochemistryChem/Biol 272

Spring 2013
MWF 10:30-11:20


Instructor: Dr. Joseph Osmundson
Office: 214
Phone: x7419
Email: joosmundson@vassar.edu
Office hours: M/F 12-1p and by appointment
Prerequisites: Introductory biology and one semester of organic chemistry
Text: Nelson, D. L., and Cox, M. M. Lehninger Principles of Biochemistry (5
th
Edition). 2009.
W. H. Freeman and Company.

Overview: This course is designed to cover the important aspects of biochemistry in one
semester. We will focus on macromolecular structure and function, with an emphasis on protein
structure and function, and on metabolism, or energy flow, in biological systems.

Reading Assignments: Designated chapters are designed to reinforce, reiterate and supplement
lecture material. I recommend that you read all assigned chapters. The material for the exams
will be drawn solely from what I go over in class.

Attendance and Participation: Attendance and participation in class are strongly encouraged.
Please participate in class discussions, answer questions posed in class and ask questions about
material that is confusing. Asking a question in class helps me see where I may be confusing
the class. If you are confused chances are someone else is as well. ASK!! A reduction in your
grade may be warranted for unexcused absences.

Moodle: We will use a web based course management system called Moodle. I will post class
handouts, homework assignments and answer keys, announcements, etc on Moodle. You should
all have access to Moodle. Direct your browser to http://moodle.vassar.edu and login using your
Vassar ID and password. If there are any problems accessing this course with Moodle please let
me know immediately.

Communication: I am available during office hours or by email. Please think ahead if you have
questions on an assignment to ensure that you can get sufficient assistance.

Problem sets: There will be several problem sets throughout the semester (as indicated on the
syllabus). These problem sets are designed to give you practice on problems you may encounter
on exams. You may discuss these problems with your classmates but what you turn in MUST
BE YOUR OWN WORK. Problem sets must be turned in by 3:00 pm on the day they are due.
A late assignment will lose 10% points for each day or fraction of day that the assignment is late.
Additional problems (mostly from the text book) will be suggested for extra practice.

Exams: Five 50-minute exams will be given as indicated on the course schedule. The exams
will consist of a mixture of problems and short answer. The material covered on each exam is
indicated on the course schedule.

Final portfolio: To demonstrate your learning over the course of the semester you will prepare a
comprehensive portfolio of your work. More information will be given on this assignment.

Laboratory: The laboratory component of this course is required. Your lab instructor will
determine your grade. Satisfactory completion of the lab is required to pass the course.

Make-up exams/homework: Make-ups for exams will only be given for extreme
circumstances/emergencies. Every effort should be made to contact me as soon as a situation
arises.

Cell phones/Computers: Cell phones are to be turned OFF (not on silent) for the duration of the
class. Computers are not to be used in class (including for note taking).

Calculators: Please bring a calculator to class, you may need to use it to do small group
exercises.

Grading:
Problem sets 25 %
Laboratory 20 %
Exams 40 %
Class Portfolio 15%

% Points Final Grade
100-93: A
92-90: A-
89-87 B+
86-83 B
82-80 B-
79 -77 C+
76-72 C
71-70 C-
69-67 D+
66-60 D
59 -0 F


Students with Disabilities: Academic accommodations are available for students with disabilities
who are registered with the Office of Disability and Support Services. Please schedule an
appointment with me early in the semester to discuss any accommodations for this course which
have been approved by the Director of Disability and Support Services as indicated in your DSS
accommodation letter.

Course Schedule
Date Topic Reading Due Dates
W Jan 23 Introduction (Review Chapter 1)
F 25 The Chemistry in Biochemistry Chapter 13.1-13.2

M 28 Water and pH / Buffers Chapter 2
W 30 Amino Acids and Peptides Chapter 3.1-3.2
F Feb 1 Protein Structure Chapter 3.4, 4 PS #1

M 4 Protein Structure Chapter 4
W Feb 6 Xray Crystallography TBD
F 8 Exam #1 (Material covered through 2/6)

M 11 Enzymes /Catalytic Strategies Chapter 6.1-6.4
W 13 Enzymes /Catalytic Strategies Chapter 6.1-6.4
F 15 Studying Proteins/Protein Purification Chapter 6.1-6.4

M 18 Regulation of Proteins and Enzymes Chapter 5, 6.5
W 20 Regulation of Proteins and Enzymes Chapter 5, 6.5
F 22 Carbohydrate Structure Chapter 7.1 PS #2

M 25 Carbohydrate Structure Chapter 7.2-7.3
W 27 Nucleic Acid Structure Chapter 8.1-8.2, 8.4
F Mar 1 Exam #2 (Material covered through 2/27)

M 4 Lipids Chapter 10.1-10.3
W 6 Membrane Proteins Chapter 11, 12.6
F 8 Protein structure/function TBD

Spring Break (March 9-24)

M 25 Introduction to Metabolism Chapter 13.1, 13.3-13.4
W 27 Glycolysis Chapter 14.1-14.2
F 29 Glycolysis Chapter 14.1-14.2 PS #3

M Apr 1 Gluconeogenesis Chapter 14.4
W 3 Gluconeogenesis/Pentose Phosphate Shunt Chapter 14.4-14.5
F 5 Exam #3 (Material covered through 4/3)

M 8 Citric Acid Cycle Chapter 16.1-16.3
W 10 Citric Acid Cycle Chapter 16.1-16.3
F 12 Oxidative Phosphorylation Chapter 19.1-19.3

M 15 Oxidative Phosphorylation Chapter 19.1-19.3 PS #4
W 17 Amino Acid Catabolism/Urea Cycle Chapter 18
F 19 Fatty Acid Oxidation Chapter 17

M 22 Exam #4 (Material covered through 4/19) PS #5
W 24 Fatty Acid Synthesis Chapter 21.1
F 26 Glycogen Metabolism Chapter 15.1, 15.3-15.5

F 29 Glycogen Metabolism Chapter 15.1, 15.3-15.5
F May 1 Carbohydrate Metabolism in Other Systems Chapter 20
F 3 Integration of Metabolism Chapter 23 Portfolios

R 6 Integration of Metabolism Chapter 23

Study Period (May 8-14)

Exam #5 (May 15-21)