CHEM 328- Biochemistry II-Lecture
Spring 2009
Instructor: Didem Vardar-Ulu
Time and location: T,W&F 8:30-9:40 AM; SCI-273
Contact Info: SCI-276, x3255 (office), SCI-L301, X3285 (lab), dvardar@wellesley.edu
Office hours: T: 11:15 am – 12:30 pm, W: 2:15 – 3:45 pm (or by appointment)
Text: Lehninger Principles of Biochemistry, 4th edition: David L. Nelson, Michael M. Cox (Primary)
Biochemistry 3rd edition: Reginald H. Garrett, Charles M. Grisham (Supplemantary)
Biochemistry 6th edition: Jeremy M Berg, Lubert Stryer, John L. Tymoczko (Supplemantary)
Biochemistry 3rd edition: Donald Voet and Judith Voet (Supplemantary)
Biochemical Methods (2002): Pingoud, Urbanke, Hoggett, and Jeltsch (Supplementary)
Scope of the course and content overview:
This course is the second half of a one-year sequence intended for Biological Chemistry majors
and others who want an in-depth introduction to biochemistry. Throughout the semester we will focus on
the interactions between biomolecules and macromolecular assemblies to study the mechanism of action
and regulation of different functional biological systems with special emphasis on enzymes. We will also
discuss how various biological macromolecules come together in metabolic pathways central to the life of
cells and organisms. We will revisit many concepts that were covered in Chem221, as we study variuos
examples of structure-function relationship in different areas of biochemistry. We will also pay
particular attention to experimental methods used to study these systems with examples from current
published literature.
Course Goals:
The specific learning goal for this course is to expand on the core biochemical knowledge
necessary to provide you with the fundamental understanding of a functional biochemical system and
enable you to analyze it both qualitatively AND quantitatively.
The general learning goal for this course is to help you build-on to the customized learning
techniques you have developed in Chem221 and apply them to studying a specific biochemical topic of your
own interest in great detail throughout the semester.
Course Expectations:
As we have extensively discussed in Chem221, biochemistry is an interdisciplinary field that
requires both biological and chemical understanding and description of the problems at hand. It is also an
experimental science. Therefore, throughout the semester you will be expected to utilize and
demonstrate understanding from various areas of science as well as scientific literature and the
laboratory section of the course.
I expect that through the different studying techniques you were exposed during Chem221 you
have already developed a better sense for what kinds of activities help you learn biochemistry most
efficiently. Since biochemistry is a collaborative enterprise, I will still strongly encourage you to work in
groups both in and out of class for any different parts of the course work, but you will also have ample
opportunities to practice your own learning styles and individually demonstrate your mastery of the new
material. Remember, you will NEVER be in competition with one another in this class since you are
evaluated against an absolute standard of excellence.
Finally, I want to reemphasize that in-class participation is an extremely integral part of your
learning experience for this course. Your preparedness, presence, and contributions are not only vital for
your learning, but also for your classmates. Therefore I expect you to attend all classes, be on-time, and
come prepared, unless you have previously provided me with a written explanation of a foreseeable
conflict or a same day note about an EXTREMELY serious unforeseeable circumstance. Failure to do so
for more than 10% of the classes (4 classes) will result in a sign deduction from your final grade.
Course conferences:
We will use CHEM328-S09 conference as our platform to exchange information and discuss ideas.
All additional course materials will also be available through this conference.
Evaluation of work:
Your final grade will reflect your performance on your mastery of the new biochemistry material
that will be covered this semester as well as your performance on the application of all the biochemistry
you have learned so far with the following weights:
New Biochemistry Material: (25%)
Content Exams (3): 15% (Each 5%)
PSets (2): 10% (to me completed in groups of three students)
Application of Biochemistry: (75%)
Research Grant Proposal: (45%)
o Specific Aims: 5%
o Grant Proposal Initial Submission: 10%
o Grant Proposal Final Written Submission: 15%
o Written Questions for the other proposals: 5%
o Grant Proposal Oral Presentation: 10% (5% presentation/ 5% handling questions)
Laboratory: 30%
Extra Help:
There will be an attached tutor, who will be holding weekly question/answer sessions for all
interested students throughout the semester for this course. Although these sessions are not
mandatory, I strongly encourage you to attend and make use of the opportunity to facilitate your
studying. You should also make every effort to arrange for regular group study sessions to discuss class
and lab material and also feel free to make use of the tutoring services offered through PLTC.
Suggestions:
As you know, I highly value and appreciate any suggestion and constructive criticism you might
have regarding any aspect of this course and hope that you would feel comfortable enough to voice your
opinions. However, if any time during this semester you feel that you would rather send me an anonymous
email please use the following yahoo account:
Login name: Chem221wellesley Password: Spring09
Additional information:
Please let me know immediately if you foresee any conflict of important dates due to any personal
or religious reasons. I will be happy to consider making any necessary changes or accommodations for
requests voiced until February 6th 2009.
Students with disabilities who are taking this course and who need disability-related
accommodations are encouraged to work with Verónica Darer, the Directory of Programs of the
Pforzheimer Learning and Teaching Center (for learning or attention disabilities), and Jim Wice, the
Director of Disability Services (for physical disabilities) to arrange these accommodations. Their offices
are in the Pforzheimer Learning and Teaching Center in Clapp Library.
CHEM328-S09 Schedule
# Date Topic Reading Work Due
Thermodynamics of Molecular Interactions
1 02/03/09(T) Course goals / Grant Writing Principles Handouts posted on the
conference
Ch 1.3 Physical
Foundations
Ch3 from Garrett&
Grisham; can be
accessed:http://web.vir
ginia.edu/Heidi
2 02/04/09(W) Thermodynamics of Ligand Binding Ch 5.1 and 5.2 (optional)
Understanding Allostery, Cooperative Binding, Ch12 Box 12.1
Hill and Scatchard Plots
3 02/06/09(F) Examples: Hemoglobin and Immunoglobulins Submission of ranked
choices for Research
Grant Proposal Topic
4 02/10/09(T) IPT 1: Thermodynamics of Ligand Binding
(Hemoglobin)
5 02/11/09(W) Experimental Biochemical Techniques (non- Biochemical Methods:
structural methods and structural methods) Ch7.3.1-7.3.6
Spying on HIV with
SPR: Rebecca L.
Richand David G.
Myszka TRENDS in
Microbiology Vol.11
No.3 Mar 2003
Ligand binding by TPR
domains: Cortajarena,
et.al. Protein Sci. 2006
15: 1193-1198
6 02/13/09(F) Class visit by Enriqueta Bond '61 http://www.wellesley.ed Decision on Group
Health Policy Leader, u/Alum/Awards/AAA/w Aim for the Research
Medical Research Champion inners/bond.html Grant Proposal
Recipient of the Wellesley College Alumnae
Achievement Awards 2009 PSet #1 due
Enzyme Kinetics and Catalysis
7 02/17/09(T) Chemical Kinetics - Review Ch 6.1, 6.2 Decision on Specific
Class time for grant proposal work Individual Aims for
(Group work on specific aims) Research Grant
Proposal
8 02/18/09(W) Intro to Enzymes
Class time for grant proposal work
(Group work on specific aims)
9 02/20/09(F) Catalytic Strategies Specific Aims for
Reseach Grant
Proposal due
10 02/24/09(T) Enzyme Kinetics I Ch 6.3
11 02/25/09(W) Enzyme Kinetics II
12 02/27/09(F) Content Exam I: Thermodynamics of
Molecular Interactions
13 03/03/09(T) IPT 2: Enzyme kinetics (DNA Polymerase I) DNA polymerase I
Astatke, et al. PNAS
Vol.95,pp.3402–3407,
March 1998
Astatke, et al. JBC
270 (4), p. 1945-1954
27 Jan 1995
14 03/04/09(W) Enzyme Mechanisms (serine proteases) Ch 6.4 Submission of grant
drafts to group
members
15 03/06/09(F) Enzyme Mechanisms (other examples)
16 03/10/09(T) Class time for grant proposal work
(Group work on grant drafts)
17 03/11/09(W) Enzyme Regulation Ch 6.5
Medicinal Biochemistry - Metabolism
18 03/13/09(F) Overview to Metabolism Part II (section before Initial Research
Review of important chemical reactions Ch 13) Grant Proposal due
19 03/17/09(T) Bioenergetics Ch 13.1
20 03/18/09(W)
21 03/20/09(F) Enzyme Inhibition Ch 6.3
(by Elizabeth Oakes)
22 03/24/09(T)
SPRING VACATION
23 03/25/09(W)
24 03/27/09(F)
25 03/31/09(T) Carbohydrate Metabolism Ch 14.1, 14.2, 14.4 PSet#2 due
26 04/01/09(W)
27 04/03/09(F) IPT 3: Carbohydrate Metabolism –
a specific enzyme in the pathway
28 04/07/09(T) Tricarboxylic Acid Cycle Ch 16.1, 16.2
29 04/08/09(W) Electron Transport Chain/ Oxidative Ch 19.1, 19.2
phosporylation
30 04/10/09(F) Content Exam II: Enzyme Kinetics and
Catalysis
31 04/14/09(T) Fatty Acid Biosynthesis Ch 21.1
32 04/15/09(W) Fatty Acid Catabolism Ch 17.1, 17.2
33 04/17/09(F) Group time for grant proposal work
34 04/21/09(T) MONDAY SCHEDULE
35 04/22/09(W) IPT 4– Lipid Metabolism – a specific enzyme in
the pathway
36 04/24/09(F) Alternative fates for metabolic intermediates Ch 14.3, 14.5 Final Research Grant
Proposals due
37 04/28/09(T)
38 04/29/09(W) RUHLMAN
39 05/01/09(F) Principles of Metabolic Regulation Ch 15.2, 19.3 Two questions for
each of the other
proposals due
40 05/05/09(T) Proposal Presentations I
41 05/06/09(W) Proposal Presentations II
42 05/08/09(F) Proposal Presentations III
43 05/12/09(T) Content Exam III: Metabolism
44 05/13/08(W) Discussion: Who gets the funding?