BIOLOGY 202
Cell Biology & Biochemistry
Fall 2006 (Thursdays,
Instructor: Bob Loudon, Ph.D.
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Sept. 7 |
Introduction to
protein structure & function ppt.#1 slides,
ppt. #2
slides |
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Sept. 14 |
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Sept. 21 |
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Sept. 28 |
First Midterm Exam |
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Oct. 5 |
Receptor tyrosine
kinases |
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Oct. 12 |
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Oct. 19 |
Second Midterm Exam |
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Oct. 26 |
Small G proteins and the actin
cytoskeleton (neutrophil chemotaxis movie and
keratinocyte GFP-actin movie [need
Windows Media Player to view]) ppt. slides |
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Nov. 2 |
Small G proteins and the actin cytoskelelton (continued) |
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Nov. 9 |
Mapping signal transduction pathways and the yeast two-hybrid system:
no notes for this lecture just the powerpoint slides (ppt. slides) |
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Nov. 16 |
Third Midterm Exam |
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Nov. 23 |
NO CLASS |
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Nov. 30 |
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Dec. 7 |
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Dec. 14 |
Final exam (cumulative: ~40-50% covering material from the first three sections
with the remainder covering the last section) REMEMBER TO BRING A STAMPED
SELF-ADDRESSED ENVELOPE TO THE EXAM IF YOU WANT ME TO SEND YOU YOUR GRADED
EXAM. I CANNOT LEAVE IT AT PENN FOR YOU TO PICK UP AT A LATER DATE. |
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ANNOUNCEMENTS:
OLD EXAM AND PRACTICE QUESTIONS
Course description
Biology 202 is an introductory-to-intermediate level CGS course that covers essential topics in biochemistry and cell biology. It assumes that you’ve had at least some basic biology and chemistry either in high school, college, or both. If you are someone who has had no biology or chemistry, this course may be a bit much for you and you might look into taking the prerequisite [or equivalent] introductory Biology 101 course first. If you have had gobs of biochemistry and/or cell biology already and you take this course, you run the risk of being bored silly. In this case, you may want to consider one of the upper-level courses offered at Penn. If you have any questions or concerns about this please feel free to talk to me.
Textbook
There is no required textbook for Biology 202. I have
included a list of suggested reading materials with links to on-line
texts of both Stryer's Biochemistry (5th ed.) and Alberts' Molecular
Biology of the Cell (4th ed.). For the most part, the readings are meant to
enhance your overall understanding of the topics covered in class and it is up
to you to decide whether you want to read these texts.
Grading for the course
During this semester, you will be given three midterm exams
and one final exam. The two highest midterm scores plus the final exam score
will count towards your course grade. Everyone MUST take the final exam. Any
student who misses a lecture for any reason will be responsible for getting
notes and other lecture materials from a fellow classmate. Three in-class exams
(2 highest midterms, 1 final [cumulative]): each exam is worth 33.3% (2 x 33.3%
for 2 highest score midterm exams + 33.3% for final exam = 100%). No make-up
exams will be given if you miss one for any reason, so do NOT ask me if you can
take an exam at another time please. Please note that the final exam is cumulative.
In terms of coverage of course material, the final exam will contain questions
up to and including the first three sections (midterms 1, 2, & 3) worth
roughly 40-50% of the final exam point total with the remainder of the exam
including “new” material (material covered after the third midterm exam up to
the final exam). Please note that I often times present
information in the lectures that is NOT always in the lecture notes. Thus, it
is in your best interest to attend the lectures!
I do my best to be available to you should you have any questions or concerns. Please feel free to contact me at my e-mail address or telephone number. Optional review sessions will be set up after class, one week prior to an exam. All students are expected to be familiar with the University's Code of Academic Integrity and to behave in a manner consistent with the principles outlined therein. Any violation of the Code will be dealt with severely.
Suggested readings (not required for the course but may be
helpful to you)
A website devoted to online versions of some of the classic, big-name textbooks in cell & molecular biology, other titles may be of less use to you: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Books
Also, the entrez-pubmed web site contains a huge database of scientific articles on wide ranging topics and can serve as a great place to find more detailed information about topics presented in class: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Introduction to protein structure & function
Proteins
are made up of 20 different amino acids: Berg, J., Tymoczko, J., & Stryer,
L. Biochemistry (5th edition), W.H. Freeman & Co.
Amino
acids are linked together by peptide bonds: Berg, J., Tymoczko, J., &
Stryer, L. Biochemistry (5th edition), W.H. Freeman & Co.
Structure
determines function!: Berg, J., Tymoczko, J., & Stryer, L. Biochemistry
(5th edition), W.H. Freeman & Co.
Protein allostery (actin,
heterotrimeric
G proteins): Berg, J., Tymoczko, J., & Stryer, L. Biochemistry
(5th edition), W.H. Freeman & Co.
Enzymes & enzyme kinetics
Enzyme regulation (covalent
modification [overview
of glycogen metabolism], feedback
inhibition, regulatory
molecules [calmodulin], proteolysis
[digestive enzymes]): Berg, J., Tymoczko, J., & Stryer, L. Biochemistry
(5th edition), W.H. Freeman & Co.
Enzyme kinetics (Michaelis-Menton
Model of enzyme kinetics, ): Berg, J., Tymoczko, J., & Stryer, L. Biochemistry
(5th edition), W.H. Freeman & Co.
Enzyme
inhibitors (competitive & noncompetitive inhibitors, irreversible
inhibitors): Berg, J., Tymoczko, J., & Stryer, L. Biochemistry
(5th edition), W.H. Freeman & Co.
G
proteins: Alberts, B., et al. Molecular Biology of the Cell (4th
edition), Garland Publishing, Inc.
More
specific information on heterotrimeric G proteins: Alberts, B., et al. Molecular
Biology of the Cell (4th edition), Garland Publishing, Inc.
Second
messengers: Alberts, B., et al. Molecular Biology of the Cell (4th
edition), Garland Publishing, Inc.
Receptor tyrosine kinases
Receptor
tyrosine kinases & the MAP kinase pathway: Alberts, B., et al. Molecular
Biology of the Cell (4th edition), Garland Publishing, Inc.
Review articles on RTKs, Ras, and the MAP kinase pathway:
Schlessinger,
J. Cell signaling by receptor tyrosine kinases. 2000. Cell. 103:
211-225.
Protein Phosphatases (NOT COVERED THIS SEMESTER!)
Protein phosphatases: Alberts, B., et al. Molecular
Biology of the Cell (4th edition), Garland Publishing, Inc.
Review articles:
PTP-1B
review article by Nick Tonks
CD45
review article by N.D. Huntington and D.M. Tarlinton
Lipids and cell signalling
Phospholipid
structure and the plasma membrane: Alberts, B., et al. Molecular Biology of
the Cell (4th edition), Garland Publishing, Inc.
Phospholipase
C and activation of PKC: Alberts, B., et al. Molecular Biology of the Cell
(4th edition), Garland Publishing, Inc.
Mapping signal transduction pathways and the yeast
two-hybrid system
Review article:
Fashena, et al.
Cell signaling and drug addiction(NOT COVERED THIS SEMESTER!)
Check out the NIDA website on issues related to drugs, drug abuse & addiction, and treatment strategies: http://www.nida.nih.gov/
The cell cycle
Extracellular
ligands control cell division & apoptosis (cell death): Alberts, B., et al.
Molecular Biology of the Cell (4th edition), Garland Publishing, Inc.
Cell
cycle checkpoints: Alberts, B., et al. Molecular Biology of the Cell
(4th edition), Garland Publishing, Inc.
A good website to check out if you need some general info about the cell cycle.
Also has a nice description of the 2000 Nobel Prize winners whose
ground-breaking work in understanding cell cycle regulation has revolutionized
the field. When you click on the link you will be redirected to an updated
version of Dr. Forsburg's webpage. Once there, scroll all the way to the bottom
of this page and look for a link that says "All purpose cell cycle lecture
notes" and click on this link to reach her notes. Contains links to
other useful mitosis and cell biology sites as well: http://www-rcf.usc.edu/~forsburg/cclecture.html
Small G proteins and the actin cytoskeleton
Bar-Sagi,
D. and Hall, A. Ras and Rhofamily GTPases: a family reunion. 2000. Cell
103: 227-238.