Winner of 2008 BMS Challenge: Genevieve Abbruzzesse
Runners Up: Lawrence B., David B., Tsung-Yi L. & Yash, P.
Fall 2008
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| T & H 9:30-10:45 am LGRT 1234 |
Chemistry 791a
Spire number 72101
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Instructor:
Jeanne Hardy |
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Last Updated:
7-8-08
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| Textbooks |
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"Protein Structure & Function," Gregory A. Petsko & Dagmar Ringe, Sinauer Press, 2004
By visiting http://www.new-science-press.com/browse/protein you can access the text for free from UMass IP addresses. While on a UMass IP address, you can get a personal subscription for free, which then allows you to log in from anywhere and read the book.
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"Introduction to Protein Structure," Carl Branden & John Tooze (supplementary) |
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"Proteins" David Whitford, Wiley Publishing (supplementary) |
| Course Content |
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| This course is designed for first and second year graduate students whose research focuses or just touches on macromolecular structure or function. This course is a must for students who wish to pursue research in chemical biology, structural biochemistry or enzymatic function. It is also a tremendously useful course for synthetic organic or inorganic students who will synthesize molecules to interact with biological structures. In this course you will learn how to think about protein and nucleic acid structure, the physical basis from which those structures come, and gain a functional understanding of tools such as x-ray crystallography, NMR, and circular dichroism that are used to determine biological structure. In the course you will also get a flavor of the most recent advances in biological structure determination, prediction and design. |
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| Prerequisites |
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| Undergraduate organic chemistry, a desire to learn about protein structure and function. |
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| Grading |
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A = 90 - 100 |
B = 80-89 |
C = 70 - 79 |
D = 60 - 69 |
F = below 60 |
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The grading cutoffs listed above are the minimal cutoffs. If you score 80 points you will earn at least a "B" grade. Grading may be curved to reflect class performance. |
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Grading Breakdown |
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Exam I |
25% |
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Exam II |
25% |
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Presentation |
20% |
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Quizzes |
15% |
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Homework |
15% |
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| Syllabus |
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| Week |
Dates |
Reading |
Topic |
1 |
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1-0 to 1-8 |
Amino Acids & Primary Structure |
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1-10 to 1-15 |
Secondary and Tertiary Structure |
2 |
Sept. 9 |
Pymol Manual
Pymol Handout
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PyMol Workshop I in Goessman 151 |
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1-9, 1-12
Matthews
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Protein stability and circular dicroism (CD). |
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4-15, DW 11, Dobson
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Protein Folding. Homework 1 due. |
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1-16 to 1-22 Metamorphic Proteins
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Quaternary Structure and AUC |
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1-13, 3-12 to 3-20
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Post-translational Modification and effect on structure |
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5-1 to 5-3
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X-ray Crystallography |
5 |
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B&T p. 373-386
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X-ray Crystallography Homework 2 due. |
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B&T p.387-392
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NMR by Qinghua Wang |
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Oct. 7 |
Biotechniques
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NMR by Qinghua Wang |
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Oct. 9 |
map, ps, cal |
PyMol workshop II Take-home exam I distributed. Spectra file |
7 |
Oct. 14 |
NO CLASS |
NO CLASS - Monday Schedule Followed Due to Columbus Day |
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Oct. 16 |
Structural Proteomics, NSB1, NSB2,
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Structural Genomics. Reading Papers. Take-home exam I due by 9:30 am. Key to Exam 1.
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1-22, 2-0 to 2-7
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Binding sites
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2-8 to 2-16
How Enzymes Work Enzymes w/o Borders
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Flexibility in Protein Structure |
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3-0 to 3-10 |
Relating Protein Structure to Function: Active sites, catalysis |
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3-11 to 3-20 |
Regulation of Protein Function. Homework 3 distributed. |
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4-0 to 4-10 |
Protein Structure Prediction and Design Homework 3 due. |
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4-11 to 4-17
Baker, Supp. Data |
The "Omic Era." |
11 |
Nov. 11 |
NO CLASS |
NO CLASS - Veterans Day |
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Fun with photochemistry by Jim Chambers. |
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Nov. 13 |
Craig's notes and jmol files |
DNA, RNA, riboproteins, ribozymes, aptamers by Prof. Craig Martin. Presentation topic due by Nov 14th. |
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Nov. 18 |
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Nucleic Acid Structure by Prof. Craig Martin Take home exam II distributed. Exam 2 Due Dec. 1, 9:00 am. |
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Nov. 20 |
view, movie, load
new load, new movie |
PyMol Presentation Prep & Movie Making with Witold Witkowski. Meet in CRC. |
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Nov. 25 |
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Proteopedia workshop. Meet in CRC. |
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Nov. 27 |
NO CLASS |
No Class Thanksgiving Day |
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Dec. 1 |
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Exam 2 Due 9:00 am, paper and electronic copies. Exam 2 Key. |
14 |
Dec. 2 |
Student Selection |
Presentations: David, Jamie, Mariel & Max |
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Dec. 4 |
Student Selection |
Presentations: Daniel, Lawrence, Luis & Mangai |
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Dec. 9 |
Student Selection |
Presentations: Burcu, Serap, Shiela & Yash |
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Dec. 11 |
Student Selection |
Presentations: Jung Won, Michael, Muslum & Steven |
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