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Biomolecular Structure
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Fall 2006
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| T & H 9:30-10:45 am LGRT 202 |
Chemistry 791a
Spire number 72543
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Instructor:
Jeanne Hardy |
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Last Updated:
9-5-06
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| Textbooks |
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"Protein Structure & Function," Gregory A. Petsko & Dagmar Ringe, Sinauer Press, 2004 |
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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 |
30% |
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Presentation |
20% |
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Quiz |
10% |
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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 |
2 |
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1-10 to 1-15 |
Secondary and Tertiary Structure |
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Pymol Manual |
PyMol Workshop I in Goessman 151 |
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1-9, 1-12 |
Protein stability and circular dicroism (CD). Homework 1 due. |
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4-15, DW 11, Dobson |
Protein Folding |
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1-16 to 1-22 |
Quaternary Structure and AUC |
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1-13, 3-12 to 3-20 |
Post-translational Modification and effect on structure |
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5-1 to 5-3 |
X-ray Crystallography. Homework 2 due. |
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B&T p. 373-386 |
X-ray Crystallography |
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B&T p.387-392 |
NMR by Prof. Joanna Swain. |
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Biotechniques |
NMR by Prof. Joanna Swain Take-home exam I distributed. |
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map, ps, cal |
PyMol workshop II Take-home exam I due by 9:30 am. |
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NSB1, NSB2 |
Structural Genomics. Reading Papers. |
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1-22, 2-0 to 2-7 |
Flexibility in Protein Structure |
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2-8 to 2-16 |
Relating Protein Structure to Function: Active sites, catalysis |
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3-0 to 3-10 |
Regulation of Protein Function |
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3-11 to 3-20 |
Discussion of Homework 3 reading. Homework 3 due. |
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4-0 to 4-10 |
Protein Structure Prediction and Design |
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TBA |
Nucleic Acid Structure by Prof. Craig Martin |
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Nov. 14 |
TBA |
DNA, RNA, riboproteins, ribozymes, aptamers by Prof. Craig Martin |
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4-11 to 4-17 |
The "Omic Era." Take home exam II distributed. |
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view, movie, load |
PyMol Presentation Prep. Exam II due at 9:30 am |
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Nov. 23 |
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No Class Thanksgiving Day |
13 |
Nov. 28 |
Student Selection |
Student Presentations (Dobson ppt, pdf ,Witkowski pdf, mov1, mov2, mov3) |
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Nov. 30 |
Student Selection |
Student Presentations (Paczkowski mov1, mov2, pdf, ppt, pse Pearse pdf pse, Craney pdf, ppt) |
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Dec. 5 |
Student Selection |
Student Presentations (Viana pdf pse ppt, Ankit mov1, mov2, pdf, ppt, Aruni pdf, ppt) |
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Dec. 7 |
Student Selection |
Student Presentations (Nivas ppt, pdf, Ake ppt, pdf pse, Adam ppt, pdf, mov1, ) |
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Dec. 12 |
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In-class quiz on student presentations. |
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Lab Updates
Hardy appeared on EcoExchange on PBS.
Elih named Nano IGERT Fellow!
Kristen's Paper Published.
Witold's Paper Published with a movie.
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