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Bioorganic Chemistry Fall 2008 T, Th 8:10 - 9:25 AM Room SC 1432 |
 Carmelo Rizzo
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updated: 11/17/2008
| Tentative Course Content | |
| Â I. Amino Acids, Peptides and Proteins | |
| Â A. Amino Acid structure, synthesies and analysis | |
| Â B. Peptide and Protein structure, synthesis and analysis | |
| Â II. Enzymes Mechanisms | |
| Â A. Catalytic Sidechains | Â |
| Â B. Cofactors | Â |
| Â III. Nucleosides, Nucleotides and Nucleic Acids | |
Prerequisite: Chem 220 a and b (Organic Chemistry)
Text: There is NO required text for this course. Exams and assignments will come entirely from class notes. The bookstore has the following recommended texts:
Chemical Approaches to the Synthesis of Peptides and Proteins, P. Lloyd-Williams, F. Albericio, E. Giralt, CRC Press, Boca Raton,1997. ISBN 0-8493-9142-3
An Introduction to Enzyme and Coenzyme Chemistry (2nd ed),Tim Bugg, Blackwell Science, Oxford, 2004, ISBN: 1-4051-1452-5
Nucleic Acids in Chemistry and Biology (3rd ed), G. Michael Blackburn, Michael J. Gait, David Loakes, and David Williams, Royal Society of Chemistry Publishing, 2006, ISBN: 978-0-85404-654-6
Bibliography and suggestions for further reading
Exams: Two mid term exams and a Final. The dates of the midterm exams are Thur. Sept 25 and Tue., Oct. 30.
The Final Exam is scheduled for Wed., Dec. 17, 2008 at 9:00-11:00 am in SC 5502. No Alternate Final will be offered.
Please make your travel plans accordingly.
Grading: Each exam with count equally toward the final grade. Graduate students are also required to write a short paper (10 page limit) on a topic of their choice (with approval from me), related to bioorganic chemistry. In addition, they will present a short lecture (15 minutes) on their topic. You should choose a topic by Oct. 30.
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Questions & Answers Page: I am posting questions and answers from the class, sent to me via email.
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Exams from Spring 2000:
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 Exam 1 |
 Exam 2 |
 Exam 3 |
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 Tentative class schedule |
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| Â Tue., Aug. 26 | Â Amino acid struture and synthesis |
 slides 1-46 (revised 9/08) |
| Thur., Aug. 30 | Â Asymmetric synthesis of amino acids, and peptide synthesis | |
| Tue., Sept. 2 |
Solid phase peptide synthesis and peptide ligation; cyclic peptides |
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| Â Thur., Sept. 4 |
 Protein Structure: Amino Acid Analysis and peptide sequencing "Introduction to Proteomics: Tools for the New Biology," Liebler, D. C., Human Press: 2002 available as an ebook through ACORN. |
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Amino Acid Masses
 slides 47-104 (revised 9/08) |
| Â Tue., Sept. 9 | Â Protein Structure: Methods of protein structure determination |
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| Â Thur., Sept. 11 | Protein Structure: Hydrogen Bonds, the Hydrophobic effect, alpha-helices, beta-sheets, beta-turns | ÊÂ |
| Â Tue., Sept. 16 | Â Protein Structure: Hydrogen Bonds, the Hydrophobic effect, alpha-helices, beta-sheets, beta-turns (con't); Combinatorial Synthesis | Â slides 105-141 (revised 9/08) |
| Thur., Sept. 18 |
 Combinatorial Synthesis (con't) |
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| Â Tue., Sept. 23 | Â Peptidomimetics | Â |
| Â Thur., Sept. 25 |
  First Hour Exam |
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| Tue., Sept. 30 | Enzyme Chemistry- proteases | Â Â slides 142-186 (revised 9/08) |
| Â Thur., Oct. 2 | Enzyme Chemistry- phosphatases | |
| Â Tue., Oct. 7 | Â Cofactor Chemistry- Thiamin and pyridoxal dependent enzymes | Â |
| Thur., Oct. 9 | Â Cofactor Chemistry- Pyridoxal dependent enzymes | |
| Â Tue., Oct. 14 | Â Cofactor Chemistry- Nicotinamide dependent enzymes |
  (mid-semester dificiency report due) slides 187-240 (revised 9/08) |
| Â Thur., Oct. 16 | Â Cofactor Chemistry- Flavin dependent enzymes | Â |
| Oct. 20-21 | Â October Break- no class | |
| Thur., Oct. 23 | Â Cofactor Chemistry- Flavin dependent enzymes | Â |
| Â Tue., Oct. 28 | Â Cofactor Chemistry- Heme and Vitamin B12 dependent enzymes | |
| Â Thur., Oct. 30 | Â Â Second Hour Exam | Â |
| Â Tue., Nov. 4 | Structure and Properties of Nucleosides, Nuceotides and Nucleic Acids; DNA replication | Â slides 241-309 (revised 11/08) |
| Â Thur., Nov. 6 | Â Nucleoside and oligonucleotide synthesis, solid-phase oligonucleotide synthesis | Â Â PCR Animation |
| Tue., Nov. 11 | Â DNA sequencing | Â |
| Â Thur., Nov 13 | Â Nucleotide Biosynthesis | |
| Â Tue., Nov. 18 | Nucleoside Analogues as Therapeutic Agents | Â slides 310-359 (revised 11/08) |
| Thur., Nov. 20 | Â RNA & Transcription | Â Topoisomerase animation |
| Nov 22-Nov 30 | Thanksgiving Break- no classes | |
| Â Tue., Dec. 2 | Â Nucleic Acids as Therapeutic Agents | Â Â RNAi animation |
| Â Thur., Dec. 4 | Â DNA Damage & Repair | |
| Â Tue., Dec. 9 | Graduate Student Presentations (no class for the undergraduates) | Â |
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| Wed., Dec. 17 | Â Final Exam, Room SC 5502, 9:00 - 11:00 am | Â term papers due for graduate students |