Chem 224
Bioorganic Chemistry
Fall 2008
T, Th 8:10 - 9:25 AM
Room SC 1432

 Carmelo Rizzo
office: SC 7662
Tel.: 322-6100
e-mail: c.rizzo@vanderbilt.edu

updated: 11/17/2008

Tentative Course Content
 I. Amino Acids, Peptides and Proteins
  A. Amino Acid structure, synthesies and analysis
 B. Peptide and Protein structure, synthesis and analysis
 II. Enzymes Mechanisms
  A. Catalytic Sidechains  
  B. Cofactors  
 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.

Syllabus

 

Questions & Answers Page: I am posting questions and answers from the class, sent to me via email.

 

Exams from Spring 2000:

 Exam 1

Answers

 Exam 2

Answers

 Exam 3

Answers

 Tentative class schedule

     
 Tue., Aug. 26  Amino acid struture and synthesis

 amino acids

 slides 1-46 (revised 9/08)

Thur., Aug. 30  Asymmetric synthesis of amino acids, and peptide synthesis
Tue., Sept. 2

Solid phase peptide synthesis and peptide ligation; cyclic peptides

 "Synthesis of Native Proteins by Chemical Ligation" Dawson, P. E.; Kent, S. B. H. Annu. Rev. Biochem. 2000, 69, 923-960.

 
 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.

  Amino Acid Masses

 slides 47-104 (revised 9/08)

 Tue., Sept. 9  Protein Structure: Methods of protein structure determination

 

 Thur., Sept. 11 Protein Structure: Hydrogen Bonds, the Hydrophobic effect, alpha-helices, beta-sheets, beta-turns  
 Tue., Sept. 16   Protein Structure: Hydrogen Bonds, the Hydrophobic effect, alpha-helices, beta-sheets, beta-turns (con't); Combinatorial Synthesis

 "Synthesis and Applications of Small Molecule Libraries." Thompson, L. A.; Ellman, J. A. Chem. Rev. 1996, 96, 555-600.

 slides 105-141 (revised 9/08)
Thur., Sept. 18

 Combinatorial Synthesis (con't)

 "Concepts and Progress in the Development of Peptide Mimetics." Olson, G. L. et al. J. Med. Chem. 1993, 36, 3039-3049.

 
 Tue., Sept. 23  Peptidomimetics  
 Thur., Sept. 25

  First Hour Exam

 
Tue., Sept. 30 Enzyme Chemistry- proteases   slides 142-186 (revised 9/08)
 Thur., Oct. 2 Enzyme Chemistry- phosphatases
 Tue., Oct. 7  Cofactor Chemistry- Thiamin and pyridoxal dependent enzymes  
Thur., Oct. 9  Cofactor Chemistry- Pyridoxal dependent enzymes
 Tue., Oct. 14  Cofactor Chemistry- Nicotinamide dependent enzymes

  (mid-semester dificiency report due) slides 187-240 (revised 9/08)

 Thur., Oct. 16  Cofactor Chemistry- Flavin dependent enzymes  
Oct. 20-21  October Break- no class
Thur., Oct. 23  Cofactor Chemistry- Flavin dependent enzymes  
 Tue., Oct. 28  Cofactor Chemistry- Heme and Vitamin B12 dependent enzymes
 Thur., Oct. 30   Second Hour Exam  
 Tue., Nov. 4 Structure and Properties of Nucleosides, Nuceotides and Nucleic Acids; DNA replication  slides 241-309 (revised 11/08)
 Thur., Nov. 6  Nucleoside and oligonucleotide synthesis, solid-phase oligonucleotide synthesis   PCR Animation
Tue., Nov. 11  DNA sequencing  
 Thur., Nov 13   Nucleotide Biosynthesis
 Tue., Nov. 18 Nucleoside Analogues as Therapeutic Agents  slides 310-359 (revised 11/08)
Thur., Nov. 20  RNA & Transcription  Topoisomerase animation
Nov 22-Nov 30 Thanksgiving Break- no classes
 Tue., Dec. 2  Nucleic Acids as Therapeutic Agents   RNAi animation
 Thur., Dec. 4  DNA Damage & Repair
 Tue., Dec. 9 Graduate Student Presentations (no class for the undergraduates)  
 
Wed., Dec. 17  Final Exam, Room SC 5502, 9:00 - 11:00 am  term papers due for graduate students