Chemical Biology

Instructor: Teaching Assistant: Lectures: Recitation section: To be named.

Chem 421b

Professor Alanna Schepartz (Alanna.Schepartz@yale.edu) KCL 120, 432-5094

Tuesdays and Thursdays, 9:00 – 10:15, in SCL 19 Date and time TBA (1 hr)

Course description: A comprehensive introduction to the origins and emerging frontiers of chemical biology. This course develops the fundamental chemistry of molecules found in nature, a quantitative description of their interactions with themselves and each other, and subsequent effects on biological function. Topics include protein design, molecular evolution, chemical genetics, metabolic engineering, and methods in genomics and proteomics research. Grades: Grades will be based on problem sets (40%), two exams (40%) and, in lieu of a final exam, a term paper written on a chemical biology topic not covered in class. Problem sets: following Tuesday. Problem sets will be distributed each Tuesday and will be due on the

Texts and readings: Most readings will be from the primary literature and can be viewed and downloaded from the Yale classes server (https://classes.yale.edu). No text is required, but the following books are great sources for background material and as a reference guide. Each will be placed on reserve in Kline Science library. Blackburn, G.M. & Gait, M.J. Nucleic Acids in Chemistry and Biology. Oxford (1996) Branden, C. & Tooze, J. Introduction to Protein Structure. Garland (1999) Creighton, T.E. Proteins: Structures and Molecular Properties. Freeman (1993) Fersht, A. Structure and Mechanism in Protein Science. Freeman (1999) Syllabus: Date Jan. 11 Jan. 13 Section References (not a complete list, pls see classes server) What is chemical biology, and how does chemical biology differ from biochemistry or bio-organic chemistry? Chemical Solid phase Merrifield1963.pdf methods to peptide synthesis Merrifield1964.pdf synthesize proteins and peptides I Chemical Inteins.ppt Native chemical Casi2003.pdf methods to ligation methods, Dawson2000.pdf synthesize inteins Moots2002.pdf proteins and Moot2003.pdf peptides II Giriat2003.pdf Foldamers I Foldamers-part-I Foldamers with MinterJACS2003.pdf structure PowerPoint file Topic

Jan. 18

Jan. 20

pdf Li2003.pdf Feb.pdf Wilson2001. 22 Protein-protein-int.pdf Grandl2003.Jan. 17 No class today DNA recognition Case study: Artificial transcriptional activators Protein-protein interactions I DNArecognition. 15 Feb.pdf Dervan2001.pdf Best2003.pdf Chin2003.pdf Kritzer2004a.pdf Kritzer2004.pdf Rutledge2003.pdf Liu2003a.pdf Ansari2002.pdf Golemi-Kotra2004. 8 Evolution II Hoess2001.pdf Macbeath2000.pdf Ofran2003. 3 Case study: The first example of a foldamer ligand for a medicinally relevant target Chemical methods to synthesize DNA and RNA Case study: A four-base paired helix with expanded size Evolution methods Foldamers-part-II Foldamers-part-III structure Foldamers with function Hart2003.pdf Arkin2003.pdf Solid phase oligonucleotide synthesis Non-naturalDNA.ppt Feb.ppt Westheimer1987.ppt Feb.pdf Wells1995.ppt Feb.pdf Stemmer1994.pdf Dervan2003.pdf Hopkins2002.pdf Atwell1997. 24 March 1 March 3 March 22 Protein-protein interactions II Ligands for protein surfaces I Mid-term exam Ligands for protein surfaces II Structuralplasticity. 25 Jan.pdf Keefe2001.pdf Ma2003. 10 Feb.pdf Chin2001.pdf Gemperli2004.ppt Artificialactivators.pdf Li2002.pdf Berg2003. 1 Feb.pdf LoConte1999.pdf Schwarze1995.pdf Gartner2002.pdf Arndt2003.pdf . 27 Feb.pdf Doyon2003.pdf Evolutionmeth-II.pdf Chakabarti2002.pdf Gemperli2004.ppt March 24 March 29 March 31 Case study: paralog selective ligands for Bcl-2 proteins Genomics and proteomics DNA arrays Protein arrays Pirrung2002.

pdf Barnes-Seeman2003.pdf Shogren-Knaak2001.pdf Schreiber2003.pdf Knooh2003.pdf .pdf Koehler2003.31 April 5 Case study: Small molecule arrays Chemical Genetics I Chemical Genetics II [open] Exam April 12 April 14 April 19 April 21 Zhu2001.pdf Koh2002.pdf Macbeath1999.pdf Newman2003.

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