Biochemistry 565

Proteins and Enzymes - Cordes section

useful website links

Dates in bold black, e.g. Monday Aug 20, are completely updated for 2007. Dates in bold red are not updated at all from 2006, while dates in bold brown are "beta" versions that are partly updated but still in progress! The section will follow the same general structure as in 2006, but specific powerpoint notes, readings and assignments will change.

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Date	Title	Reading	Homework, Links, Info, Notes
Monday Aug. 20	Review of amino acid backbone and side chain properties (ppt file)	none	IUPAC amino acid nomenclature rules: http://www.chem.qmw.ac.uk/iupac/AminoAcid/index.html
Wednesday Aug. 22	Chemistry of side chains/Anatomy of Protein Structure I (ppt file)	Muralidharan paper, p.429-434 plus box 2	Muralidharan & Muir, Nat Methods 3, 429 (2006); related, possibly helpful readings: Tam et al. Biopolymers 60, 194 (2001); Perler & Adam, Curr Opin Biotech, 11, 377 (2000). Reading guide
Friday Aug 24	Anatomy of Protein Structure II (ppt file)	Richardson online paper, Anatomy section up to turns	"The Anatomy and Taxonomy of Protein Structure," J.S. Richardson, Adv. Protein Chem, 34, 167 (1981) updated, annotated online version: http://kinemage.biochem.duke.edu/~jsr/index.html Reading guide
Monday Aug. 27	Anatomy of Protein Structure III (ppt file)	Richardson online paper, rest of Anatomy section	Also work on Deep View tutorial (tips handout), and try to finish by Wednesday. Deep View tutorial link: http://www.usm.maine.edu/~rhodes/SPVTut/index.html see updated reading guide for Friday above
Wednesday Aug. 29	catch up on previous lectures	No new reading, work on problem set	Problem set 1, due September 5 Lovell article for problem set Optional review session, BSW 219, 5-6 pm
Friday Aug. 31	Thermodynamic stability of proteins (ppt file)	Razvi review on thermophiles	Razvi & Scholtz, Protein Science, 15, 1569-78 (2006) . optional additional reading on osmolytes: Street, Bolen & Rose, PNAS 103, 13997-14002. In-class handout on water properties, vdW radii, H-bonds (see Matt if you didn't get a copy). Reading guide for Razvi, Street
Monday Sept. 3	NO CLASS
Wednesday Sept. 5	Determinants of protein stability and structure ppt file	Matthews review	Problem Set 1 due; see Wed Aug 29 (answer key for Problem set 1) Matthews, Annu Rev Biochem 62, 139-60 (1990) Reading guide for Matthews
Friday Sept. 7	continuation from Wednesday, with discussion of Matthews review	no new reading	Problem set 2, due Wed Sep 12. In-class handout on double mutant cycles.
Monday Sept. 10	Evolution and comparison of protein sequences ppt file	Suel paper	Suel et al Nat Struct Biol 10, 59-68 (2003) Reading guide for Suel Also work on problem set 2. In-class handout on substitution matrices.
Wednesday Sept. 12	Evolution, classification and comparison of protein structures ppt file	Orengo paper	Problem set 2 due; answer key Review session, 5-6 pm in BSW 208 Orengo et al Structure 5, 1093-1108 (1997) Reading guide (optional) Holm & Sander J Mol Biol 233, 123-38 (1993). (optional)Ppt appendix on automated structure comparison
Friday Sept. 14	In class exam covering first four weeks		2006 exam with answers 2007 exam key

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Department of Biochemistry
The University of Arizona

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