Biochemistry 565

Proteins and Enzymes - Cordes section

useful website links

Dates in bold black, e.g. Monday Aug 25, are completely updated for 2008. Dates in bold red are not updated at all from 2007, 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 2007, but due to some course reorganization additional subjects will be inserted in the sequence as we g, and some specific existing powerpoint notes, readings and assignments will also change.

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Date	Title	Reading	Homework, Links, Info, Notes
Monday Aug. 25	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. 27	Topics in chemistry of the protein backbone and side chains (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 Class handout (on Wed) on additional protein chemistry
Friday Aug 29	Anatomy of Protein Structure (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 Sep 1	NO CLASS
Wednesday Sep 3	Anatomy of Protein Structure cont. (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
Friday Sep 5	Anatomy of Protein Structure cont. cont. (ppt file)	No new reading	Problem set 1, due September 12 (as doc) Lovell article for problem set
Monday Sep 8	Catch up on previous material	No new reading	possible class handouts-TBA
Wednesday Sep 10	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 Reading guide for Razvi, Street Optional review session 5-6 pm Biosciences West 210
Friday Sep 12	Determinants of protein stability and structure ppt file	Matthews review	Matthews, Annu Rev Biochem 62, 139-60 (1990) Reading guide for Matthews
Monday Sep 15	continuation from Friday, with discussion of Matthews review	no new reading	Problem Set 1 due; see Fri Sep 5 Problem set 1 key In-class handout on double mutant cycles.
Wednesday Sep 17	Evolution and comparison of protein sequences ppt file	Suel paper	Suel et al Nat Struct Biol 10, 59-68 (2003) Reading guide for Suel In-class handout--supplement on substitution matrices.
Friday Sep 19	Continue protein sequence material	No new reading	Problem set 2 as doc, pdf Due Friday Sep 26
Monday Sep 22	Evolution, classification and comparison of protein structures ppt file	Orengo paper	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
Wednesday Sep 24	Continue Monday's material	No new reading	Work on your problem set Review session 5-6 pm, BSW 210 tentative location
Friday Sep 26	Finish previous material; wrap up of section	No new reading	Problem set 2 due (see Friday Sep 19) key
Monday Sep 29	In class exam covering first five weeks		2006 exam with answers 2007 exam key 2008 exam key

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Department of Biochemistry
The University of Arizona

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