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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