screen shot of KiNG kinemage viewer

BCH 258
Structural Biochemistry I

1st-half Fall Semester
MWF 3:05-3:55
Nanaline Duke 147
Course Director: Lorena Beese

pol A ribbon on diffraction pattern

This course introduces students to the principles of modern structural biology. The objective is to convey the importance of understanding fundamental biological processes in terms of the atomic properties of the macromolecules that participate in them. In this course we identify reoccurring structural principles and motifs and show how proteins with unrelated functions are built up from combinations of these. We then introduce methods of structure determination by X-ray crystallography and NMR. Finally, we use specific examples from the current literature to illustrate general structural principles.

Immediately below are PDFs with general information about the course. Following the general info is the tentative class schedule in columnar format. Listed with the date and topic are downloadable resources - PDFs, kinemages, and text files. The topics and/or resources may change during the course of the course. An assigned worksheet is generally expected to be done between the day it is listed and the following class. After the class schedule are links to additional resources on using kinemages and KiNG, both for class exercises and for projects.

Be attentive with your downloads! Kinemage files are text files and may display in the browser. If necessary, use some type of "right-click"; option-click; shift-right elbow-click combo to download the file or link. This may be true for some browsers even with PDF files.

Structural Principles

Mon - 8/25/08

Macromolecular computer graphics
KiNG basics
3D literacy

download arrow WrkSht1_Intro2008.pdf (120KB pdf) | download arrow Demo5_4a-KiNG.kin (100KB)
KiNG basics | download arrow QuickStartKing.pdf (36KB pdf)
download arrow LectureNotesMonAug25-2008.pdf (56KB pdf)

Wed - 08/27/08

Peptide geometry & handedness

download arrow Wrksht2_handedAAroles2008.pdf (148KB)
download arrow LectureNotesWedAug27-2008.pdf (60KB)
download arrow c1Basics-A-KiNG.kin (120KB)

Fri - 08/29/08

Polypeptide chain & amino-acids

download arrow howdotswork3KiNG.kin (515KB)
(requires mage) download arrow ala_dipept_geom_dotball5.1.kin (4.9MB)
(requires mage) download arrow idealpolyala12.kin (16KB)
(requires mage) download arrow appendstuff2.kin (3.8MB)
download arrow c1Basics-B-KiNG.kin (16KB)
download arrow Wrksht3-.pdf (120KB)
download arrow 4FXN.pdb (120KB)

Mon - 09/01/08

Labor Day -- (no class)

Wed - 09/03/08

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Structure, Function & Engineering

Mon - 09/15/08

Protein-nucleic acid recognition:
General Principles

download arrow Prot-DNAInteractionsWksht.pdf (32KB)
download arrow 258protDNAinter.kin (240KB)
download arrow c7DNA.kin (156KB)
download arrow c8HthTF.kin (312KB)

Wed - 09/17/08

Sequence-specific DNA recognition:
Procaryotic and eucaryotic transcription factors

download arrow Prot-DNAInteractionsWksht.pdf (32KB)
download arrow 258protDNAinter.kin (240KB)
download arrow c9EuTF.kin (316KB)
download arrow c10TFfam.kin (312KB)

Fri-09/19/08

Enzyme catalysis: Serine & HIV-1 proteases

download arrow Wkst-SerineProtease.pdf (36KB)
download arrow c11SerPr.kin (316KB)

Mon - 09/22/08

Enzyme catalysis:
DNA polymerases & HIV-1 reverse transcriptase

Polymerase movie

(local download)
download arrow polymerase.mov (10.6MB)

Wed - 09/24/08

The Ribosome

Ribosome movie download arrow ribosome.mov (32.4MB)
download arrow 1ffk.bb.kin (704KB)
download arrow 1ffk_hlx7H.kin (1.3MB)
download arrow 1ffk_5Sto38.kin (436KB)
download arrow 1ffk_pieceH.kin (116KB)
download arrow 1ffk5S_mcdots.kin (1.1MB)
download arrow 1ffk5SHstack.kin (1.9MB)
download arrow 1JJ2s.L24.kin (72KB)

Structural Techniques

Fri - 09/26/08

Structure determination by X-ray crystallography

download arrow c18StDet.kin (204KB)

Mon - 09/29/08

Structure determination (continued)

Wed - 10/01/08

Structure determination by NMR

Fri - 10/03/08

Immunoglobins

Mon - 10/06/08

Fall Break(no class)

Wed-10/08/08

Frontiers in Structural Biology

Fri - 10/10/08

Biochemistry Departmental Retreat
(no class)

Resources on using KiNG and kinemages