ABC97 Home Page

Advanced Biochemistry Fall Term, 1997

[NOTE: The course page for the Fall Term, 1998 is ABC98 Home Page.]

These pages provide background and describe general aspects of the course:
Problem set and lecture schedule.
Course description and requirements.
Books and folders on Reserve in the MI and E&S Libraries.
Other sites of general interest for the course.
Viewing and downloading text and graphics from these pages.
for Biochemistry: Tutorials and quizzes on biochemistry.
is an on-line version of the tutorial written by Dr. Hackney.
The remainder of the page is organized by problem set number.

Go to problem set materials for

Select problem set number:   0   1   2   3   4   5   6   7   8   9   10   11.

PS #0: Review of (some) Quantitative Biochemistry Topics.

The Graphs that accompany the answer sheet for this problem set.
A page dealing with first-order decay and some practice kinetics problems.

PS #1: Protein and Nucleic Acid Structures: Graphics Display.

Check your understanding of RasMol commands with an interactive RasMol Quiz.
An annotated Example of a PDB file from the online RasMol manual.
The links submitted for this problem set were added to the WWW Links page.

PS #2: Protein Folding: Mutagenesis and Energetics of T4 lysozyme.

Problem set topics illustrated with "Chimed images" of T4 Lysozyme.

PS #3: Negative Cooperativity in Binding Processes: The Bacterial Aspartate Receptor.

Problem set scripts shown as "Chimed images" of the Aspartate Receptor Protein.

PS #4: Abzymes: Catalytic Antibodies through High Affinity for Transition State Structures.

PS #5: ATP Sulfurylase: Enzyme Kinetics and Mechanism and Coupling to GTP hydrolysis.

PS #6: DNA & RNA Structures and the in vitro Selection of RNA Molecules.

Overviews of DNA and RNA Structure.
Yeast tRNAPhe: A Chime & RasMol-scripted tour of the structure.

PS #7: Protein-DNA Interactions: Zinc Finger Structures and Specificity.

Zif268 Structure and residues randomized by Greisman & Pabo.
Students' scripts (as Chime buttons) and figure captions were added to this page.
Zif268-DNA Recognition based on the Pavletich & Pabo (1991) structure.
Hydrogen Bonding Patterns by Proteins to DNA Base Pairs

PS #8: The F1 ATP Synthase.

An excellent lecture on ATP Synthase with acompanying figures by Antony Crofts for a biophysics course at the Univ. Illinois, Urbana-Champaign.
There is also a link from the lecture page to: F1-ATPase as a Chime tutorial. (Note: this "Chimed page" requires the transfer of about 2Mb of PDB coordinates; be warned or be patient while the page loads.)

The F1-ATPase structure: The residues that were cross-linked by Duncan et al. are highlighted.

PS #9: Single Molecule Measurements: RNA Polymerase & lac Repressor.

The Gelles Laboratory Homepage describes several single molecule measurements and provides a movie of Brownian motion of a DNA-tethered bead in a laser trap.

PS #10: Protein Folding Assisted by Chaperones.

Color images of GroEL & GroES Structures.
Additional images and information are at The Chaperonin Home Page.

PS #11: ATP Binding Sites in Enzymes.

Chime images of several ATP conformations as bound to enzyme active sites.
Chime images of ATP bound at the active site of:
Src-Family Tyrosine Kinase: Hck.
Green Fluorescent Protein GFP
Aspartate Carbamoyltransferase (ATCase).

PS #13: Students' Selectionsfor Problem Set #13
HIV Reverse Transcriptase; Nitrogenase;Cytochrome Oxidase; Photo Reaction Center; GCN4-DNA Complex Leu zipper

Chime images of   HIV-1 RT in the Cartoon display with Structure as bound to enzyme active sites to make DNA .
Chime images of Nitrogenase
Chime images of Cytochrome Oxidase
Chime images of Photo Reaction Center
Chime images of GCN4-DNA Complex


Advanced Biochemistry at CMU. William McClure David Hackney
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh, PA 15213
Last modified: December 3, 1997