W E L C O M E to the Biochemistry & Molecular Biology 100C Home Page

BIOC 100C: Integrative Biochemistry

Bob Ludwig, Professor
Office: Sinsheimer Labs 425
Office hours: Tuesdays 2:00-4:00 PM
Office TEL: (831)459-4084

Robert Darneal, CA
Office: Thimann Labs 329
Office hours: Mondays, Wednesdays 9:50-10:50 AM

Drew Wagner, CA
Office: Thimann Labs 329
Office hours: Wednesdays 3:00-5:00 PM

LECTURE MEETS:
Monday, Wednesday, and Friday, 11:00 AM - 12:10 PM, Natural Sciences Annex 101

SECTIONS MEET:
Wednesday       8:00-9:10 AM, Physical & Biological Sciences 130
Friday                2:00-3:10 PM,  Physical & Biological Sciences 130

SYLLABUS

News:

· The third BIOC 100C exam is scheduled for Thursday, June 9, at 9:00 AM.

· Special study section Monday, June 6, 5:00-7:00 PM, Physical & Biological Sciences 130

· Bob’s Powerpoint presentations may be downloaded from the course eCommons page.

· Due to copyright laws, published articles for class discussion may not be distributed locally.

Aerobic Energy Transduction: the Orthodox Model vs. the Reform Model

Problem Sets on eCommons:

· Problem Set #1       due April 11, 2011

· Problem Set #2       due April 18, 2011

· Problem Set #3       due May 2, 2011

· Problem Set #4       due May 9, 2011

· Problem Set #5       due May 16, 2011

· Problem Set #6       due May 27, 2011

· Problem Set #7       due June 3, 2011

(Problem Set Answers available at the UCSC Science Library on closed reserve)

Enzyme Mechanisms:
Fructose bisphosphate aldolase
Malate exchange between cytosol and mitochondrion (Reform Model)
PEPCK activity

( Pssssst--Wanna see some movies of ATPase? )
(red and green ribbons = b subunit domains;
yellow ribbon = a subunit (180° opposite);
blue and gray ribbons = g subunit)
courtesy of Prof. Hong Yun Wang, Applied Mathematics

 Metabolic Pathways:
Boehringer Metabolic Pathways
EcoCyc: Encyclopedia of E. coli Genes and Metabolism
Oxidative Phosphorylation

Protein Structures (Require JMOL Java browser plug-in):
Interactive Study of a FLAVOPROTEIN University of Virginia
Respiratory complex I: NADH-Ubiquinone oxidoreductase (Scripps Research Institute)
Respiratory complex III: chicken heart mito cytochrome bc₁ complex University of Illinois
Respiratory complex IV: bovine mito cytochrome c oxidase complex (CHIME Tutorial)
Respiratory complex IV: bacterial cytochrome c oxidase complex (CHIME Tutorial; Rice University)

Protein Databank 3D Browser
As one example: to retrieve Paracoccus denitrificans cytochrome c oxidase (catalytic subunit),
type its PDB ID code: 1AR1

Links:

“Mystery of the Poisoned Expedition”, Earl, J.W. and McCleary, B.V., Nature 368: 683-684 (1994)
(accessible at machines with UC Santa Cruz IP addresses)

NCBI Genome Database Access

Tad W. Patzek, Dept. of Petroleum Engineering, University of Texas
A First-Law Thermodynamic Analysis of the Corn- Ethanol Cycle, by Tad W. Patzek,
Natural Resources Research, Vol. 15, No. 4, 255-270, February 2007
download PDF file

Class Project:
Exploring the Metabolic and Genetic Control of (Yeast) Gene Expression on a Genomic Scale by Joseph L. DeRisi*, Vishwanath R. Iyer, and Patrick O. Brown, Stanford University, SCIENCE v. 278: 680, 1997. (*UCSC graduate)
Note: Access to the SCIENCE magazine website is by paid subscription; you will need to connect from a UCSC computer
(with domain UCSC.EDU) starting from the UCSC Science Library Electronic Journals page.

Follow-up article on yeast evolution in the chemostat:
Systematic changes in gene expression patterns following adaptive evolution in yeast
Tracy L. Ferea*, David Botstein, Patrick O. Brown, and R. Frank Rosenzweig.
Proceedings of the National Academy of Science USA v. 96: 9721, 1999. (*former UCSC graduate student)
Note: Access to the Proceedings website is by paid subscription; you’ll need to connect from a UCSC computer
(with domain UCSC.EDU).