Biology 100: Biochemistry
Fall Quarter, 2009
Bob Ludwig, Professor
Office: 425 Sinsheimer Labs
Office hours: Tuesdays 2:00—4:00 pm
Office telephone: 459-4084
Amanda Sugay, TA
Office: 347 Thimann Labs
Office hours: Thursdays 1:30—3:30 pm
Sean O’Rourke, TA
Office: 347 Thimann Labs
Office hours: Mondays 11:00 am—1:00 pm
CLASS MEETS: Monday-Wednesday-Friday, 2:00 PM - 3:10 PM
Stevenson College 150
TEXT: LEHNINGER: PRINCIPLES OF BIOCHEMISTRY, either 4th or 5th ed.
by David L. Nelson and Michael M. Cox
All Students should read Chapters 1-2 (background and review material)
in advance as preparation for the class
LINKS:
SYLLABUS
ELECTRONIC RESERVES (ERES)
· (Note: for Password to Electronic Reserves, please e-mail Bob, Amanda or Sean)
DISCUSSION SECTIONS:
Monday 9:30 - 10:40 am Nat Sci Annex 103
Tuesday 6:00 - 7:10 pm Earth & Marine Sci B214
Tuesday 7:30 - 8:40 pm Earth & Marine Sci B214 (suspended until further notice)
Thursday 4:00 - 5:10 pm Earth & Marine Sci B210
NEWS:
· Exam 2 scores posted to ERES through Monday Nov. 16 (4 days only)
· In Monday (Nov. 2) class, someone left an electronic device; describe it accurately and it’s yours
· Tuesday 7:30 PM section suspended until further notice (Please attend one of three other sections)
· For molecular visualization software, please try Jmol; use Chime at your own risk.
PROBLEM SETS / PRACTICE EXAMS (posted on ERES):
· Problem Set #1: due Oct 5
· Problem Set #2: due Oct 12
· Problem Set #3: due Oct 19
· Problem Set #4: due Oct 30
· Problem Set #5: due Nov. 9
· Problem Set #6: due Nov. 20
LECTURE NOTES:
Protein-Ligand 1:1 interaction (Bob does the math!) (Powerpoint)
Michaelis-Menten Equation (derivation)
Enzyme Inhibition Equations
Na+ K+ ATPase cycle (Quicktime movie, 12 Mb!)
Biosignalling (Powerpoint)
Mechanism of G3P Dehydrogenase
(Pssssst--Wanna see some movies of ATP synthase? )
(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, UCSC
INTEGRATIVE BIOCHEMISTRY (METABOLISM):
Boehringer Metabolic Pathways
EcoCyc: Encyclopedia of E. coli Genes and Metabolism
PROTEIN STRUCTURES (REQUIRE CHIME BROWSER PLUG-IN; SEE BELOW):
Interactive Study of a FLAVOPROTEIN (University of Virginia)
NADH-DH (respiratory complex I) homepage
Cytochrome bc1 complex (Lawrence Berkeley Lab)
Bovine mito cytochrome c oxidase complex (CHIME Tutorial)
To retrieve Paracoccus denitrificans cytochrome c oxidase (catalytic subunit),
type its PDB ID code: 1AR1
When viewing the molecule, toggle its "Display" to "Ribbon" and its "Color" to "Chain"
This is an integral membrane protein; Where is the membrane bilayer?
This crystal structure was determined from an antibody complex: Where is the antibody?
Where are the heme(s)!
CHIME Plug-In to your Browser (allows on-line viewing of 3D protein structures)
What is CHIME? (Tutorial)
Click here to obtain RasMol viewer program
