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CHEM 440 - Biochemistry

Instructor: Megan Bestwick

Office: Murdock Hall room 120

Office Hours: M, W 11:00 am – 12:30 pm; Th 8:30 – 9:30 am; 
                        or by appointment

Phone: 503.883.2265



Course Materials

Lecture: MWF, 9:30 - 10:35 am, TAYH 102

 F, 2:00 - 5:00 pm, MRUD 106

Lecture & Lab Syllabus

Protocols for Lab Experiments

Micropipette Use & Calibration

        - Density of Water vs. Temperature
        - Gilson Guide to Pipetting

Preparation of Buffers

Spectrophotometric Analysis

Gel filtration chromatography

Lysozyme: Isolation and Optimum pH

Kinetics of Chymotrypsin Catalysis

Lactate Dehydrogenase: Extraction, Purification & Kinetic Behavior

Independent Biochemistry Project
     - Example Introduction
     Due Dates:
          Introduction - Monday, November 17th
          Final Report - Wednesday, December 3rd

Useful Course Links

Current Lecture Schedule & Course Content

Format & Guidelines for Laboratory Reports
Examples of Biochemistry Related Scientific Papers:
          Cobine PA, et al. (2006).  J. Biol. Chem281, 36552–59.
          Liu L, et al. (2011).  J. Biol. Chem286, 41253-64.
          Bestwick ML, et al. (2010). Mol. Cell. Biol30, 172-185.
          Brown BM, et al. (2004). Biochem43, 13541-48.
Lehninger, Principles of Biochemistry, 6th ed: Book Companion Website

Useful Biochemistry Links

Titration Curve of a Weak Acid
Titration Curves for Acetic Acid, Phosphate, and Ammonia

Titration of a Polyprotic Acid

Animation: Peptide Bond Formation (1)
Animation: Peptide Bond Formation (2)

Animation: The Alpha Helix
Animation: Beta Sheets

Common Protein Chromatography Methods: Ion-exchange & Gel filtration

Protein Sequence, Stucture & Function Resources

How Enzymes Work
Enzyme Catalysis
Enzyme Kinetics
     Progress Curves for a Simple Enzyme-catalyzed Reaction 
     Double-reciprocal (Lineweaver-Burk) Plot
     Lineweaver-Burk Plot for Competitive Inhibition
     Lineweaver-Burk Plot for Uncompetitive Inhibition
     Lineweaver-Burk Plot for Mixed Inhibition

Map of Metabolic Pathways 
Interactive Metabolic Pathways Map

Carbohydrate Metabolism Tables

     Animation: Overview of Glycolysis
     Interactive Animation: Glycolysis Enzyme/Reactant Name/Reactant Structure Match-up

     Interactive Animation: Gluconeogenesis
     Animation: The Transport of PEP and Oxaloacetate from the Mitochondrion to the Cytosol
     Comparison of the Pathways of Gluconeogenesis and Glycolysis

Pyruvate Dehydrogenase Complex: Interactive Animation

Citric Acid Cycle
     Interactive Animation: Carbon, Energy, Regulation, Intermediates, Pathway
     Animation: The Reactions of the CAC
     Animation: Regulation of the CAC
     Animation: Amphibolic Function of the CAC

Oxidative Phosphorylation
     Mitochondria, review of OXPHOS
     Animation: Electron Transport Chain major events
     Molecular Animation of ATP Synthase

     Photosynthesis Light Reactions

Summer Research Opportunities

Amgen Scholars Program for undergraduate students
Fred Hutchinson Cancer Research Center: Summer Undergraduate Research Program
Oregon Health Sciences University: Listing of various research opportunities


For Fun

Glucose song (YouTube video)
Bio-Rad GTCA SsoFast (YouTube video)
Powering the Cell: Mitochondria (YouTube video)