Spring 2008 Syllabus,

Dr. Koni Stone

Professor of Chemistry

Links to Medical School application information.

Be sure to visit Laura Boyer's page for searching the literature. Be sure to use the full text articles that are available at Science Direct and Wiley Interscience.

Group activities

• DNA technology
• Chapter 11
• Chapter 12

Course materials:

Homework and assignments 

Reading notes:

• Chapter 8 notes: pages 273-305
• Chapter 9 notes:  pages 306-337, 
  • Arsenic is a carcinogen.  It is also used to treat a form of leukemia.  What is the mechanism?
  • Decoding the Procainamide paper
• Chapter 11 notes: pages 369-389 and 389-417
• Chapter 12 notes: Biosignaling
• Chapter 13 notes: part I,  part II. Here is a review of kinetics vs thermodynamics.
• Chapter 16: practice problems for chapter 16
• Chapter 17: pages 598-607 and pages 607- 618. Here are the chapter 16 homework problems: 1,2,5,6,7,9,12,13,14,16,17,18,19,20!
• Chapter 18: pages 623-637 and pages 637-654.
• Chapter 19: pages 659-677.
• Chapter 20: Highlights.
• Chapter 23: Reading notes.

Biochemistry related sites

Membranes, transporters, channels, signaling and more...

• Cystic fibrosis chloride channel
• Information on transporters 
• How does serotonin get back into its neuron?
• Animated Sodium/Potassium Pump! 
• Another Animated Sodium Potassium Pump 
• Animated Ion pump animated="">Sodium Potassium pump
• Links to Opiate Receptor Information. Be sure to find out what type of receptor it is.
•  Phospholipid derived secondary messengers.
• Adrenergic receptor links!
• Capsaicin binds to a vanilloid receptor.  This receptor senses heat, pain and chemical stimuli.  When Capsaicin binds, the message "heat" goes to the brain, the brain then ilicits a "cooling down" process: vasodilation and sweating occur.  
• Capsaicin binds to a vanilloid receptor.  This receptor senses heat, pain and chemical stimuli.  When Capsaicin binds, the message "heat" goes to the brain, the brain then ilicits a "cooling down" process: vasodilation and sweating occur.

Ammonia is Toxic

• Neurobiology of ammonia toxicity
• Hyperammonemia case study ( A must read!)
• Glutamate dehydrogenase defect causes hyperinsulinemia and hyperammonemia, find out why!
• Ammonia causes protein phosphorylation.
• Role of NMDA (n-methyl aspartic acid) receptors in ammonia toxicity
• Glutamine synthesis is regulated by NMDA receptors

Glycolysis sources:

• Here is a great glycolysis page.
• Great Biochemistry links!   Check out the glycolysis reactions.
• Summary of Glycolyis
• To find out information about diseases due to defects in glycolysis enzymes go to this search engine on the NIH site and type in the enzyme you are studying.

• Some nice diagrams
• This site has a really nice animation of the conversion of pyruvate to Aetyl-CoA by pyruvate dehydrogenase.
• Some other animations and interactive learning tools.  Check out the TCA cycle.  You need to know this.

Peroxisome website (Maintained by the laboratory of  Stephen J. Gould at The Johns Hopkins University School of Medicine.)  The following links are part of this website.  (Information from these pages will be incorporated into future assessment devices.)

• Peroxisomal diseases (a must read!)
• Information about branched chain fatty acid metabolism (where are these branched chain fatty acids in the diet?)
• Refsum's disease
• a oxidation (Where does a oxidation occur in the cell?)

• Lactic acidosis and mitochondrial encephalopathy. (We may have muscles in our head, but that is not what this disease is about--its about a brain disorder)

• Calmodulin movie This page is from the Molecular Biochemistry class at Rensselaer. You will need to down load shock wave player to see the animations.
• This will help you with the acyl CoA dehydrogenase case studies. 
• Smooth muscle contraction This page is from the University of Indiana Medical School page. It has some other really great stuff.
• Black Widow Spiders!
• Cancer may not be as complicated as once thought. Check out this news article from BioMedNet News.
• Arsenic is a carcinogen.  It is also used to treat a form of leukemia.  What is the mechanism?
• Read about rat poison in this article by Joseph M. Newcomer
• Decoding the Procainamide paper
• Why can't patients take lipitor and eat grapefruit?  (Red Wine has the same effect.

Eric Martz's pages:

Protein Secondary structure
DNA

An electronic overview of biochemistry, written by Dr. William McClure, Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213

University of Kansas Medical Center's Medical Biochemistry site. This is what you have to look forward to learning! Be sure to check out their practice exams. There are some lovely questions on them!

Practice (old) exam questions

• Exam I - Spring 2002
• Exam I - Spring 2003
• Exam I- Spring 2006, Fall 04 CHEM 4400 Exam III (lipid questions).
• Exam I- Spring 2007
• Membrane transport questions and one lipid question.
• Exam II- Spring 1995
• Exam II -Spring 1997
• Exam II- Spring 2002
• Exam II- Spring 2003
• Exam III-Spring 1999
• Exam III- Spring 2002
• Exam III- Spring 2003
• Exam III -Spring 2004, Topics for exam 3, Exam III -Spring 2004

Supplementary materials

• Disaccharides
• Glucose and fructose
• UDP-Glucose:UDP-Galactose Uridyl transferase mechanism
• Phosphoglucomutase mechanism
• Abstracts related to the lead poisoning case study problem.

Stanislaus Journal of Biochemical Reviews

This is a peer reviewed electronic journal comprised of the research papers that were submitted as partial fulfillment of the requirements for Biochemistry II (CHEM4420). The papers were written in an iterative process: students used feed back from the instructor and their peers to enhance their writing ability. Each manuscript was anonymously reviewed by two classmates. This course is taught annually, so there will be a new volume published every May.

Comments? Please use e-mail to koni@chem.csustan.edu

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This page was designed by Koni Stone at CSU, Stanislaus. It was most recently revised on February 7, 2006. Please send comments to koni@chem.csustan.edu