Biochemistry Calendar

CHY 463, Spring 2008

Subject to Revision: LAST REVISION 200/02/06

This schedule is pretty sketchy now -- will be filled in as course goes along.

See Topic List for specific assignments.

Week of	M	W	F
Week of January 14	SNOW DAY	Introduction; Looking Ahead to Your Seminar PLEASE Click HERE to join the Biochemistry Discussion List TODAY, in order to get next Wednesday's reading by email.	Chapter 12 Carbohydrate Metabolism II
Week of January 21	No Class	Discussion of "Biochemistry of exercise-induced metabolic acidosis," by Robergs, et al, reading provided by email (you must join discussion list). Read paper and be prepared to summarize its main conclusion in a short quiz. To help you understand this paper better, review the metabolic pathways we have covered so far.	Quiz: See Learning Strategy for Pentose Pathway.
Week of January 28	Chapter 15 Photosynthesis	Quiz: See Learning Strategy for Photosynthesis	Photosynthesis The sun's wind blows the fire green, sails the chloroplasts, lifts banks, bogs, boughs into flame: the green ash of yellow loss. A.R. Ammons (MORE about Ammons)
Week of February 4	Chapter 16 Lipid Metabolism Quiz: See Learning Strategy for Fatty Acid Catabolism • Fatty-acid biosynthesis and oxidation	• Cholesterol metabolism • Regulation of lipid metabolism • Catch-up and review NOTE: Next Meeting in Science 165	Biochemistry Seminar Series Begins Seminar: Sri Dhyana, Connexins, and Research at Scripps Research Institute, Science 165
Week of February 11	Exam #1 Click HERE for the exam key. Key will appear after second-chance submission of exam.	ANOTHER SNOW DAY	Chapter 17 Amino Acid Metabolism Quiz: see Learning Strategy for Amino-Acid Catabolism • Transamination and deamination of amino acids • Urea cycle • Selected pathways of amino-acid catabolism Your Seminar: Preliminary Proposal (tentative title, brief description, COPIES of 1 or 2 lead papers)
Week of February 18	Winter Break	Winter Break	Winter Break
Week of February 25	Due today: Exam 1, Second-Chance Submission Readings Provided: Sections 1, 2 The Five Senses • Nerve impulses and symapses • From stimulus to nerve impulse: what the senses have in common • The senses one by one: smell and taste For background, see The Nervous System (read about nerve cells, nerve impulses, and synapses) and Animations of Nerve Action	Readings Provided: Sections 3,4,5 The Five Senses • The senses one by one: vision, hearing, and touch. As you study this subject, consider these questions: • Where, in all this molecular machinery, is the knower? • How do all of these molecular somethings make a someone?	Due today: Last Exam 1, Second-Chance Submissions (for those who justifiably missed last class before break) Discussion Biological Naturalism, by John Searle (get article from Searle's web site) The Mind-Body Problem You might also find THIS interesting.
Week of March 3	Crystallography Made Crystal Clear (CMCC): Read Chapters 1-5, provided. Molecular Structure Determination I. X-ray Crystallography Crystal growth, data collection, from diffraction data to structure.
Week of March 10	CMCC: Read Chapters 6-7, provided. Molecular Structure Determination I. X-ray Crystallography Phase problem,	Completion and refinement of X-ray models.	Exam #2 Click HERE for the exam key.
Week of March 17	CMCC: Read Chapter 8, provided Molecular Structure Determination IV. Judging Model Quality a. Crystallographic models b. NMR models c. Homology models See CMCC Chapter 8 (will provide) and Principles of Protein Structure, Comparative Protein Modelling and Visualisation For future reference: Judging the Quality of Macromolecular Models: A Glossary of Terms from Crystallography, NMR, and Homology ModelingBioinformatics	Brief Intro to Tutorial: Bioinformatics for Beginners Note: Exam #3 is Parts 1 and 2 of the Test Yourself section of Bioinformatics for Beginners. Due Monday, April 2, at beginning of class. CMCC: Read Chapter 10, sections I and II, provided. Molecular Structure Determination II. NMR a. Basic and multidimensional NMR b. NMR models: ensembles and averaged structuresof Chapters 19-22 (tentative) DUE TODAY: Your Seminar: Final Plan: title, outline of seminar, full citations of all papers you plan to use; your outline must show plainly how you plan to meet the four main REQUIREMENTS in the Seminar Guidelines ALSO: LAST DAY TO SWAP SEMINAR DATES!	CMCC: Read Chapter 10, sections III and IV Molecular Structure Determination III. Homology Modeling Chapter 10, Sections III, IV, Also see Principles of Protein Structure, Comparative Protein Modelling and Visualisation Parts II and IV
Week of March 24	Spring Break	Spring Break	Spring Break
Week of March 31	Turn in Exam #3 at beginning of class. Submit files and responses by beginning of class (10:15 AM) April 9. NOTE: Schedule for this week revised Thursday 3/27. Homology Modeling, CMCC, Chapter 10, Sections III and IV. If time, discussion of this Reading: Realms of Belief Beliefs, Models, and Reality	Chapter 23 Recombinant DNA Technology For deeper understanding of the methods presented in this chapter, skim these sections: • 19.1, 2, 4, 6, 7 • 20.2-5 • 21.1-4, 7 • 22.1, 6 Download Outline and Slides Distribute Abstract: 4/9 Speaker	Recombinant DNA Technology, continued IF TIME ALLOWS: Discussion of a Recent Structure-Determination Paper Download Paper. This is a zipped file containing the paper, supplemental online material, and a perspective about the work. Distribute Abstract: 4/11 Speaker
Week of April 7	Biochemistry Seminar Series Begins Seminar John Lippert, USM class of 1994, Albany Molecular Research, Inc. Synthetic Derivatives of Combretastatin A-1 Please join us for lunch and discussion at Great Lost Bear after the talk. If you are interested in employment at Albany Molecular Research, make an appointment with me to meet with John after lunch. Distribute Abstract: 4/14 Speaker	Seminar: Michael Esty Whole-Genome Comparisons of Orthologous Proteins Distribute Abstract: 4/16 Speaker	Seminar: Trevor Bozeman Enzymatic Incorporation of Acid and Alpha-Hydroxy Acid Analogues of Phenylalanine Using Aminoacyl-tRNA Synthetases Distribute Abstract: 4/18 Speaker ALL STUDENTS: Provide an email evaluation by 8:00 PM the day of each seminar. Use the form I sent you by email. Send to me with subject line as follows: #evaluation of (name of speaker)
Week of April 14	Seminar: Tru Nguyen Detecting Uric Acid with Biosensors Distribute Abstract: 4/21 Speaker	Seminar: Kevin McKelvey Bacterial Electron Transport Protein Modifications She LIGHT on Structural Significance of Proteins in Electron Transport from Photosystem I to Ferredoxin-NADP⁺ Reductase. Distribute Abstract: 4/23 Speaker	Seminar: Joshua Watson Investigating How Protein Dynamics Control the Kinetics of Initial Electron Transfer in Photosynthesis Distribute Abstract: 4/25 Speaker
Week of April 21	Seminar: James Suriyodorn Mutation of CTFR Protein in Cystic Fibrosis Distribute Abstract: 4/28 Speaker	Seminar: Devin Layton *Structure of E. coli* Signal Peptide Peptidase Distribute Abstract: 5/30 Speaker**	Seminar: Nadia Conti Prions—The Mystery Unfolds: A Brief Look into the Molecuar Architecture of Human Prion Protein Amyloid Using Electron Paramagnetic Resonance and Hydrogen/Deuterium Exchange Distribute Abstract: 5/2 Speaker
Week of April 28	Seminar: Sri Dhyana Direct Observation of Chaperone-Induced Changes in a Protein-Folding Pathway Using Optical Tweezers Distribute Abstracts: Exam Period Speakers, if any (hope not)	Seminar: Russel Rogers *Estrogen Reduction of Ortho-Quinones Catalyzed by NQO1: And ESI-MS Perspective*	Seminar: Mina Assadollazadeh Limb Regeneration in Newts: It Got Better!
Week of May 5 (Exam Week)	No meeting during final exam week, unless snow moves a seminar into this slot. Best wishes on all your finals!!!		Spare Parts IF TIME ALLOWS: Discussion of a Recent Structure-Determination Paper Download Paper. This is a zipped file containing the paper, supplemental online material, and a perspective about the work.