Biochemistry Calendar

CHY 563, Spring 2006

Subject to Revision: EXTENSIVE REVISION 2006/01/31

See Topic List for specific assignments.

Daily Study Questions

For each class day the calendar specifies sections of the text (signified by "VVP: ") for you to read before class. You are required to prepare three study questions from the assigned sections, and to turn them in at the beginning of every class. Your study questions should be your own work. Ask questions about specific subjects in the assigned sections that you find difficult or unclear. Ask about subjects that arouse your curiosity. I will use your questions in class, in an effort to spend most of our class time on subjects with which you really need help, not on things you can read and understand on your own.

Study questions are required for every class, including quiz days (but not exam days).

Week of	M	W	F
Week of 1/16	No Class	Introduction; Looking Ahead to Your Seminar Unfinished business from CHY461	Oxidative Phosphorylation VVP: Section 17.3
Week of 1/23	Pentose Phosphate Pathway VVP: Section 14.6 Quiz: See Learning Strategy for Pentose Pathway. Reactions and roles of the pentose pathway	SNOW	Photosynthesis VVP: Sections 18.1,2 Chloroplasts; from light to chemical energy
Week of 1/30	Photosynthesis VVP: Section 18.3 From chemical energy to carbohydrates Quiz: See Learning Strategy for Photosynthesis	Finish Photosynthesis	Carbohydrate Metabolism II VVP: Sections 15.1, 2 Glycogen breakdown and synthesis
Week of 2/6	Carbohydrate Metabolism II VVP: Sections 15.3, 4, 5 Regulation of glycogen metabolism; gluconeogenesis.	Review or catch up for exam.	Exam #1 Click HERE for the exam key.
Week of 2/13	Lipid Metabolism VVP: Sections 19.1, 2 Quiz: See Learning Strategy for Fatty Acid Catabolism. Fatty-acid oxidation Seminar: Preliminary Proposal (tentative title, brief description, COPIES of 1 or 2 lead papers)	Lipid Metabolism VVP: Sections 19.3, 4, 5 Ketone bodies; fatty acid biosynthesis; regulation of lipid metabolism Click HERE for a diagram of fatty-acid biosynthesis.	Amino Acid Metabolism VVP: Sections 20.1, 2, 3, 20.4.A, B,C; 20.5.A; 20.6.C Nitrogen removal and excretion; selected pathways of amino-acid catabolism Quiz: see Learning Strategy for Amino-Acid Catabolism
Week of 2/20	Winter Break	Winter Break	Winter Break
Week of 2/27	Regulation of Metabolism in Humans VVP: Sections 21.1, 2, 3, 4 Inter-organ communication; Signal transduction, underlying mechanisms; starvation, diabetes, and obesity	The Five Senses VVP: Sections 9.4.F, 10.2C Readings Provided: Sections 1, 2 From stimulus to nerve impulse: what the senses have in common; The senses one by one: smell and taste	The Five Senses Readings Provided: Sections 3,4,5 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?
Week of 3/6	Molecular Structure Determination I. X-ray Crystallography a. Crystal, data collection, from diffraction data to structure. Chapters 1-2, Crystallography Made Crystal Clear (CMCC, provided)	Molecular Structure Determination I. X-ray Crystallography b. Phase problem, refinement of X-ray models. NOTE: Seminar by GR, Judging Model Quality, Thursday, March 9, 2:00 PM, Science Room 7.
Week of 3/13	Seminar: Final Proposal (title, outline of seminar, full citations of all papers you plan to use) LAST DAY TO SWAP SEMINAR DATES!	etc	Exam #2
Week of 3/20	Molecular Structure Determination II. NMR a. Basic and multidimensional NMR b. NMR models: ensembles and averaged structures Chapter 10, Sections I, II, CMCC Molecular Structure Determination III. Homology Modeling Chapter 10, Sections III, IV, CMCC Also see Principles of Protein Structure, Comparative Protein Modelling and VisualisationParts II and IV	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 Modeling	Bioinformatics 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 Friday, April 7, at beginning of class.
Week of 3/27	Spring Break	Spring Break	Spring Break
Week of 4/3	Bioinformatics Q/A, if any Recombinant DNA Technology VVP Chapter 3, Sections 4 , 5, and Boxes 3.1, 2, 3. Packet of slides provided. Download this Outline and these Slides. Exam #3: Take-home exam: Complete Parts 1 and 2 of the Test Yourself section of Bioinformatics for Beginners. Submit files and responses by beginning of class (10:15 AM) April 7.	Recombinant DNA Technology	Recombinant DNA Technology Distribute Abstract: 4/14 Speaker Turn in Exam #3 at beginning of class.
Week of 4/10	Biochemistry Seminar Series Begins Bioinorganic Perspectives on Environmental Alkane Oxidation Rachel Narehood Austin Associate Professor of Chemistry, Bates College Distribute Abstract: 4/17 Speaker Lunch afterward, Great Lost Bear	Seminar (tentative) Building a Brain; Neurons, Second Messengers, and Arsenic Douglas Currie, Assistant Professor of Biology, USM Lunch afterward, Great Lost Bear Distribute Abstract: 4/19 Speaker	Seminar Title Sarah Sandwick Distribute Abstract: 4/21 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 4/17	Seminar Title Heidi Tate Distribute Abstract: 4/24 Speaker	Seminar Title Justine Roths Distribute Abstract: 4/26 Speaker	Seminar Title Jeff Averill Distribute Abstract: 4/28 Speaker
Week of 4/24	Seminar Title Daniel Moore Distribute Abstract: 5/1 Speaker	Seminar Title Patrick Seitz Distribute Abstract: 5/3 Speaker	Seminar Title Megan Stackpole
Week of 5/1	Seminar Title Abby Culberson	Seminar Title Virginia Flood
Week of 5/8	No Final Exam