CHEM 451 BIOCHEMISTRY I. SUNY Cortland Fall 2010

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1 CHEM 451 BIOCHEMISTRY I SUNY Cortland Fall 2010 Instructor: Dr. Frank Rossi Office: Bowers 135 Office Hours: Mon. 2:30-4:00, Wed. 4:00-5:30, Friday 2:30-3:00, or by appointment. Extra evening office hours on exam weeks TBA. If my office door is open, feel free to stop in. frank.rossi@cortland.edu Classroom: Bowers 051 Meeting Time: MWF 12:40-1:30 Prerequisite: CHE 301 Texts: Required Biochemistry, 6 th ed., Berg, Tymoczko & Stryer Electronic Problem Sets: Sapling Learning. Purchase online Catalog Description: Compounds, reactions of biological importance, amino acids, nucleic acids, proteins, lipids, carbohydrates, vitamins, enzyme systems, digestion, absorption and pathways of intermediary metabolism. Prerequisite: CHE 301. Lecture/Lab Hours: Three lectures. Fulfills Liberal Arts Requirement: LASR (3 cr. hr.) Detailed Description: Chem 451 is part of a two-semester biochemistry sequence, Chemistry 451/452. Lectures will emphasize content that is accessible to students with the stated prerequisite of one semester of Organic Chemistry (CHE 301). All major classes of biological molecules are discussed with an emphasis on the on the chemistry of proteins. In addition, a portion of the course will discuss the discovery and development of pharmaceuticals, an area that integrates many of the topics of biochemistry. Learning Objectives: Students successfully completing CHE 451 are expected to be able to: Utilize fundamental concepts from General Chemistry and Organic Chemistry to explain the structure and properties of biological molecules. Apply concepts encountered in the text and lecture to explain related, but previously unencountered, biochemical problems. Develop the skills required to visualize biomolecules and explain the relationship of structure to function.

2 Drop Policy: University Policy will be followed. Attendance: Your attendance at lecture is expected. Excessive absences will reduce your grade. Posted Materials: Keys to exams will be posted in the hallway outside my office, Bowers 135, until the next test date. Be sure to record any correct answers you wish during that period, since these keys may not be available later. Disabilities: SUNY Cortland is committed to upholding and maintaining all aspects of the Federal Americans with Disabilities Act of 1990 (ADA) and Section 504 of the Rehabilitation Act of If you have a disability and wish to request accommodations for this class (e.g., note-taking, testing environments, etc.), please contact me or the Office of Disability Services located in B-40 Van Hoesen Hall at (607) Any information regarding your disability will remain confidential. Privacy Issues: Graded work is usually returned in class ASAP -- spread out alphabetically on the front desk. If you do not wish to have your work distributed in this fashion, you may request to have it returned in a sealed envelope or during office hours. Academic Integrity: Your commitment to learning, as evidenced by your enrollment at SUNY Cortland requires you to be honest in all of your academic course work. Incidents of academic dishonesty may be referred to university officials, and will be dealt with in accordance with chapter 340 of the SUNY Cortland College Handbook.

3 Grading Your grade will consist of points earned from problem sets, papers and exams. Your grades in each of these areas will be weighted according to the distribution below: Problem Sets 20% Exam I 10% Exam II 20% 1 st Visualization Paper 10% 2 nd Visualization Paper 20% Final 20% Numerical grade converted to a letter grade using the table below: A B C D Problem Sets: The majority of problem sets will be online. The due dates given online. You can access the online homework at: Log into CHE 451. Occasionally there may be written problem sets that will be distributed in class. If these occur, they will be announced and distributed at least one week prior to the due date. Visualization Papers: The ability to visualize the structure of macromolecules is critical to understanding modern biochemistry and molecular biology. This skill is difficult to assess in traditional exams. You will be asked to write two visualization papers containing illustrations of proteins generated with the program Chimera. The first will be short (~2-3 pages) and focus on protein quanternary structure. The second will be longer (~4-6 pages) and illustrate either the mechanism of an enzyme, pharmaceutical, or signal transduction protein. Details of the assignments will be discussed in class. Hour Exams: The focus of the hour exams will be the most recently covered material, but concepts from prior exam(s) may be needed to answer some questions. Content from problem sets may appear on the hour exams. Occasionally you may be asked to further analyze information that was initially encountered in a problem set. Makeup exams will only be given for excused absences and must be arranged for at least 48 hours before the scheduled exam. Final Exam: The final exam will emphasize material covered in class after the second hour exam. It will not be comprehensive.

4 CHE 451 Rossi Fall 2010 Schedule # Date Topic* Reading** 1 8/30 Basic Cell Biology: BIO 210 in 50 Minutes or Less 2 9/1 Classes of Biomolecules: Fatty Acids, Lipids, Membranes 3 9/3 Classes of Biomolecules: Nucleic Acids 4.1, 4.2 Labor Day, No Class 4 9/8 Classes of Biomolecules: Nucleic Acids 4.1, /10 Classes of Biomolecules: Carbohydrates 11.1, /13 Classes of Biomolecules: Amino Acid, Peptides and Proteins 7 9/15 Classes of Biomolecules: Amino Acid, Peptides and Proteins 9/17 Exam I (Lectures 1-7) 1.3, /20 Protein Visualization: Tertiary and Quaternary Structure 9 9/22 Protein Folding /24 Protein Folding /27 Protein Purification /29 Protein Sequencing; Protein Mass Spectroscopy /1 Experimental Determination of Higher Order Structure: X-Ray crystallography /4 Experimental Determination of Higher Order 3.6 Structure: NMR Spectroscopy 15 10/6 Immunological Techniques; /8 Introduction to Enzymatic Catalysis /8 1 st Visualization Paper (Lectures 8-15) Due 5 PM 17 10/11 Michaelis-Menten Kinetics /13 Kinetics of Enzyme Inhibitors /15 Fall Break, No Class 19 10/18 Hemoglobin: the relationship of structure to 7.1 function 20 10/20 Hemoglobin: Allosteric Binding /22 Hemoglobin: Mechanism of Allosteric Binding 7.3

5 22 10/25 Case Study in Catalytic Strategies: Chymotrypsin /27 Case Study in Catalytic Strategies: Chymotrypsin /29 Drug Development: Challenges, Approaches and Stages /1 Drug Development: Case Study- ACE Inhibitors Handout 26 11/3 Regulatory Strategies: Allosteric Inhibition /5 Regulatory Strategies: Covalent Modification and Proteolytic Cleavage /8 Biological Membranes Revisited /10 Exam II (Lectures 16-27) 29 11/12 Membrane Proteins /15 Membrane Channels and Pumps /17 Signal Transduction /19 Signal Transduction /22 Signal Transduction /24 Thanksgiving No Class 11/26 Thanksgiving No Class 33 11/29 Bioenergetics /1 ATP and Phosphoryl Transfer /3 Biological Redox /3 2 nd Visualization Paper Due 5 PM 36 12/6 Glycolysis /8 Glycolysis /10 Glycolysis 16.2 Final Exam Tuesday 12/14 10:30-12:30 pm * Modifications to this schedule may occur. Any modifications will be announced in class. Exam dates will not be changed. ** Reading may be modified. Any modifications will be announced in class.

6 Students majoring in Adolescence Education: Chemistry 7-12 will focus on acquiring knowledge and developing skills aligned with learning outcomes from the College's Conceptual Framework for Teacher Education and those established by the National Science Teachers Association. In particular, this course addresses Conceptual Framework Learning Outcome 2: Possess in-depth knowledge of the subject area to be taught; Conceptual Framework Learning Outcome 13: Demonstrate sufficient technology skills and the ability to integrate technology into classroom teaching/learning; NSTA Standard I: Content; NSTA; Standard 2: Nature of Science; NSTA Standard 3: Inquiry; NSTA Standard 4: Issues; and NSTA Standard 7: Science in the Community.