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CHEM 351 • BIOCHEMISTRY I Syllabus • Fall 2016 INSTRUCTOR Professor Charles H. Clapp, RB 216 E-mail: [email protected] GENERAL LEARNING GOALS (Mapped to Chemistry Department Learning Outcomes) In Chemistry 351, students will: •Develop the ability to apply chemical principles to understanding the structures and properties of the major classes of biological molecules. (2, 3) •Become familiar with major biochemical pathways and develop an understanding of the energetics, chemical logic, and regulation of these pathways. (2, 3) •Develop the ability to solve problems requiring the interpretation of biochemical data and the application of chemical principles to biological problems (2, 3) •Gain experience using computer graphics to study the structures of biological molecules and learn to access data in the Protein Data Bank (2, 5). •Become aware of some important unsolved problems in biochemistry and medicine, and think about how basic biochemical tools and principles might be used to make headway in addressing these problems. (3, 8) COURSE FORMAT There will be three lectures (M W F, 10:00 a.m.) per week. In addition, each student has been assigned to one of two recitation sections, M, 1–2 p.m. and T, 11 a.m.–12 noon. These sessions will be used to discuss in more detail material presented in lecture or in readings, to present new material for discussion, and to discuss problem assignments. It is very important that you attend recitation each week. The lectures will utilize both PowerPoint and the chalk board. PowerPoint slides for a particular lecture will be placed on Moodle the day before the lecture. You should print copies of these slides and bring them with you to class. There will be no laboratory in CHEM 351. An intensive laboratory course in Biochemical Methods (CHEM 358/BIOL 340) will be offered in the spring semester. READINGS th The textbook for the course is Lehninger Principles of Biochemistry (6 ed.) by D. L. Nelson and M. M. Cox. In reading the textbook, you should keep in mind that the goal of the course is to develop a conceptual understanding of biochemistry that you will be able to apply to problem solving. Rather than trying to memorize all of the factual details, you should ask yourself whether these details fit into a coherent conceptual framework. When they do not, you should consult the instructor or one of your classmates or raise the point as a question in recitation. Comments on chapters in the textbook will be posted on Moodle to help you focus your reading and thinking on the most important points. The lectures will be designed to be complementary to the reading in the textbook. To optimize your grasp of the material, you should carefully study both the text and the class notes. I recommend that you read the sections relating to a particular class prior to that class. After the class, you can then review the reading and reread key sections that you did not fully understand the first time through. You will then be prepared to start working problems. Some important topics will not be covered in class or will only be partially covered in class, and you will be expected to master the topic from reading and doing problems. I will alert you to these topics as the course progresses Some of the topics we will cover are not covered adequately in your textbook. In these cases, the textbook readings will be supplemented by readings from the biochemical literature. These will be available in electronic form on Moodle, and I will alert you to them in class. CHEM 351 • BIOCHEMISTRY I Syllabus • Fall 2016 • p. 2 PRACTICE PROBLEMS Since the purpose of the course is to develop a working knowledge of biochemical principles, considerable emphasis is placed on problem solving. Problems will be assigned regularly. Some of these will be from the textbook; others will be in the form of weekly problem sets that will be posted on Moodle. It is recommended that you do them as soon as possible. Most of these assignments will not be collected, but they will be discussed at the recitation sessions, and a few will be discussed in class. The problems vary considerably in difficulty. Some are straightforward; others will challenge you to apply ideas presented in class to topics that have not been covered in class. In some cases problems will be used to introduce new topics. In all cases it is critical that you make a determined effort to solve these problems before they are discussed in recitation or class. If you have difficulty, stop by my office, send me an email, or talk about the problem with a classmate. If you do this, your learning will be active and much more effective than it will be if you simply listen to other people’s solutions. Answers to the problem sets will be posted on Moodle. I urge you not to consult these answers until you have worked through the problems thoroughly on your own. If you get stuck on a problem, feel free to contact me, and I will assist you without giving you the answer. Consulting one of your classmates may also be helpful. GRADED ASSIGNMENTS There will be about five short written exercises to be turned in. These will be assigned at least one week before the due dates. Some of these graded assignments will require the use of JMol, a molecular graphics program. Other assignments will require you to interpret results from the biochemical literature. OFFICE HOURS Biochemistry is a complex subject, and your goal is to understand it at a conceptual level. If you make a diligent effort to do this, you will have many questions. I am happy to meet with you individually to discuss your questions. Rather than setting aside specific office hours, I encourage you to see me after class or send me an e-mail, and we will arrange to meet at a mutually satisfactory time. You are also welcome to stop by my office without an appointment. If I am there and doing something that can be interrupted, I will be glad to talk with you. OTHER SUGGESTIONS The amount of material to be covered in the course is considerable, and the pace will therefore be fast. In addition, the course is designed so that topics build on what has been taught earlier. It is important that you make a determined effort to avoid falling behind. I expect that the reading, practice problems and written assignments will require at least eight hours per week outside of class. As indicated above, if you study and think about the course material carefully and critically, you are likely to have many questions. An excellent way to clarify your understanding is to discuss these questions with your classmates. GRADING There will be three hour exams and a final exam. The hour exams will be given at 10:00 a.m. on the days listed at right: 1. Wednesday, September 21 2. Wednesday, October 19 3. Wednesday, November 16 There will also be two or three short quizzes. They will be announced at least one week in advance. The first quiz will be on Wednesday, September 9. Grades will be computed in two ways: I. Hour exams.................................... 48% Graded assignments & quizzes ..... 20 % Final exam ..................................... 32% II. Two best hour exams .................... 32% Graded assignments & quizzes .... 20% Final exam ..................................... 48% The higher of the two computed numerical grades will be used in determining your letter grade. No make-up hour exams will be given; students who miss an hour exam will have their grades computed by the second method. ACCESS STATEMENT Any student who may need an accommodation based on the impact of a disability should contact Heather Fowler, Director of the Office of Accessibility Resources, at 570-577-1188 or [email protected], who will help coordinate reasonable accommodations for those students with documented disabilities. CHEM 351 • BIOCHEMISTRY I Syllabus • Fall 2016 • p. 3 TENTATIVE LECTURE OUTLINE 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 Mon 22 Aug Wed Aug 24 Fri Aug 26 Mon Aug 29 Wed Aug 31 Fri Sept 2 Mon Sept 5 Wed Sept 7 Fri Sept 9 Mon Sept 12 Wed. Sept 14 Fri. Sept 16 Mon Sept 19 Wed Sept 21 Fri Sept 23 Mon Sept 26 Wed Sept. 28 Fri Sept 30 Mon Oct 3 Wed Oct 5 Fri Oct 7 Mon Oct 10 Wed Oct 12 Fri Oct 14 Mon Oct 17 Wed Oct 19 Fri Oct. 21 Mon Oct 24 Wed Oct 26 Fri Oct 28 Mon Oct 31 Wed Nov 2 Fri Nov 4 Mon Nov 7 Wed Nov 9 Fri Nov 11 Mon Nov 14 Wed Nov 16 Fri. Nov 18 39 40 41 42 Mon Nov 28 Wed Nov 30 Fri Dec 2 Mon Dec 5 Cells. Molecules and Energy Water and Aqueous Solutions Intro. to Peptides and Proteins Amino Acids Primary Structure. Mass spectrometry Mass spec (cont). Solid-phase synthesis Three-dimensional Structure Quiz 1 Quaternary Structure Protein Folding Collagen. Post-translational Modification. Myoglobin Hemoglobin. Allosteric Regulation Allosteric regulation (cont.). Sickle-Cell Hemoglobin Enzyme Catalysis and Kinetics Exam I Enzyme Kinetics (cont.), Inhibition Serine Proteases Acetyl Cholinesterases, Nerve Agents, Cysteine Proteases Aspartyl and Metalloproteases Kinases Synthetases. Allosteric Regulation of Enzymes Carbohydrates Fall Break Carbohydrates and Glycoproteins Nucleic Acids. Structure and Conformation Polymerases, Nucleases and Ligases Exam II Lipids and Membranes Membrane Proteins Receptors. Signalling Bioenergetics Biological Redox Reactions Glycolysis Metabolism of Pyruvate Citric Acid Cycle Oxidative Phosphorylation Oxidative Phosphorylation Gluconeogenesis Exam III Regulation of Carbohydrate Metabolism Thanksgiving Break Fatty Acid Oxidation Pentose Phosphate Pathway Glycogen Synthesis and Breakdown Regulation of Glycogen Synthesis and Breakdown. Wrap up Chapter 1 Chapter 2 3.1–3.3 3.1 3.4 3.4 4.1–4.3 4.3 4.4 pp. 127–130, 157–163 5.1 5.1 6.1–6.3 6.3 pp. 214–218, 231-232 pp. 218–219, 219-220 pp. 206–207 6.5 7.1 7.1–7.3, pp. 221–223 8.1, 8.2 8.3, pp. 1013–1014, 1024 Chapter 10 11.1–11.3 12.1–12.3, 12.12 13.1–13.3 13.4 14.1 14.3, 16.1–16.2 16.2 19.1–19.2 19.1–19.2 14.4 15.1, 15.3, 16.3, 19.3 17.1–17.3 14.5 15.4–15.5 15.5, 12.2