Spring 2003Prof.: David FushmanTeaching Assistant: Ms. Ranjani VaradanCourse DescriptionCourse Outlinep. 1 BCHM 461: Biochemistry I Section 0101: TuTh, 8:00-9:15 am, Chemistry 1402 Spring 2003 Prof.: David Fushman Office: Room 1121 Agriculture/Life Sciences Surge Bldg (#296); x53461, [email protected] (much preferred to phone), Please restrict telephone inquiries to office hour times, except in “emergencies”. Email is welcome anytime. Office hours: Tuesday, 3:00pm-4:00pm, Thursday, 11:00am-12:00noon, Teaching Assistant: Ms. Ranjani Varadan Office hours: Monday, 4-5pm, Wednesday, 4-5pm, Room 1122, Agriculture/Life Sciences Surge Bldg., x58710, [email protected] Course Description Biochemistry is the study of the molecular basis of life. Biochemistry 461 is an introductory course that will focus on basic concepts in biochemistry and will provide the vocabulary and grammar needed to pursue further course work and research in this field. We will cover the four major classes of biological molecules: proteins, carbohydrates, lipids, and nucleic acids. The emphasis will be on the chemical properties and three-dimensional structure of these molecules in relationship to their biological function. Textbooks: Required: Lehninger Principles of Biochemistry, 3rd edition, by Nelson and Cox. Recommended: The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry, 3rd edition, by Osgood and Ocorr. The publisher’s web site (http://www.worthpublishers.com/lehninger) that accompanies the Lehninger textbook, contains interactive tutorials to further illustrate the class material, study aids, links to protein data bases, and suggestions for further reading about some topics. Additional recommended sources (on reserve in the Chem. library, no need to buy them): Biochemistr,y 2nd edition, by Voet and Voet. Biochemistry 3rd edition, by Mathews, van Holde, and Ahern. There is a course homepage at: http://gandalf.umd.edu/BCHM461/ where you will find a copy of the syllabus, practice problems, study hints, and extra materials. Some of these materials will be posted as we proceed with the course. You are welcome to email your questions and comments. I do not guarantee individual responses, but errors or common points of confusion will be addressed in class.p. 2 Course Outline The exact order of topics and the number of lectures on each may change. 1. Introduction (2 lectures) ∗ The molecular logic of life Ch. 1 Biomacromolecules: Composition and principles of organization Ch. 3 pp. 53-65, 69-73 Energy and principles of bioenergetics Ch. 1, pp. 9-12 Ch. 14, pp. 490-499 2. Water (3 lectures) Ch. 4 Non-covalent interactions pp. 82-84, 86-91 Properties of water pp. 83-91 Acid/base properties, pH buffering capacity pp. 95-107 3. Protein structure and stability (8 lectures) Ch. 5 Amino acids – structures, nomenclature, chemistry. pp. 115-126 Primary structure – the peptide bond, sequence homology and evolution, synthesis pp. 126-129, 150-153 Methods for protein purification and analysis. pp. 130-150 Secondary structure – α-helices, β-sheets, turns, Ramachandran plot, structure prediction pp. 159-169 Tertiary structure, protein motifs & structure classification. pp. 170-177, 182-188 Quarternary structure pp. 171-172, 188-191 Protein folding and dynamics pp. 191-198 Methods for protein structure determination pp. 178-181 4. Protein function (8 lectures) Protein-ligand interactions. Oxygen binding proteins Ch. 7, pp. 203-221 Quantitative analysis of protein-ligand interactions Ch. 7, pp. 206-209 Cooperativity, allostery Ch. 7, pp. 214-216 Enzymes -- how they work Ch. 8, pp. 243-257 Enzyme kinetics – Michaelis-Menten equation, Lineweaver-Burke plots Ch. 8, pp. 257-266 Enzyme inhibition -- mechanisms Ch. 8, pp. 266-269 Examples of enzymatic reactions Ch. 8, pp. 269-289 5. Carbohydrates and glycobiology (2 lectures) Ch. 9 6. Nucleotides and Nucleic Acids (2 lectures) Ch. 10 7. Lipids and Membranes (2 lectures) Ch. 11, 12 ∗ Note that Chapter 3 in Lehninger includes a short review of some basic chemical principles, structures, and reactions. I will not go over this material in the lecture but I urge you to review it yourself, especially if it has been some time since you last saw these topics.p. 3 Examinations will be given on the following dates: I Tuesday, February 25 II Tuesday, March 18 III Tuesday, April 29 Final exam: Wednesday May 21, 10:30am-12:30 pm These exam dates are firm. The quiz dates will be announced on a previous lecture or earlier. Grading Policies. Each exam during the semester will be worth 100 points and the final exam will be 150 points. Exams during the semester will include only the material covered since the previous exam but will inevitably draw on information from earlier in the semester. The final will cover the entire course material. The exams will include material covered in the lectures and in the corresponding sections of the textbook. Problem sets given as homework are optional, however, completing them is likely to be very helpful in your preparation for the exams. All mid-term exams will be 75 min long and will be given in the lecture hall (Chem 1402). You will be allowed to use calculators for computation only. Two of your three mid-term exams with the highest scores will count toward the final grade. In addition, you will be given five 10-15 minutes quizzes, each worth 20 points. You will be notified about their date in advance. Your final letter grade will be based on your total score calculated as a sum of your scores on all quizzes, on the two out of the three mid-term exams, and on the final exam (maximum 450 points). Grading will be done on a curve based on the overall distribution of the class scores. You will be guaranteed an A if your total score is 85% or better, a B if it is 60% or better and a C if it is above 30% of the class. Final grading will then be done using the “+/-“ grading system, as follows. The cut-offs for A, B, etc grades will be determined first. Then each letter-range will be divided into three groups: all students whose scores are in the upper third of, e.g. B range will be given a B+, those in the middle will receive a B, and the lower third will receive a B-, and so on. Regrades. If you think a mistake