BIOCHEMISTRY 302 / BIOLOGY 302 / 502 BIOCHEMISTRY: METABOLIC ASPECTS

Transcription

1 BIOCHEMISTRY 302 / BIOLOGY 302 / 502 BIOCHEMISTRY: METABOLIC ASPECTS Dr. Anna Tan-Wilson Spring 2004 For more information on the course including how to contact your instructor and teaching assistant, log on to Also purchase the course pack available at the campus bookstore. OBJECTIVES AND EXPECTATIONS Goals: to learn (i) how the structures of major macromolecular components of cells make them suitable for their function; (ii) the biochemical reactions that are central to cell function; and (iii) the regulation of such reactions. Students will apply these basic concepts to understanding of cellular and physiological functions as well as to practical medical and industrial applications. Another set of goals: to develop skills needed in scientific work such as formulating and testing hypotheses, constructing and analyzing graphs, retrieval of information, computation, problem-solving and communication skills. PREREQUISITE You must have completed and remembered the basic principles learned in: Organic Chemistry I and II, especially bonding and the reactions / mechanisms relating to alcohols, aldehydes, ketones, carboxylic acids, carboxylic acid derivatives, amines, saturated and unsaturated aliphatic hydrocarbons Introductory Chemistry, especially bonding, free energy, enthalpy, entropy, chemical equilibria, chemical kinetics, electrochemistry, and uv-visible spectroscopy Introductory Cell and Molecular Biology - concepts of protein structure, how enzymes catalyze reactions, membranes and subcellular compartments, glycolysis and the TCA cycle, electron transport, oxidative phosphorylation, photophosphorylation, signal transduction. In this course, you will review these concepts, learn more detail, and do so in the context of chemical principles and chemical structures. CREDITS Four credits, also W credit as partial fulfillment of Harpur College writing requirement COURSE FORMAT Four one-hour sessions a week. Each session may be a combination of lecture, discussion, in-class work, and quizzes. Attendance of all sessions is mandatory. Lectures and in-class work define the scope and depth of the information that you are expected to learn. Classes are also designed to strengthen skills that scientists need: data analysis and interpretation, experimental design, information retrieval and selflearning, practical problem-solving and communication. Skills learned during these sessions will be needed to do well in all the exams.. 1

2 TESTS Scope and depth - based on lectures and in-class work Some questions are based on factual information. Others test your ability to relate one fact to another, and to suggest solutions to hypothetical problem situations. Although questions focus on new lessons, I presume that you will have understood and remembered the most important points covered in previous tests. Three one-hour essay tests, plus a fourth given during finals week. All four tests are mandatory. Part of each test will be take-home essay format. Test details: There will be 110 points on each test, but 100 will be counted as maximum. This will allow students to skip 10 points worth of questions or miss answering 10 points correctly without penalty. However, there will be a cut-off at 105. In other words, a grade of 108 will be recorded as 105. Due to the nature of the material covered, students will be allowed to bring notes on a 4 x6 card in to Tests III and IV. [not the first two exams]. Test average will be calculated as follows: Test with highest grade 30% Test with lowest grade 20% Other two tests each 25% Missed tests: If you have a conflict with an interview, official athletic competition, or other event that cannot be rescheduled - arrange to take the test earlier. In case of illness or unexpected calamity that prevents a student from taking any one of the first three tests, you must inform me ahead of the test. No acceptable reason for missing a test student gets a zero for the missed test. WRITTEN PROJECTS, GRADED IN-CLASS WORK, QUIZZES From time to time, we will assign homework, give an unannounced quiz, or collect and grade in-class work. There will be no make-up for these. Students who miss one due to illness, unexpected calamity or unavoidable circumstance such as interviews must inform the TA before class. Only in such circumstances will the absence of a score not be counted; ie. if 10 quizzes are given and one is missed, the sum of the 9 scores will be averaged over 9 quizzes. Students should not keep missing class, however. Note the following excerpt from the Academic Bulletin: Students are expected to attend all scheduled classes and laboratories. An instructor may deny a student the privilege of taking the final examination or of receiving credit for the course, or may prescribe other academic penalties, if the student misses more than 25 percent of the total class sessions. Excessive tardiness may count as absence. In cases of excessive absence, the instructor may request the appropriate academic advising office to investigate. 2

3 GRADUATE CREDIT Students earning graduate credit will have additional assigned work such as additional written assignment, to be graded on Pass/Fail basis. All such assigned work MUST be completed. Aside from that, final grades will be calculated as described below. CALCULATION OF FINAL GRADES Test average - 90% Projects, graded in-class work, quizzes - 10% LETTER GRADES Students who get grades of 90% and above will receive an A for the course. Grades in the B and C range are usually pegged to the average, which may be the mean. [In cases where there are some unusually low grades, the median may be taken instead.] The passing grade is usually 60%. D is a passing grade. INC is given only for a missed final exam due to illness or unexpected calamity GRADES OF INCOMPLETE ARE NOT GIVEN IN LIEU OF FAILING GRADES! Please do not ask! Every student gets the same chance to earn a good grade. This is why work for extra credit to make up for low grades is NOT given on an individual basis. Please do not ask! All students in the class will be given ample opportunity to earn extra credit through extra questions in tests. ACADEMIC HONESTY For all incidences of cheating or plagiarism, a student will receive a grade of zero for the test, project, or assigned work. Note that aside from the usual definitions of cheating with regard to tests and quizzes, working beyond the circle of accepted partnerships is also considered cheating. In other words, if you are assigned individual work, do it alone. If you have group work, keep to your own group. Furthermore, all incidences will be prosecuted according to the guidelines set by Harpur College. RESOURCES AND OTHER MATERIALS 1. Course booklet - bring to all lectures 2. Textbook Lehninger Principles of Biochemistry, by Nelson and Cox, 3 rd edition, Worth Publishers, 2000 [If 2004 edition is available, purchase that instead.] 3. Blackboard you must be registered and your university computer account must be active. If not, go to a computer pod and activate your account. 3

4 4. Course prerequisites are Organic Chemistry II (and the general chemistry courses that are prerequisite to Organic Chemistry) and Biology 113 / 114. These courses must be completed since Biochemistry relies heavily on them. 5. Science library and Internet resources Several other Biochemistry textbooks will be on reserve at the Science Library. Learn how to use the library databases on the web. 6. Electronic listserv You must check your university account regularly for supplemental information and instruction. Also use to ask questions and to share information with the rest of the class. Off-campus, you can access university through webmail.binghamton.edu 7. Consultation with instructor and teaching assistants My office is in Science III Room 110 Graduate TA is Zhenzhen Zhou. Her office is in Science III, Room 108. Hours will be announced. 8. Form a study group and meet regularly to review lectures and to answer practice questions. HOW TO DO WELL IN THE COURSE Biochemistry is cumulative. Keep up week by week. Do not assume that once a lesson is over that you can forget it. Study by reading AND writing. 4

5 Schedule of Topics Biochemistry, Spring 2004 UNIT I PROTEIN STRUCTURE AND FUNCTION Biomolecules: macromolecules & their monomeric subunits Water: weak interactions in aqueous systems, ionization, buffering, water as reactant Amino acids, Peptides and Proteins: amino acids, peptides and proteins, working with proteins, covalent structure of proteins The Three-dimensional Structure of Proteins: overview, protein secondary structure, tertiary and quaternary structures, protein domains, denaturation and folding Protein function: reversible binding of ligand to a protein, complementary structures between proteins and ligands, protein interactions Laboratory procedures: protein separation, isolation, analysis, study of protein-protein interactions Test I on Monday, February 15 UNIT II MEMBRANE STRUCTURE AND FUNCTION ENZYME KINETICS AND MECHANISM Lipids: structural lipids in membranes Biological Membranes and Transport: transporters and receptors on plasma membrane, molecular constituents of membranes, supramolecular architecture of membranes, solute transport across membranes Major Structural Features of Eukaryotic Cells Thermodynamics of Enzyme Reactions Enzyme Kinetics: Michaelis-Menten assumptions, kinetic parameters, inhibitors, two-substrate reactions Enzyme Mechanism: basis of enzyme catalysis, experimental evidence for mechanism using classical examples Enzyme Regulation: environmental factors that affect rates of enzyme reactions, inhibitors, activators, covalent modifications especially proteolysis and phosphorylation, allosteric regulation Biosignaling: molecular mechanisms of signal transduction, receptor enzymes, G-protein coupled receptors and second messengers, phosphorylation as a regulatory mechanism Test II on Wednesday, March 10 5

6 UNIT III BIOENERGETICS [CARBOHYDRATE METABOLISM] Carbohydrates and Glycobiology: monosaccharides, disaccharides, polysaccharides glycoconjugates, glycoproteins, glycolipids Principles of Bioenergetics: bioenergetics and thermodynamics, phosphoryl group transfers and ATP, biological oxidation-reduction reactions Glycolysis and the Catabolism of Hexoses: glycolysis, fates of pyruvate, feeder pathways for glycolysis, regulation of carbohydrate catabolism, pentose pathway pathway of glucose oxidation Citric Acid Cycle: production of acetate, reactions of the citric acid cycle, regulation of the citric acid cycle, glyoxylate cycle Oxidative Phosphorylation: electron transfer reactions in mitochondria, ATP synthesis, regulation of oxidative phosphorylation Carbohydrate Biosynthesis: gluconeogenesis, biosynthesis of glycogen, starch, sucrose Photosynthesis: general features, light absorption, light-driven electron flow, ATP synthesis by photophosphorylation Carbohydrate Biosynthesis: photosynthetic carbohydrate synthesis, regulation of carbohydrate metabolism in plants Test III on Wednesday, April 14 UNIT IV BIOENERGETICS [LIPID METABOLISM] NITROGEN METABOLISM INTEGRATION OF METABOLISM Lipids: storage lipids Oxidation of Fatty Acids: digestion, mobilization and transport of fatty acids,?-oxidation, ketone bodies Lipid Biosynthesis: biosynthesis of fatty acids and eicosanoids, biosynthesis of triglycerides, biosynthesis of membrane phospholipids, biosynthesis of cholesterol, steroids and isoprenoids Amino Acid Oxidation and Production of Urea: metabolic fates of amino groups, nitrogen excretion and urea cycle, pathways of amino acid degradation Biosynthesis of Amino Acids: overview of nitrogen metabolism, biosynthesis of amino acids Integration and Hormonal Regulation of Mammalian Metabolism: tissuespecific metabolism, hormonal regulation of fuel metabolism, hormones: diverse structures for diverse functions, long-term regulation of body mass Test IV during Finals Week, as scheduled by the Registrar 6