Syllabus for MCB 3010/5001: Biochemistry Fall Semester 2011

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1 Syllabus for MCB 3010/5001: Biochemistry Fall Semester 2011 Instructor: Dr. Wolf-Dieter Reiter Office: TLS 406 Phone: Office hours: Wednesday, 11:00 12:00 a.m., Thursday, 2:00 3:00 p.m., and by appointment. Laboratory Instructor: Dr. Linda Guilani Office: TLS 260/266 Phone: Teaching Assistants: Katherine Launer-Felty Alessandro Rizzo Margaret Suhanovsky Topics Chapters Foundations of Biochemistry 1, 13 Cellular structure and organelles Chemical foundations Physical foundations, including bioenergetics and thermodynamics Molecules in Water 2 Weak interactions in aqueous systems ph: acids, bases and ionization Buffering against ph changes Amino acids, Peptides and Proteins 3 Amino acids Peptide bond and primary structure Purification and characterization of proteins page 1

2 The Three-Dimensional Structure of Proteins 4 Overview of protein structure Protein secondary structure Protein tertiary and quaternary structures Protein denaturation and folding Protein Function: Ligand Binding 5 Myoglobin and hemoglobin Protein Function: Enzymes 6 Introduction to enzymes Enzyme mechanisms Enzyme kinetics and inhibition Regulatory enzymes Exam I (9/26) Lipids 10 Structure and chemistry Structural lipids in membranes Carbohydrates and Glycobiology 7 Monosaccharides and disaccharides Polysaccharides Glycoconjugates Nucleotides and Nucleic Acids 8 Structure and properties of nucleotides Nucleic acid structure DNA sequence determination Principles of Bioenergetics 13 Chemical logic of biochemical reactions Phosphoryl group transfers and ATP Biological oxidation-reduction reactions DNA Metabolism 25 Replication of DNA DNA repair RNA Metabolism 26 DNA-dependent RNA Synthesis RNA processing Exam II (10/24) page 2

3 Protein Metabolism 27 The genetic code Protein synthesis Protein targeting Biological Membranes and Transport 11 Membrane proteins Transporters and channels Carbohydrate Metabolism 14, 20 Glycolysis Fermentation of glucose Gluconeogenesis in animals Photosynthetic carbohydrate synthesis The Citric Acid Cycle 16 Production of acetyl-coa Reactions of the citric acid cycle The glyoxylate cycle Exam III (11/28) Metabolism of Fatty Acids 17, 21 Oxidation of fatty acids Biosynthesis of fatty acids Light Reactions of Photosynthesis 19 Light-driven electron flow ATP synthesis by photophosphorylation Oxidative Phosphorylation 19 Electron flow in mitochondria Mitochondrial ATP synthesis Exams and Grades Exams will be given from 8 10 p.m. on the dates below: 1. Monday, 9/26 2. Monday, 10/24 3. Monday, 11/28 The final exam has tentatively been scheduled for Monday, Dec. 12, 10:30 12:30. page 3

4 Final grades will be determined with 75% weight given to the exams and 25% weight given to the laboratory grade. At the end of the semester, we will identify the lowestscoring among the first three exams, and replace its grade by the grade of the final examination if this leads to a better course grade. For instance, if the grades for exams 1, 2 and 3 are 90%, 60%, and 85%, respectively, and the grade for the final examination is 80%, a value of 80% will be entered for exam 2. If the grade for the final examination is 55% in the above example, the scores for the first three exams will remain unchanged. The final examination will be cumulative, i.e. it will cover the material of the entire course. We do not intend to apply any curving scheme to modify grades. To translate percentage grades into letter grades, we expect to use the following conversion table: A C A C A C B D B D B D Below 50 F If any of the first three exams is not taken, the score of the final examination will be entered for the missed exam. The final examination is mandatory in accordance with University regulations. As a general rule, make-up exams will not be provided. Students need to earn a passing grade for the lecture component to obtain credit for the entire course. For instance, if the grade for the lecture component of MCB 3010 translates into an F, this grade will be reported to the Registrar s Office regardless of the performance in the lab. In case of MCB 5001, lecture grades in the D range will be considered failing grades in accordance with the rules of the Graduate School. For instance, if a graduate student receives a lecture grade of D+, this grade will be reported as the final course grade regardless of the performance in the lab. During examinations, textbooks or notes may not be used. Bags and backpacks should be left in the front of the classroom. You need to bring a standard scientific calculator such as a TI-30XA to all exams. The use of graphics calculators and any other electronic devices with substantial memory capacity is prohibited. Students are strongly encouraged to check their graded exams for obvious grading errors such as arithmetic mistakes or receiving no points for entirely correct answers. In these cases the problem will be corrected by the instructor. What are you responsible for? 1. Material covered in class. A good set of lecture notes is advisable for most students but reliance on the text and the lecture slides works well for others. Slides used during the lectures will be available on HuskyCT in PowerPoint and PDF format. page 4

5 2. Extensive use of the textbook to better understand the course material. Solving the problem sets in the main text and the study guide is of particular importance. 3. Firm knowledge of the structures of metabolic intermediates and the major biochemical building blocks including amino acids, nucleotides, and selected carbohydrates. 4. Graduate students need to be able to translate the one-letter codes for amino acids and nucleotides into the respective structures. Undergraduate students need to be familiar with the one-letter codes for nucleotides and the three-letter codes for amino acids. 5. Material covered in laboratory. The lab generally reinforces theory presented in the class, but some material will mostly be covered in the lab sections. 6. Strict adherence to the Student Conduct Code. Serious academic misconduct such as cheating during exams will lead to a failing grade for the entire course and be reported to the University administration for further disciplinary action. Textbook: The primary textbook will be Lehninger: Principles of Biochemistry by Nelson and Cox, 5 th Edition. The Study Guide and Solutions Manual is also suggested. Lehninger is a classic biochemistry text that was recently revised. It contains a comprehensive overview of the basics and includes coverage of several topics at an advanced level. The text will serve as a useful reference source after you complete the course. Information related to the final examination from the Dean of Students Office: The final examination has tentatively been scheduled for Monday, December 12 from 10:30 to 12:30. Students are required to be available for their exam during that time. Students must visit the Dean of Students Office if they cannot make their exam. The DOS will give the student his or her instructions thereafter. Please note: vacations, previously purchased tickets or reservations, weddings (unless part of the wedding party), and other large or small scale social events, are not viable excuses for missing a final exam. Please contact the Dean of Students Office with any questions. page 5

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