BME 50A Cell and Molecular Engineering I Winter 2016 Prof. Chang Liu Lectures: MWF 12:00-12:50pm (RH101) Discussions (tentatively): Xiang Li M 9:00-9:50am; W 1:00-1:50pm Kamran Ali M 4:00-4:50pm; M 5:00-5:50pm No discussion for weeks of Jan 4, Jan 18, Feb 15 Office Hours: Prof. Liu M 8:30am, NSII 3105 Xiang Li W 8:00-9:00am, NSII 3212 Kamran Ali F 9:00-10:00am, NSII 3202 Theme Class Date Topic Reading (done BEFORE class) HW (turned in during the following discussion section) Chemistry and Structure 1 Jan 4 Introduction and Chemical Bonding 2 Jan 6 Organic Chemistry Crash Course pp 12 figure, 39-50, 66-69, 78-79 Handout 1: On Chemical Bonding (5 files in this handout) 3 Jan 8 Nucleic Acids pp 50-51, 55-58, 76-77, 171-187 Handout 2: Crick’s letter to his son 4 Jan 11 Proteins 1 pp 58-64, 74-75 Handout 3: Reasons for the 20 amino acids 5 Jan 13 Proteins 2 pp 121-1576 Jan 15 Lipids and Carbohydrates pp 51-55, 70-73, 360-372 HW1 (Turn in today in class) – Answer key will be released on dropbox Information 7 Jan 20 The Significance of the Central Dogma pp 3, 55-56, 58-64, 224 Handout 4: Philosophy of science entry on molecular biology Jan 22 EXAM 1 (Covers material up to and including class 6) 8 Jan 25 DNA Replication pp 197-210 Handout 5 (optional): Schrodinger’s Essay “What is Life?” 9 Jan 27 DNA Repair, and Recombination pp 211-220 10 Jan 29 Transcription pp 223-238 11 Feb 1 Translation 1 pp 238-256 12 Feb 3 Translation 2 Handout 6: Crick’s On Protein Synthesis 13 Feb 5 Basic Mechanisms of Gene Evolution pp 289-306, 652 HW2Regulation and Signaling 14 Feb 8 Levels of Control pp 261-268 Handout 7: Monod’s chapters on Molecular Cybernetics and Molecular Ontogeny from “Chance and Necessity” 15 Feb 10 Transcriptional control and the lac Operon pp 268-269 16 Feb 12 Post-transcriptional Control pp 280-284 Feb 17 EXAM 2 (Covers material associated with classes 7-15 inclusive) 17 Feb 19 Cell Signaling Principles pp 525-539 HW3 Energy 18 Feb 22 Free Energy and Catalysis pp 90-102, 104-106 19 Feb 24 Glycolysis and Fermentation pp 103-115, 420-429 20 Feb 26 The Citric Acid Cycle pp 430-437 21 Feb 29 Mitochondria and Oxidative Phosphorylation pp 438-443, 447-469 Modern Genetic Engineering Techniques and Trends 22 Mar 2 PCR and Cloning 1 pp 325-341 23 Mar 4 PCR and Cloning 2 HW4 24 Mar 7 DNA Synthesis, Sequencing and Genomics pp 339-35525 Mar 9 Synthetic Circuits Handout 8: Popular press piece on synthetic biology 26 Mar 11 Gene Editing and Therapy Handout 9: Popular press piece on CRISPR Mar 14 Final Exam (covers all material) Textbook: Alberts et al., Essential Cell Biology, 4th Edition Also available as e-book: http://store.vitalsource.com/show/9781317806271 Handouts: These will be uploaded on the course Dropbox (Cell & Mol Eng I/Course Files/Handouts). The Dropbox can be accessed through the Electronic Educational Environment (EEE) website. Lecture Slides and Notes: Lectures will be done on the board. Each lecture may have a couple of slides associated, which will be posted on the Dropbox, but please note that these slides do not cover the lecture material. As for lecture notes, you are responsible for taking your own notes. If you are not able to attend a class, please get notes from someone else. There are some lectures where I’ll draw precise or intensive figures; for these, I will upload a copy of my notes on the Dropbox. Reading: The reading load varies, so please plan ahead. You are expected to have read the material before each class.HW: HW will be graded for completeness and answers will be discussed at the following discussion section. HWs and answers will be uploaded in the course Dropbox (Cell & Mol Eng I/Course Files/HWs). Grading: HW: 5% Exam 1: 22.5% Exam 2: 22.5% Final Exam: 50% (will replace lowest midterm if it helps) Late Policy: HW will not be accepted if late. Missed Exam Policy: Your final exam grade has the power to replace one (but not both) of your other exam grades. I will automatically replace one of your exam grades with the final exam grade if the final exam grade is higher than one of your exam grades. If your final exam grade is higher than both of your exam grades, I will replace the one that maximizes your course grade. Because this policy allows you to miss one exam, there will be no makeup exams, except under truly exceptional circumstances. Academic Honesty: Exams are meant to test each student’s individual command of the material at the time of the exam. Any action that violates this intent will be considered academically dishonest and will be dealt with appropriately. During the course of an exam, obvious violations include copying from someone else’s exam, communicating using text messaging, searching the Internet, bringing in outside materials, etc. Any such violation will result in an F.Outside of exams, you are encouraged to work together, especially when preparing for class and discussing reading. For HW, you are allowed to help each other on the HW; but work through the HW yourself before collaborating to get the most out of