Macromolecules (Biochemistry 200A) 2009 Lectures
Course Goals: The primary goal of this course is to make students more familiar with proteins: How to handle them; how to purify them; how to determine and understand their structures; and how to detect and characterize their interactions. We begin by discussing the physical and chemical properties of proteins and by outlining strategies for detecting biochemical activity in complex cell extracts and then purifying the protein responsible. Next, we will discuss ways to characterize the activities and interactions of purified proteins using basic thermodynamics and pre-steady state kinetics. We will then explore the wonderful world of structural biology and describe how to determine molecular structure at various levels of resolution using electron microscopy, x-ray crystallography, and NMR spectroscopy. Finally, we will explore modern techniques for studying the structure and function of single protein molecules. At the end of the course you will not only be more comfortable hanging out with large, biological molecules, you will love them. Oh yes, you will love them. Lectures are 9:00-10:00 in BH 212 and Review Sessions are Thursdays 10:30-12:00 in BH 212. Week 1: January 5-8 Lecture 1: Protein Structure I – JJ Miranda (Molecular forces, intro) Lecture 2: Working With and Purifying Proteins – Jonathan Weissman - Postponed until 1/8 at 10:30 Lecture 3: Determining and Analyzing Molecular Interactions - Geeta Narlikar Lecture 4: Introduction to Thermodynamics, Binding and cooperativity I – Geeta Narlikar Lecture 2 Makeup: Thursday 1/8 at 10:30-12 in BH215, Working With and Purifying Proteins – Jonathan Weissman Week 2: January 12-15 Lecture 5: Binding and Cooperativity II – Geeta Narlikar Lecture 6: Binding and Cooperativity III – Geeta Narlikar Lecture 7: Kinetics Workshop – Dyche Mullins Lecture 8: Enzyme Kinetics – Geeta Narlikar Review: 10:30-12, Thursday: lectures 1-7 Week 3: January 20-22 (Jan 19: Martin Luther King Jr. day – no class) Lecture 9: Systems Biology – Jonathan Weissman; Problem Set 1 Due in class Lecture 10: Statistics and Data Analysis – Jonathan Weissman Review session: 10:30-12, Wednesday, Lectures 8-10 and prepare for midterm. Extra Review Session Week 4: January 26-29 Lecture 11: Mass Spectrometry – Jonathan Weissman; Midterm Distributed Lecture 12: Protein Structure II – JJ Miranda
Lecture 13: X-Ray Crystallography I – David Agard; Midterm Due 5pm. Argenta’ Desk. Lecture 14: X-Ray Crystallography II – David Agard Week 5: February 2-5 Lecture 15: Cryo-Electron Microscopy – Yifan Cheng Lecture 16: Fluorescence Spectroscopy – Dyche Mullins Review: 10:30-12:00 Tuesday 2/3. Lectures 11-15 Lecture 17: Single Molecule Techniques – Dyche Mullins; Problem Set 2 Due in class Lecture 18: NMR Spectroscopy – John Gross Feb 10: Review Session with Geeta. 9-12. BH212. Feb 11: Discussion Session with Robert Fletterick and Dave Agard. GH S204 and S271 February 13: Final Distributed. Final Due: 2/16/09 by 5 PM sharp on Argenta Price’s desk (Guthrie Lab, GH N374) Supplemental Workshops – Location TBA Jan 27, 2:30-3:30 PM. Workshop1: Primer to X-ray crystallography and how one turns a diffraction pattern into structural data. (Dave Agard) Feb 3, 2:30-3:30 PM. Workshop 2: Diffusion and centrifugation. (Dyche Mullins) TA Office Hours The TAs will be holding "office hours" throughout the course. These are designated times when we will definitely be in our respective labs to answer your questions. You are of course welcome to stop by at other times, though we may not be around. You can also email us (addresses below) and we will do our best to respond in a timely manner. Please please please please don't email us late the night before something is due because each of your classmates is doing the exact same thing and we can't guarantee a(n adequate) response. Day Monday Tuesday Wednesday Thursday Time 1-3 2-4 1-3 2-4 TA Silvi Colin Argenta Ashley Location Weissman Lab, BH 403 Reiter Lab, RH 446 Guthrie Lab, GH N274 Andino Lab, GH S572