CourseInfo_2006

Most serious i encourage simultaneous enrollment in

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most serious I encourage simultaneous enrollment in the laboratory course, APh162 - Physical Biology Laboratory, which will be built around a series of experiments which are designed to correspond with material covered in the lecture course APh161. 2 Tentative Course Outline The course outline given below is intended to provide an overall sense of the topics we will cover and the general flow of the course. Certain individual topics might be added or deleted as I see fit. 1. Biology - A Feeling for the Numbers 2
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Spatial scales. The size of things - molecules, macromolecular assemblies, organelles, cells, tissues, organisms. Temporal scales in cells. How fast? From molecular vibrations to development - a hierarchy of time scales. Balancing the budget of the cell. Mass budget of the cell. Energy budget of the cell. 2. Genome Management Genomes and the Central Dogma. Information content of genomes (aside on central dogma and “the two great polymer languages”). Gene Expression. How much, when, where and how fast? Case studies from metabolism and development. The mechanisms of genetic control. Transcriptional Control. Statistical mechanics of gene expression. The fabled case of the lac operon. The fabled case of the lambda switch. Dynamics of gene expression. Biological Accuracy. Error rates during translation. Kinetic proof- reading. Packing the Genome. Physical size of genomes. Packing the genome in viruses, prokaryotes, eukaryotes. DNA Management During the Cell Cycle. The cell cycle. The machines of replication. Chromosomal territories and DNA seg- regation. The case of ParM and plasmid segregation during cell division. 3. Dynamics in and of Cells Phenomenology of Cellular Dynamics. Dynamics in the cell. Dy- namics of the cell. Enzyme dynamics. Phenomenology of enzyme action. Rate equa- tions. Michaelis-Menten dynamics. Molecular Motors. A rogue’s gallery - translational and rotary motors. Experimental backdrop. What is a muscle and how does it work? Theories of motor action. The case of kinesin. Traffic within cells. 3
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4. Processes at Membranes Membrane Phenomenology. lipids, membrane area, membrane composition, ions and ion transport. Membrane structures and deformation. A tour of vesicles and membranes. The plasma membrane. Mitochondria, the endo- plasmic reticulum and the Golgi apparatus. Modelling membrane deformation - the Helfrich free energy. Curvature management - making vesicles, viral budding and beyond. Ion Channels. Mechanosensation and tension gating. Action po- tentials and voltage gating. 5. Miscellany on Physical Biology Motility. Physical content of cells - how many copies of the vari- ous molecular actors in the cellular drama. The mean spacing of molecules. Signaling and Chemotaxis. Phenomenology of signaling. Statisti- cal mechanics of snip and stitch. The case of chemotaxis.
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