Cell Physiology of Disease A)Good Parasites Gone Bad B)Weak Parts Make Weak Machines

1. Cell Physiology of DiseaseA)Good Parasites Gone Bad B)Weak Parts Make Weak Machines Professors: Michael Sheetz, 713 Fairchild, ms2001@columbia.edu Julio Fernandez, 1013 Fairchild, jfernandez@columbia.edu Teaching Assistant: Tim Marmo, tpm2003@columbia.edu

2. Plan for Course Jan. 21-March 8 Cellular Physiology of Pathogens March 10 Mid-term March 22-May 3 Physiology & Diseases of Nerve and Muscle Final

3. Grading Mid-term 33% Final 67% Exams will be written problems analogous to the problems given at the end of each lecture syllabus. Extra Credit: There will be extra credit assignments that can add up to 20% of the final grade.

4. Office Hours and TA Discussions Dr. Sheetz 713 Fairchild Tuesdays 11:30-1 Questions from the lectures or the syllabus Tim Marmo 800 Fairchild Thursdays 4:10-6 Discussion of the problems at the end of each syllabus. It is most beneficial if you have worked on the problem.

5. Cells have been around for about 2 billion years. Just imagine the sophistication of PDAs in 2 billion years

6. This is a comparison of the % identity between sequences of human hemoglobin and other species as a function of the time since they diverged in evolution. Note: the sequences of human and tuna hemoglobin are 55% identical because they evolved independently for 450 million years.

7. Systems Engineering and Cells Systems Engineering in Chemical Engineering involves the optimization of a process for the production of a chemical from raw material Cell Selection The process of selection of cells for survival with limited resources or changing environmental conditions results in a similar optimization. Computer or Automobile Evolution Many commercial products have evolved similarly from a basic functioning unit to a highly sophisticated system with many engineered features.

8. Cell Optimization and Robustness Robustness in the context of cellular functions means that the important task can be completed even as conditions vary. Some of the obvious variables for cells are listed below: number of proteins per cell salinity and pH temperature nutrient level environmental factors.

9. Engineering Cells for Robustness Compartmentalization of Functions: It is much easier to perform a complex function if the local environment can be customized Modularity in Functions: If we consider highly engineered items, they typically have modules that contain the machinery to complete a given function. Term limits: If a cell continues down a given path for a long period, there

11. Cells Have Different Phases for Different Functions Specialized Functions Require Phase Change: Many functions of cells are so complex that the phase of the cell must be altered through changes in state of many proteins or expression. Phase Changes Are Discontinuous: Cells appear most often to undergo a rapid switch from one phase to another with the appropriate signal. Populations of Clonal Cells Can Be in Many Phases: Even though a group of cells originated from the same cell and are grown in the same medium, they can be in different phases.

12. Phases of the cell cycle are bounded by definite checkpoints that aid in making the transitions abrupt.

13. The Critical Function of Cells is to Propagate DNA DNA Encodes Plan for the Organism: Survival of the organism means propagation of the DNA. Information Exchange is Critical for Survival: When one organism in a population has a mutation that enables it to survive a challenge, others will potentially benefit by sharing that information.

17. Parasitic Relationships Exist at Many Levels Not All Small Organisms Are the Food of Larger Ones: Many small organisms can survive with material that they obtain from larger organisms. Subcellular Parasites Cannot Survive Outside the Cell: Bacteriophage and viruses have found ways to propagate their DNA (RNA) through co-opting many functions of the cells that propagate them.

19. Reading for next lecture: Molecular Biology of the Cell, Alberts et al., 4th Edition Chapter 25 Pathogens