BIOL 5099 Syllabus for Fall 2002

1. Introduction: Educational Philosophy, Key Ideas and the Central Dogma
2. Evolution
   1. Replicating Systems & Inheritance
   2. Natural Selection
   3. Sources of Variation
      1. Mutation
      2. Mendelian Genetics
   4. Fitness landscapes
   5. CoEvolution
      1. Predator/Prey
      2. Symbiosis
   6. Mathematical and computational models of evolution (e.g. genetic algorithms).
3. A bit about the history of life
   1. Evolutionary time scales
   2. Metabolism recapitulates biogenesis
      1. Self-reproducing chains of chemical reactions
      2. Membranes and insides vs. outsides
   3. Mass extinction as a way of life
   4. Some eras and their critters
      1. Pre-Cambrian (early life)
      2. Cambrian (great weird critters)
      3. Paleozoic (duncleosteous and sharks)
      4. The Mesozoic (dinosaurs)
      5. The Quaternary (human ancestors)
   5. Today's mass extinction event and the end of wilderness.
4. Just a little chemistry
   1. Atoms & Molecules
   2. Relevant environmental conditions: temperature, pH, pressure
   3. Covalent bonds
   4. Reactions & Stoichiometry
   5. Catalysis
   6. Non-covalent bonds
5. Simple Life: Prokaryotes
   1. Survival of the fastest reproducer
   2. Autotrophs vs. heterotrophs
   3. Energy capture and management
      1. ATP and other energy carriers
      2. Photosynthesis
   4. Materials & Metabolism: The components of a cell and their synthesis
      1. Cellular components, membranes & biomolecules
      2. Intermediary metabolism
      3. DNA replication
   5. Chemotaxis: Sensation, Awareness and Action
   6. Horizontal transmission and bacterial sex
   7. Modern is not ancient: bacteria are contemporary organisms
6. Eukaryotes
   1. Symbiosis and the origin of the eukaryote
   2. Eukaryotic cellular organization and organelles
   3. Chromosomal structure, chromatin and Eukaryotic DNA
   4. Ribosomes, Mitochondria and chloroplasts
   5. The classes of Eukaryotes
7. Biological Macromolecules
   1. The molecules and their assays:
      1. DNA sequencing, PCR, genotyping
      2. RNA, alternative splicing and cDNAs
      3. Proteins, gels and mass spec
      4. Antibodies, and immunological staining
   2. From DNA to activity
      1. Transcription
         1. Gene structure
         2. Transcriptional Control
         3. Gene expression array instrumentation
      2. Translation
      3. Post-translational modifications
   3. How biomolecules work together: Pathways and Molecular Machines
      1. Intermediary metabolism in more detail (TCA)
      2. Signal Transduction (cAMP?)
      3. Genetic regulation (lac operon?)
8. Death, rebirth and differentiation: The grand deal of multicellullar organisms
   1. Why be somatic?
   2. The genetics of altruism
   3. Mitosis & Meiosis
   4. Intercellular signaling: ligands, receptors and signal transduction
   5. Development and differentiation
      1. Stem cells
      2. A little embryology
   6. Apoptosis and cell death
   7. Cancer as a breakdown in the deal
9. Genome Projects and Genetic Engineering
   1. Genome Projects, human and others
   2. Cloning
   3. Knock-ins, knock-outs, transgenics
   4. Commercialization and ethical considerations
10. Model organisms
    1. E Coli
    2. Yeast
    3. C elegans
    4. Arabidopsis
    5. Drosophila
    6. Mice and other mammals
    7. Human cell lines
    8. Computational modeling
11. A quick tour of the human body
    1. Systems and physiology
    2. Tissues and cell types
    3. The nervous system
    4. The immune system
12. Pathology & Disease
    1. General Principles
    2. Sepsis
    3. Cancer
    4. Aging
13. The Future of Medicine
    1. Molecular therapeutics and drug design
    2. Pharmacogenomics and individualized therapy
    3. From Curative to Predictive