Biological Systems

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  1. Genetic Engineering
    1. Restriction Enzymes
    2. Polymerase Chain Reaction (PCR)
    3. Primer Design
    4. Ligase
    5. Plasmids
    6. How to prepare electrocompetent ''E. coli''
    7. Transformation with ''E. coli''
  2. Cell Physiology
    1. Bacterial Growth
    2. Metabolism
      1. Glycolysis and Gluconeogenisis
      2. Tricarboxylic Acid Cycle (also Krebs or Citric Acid Cycle)
      3. Cellular Respiration (also Oxidative Phosphorylation, mediated by the Electron Transport Chain)
      4. ATP Synthase
      5. Pentose Phosphate Pathway
  3. Cell Signaling
    1. lac operon
    2. Gene Regulation and Protein Levels
    3. Simple Gene Regulation
    4. Statistical Mechanics of Binding
    5. Stochastic Gene Expression
    6. Optimality and Evolution
    7. Genetic Toggle Switch
    8. The Repressilator
    9. Transcription Networks
    10. Network Motifs
      1. Lever
      2. Buzzer (Goldbeter-Koshland switch)
      3. Fuse
      4. Autoregulation
        1. Negative Autoregulation (NAR)
        2. Positive Autoregulation
      5. Feed Forward Loop (FFL)
      6. Single Input Module (SIM)
    11. Hill Function
    12. Robustness
  4. Biochemical Kinetics and Theromdynamics
    1. Isolated, Closed and Open Systems
    2. Chemical Potential
    3. Fluctuations about the mean energy
    4. Law of Mass Action (Reaction Rate Law)
    5. Michaelis Menten Kinetics
    6. Reversible Michaelis Menten Kinetics
    7. Brusselator
    8. Glycolytic Oscillations
    9. Stoichiometric Matrix
    10. Separation of Timescales
    11. General Enzyme Kinetics
    12. Open Systems - Mass Balance Equations
    13. Open Systems - Entropy Balance Equation
    14. Open Systems - Flux Balance Equations
    15. Flux Balance Analysis (FBA)
    16. Osmosis and the Cell Membrane
    17. Cells and Membrane Potentials - Equivalent Circuits
    18. Succinic Acid Efflux Energy Coupling
    19. Fick's Law: From Concentration Gradients to Fluxes
    20. Diffusion
    21. Bayes Theorem
    22. Markov Processes
    23. Isotopomer
    24. Elementary Metabolic Unit (EMU)
  5. Control Systems
    1. Dynamical Systems
    2. Regulating vs. Steering
    3. Convolution
    4. Transfer Function
    5. State and Output Equation
  6. Molecular Biology
    1. Saccharides
    2. DNA Structure
    3. Central Dogma
    4. Promoter Strength
    5. Chromatin
    6. Cell Cycle
    7. Antibiotics
    8. Protein Modification
    9. Protein Translocation
    10. mRNA Processing
    11. Splicing
    12. Apoptosis
    13. Protein Trafficking
    14. G-Protein Signaling
    15. Insulin Signaling
    16. cAMP Signaling
    17. PI3K/AKT Signaling
    18. MAPK Signaling
    19. Wnt Signaling
    20. Protein Kinase C