Week 1 in Review

Animal Physiology
- Nothing substantive. I'm probably going to drop this course anyway.

Computer Science for the Sciences
- Wow. I know *nothing* about programming. Eep.
- Math in Python: +, -, *, /, %
- Types in Python: str, int, float, long, bool
- Define a function: def function_name(x):
- Define a variable: variable_name=variable quantity
- I'm a clever little logic-problem solver

Organic Chemistry I
- Quick overview of Lewis structures, dipole moments, VSEPR, etc.
- Hybridization: single bonds, double bonds, and lone pairs count as "groups." The number of groups dictates the number of orbitals that hybridize.
- Lewis acids and bases are electron pair acceptors/donors
- Strength of an acid proportional to the stability of its conjugate base
- Ka = Keq[H2O]=[H+][A-]/[HA]
- pKa = -log(Ka)
- Factors that affect an acid's pKa:

  • Electronegativity of atom bonded to the proton (more electronegative, stronger acid)
  • Size of atom bonded to the proton (the larger the atom, the more acidic the compound)
  • Substituents in the molecule (electronegative substituents increase acidity, the closer the substituent is to the proton's bond, the stronger the effect)
  • Electron delocalization (resonance in the conjugate base increases its stability)
  • Hybridization (brings orbitals closer to the nucleus, increasing stability of conjugate base)
- Quite possibly the course from hell.

Animal Behaviour
- Nothing substantive, looks like a lot of fun.
- T.A. is a grad student from the lab next door. Known feminist and all around good person.
- Tutorials will be discussion-based, talking about assigned readings, marks for participation. Wheee!

Microbiology: The Bacterial Cell
- They are going to be strict about the lab rules, wow.
- Light microscopy:
  • Bright field light microscope, image determined by:
    • absorption
    • refraction
    • diffraction
    • spreading
  • Dark field light microscope, image given by reflected and refracted light
  • Phase contrast microscope, image given by refracted light only
  • Fluoresence microscope, image given by light emitted by fluorochromes excited with UV light
- Magnification, basic optics, not even highschool level
- Resolution due to numerical aperture(=amount of light the lens gathers). Physical limitations due to refractive index of air. Use oil to get better resolution. R=λ/2NA
- Confocal microscopy: laser beam reflected off specimen creates image in thin slices, compiled by computer
- Electron microscopy:
  • Transmission electron microscopy: beam of electrons through specimen (dyed with electron-dense material), specimen scatters electrons, electrons that aren't scattered are detected. Optics very similar to bright field light microscopy but with electromagnets instead of lenses.
  • Scanning electron microscopy: beam of electrons reflected off surface (coated with heavy metals)
- Scanning probe microscopy (aka atomic force microscopy, AFM): needle maintains constant distance from speciment, laser reflected off needle detects needle movement.