Biology 2120 recitation

1
Biology 2120 recitation

• (your name here)

2
Todays schedule

• Review and clarify last weeks quiz if necessary
• Review last weeks lecture (METHODS)
• Quiz
• Reading the primary literature, part 2 defining
  a hypothesis

3
Last weeks lecture

• Common Methods in Cell Biology
•  The Big Picture
•  Cell fractionation permits purification of
  cellular components Fig. 12-1
•  Detergents are amphipathic molecules that
  dissolve most cellular molecules
•  Centrifugation separates cellular components
  Figs. 12A1-12A4
•  Gel electrophoresis separates individual
  molecules based on size Fig. 7-22a-e
•  Microscopes permit close examination of cells
  and tissues
•  Magnification and resolution are distinct
  properties of microscopes Fig. A2
•  The Abbe equation defines the features that
  determine resolution
•  Lenses focus the illuminating source on a
  specimen Figs. A1, A3, A4

4
Last weeks lecture

• Common Methods in Cell Biology
• Light microscopes are powerful tools in cell
  biology Fig. A5
•  Phase contrast microscopy can be used to
  visualize living cells Figs. A6, A7
•  Fluorescence microscopes are the most widely
  used microscopes in cell biology
•  Fluorescence is a property of some molecules
  Figs. A10, A11, A13, A14
•  Antibodies are widely used probes in cell
  biology Figs. A12, A15
•  Confocal microscopes have high practical 3D
  resolution
•  Electron microscopes permit close examination of
  fixed cells Figs. A24-26

5
Whats on the test?

• What determines resolution?
• Why might we use brightfield or phase over
  fluorescence?
• What advantages do antibodies provide?
  Limitations?
• Why use confocal over traditional microscopy?

6
Detergents
Sodium Dodecyl Sulfate (SDS, aka Sodium Lauryl
Sufate)
Triton-X-100
IONIC DENATURING
NONIONIC NOT DENATURING
7
A-7 Phase Contrast Microscopy
High contrast
8
Fluorescence Light Microscopy
A-10 Principles of Fluorescence
9
Regular Fluorescence vs Confocal
10
Hypothesis

• Define the word hypothesis. Research articles
  in cell biology use experimental data to argue in
  support of a hypothesis. It is important to
  clarify what the word hypothesis means in
  science.
•  
• Exercise (1) Ask your students to write down
  their definition of the word hypothesis. Ask for
  a few volunteers to read theirs aloud, seeking a
  range of definitions. Chances are that nearly all
  of them will be correct in general usage. But in
  the sciences, there is a very rigorous
  definition, one that helps students understand
  why certain experiments are included in a paper.
•  
• The Oxford English Dictionary defines a
  hypothesis in the sciences as follows
•  
• A supposition or conjecture put forth to account
  for known facts esp. in the sciences, a
  provisional supposition from which to draw
  conclusions that shall be in accordance with
  known facts, and which serves as a starting-point
  for further investigation by which it may be
  proved or disproved and the true theory arrived
  at.
•  
• (2) Have your students copy this down right below
  their own definition. Then, make sure your
  students understand this definition. One of the
  key points in this definition is that a solid
  hypothesis is a provisional explanation for
  something already known one has to explain
  something that is already known before the
  experiment(s) are performed. It is not a
  prediction of what will happen when an experiment
  is completed. Second, a hypothesis can be proven
  or disproven.
•  

11
Hypothesis

• Note that most scientists avoid claiming that
  their hypothesis is ever conclusively proven,
  because they can never absolutely rule out a set
  of premises that cant be generated at that time
  (the Aristotle didnt have a microscope
  concept). Instead, they typically say that their
  data suggests that a given explanation is
  correct or incorrect. Many students miss these
  points, so be sure to point them out.
•  
• (3) Have them paraphrase the OED definition and
  write it down in their own words, right below the
  OED version. On the page, the progression looks
  something like this
•  
• 1. Students original definition
• 2. OED definition.
• 3. Students reworded definition.

12
Hypothesis

• Have your students look for and then write down
  the hypothesis in the paper for this week

• Then, have them rewrite it in their own words,
  and have them hand the entire exercise in at the
  end of class. Hand it back the following week.

13
For next week

• Bring two written questions about the lecture
  material to class. These will be collected.
• Bring the Chet et al. paper with you to
  recitation again.
• Check the class website for any research articles
  to be downloaded.