Course Information Physics 498Bio
       Introduction to Biological Physics   
          You’ve  (hopefully) made a good choice!   
     Prerequisites   
     Physics 111, 112 (or equivalent)
            Some knowledge of Statistical Mechanics 
     Gibb’s Free Energy,  entropy: G = H-TS 
     Boltzmann’s Constant, kB
     Boltzmann Factor: exp(-E/kT)
                             i
     ATP: Adenosine TriPhosphate (universal energy currency)
     (Remember in useful units: 
     [k T = 4 pN-nm; ATP = 80-100 pN-nm ~ 25 kT])
       B
     Some elementary calculus. 
     No previous biology assumed. I teach it in course.
     Required Reading
     Essential Cell Biology, 3rd edition: 
     by Bruce Alberts et al. 
      Excellent introduction to biology. Chpt 1-5, 11-13 
            Read Chpt 1: Quiz next Wednesday.
      Need to know biology in order to do biophysics!
            Using physics to understand biology!
             Not biology to understand physics!
         Goals of course   
   1. Learn some basic molecular biology. 
       Language of Life: 4 key components
       DNA (PCR, sequencing)
       Proteins... can do everything!  
   2. Learn how to apply basic physics to biology.   
    Mechanics, Electricity & Light,  Statistical Mechanics 
    (Example today – What planets are life possible on?) 
   3. Learn about/type problems biophysicists work on. 
       Biology...
       Molecular motors (chemical  mechanical)
       Ion Channels (chemical Ion Gradients electrical)
       [Photosynthesis (light  electricalchemical 
   energy)]
       Stochastic Nature of gene expression, 
       Magnetic Navigation, Vision...
   4. Learn“back of the envelope”type calculations.
       Example today: Strength of animals   
   5. Learn experimental (bio)physics   
       How to measure (nm distances, pN forces), 
       Single molecules (Fluorescence, Optical Tweezers
       Magnetic Traps, Patch Clamp Techniques)
    Some guest lecturers– people doing the stuff!
          Klaus Schulten 
     How do birds know which way is North?
   In singulo Biophysics
  Single molecules, single cells, 
  single species, single planets…
    Heterogeneity is the norm
   Men vs. women: height, sex organs
  Important to understand (prostate cancer, 
       ovarian cancer
  It is only in last 10 (20) years that single 
   molecule detection has been possible!
                                     Course Schedule
  DNA (& Proteins…)
  1) Jan. 20th  : Intro; King Kong; Temp. of Earth; Evolution & Modern Biology 
  2) Jan 25th   : Central Dogma of Biology; Partition Function
  3) Jan 27th   : The 4 class of macromolecules; Entropy
  4) Feb 1st    : DNA Technology : FISH, PCR, Forensics
  5) Feb 3rd    : DNA Technology : Gene Chips
           th
  6) Feb 8      : DNA as Spaghetti: Magnetic Traps 
            th
  7) Feb 10   :  Magnetic Traps, Part II
            th
  8) Feb 15   :  Carbohydrates and Lipids
  Fluorescence
            th
  9) Feb 17   : ATPase Operates at near 100% Efficiency 
              nd
  10) Feb 22  : [I’m gone]: Alternative make-up day?
  11) Feb 24th : Microscopes and Resolution; X-ray Diffraction
  12) March 1st : Super-Accuracy, Super-resolution techniques:  FIONA, SHREC, 
  13) March 3rd : More super-accuracy: PALM, STORM
  14) March 8th : STED,  FRET, Part I
  15) March 10th : FRET Part II and DNA helicase—TJ Ha’s Science magazine article.
  Students Teach!
  16) March 15th : Student Presentations
  17) March 17th : Student Presentations
  March (22, 24) Vacation
  Optical Traps allow you to see Angstrom & Nanometer distance.
  18) March 29th : Optical Traps- theory and Experiment 
  19) March 31st : Optical traps, Part II
  Diffusion: Inertia doesn’t mean anything!
  Diffusion and Bacteria Moving
  20) April 5th      :How E. coli swim and tread water Diffusion: Inertia doesn't mean anything
              th
  21) April 7       :Magnetic Orientation? Klaus Schulten.
  Vision & Ion Channels
  22) April 12th   : Ion Channels – Voltage-sensitve (nerves, neuromuscular) 
  23) April 14th   : Ion Channels – Ligand sensitive (your brain)
  24) April 19th   : Vision 
  Single Cells: Most Genes are few in Number—some surprising results
  25) April 21st   :  Studying Gene Activity in Individual Cells.  
  26) April 26th   :  Gene Activity Part II 
  Students Teach!
  27) May 3rd     : Student Presentation 
  28) May 5th     : Students Presentation 
           Grading 
   30%: Homework (Must do all of them): Mostly weekly 
     assignments, but occasionally to write up something
        Work together, but turn in separately.
     Hand in at start of class– in class! (Do not be late.)
   25% Mid-term Oral and written report
   Oral & Written—the same subject
   -- 12.5% on written report: 8 pg report.
   -- 12.5% on oral report: 10-12 min plus 3-5 min for questions. 
   25%:  Final Written Project & Oral Project– Same topic
   -- 12.5% on written report: 10 pg report.
   -- 12.5% on oral report: 10-12 min plus 3-5 min for questions.
       No regular mid-term or final exams.
   10% Quizzes (~1% on each) 
     --5 min quizzes making sure that you’ve done readings
   10% on classroom participation /class evaluation