Understanding Biology with Physics

1. Welcome to Physics 498Bio Understanding biology using “simple” ideas from physics. You must know enough biology to have a sense of what to study! Monday, Wednesday, 10:30 am- 12 pm: 158 Loomis Your host: Professor Paul Selvin Office: 365 Loomis Office Hr: after class or 10:30-11:30 am Friday. (Can anyone NOT make it?) selvin@uiuc.edu: 244-3371 Your co-host (TA): Anne Cai, 2nd year physics student doing biophysics Office: 328 Loomis Office Hrs: Sunday 1-2:30pm OR Tuesday 3:30-5pm depending on whether HW due on Mon. or Wed. encai1@uiuc.edu: 305-282-9398 HW due 1 week from date of assignment Course Info: Online.physics.uiuc.edu/courses/physics498bio/spring08 Or people.physics.uiuc.edu/Selvin/PRS/PRS.html then physics498bio Spr10 Or physics.uiuc.edu, Courses, Intro to Biophysics Research (next to 498Bio)

2. 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: DG = DH-TDS Boltzmann’s Constant, kB Boltzmann Factor: exp(-Ei/kT) ATP: Adenosine TriPhosphate (universal energy currency) (Remember in useful units: [kBT = 4 pN-nm; ATP = 80-100 pN-nm ~ 25 kT]) 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!

3. 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?

4. 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!

5. 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 6) Feb 8th : DNA as Spaghetti: Magnetic Traps 7) Feb 10th : Magnetic Traps, Part II 8) Feb 15th : Carbohydrates and Lipids Fluorescence 9) Feb 17th : ATPase Operates at near 100% Efficiency 10) Feb 22nd : [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 21) April 7th :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

6. 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

7. Yes, you get to evaluate class!Three (or 4) questions: 1. What was the most interesting thing you learned in class today? 2. What are you confused about? 3. Related to today’s subject, what would you like to know more about? 4. Any helpful comments. Answer, and turn in at the end of class. (I’ll give you ~5 minutes.) I’ll typically start class with some of your questions.

8. Plagiarism Not allowed! You will flunk the course. In written project… Something has always been written… (unless you have truly come up with something new.) Usually what’s written will be clearer than you can write it. But you want to independently understand it. And show me that you independently understand it. So… Read book/article, then close it, Then write your own version. This way you know you understand it, and can explain it in your own words. Also, when you “steal” a picture from somewhere, write in your paper where you got it from. A picture is worth a thousand words, but give credit where due.

9. Mass? (density is the same): 10 x 10 x 10 = 103 Strength? a Cross-sectional area (rope): 10 x 10 = 102. 1/10… 1/dimension Strength/Mass ratio? King Kong is proportionally speaking is 10x weaker than regular gorilla! Regular gorilla with 10 gorilla’s on him—couldn’t walk.

10. In water– held up by buoyant force. Bones do not need to support weight If have to, have super big bones– would sink. If whale stranded on the beach? Bones break; also overheat (because warm-blooded and water is going at conducting away heat, whereas air is not.)

11. How much light? 1 meter 1 meter Is there water-based life on other planets?Example of physical limits to life. Idea: For water-based life, 0º < Tave < 100ºC Can we calculate Tave of planets in our solar system? Earth What determines (surface) temp? Answer: Heat (photons) from sun Ie= 1.35 kW/m2 How many (flood)lights? # Floodlight ~ 30 (1 meter away) (Incandescent light 3% efficient)

12. Why determines earth temperature? Why can life exist? Temp of earth constant Heat in = Heat out Heat out Heat in    Heatin = ?? Heatin = IinpRe2 (1-a) • = reflectivity of object • The albedo of the earth, i.e. the amount of light which is reflected (a) is about 0.3 (depending on cloud cover, the amount of snow, etc.) The remainder of sunlight is absorbed, transferred into random thermal vibrations. Iin= 1.35 kW/m2 Assume the earth is a black-body. (Stefan-Boltzmann Law) Kittel, Thermal Physics pg 91-96 Heatout = 4pRe2σ T4 σ = const (=5.7 x 10-8 W/m2K4) T = absolute Temp. We balance the incoming energy flux from the Sun and the outgoing flux due to black-body radiation. pRearth2(1- a)Iin = 4pRearth2sT4 Therefore: sT4= (1-a)Iin/4 T = 253°K

13. According to this (simple) model, TEarth should be 253°K. In reality, it’s more like 280°K? What happened? Greenhouse Effect: 280°K (Homework) When you change the balance, you get REAL effects! Add CO2, you get an artificial Greenhouse Effect

14. Physics is about great laws Some examples… Newton’s 3 Laws (Mechanics) (Electricity & Magnetism) Maxwell’s 4 Equations Isaac Newton 1642-1727 (Thermodynamics) Gibb’s Free Energy James Clerk Maxwell 1831-1879 (Quantum Mechanics) Schrodinger’s Eq’n J. Willard Gibbs 1839-1903 (Stat. Mechanics of Entropy) S= k·log W Erwin Schrödinger 1887-1961 Ludwig Boltzmann 1844-1906

15. --One of the best tested scientific theories around Evolution is a series of tricks/random events Build complex beings from simpler parts Often many ways of doing this Our life form is just one. Does Biology have any great theories/laws? Charles Darwin, Age 51, 1860, On the Origin of Species Evolution -- Life evolved from simpler forms

16. Evaluate class 1. What was the most interesting thing you learned in class today? 2. What are you confused about? 3. Related to today’s subject, what would you like to know more about? 4. Any helpful comments. Put your name in upper right-corner. Then tear off your name before turning in. (That way you can be brutally honest!) Answer, and turn in at the end of class. (I’ll give you ~5 minutes.)