Welcome to Physics 498BioUnderstanding biology using “simple” ideas from

physics.You must know enough biology to have a sense of what to study!

Your host:Professor Paul SelvinOffice: 365 LoomisOffice 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 biophysicsOffice: 328 LoomisOffice Hrs: Sunday 1-2:30pm OR Tuesday 3:30-5pm depending on whether HW due on Mon. or Wed.encai1@uiuc.edu: 305-282-9398HW due 1 week from date of assignment

Course Info:Online.physics.uiuc.edu/courses/physics498bio/spring08

Orpeople.physics.uiuc.edu/Selvin/PRS/PRS.html

then physics498bio Spr10Or

physics.uiuc.edu, Courses, Intro to Biophysics Research (next to 498Bio)

Monday, Wednesday, 10:30 am- 12 pm: 158 Loomis

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-TS 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!

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 electricalchemical 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 normMen 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 ScheduleDNA (& Proteins…)1) Jan. 20th : Intro; King Kong; Temp. of Earth; Evolution & Modern Biology 2) Jan 25th : Central Dogma of Biology; Partition Function3) Jan 27th : The 4 class of macromolecules; Entropy4) Feb 1st : DNA Technology : FISH, PCR, Forensics5) Feb 3rd : DNA Technology : Gene Chips6) Feb 8th : DNA as Spaghetti: Magnetic Traps 7) Feb 10th : Magnetic Traps, Part II8) Feb 15th : Carbohydrates and LipidsFluorescence9) 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 Diffraction12) March 1st : Super-Accuracy, Super-resolution techniques: FIONA, SHREC, 13) March 3rd : More super-accuracy: PALM, STORM14) March 8th : STED, FRET, Part I15) March 10th : FRET Part II and DNA helicase—TJ Ha’s Science magazine article.Students Teach!16) March 15th : Student Presentations17) March 17th : Student PresentationsMarch (22, 24) VacationOptical Traps allow you to see Angstrom & Nanometer distance.18) March 29th : Optical Traps- theory and Experiment 19) March 31st : Optical traps, Part IIDiffusion: Inertia doesn’t mean anything!Diffusion and Bacteria Moving20) April 5th :How E. coli swim and tread water Diffusion: Inertia doesn't mean anything21) April 7th :Magnetic Orientation? Klaus Schulten.Vision & Ion Channels22) 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 results25) 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

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

Grading

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.

PlagiarismNot 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.

Mass?

Strength?

King Kong is proportionally speaking is 10x weaker than regular gorilla!

Regular gorilla with 10 gorilla’s on him—couldn’t walk.

10 x 10 x 10 = 103

Strength/Mass ratio?

10 x 10 = 102.

1/10… 1/dimension

(density is the same):

Cross-sectional area (rope):

Bones break; also overheat (because warm-blooded and water is going at conducting away heat, whereas air is not.)

If whale stranded on the beach?

In water– held up by buoyant force.Bones do not need to support weightIf have to, have super big bones– would sink.

Is there water-based life on other planets?Example of physical limits to life.

Idea: For water-based life, 0º < Tave < 100ºC

Answer: Heat (photons) from sun

Ie= 1.35 kW/m2

# Floodlight ~ 30 (1 meter away)

(Incandescent light 3% efficient)

Can we calculate Tave of planets in our solar system?

EarthWhat determines (surface) temp?

1 meter

1 meter

How much light?

How many (flood)lights?

Why determines earth temperature? Why can life exist?

Heat outHeat inTemp of earth constant

Heat in = Heat out

= reflectivity of objectThe albedo of the earth, i.e. the amount of light which is reflected () is about 0.3 (depending on cloud cover, the amount of snow, etc.) The remainder of sunlight is absorbed, transferred into random thermal vibrations.

Heatout = 4Re2σ T4

σ = const (=5.7 x 10-8 W/m2K4)T = absolute Temp.

Assume the earth is a black-body.

Rearth2(1- )Iin = 4Rearth

2T4

Therefore: T4= (1-)Iin/4

in= 1.35 kW/m2

We balance the incoming energy flux from the Sun and the outgoing flux due to black-body radiation.

Heatin = ??Heatin = inRe

2

(1-

(Stefan-Boltzmann Law)Kittel, Thermal Physics pg 91-96

T = 253°K

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

Physics is about great laws Some examples…

Newton’s 3 Laws (Mechanics)

Isaac Newton1642-1727

James Clerk Maxwell 1831-1879

(Electricity & Magnetism)

Schrodinger’s Eq’n

Erwin Schrödinger 1887-1961

J. Willard Gibbs1839-1903

Gibb’s Free Energy

S= k·log WLudwig Boltzmann

1844-1906

Maxwell’s 4 Equations

(Quantum Mechanics)

(Thermodynamics)

(Stat. Mechanics of Entropy)

Does Biology have any great theories/laws?

Evolution-- Life evolved from simpler forms

--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 thisOur life form is just one.

Charles Darwin, Age 51, 1860, On the Origin of Species

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.)