Welcome to Physics 475 Understanding biology using “ simple ” ideas from physics.

Welcome to Physics 475Understanding biology using “simple” ideas from physics.

with an emphasis on single-molecule biophysics

Your host:Professor Paul Selvin; Office: 365 LoomisOffice Hr: after class and 10:30-11:30 am Tuesday. (Can anyone NOT make it?)[email protected]: 244-3371

Your co-host: Marco Tjioe: Biophysics student (Taught this last year).

Murat Baday: Biophysics student; graduates in May. [email protected]: 364 Loomis: [email protected]: 328 Loomis: 720-722-2787

Office Hrs: Either Sunday 3-5 pm OR Tuesday 1-3pm.[Depending on whether HW due on Mon. or Wed.]

HW due 1 week from date of assignment

Course Info: M, W, 11:00 am-12:20 pm Rm 136 LLP

go to my web site

Or: http://physics.illinois.edu/courses/ then Physics 475

You’ve (hopefully) made a good choice!

Why are you here?1. Study Biophysics--Physics to understand biology(Not biology to understand Physics.)--Most cool subject you will take in Physics.•Recently:Single Molecule Biophysics(Cool of the cool)Santa Barbara CA. vs. Urbana IL

Why Single-Molecule?

Temperatures in 2007(By ensemble measurements)

Why Single-Molecule?Daily Temperatures in 2007

Invest in a warm winter coat & a swimming trunks

in Champaign-Urbana!

Fluctuation/heterogeneity matters!

Why are you here?

2. Personal: You presumably could get 90% of information from readingYou will do plenty…. Physical Biology of the Cell by Rob Phillips et al.

Interaction with those who do biophysics…me, Murat, Marco…And with other students (do HW together)

BioPhysicsTwo areas:

Method Development

New techniques to see better.

Model Development

What it means.

We will study both.

Should you be here?Yes, if you want to know about the physics of

biology (medicine), single molecules.Prerequisites

Physics 111, 112 (or equivalent)Some Statistical Mechanics, Elementary calculus

You will have to know: (Can learn)•Boltzmann’s Constant, kB

(relationship between energy and temperature)•Boltzmann Factor: exp(-Ei/kBT)

(proportional of being in some state with energy i, given that it’s at temperature T)

• Gibb’s Free Energy, G = H-TS; ≈ -TSH ≈ S = Entropy = ln Wi , Wi = # of states

If G negative, reaction will go there spontaneously (Fall downhill);

If G is positive, takes some “push”.

No previous biology assumed. I teach it in course.

Remember in useful units: kBT = 4 pN-nm at Room Temperature; Usually small—Covalent bond 100kT

But not in Biology! Hydrogen bond 3-5kTCommon unit of energy: ATP ~ 20-25 kBT ~80-100 pN-nm

ATP is universal food(Can measure distance and get maximum force)

Boltzman factor + Partition function(review of basic Stat. Mech. – see Kittel, Thermal Physic)s

iE / kTiP E const. e

E1

E0

Temp, T

If T = 0 ºK, what proportion of particles will be in E1, Eo?

If T > 0 ºK, what proportion of particles will be in E1, Eo?

Answer: Eo= 1 E1 = 0

iP E 1

jN

-E / kT

j=0

1const.= 1/ Ze

Z = partition function j

N-E / kT

j=0

e

J= represents jth state

Partition Function for 2-state system

1

o 1

1

o

-E /kT

1 -E /kT -E /kT

- 1 E

- o E

eP E =e +e

o

1

E = mghE h = 0E h =(mg)(h meter)

P(h) = P(0)

Simple case: Ball in gravitational field.

Thermal fluctuations, finite probability of being at height, h.

E = ??

As ball gets smaller, probability gets smaller / larger ?

“Ball” the size of O2? Why can you breathe standing up?

For O2, 1/e height is ~10 km ~height of Mt. Everest.(10 kM is “death zone”)

Probability of dying if you go over 20,000 ft is 10% for every trip!!

What is 1/e height for O2?

-mgh/kT e

Physical Biology of the Cell, 2nd edition by Rob Phillips et al. Publisher Garland Press.

(www.garland.shareddbook.com)

This is the first time I have used this book, so I’m uncertain about what parts I will cover.

“Definitely” Chapter 1-5.There are several ways you can get a hold of the book.

•Buy it from Amazon.com : $102. (“good” price”)•Rent it for 180 day from Amazon: ≈ $70.

•Buy it chapter by chapter: $9/chapterFrom VitalSource e-book version, which can be

purchased or rented.https://store.vitalsource.com/show/9781134111589

Get book fast because 1st assignment is Chapter 1—assigned now! Due in 2 weeks. (There will be a quiz.)

There will also be readings assigned in class.

Need to know biology in order to do biophysics!Using physics to understand biology!Not biology to understand physics!

Required Reading

Major concepts of physics inherent to biological systems.  Basics of biology,

including protein and DNA structure and their organization into cells are discussed,

with a  focus on single molecule biophysics.  Major techniques including optical and

magnetic traps, and fluorescence microscopy, including "new" super-

resolution techniques. Applications to cytoplasmic and nuclear molecular motors,

bacterial motion, nerves, and vision.It’s only been last 10-20 years that single

molecule measurements have been possible!

Course Information Physics 475 Biological PhysicsAlternative title:

Introduction to the physics of quantitative biology with an emphasis

on single molecule biophysics

Single: molecules, cells, species (men vs. women), planets… very hot, very cold, only if you look

In singulo Biophysics

Course Syllabus Physics 498BioDNA, RNA, ATP & Proteins (Making, Folding)1. Jan 14: Introduction to Biophysics: The Earth’s Temperature, King Kong and Bacteria2. Jan 16: The Language of Life: DNA, Proteins, Carbohydrate, Lipids: How you eat!3. Jan 21: No class (Martin Luther King Day) 4. Jan 23: Protein Folding in Silico—Computer Simulation (VMD)– Klaus Schulten5. Jan 28, 30: Reg. Class 6. Feb 4: No class 7. Feb 6: Reg class

Magnetic Tweezers, Atomic Force Microscopy

About March 6: Mid-term Exam (Lec. 1-13)

Imaging and Microscopy—Seeing small things: Fluorescence, Optical Traps

Spring Break: March 18, 20

DiffusionIon Channels and Vision

Extraneous: Most Genes are few in Number—some surprising resultsStudying Gene Activity in Individual CellsStudying Gene Activity in Individual Cells II

Student lectures (given over many nights)

May 1st: Last class

Grading 25%: written Homework : (about 9 total; drop lowest 1):

(You CANNOT drop the last homework!) Work together, but turn in separately.Hand in at start of class– in class! (Do not be late.)

10% in-class Quizzes: (covering Phiilip’s or extra-reading)

25%: Written Project & Oral Project– Same topic-- 12.5% on written report: 10 pg report.-- 12.5% on oral report: 8-12 min plus 4 min for questions.

15% on midterm exam

15% on final exam

10% on classroom participation /class evaluation

Grading (may be modified slightly if changes to course )

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.

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.

Get to know each other

With someone you don’t know,Find out their:1.Name, Year, undergrad vs. grad.2.Why you’re taking the course.3.Tell one thing that’s surprising.

Take 4 minutes (2 min/person)A few people will have to report!

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.

Physics says your atoms are billions of years old!13.7 Billion years ago, Big Bang.

How old are the atoms in you? Where did they come from?

Big Ideas…the most amazing story ever…

• Dark Energy: permeates all of space:Necessary for expansion of the universe at accelerating rate.• Dark matter –unknown what it is. Look at large scale gravity affect on visible matter, need this.• Baryonic “heavy” (atomic) matterProtons and neutrons.--visible

Wikipedia

Our Universe

Formation of atomsIn Big Bang, Hydrogen was formed; within 3-20

minutes, during the rapid “expansion” of the universe, the smallest elements formed (by fusion because of super hot temp.), H, He, Li (and some radioactive Beryllium): Big Bang Nucleosynthesis.

 Within 100-200 million years, density fluctuations caused

the first stars formed.(Also [I think] dark matter appeared to form)

(Based on NASA's Wilkinson Microwave Anisotropy Probe (WMAP) released in February 2003—Nobel Prize, 2006)

Cosmic Microwave Background—nearly constant background, formed about 400,000 years after BB. Universe expanded and been cooling ever since.

Now about 2.73 ˚K.

In Sun, form He. In more massive stars, form Carbon up to

Oxygen.Therefore we are derived from a

long-dead star which exploded and reformed to make us (& sun, earth…)

Big stars: Elements up to Iron formed. (≈ 1 billion years passed and galaxies proliferated.

CMB ≈19˚K, a billion years after the BB)(Darkness to light.)

Formation of atoms up till Iron

Supernova

All atoms > Iron come from Supernova!

(Sun & Earth is 4.54 Billion years old)

(Stars that are more than 250 times more massive than the sun do not explode at the end of their lives; instead they collapse into similarly massive black holes.

A type II supernova, or stellar explosion, occurs when a star of at least eight times our sun's mass runs out of nuclear fuel at its core.

We are mostly made of water (H2O): ≈75%C —very versatile: everything made of: Nucleic acids, Proteins, Lipids (fat), Carbohydrates. (Remember these families)!O —bonding, proteins, fats, nucleic acidsN — proteins, genetic materialCa, P — bones

What are we made of?

Campbell

CH4

C2H6

C2H4

What’s so special about Carbon?Carbon is backbone of life

• Carbon, along with Oxygen, Hydrogen, Nitrogen, (and Phosphorous) make up “life”.

• C is abundant (on earth).• C has 4 valence electrons.• C can make up huge array of

C-containing polymers.• C is water-soluble.• C is small size and

intermediate energy levels (so enzymes can manipulate).

Astrobiology: life elsewhere is probably C-based: carbon chauvinism.

http://en.wikipedia.org/wiki/Carbon-based_life

Si is alternative, but larger, more stable, tends tends to form crystals.

Homework

Buy Book (or parts of it)!Read Chpt 1

You will get written homework on Wednesday, Jan 16th.

Due following Wednesday, Jan. 23rd!

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.)