MAT 272/BMSE 272Mechanical Force and

Biomolecules:Lecture 1

Introduction:

Why is force important for biomolecules?

1951: Pauling predicts alpha helix1954: Watson and Crick propose double-helixLate 50s: Perutz, Kendrew attain first protein

structures from X-ray crystallography60s: Genetic code determined70s: Amino acid sequences shown to

uniquely determine protein function (Anfinsen)

80s: Biotechnology explodes(Molecular cloning , PCR)

90s: Genomes sequenced

A eucaryotic cell

Information must be stored in an ‘aperiodic crystal’

-Schrodinger, 1944

replication

Eucaryotic genome packaging

A single-stranded RNA molecule can fold into an enzymatically active

structure (a ribozyme)

Proteins: Polypeptide chains that fold into globular structures with a wide variety of activities

Folded structures

Myoglobin : one chain of 153 monomers; 17 kDa

Proteasome: 28 chains of ~200 monomers each; 6.8 MDa total

1

2

3

4

How can you measure single molecules?

1) With electrical current through an ion channel (Neher and Sackmann, Nobel Prize 1991)

2) With a fluorescent dye

3) With manipulation That is, applying a relevant force to a biomolecule, and measuring resulting changes in length Single kinesins moving along

microtubules (Vale lab website)

From Nobel prize announcement

The common techniques

The Atomic Force

Microscope

The Optical Tweezer

The Magnetic Tweezer

The actuator A cantileverA dielectric

beadA paramagnetic

bead

Position detection Quad photodiode

Quad photodiode Video tracking

Force range 10-1000 pN 1-200 pN 0.1-100 pN

Advantages Bandwidth, sensitivity

Bandwidth, manipulation

Simplicity, constant force,

rotation

Disadvantages

Limited low-force ability Complicated

Low precision in position detection

Units, and the interesting range of forceForce~ Energy/Length; kBT ~ 4 pN nm

Process EnergyLengt

hForce

Stretching DNA

~kBT 50 nm 0.1 pN

Weak bonds ~kBT ~nm 4 pN

Unzipping DNA

2/3 H bonds = a few kBT

~nm10-15

pN

Motor motionATP ~ 20

kBT1-10 nm

8-80 pN

Denaturing a protein

[many weak bonds]

nm10-200

pN

Covalent bonds

1 eV ~ 40 kBT

0.1 nm 1 nN

AF

M

Op

tical

tweeze

rsM

ag

netic

tweeze

rs

Caveat:Reductionism

Certain proteins can only fold in the crowded interior of the cell; remove the crowding, and you’ve removed the physical impetus from the problem.Interior of an E. coli cell; from Goodsell,

1991, by way of Alberts

green: ribosomes; red: proteins; blue: Rna

Anti-reductionism tracts

1) P. W. Anderson, Science (1972) “More is Different”

This is the start of an argument that eventually killed the SSC.2) C. R. Woese, Microbio. Mol. Bio. Rev. (2004) “A New Biology for a New Century”

In which the author questions the significance of nearly the entire field of molecular biology.

“If you read trendy intellectual magazines, you may have noticed that ‘reductionism’ is one of those things, like sin, that is only mentioned by people who are against it. To call oneself a reductionist will sound, in some circles, a bit like admitting to eating babies. But, just as nobody actually eats babies, so nobody is really a reductionist in any sense worth being against.”– Richard Dawkins

Practical mattersEvaluation

-Two graded problem sets (30% of grade)

-Half-lecture presentations (70%):These will be based on a recent paper from the field. You will get a list of papers to choose from. With my approval, you can use a paper not on the list.

The rough plan: I give 16 lectures, students give last 2-3, plus during final exam week (if necc.)

Prereq: Prior knowledge of stat. mech., not of bio

Note 5/28 is a UCSB holiday.

The websitehttp://www.engr.ucsb.edu/~saleh/#Teaching

I have posted, and will continually update:

1. PPT slides from lectures (when used)

2. pdf of lecture notes

3. pdf of journal articles referenced (e.g. Woese and Anderson articles)

Also, there are some links to online resources (e.g. textbooks, journal search engines) that could be useful for background research for your presentation

Practical Matters:The syllabus

Schedule and textbooks