1. MAT 272/BMSE 272 Mechanical Force and Biomolecules: Lecture 1

2. Introduction: Why is force important for biomolecules?

3. 1951: Pauling predicts alpha helix 1954: Watson and Crick propose double-helix Late 50s: Perutz, Kendrew attain first protein structures from X-ray crystallography 60s: Genetic code determined 70s: Amino acid sequences shown to uniquely determine protein function (Anfinsen) 80s: Biotechnology explodes (Molecular cloning, PCR) 90s: Genomes sequenced

4. A eucaryotic cell

5. Information must be stored in an ‘aperiodic crystal’ -Schrodinger, 1944 replication

6. Eucaryotic genome packaging

7. 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

8. 1 2 3 4

10. 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

11. The common techniques The Atomic Force Microscope The Optical Tweezer The Magnetic Tweezer The actuatorA cantileverA dielectric beadA paramagnetic bead Position detection Quad photodiode Video tracking Force range10-1000 pN1-200 pN0.1-100 pN Advantages Bandwidth, sensitivity Bandwidth, manipulation Simplicity, constant force, rotation Disadvantages Limited low-force ability Complicated Low precision in position detection

12. Units, and the interesting range of force Force~ Energy/Length; k B T ~ 4 pN nm ProcessEnergyLengthForce Stretching DNA~k B T50 nm0.1 pN Weak bonds~k B T~nm4 pN Unzipping DNA 2/3 H bonds = a few k B T ~nm10-15 pN Motor motionATP ~ 20 k B T1-10 nm8-80 pN Denaturing a protein [many weak bonds] nm 10-200 pN Covalent bonds1 eV ~ 40 k B T0.1 nm1 nN AFM Optical tweezers Magnetic tweezers

13. Caveat: Reductionism

14. 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

15. 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.

16. “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

17. Practical matters Evaluation -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.

18. The website http://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

19. Practical Matters: The syllabus Schedule and textbooks The syllabus