4S03 Molecular Biophysics - 2016

Dr Paul Higgs

Schedule for Fall 2016: Tu We Fr 9.30, BSB 104

Course Aims

The course will focus on the single-molecule approach to biophysics experiments. Students will learn to appreciate methods for observing and manipulating single molecules and what can be understood with these techniques about the structure, function and dynamics of biological molecules. Ideas from thermodynamics and soft-matter physics will be used to explain the observations and make predictions about the behaviour of the biological molecules. Students should appreciate the interdisciplinary nature of the subject physics/biochemistry/biology and the interplay between theory and measurements. Lectures will make use of example papers from the scientific literature for each of the topics considered. Students will gain practice in reading and interpreting the primary literature in the field.

Lecture Contents

Techniques for observing and manipulating molecules, including optical tweezers, atomic force microscopy and fluorescence methods.

Force-extension curves for DNA, proteins and RNA.

DNA structure and packaging (nucleosomes, viruses).

Helix-coil transitions in nucleic acids and proteins.

Folding of RNA and Proteins observations and thermodynamic models.

Assembly and growth of microtubules and actin filaments.

Molecular Motors (myosin, kinesin, ATP synthase, flagellar motor)


There will be 3 assignments based on interpretation of papers in the biophysics field (worth 15% each). Assignments will be downloadable from this web site. Due dates will be announced when the assignment is issued. A printed version of the completed assignment should be handed in at the lecture on the due date.

There will be a mid-term test (worth 15%) and a final exam (worth 40%). The mid-term will be based on all topics covered up to that point and the final exam will be based on all topics covered in the course. The format of the exam questions will be discussed with the class prior to the exam.

Assignment 1 - Assignment 1.doc You will need the following paper for this assignment - ForceExtRNA_Liphardt2001.pdf - DEADLINE Hand in at lecture on Fri 30th Sept

Midterm - To be held in class on Friday 21st Oct. Examples of past midterm exams : Midterm2013 Midterm2010

Assignment 2 - Assignment2.doc You will need the following paper - Microtubules_Fygensen.pdf - DEADLINE Hand in on Tue Nov 8th

Assignment 3 - Assignment3.doc You will need the following paper - Microtubules_Dogterom.pdf -

Schedule for Presentations:

Tuesday 15th Nov

         Clementine - Cantilever-based microscopy in biophysics - presentation

         Lucas - Magnetosomes in Magnetotactic Bacteria

Wed 16th Nov

         Nenad - Attwater - In-ice evolution of RNA polymerase ribozyme activity

         Chris - Vaidya - Spontaneous network formation among cooperative RNA replicators

Fri 18th Nov

         Paul - Fluorescence (notes at the bottom)

Tue 22nd Nov

         Alex - Blanchard - tRNA selection and kinetic proofreading in translation

         Nathaniel - Guolla - Force transduction and strain dynamics of actin in stress fibres in response to nanonewton forces

Wed 23rd Nov

         Michael - Moerner - Single molecule spectroscopy and imaging of biomolecules in living cells

         Nia - Henon - Determination of the shear modulus of the human erythrocyte membrane using optical tweezers

Fri 25th Nov

         Paul - Proteins

Tue 29th Nov

         Paul - Proteins

Wed 30th Nov

         Julian - Subramanian - Disease-associated mutations in proteins

         Carmen - The role of protein structure in the physical properties of silk fibres

Fri 2nd Dec

         Hedwig - Molecular Mechanisms of Photosynthesis

Tue 6th Dec & Wed 7th Dec - Paul - Protein folding


Recommended Textbook

Rob Phillips, Jane Kondev, Julie Theriot (2009) The Physical Biology of the Cell This is a textbook covering many biological problems from a physics point of view. Lectures will refer to this book where appropriate, but will also use a lot of material from other research papers.

Background Reading

For those who are not familiar with Biochemistry - I would like you to have a general idea of the structure of the important types of biological macromolecules (proteins, DNA, RNA, lipids, polysaccharides) and the roles played by these molecules in the cell. There are many textbooks on this, but for something that is at the right level and not too long, I would recommend Chapter 5, "The structure and function of macromolecules", from the book "Biology" by N A Campbell and J B Reece. This should be in the library, and I have one copy that can be borrowed.

For everyone - Look at Chapters 1 and 2 of Phillips et al. This covers some ideas on sizes of molecules and cells that we talked about in class, and gives a physicist's point of view on the importance of models in biology.

The instructor and university reserve the right to modify elements of the course during the term. The university may change the dates and deadlines for any or all courses in extreme circumstances. If either type of modification becomes necessary, reasonable notice and communication with the students will be given with explanation and the opportunity to comment on changes. It is the responsibility of the student to check their McMaster email and course websites weekly during the term and to note any changes.

Stuff to Download

Pictures from Phillips Sizes and Time Scales - Notes1

Papers on Optical Tweezers Review of Scientific Instruments Neuman and Block

Pictures related to DNA force-extension experiments and DNA-histone interactions - Notes2

Papers on DNA force-extension experiments - Bustamante2000 Bustamante2003

Physics of Chromatin Review Schiessel2003 . Simulation of charged chain and sphere Kunze2000

Papers on nucleosomes that we mentioned in lectures: Schiessel2006.pdf , BrowerToland.pdf , Mihardja2006.pdf

Stat Phys notes

Recommended chapters from Phillips et al:

         Chaps 5 and 6 are relevant to what we talked about but we did not do everything in detail.

         Chap 7 gives examples of two-state transitions. Think about these in comparison with the examples of RNA unfolding and nucleosome unfolding that we did in class

         Chap 8 is very relevant - we have covered a lot of this and we will come back again to HP model later

         Chap 9 - useful derivation of the Debye Huckel theory and screening

         Chap 10 - bending beams, wormlike chains etc

         Chap 15 - sections on actin filaments and microtubules

Helix-coil transitions Notes1and Notes2

RNA folding Notes

Review of RNA secondary structure HiggsQRB. Review of ribozymes and RNA world Higgs&Lehman

Fluorescence Notes

Papers on Protein Folding - ProteinFolding_Dill.pdf CATH database PDB database

EXAM TIPS: Topics from the mid-term will not be on the exam (i.e. Debye-Huckel theory and Wormlike chains). Everything else might well be on the exam (including Helix-coil transitions, RNA folding, Protein Folding, Microtubules....). Please bring a calculator. There will be some questions where you have to look at graphs from a paper and interpret them (as with the assignments).