4S03 Molecular Biophysics - 2016
Dr Paul Higgs
Schedule for Fall 2016: Tu We Fr 9.30, BSB 104
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.
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
<![if !supportLists]>· <![endif]>Clementine - Cantilever-based microscopy in biophysics - presentation
<![if !supportLists]>· <![endif]>Lucas - Magnetosomes in Magnetotactic Bacteria
Wed 16th Nov
<![if !supportLists]>· <![endif]>Nenad - Attwater - In-ice evolution of RNA polymerase ribozyme activity
<![if !supportLists]>· <![endif]>Chris - Vaidya - Spontaneous network formation among cooperative RNA replicators
Fri 18th Nov
<![if !supportLists]>· <![endif]>Paul - Fluorescence (notes at the bottom)
Tue 22nd Nov
<![if !supportLists]>· <![endif]>Alex - Blanchard - tRNA selection and kinetic proofreading in translation
<![if !supportLists]>· <![endif]>Nathaniel - Guolla - Force transduction and strain dynamics of actin in stress fibres in response to nanonewton forces
Wed 23rd Nov
<![if !supportLists]>· <![endif]>Michael - Moerner - Single molecule spectroscopy and imaging of biomolecules in living cells
<![if !supportLists]>· <![endif]>Nia - Henon - Determination of the shear modulus of the human erythrocyte membrane using optical tweezers
Fri 25th Nov
<![if !supportLists]>· <![endif]>Paul - Proteins
Tue 29th Nov
<![if !supportLists]>· <![endif]>Paul - Proteins
Wed 30th Nov
<![if !supportLists]>· <![endif]>Julian - Subramanian - Disease-associated mutations in proteins
<![if !supportLists]>· <![endif]>Carmen - The role of protein structure in the physical properties of silk fibres
Fri 2nd Dec
<![if !supportLists]>· <![endif]>Hedwig - Molecular Mechanisms of Photosynthesis
Tue 6th Dec & Wed 7th Dec - Paul - Protein folding
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.
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:
<![if !supportLists]>· <![endif]>Chaps 5 and 6 are relevant to what we talked about but we did not do everything in detail.
<![if !supportLists]>· <![endif]>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
<![if !supportLists]>· <![endif]>Chap 8 is very relevant - we have covered a lot of this and we will come back again to HP model later
<![if !supportLists]>· <![endif]>Chap 9 - useful derivation of the Debye Huckel theory and screening
<![if !supportLists]>· <![endif]>Chap 10 - bending beams, wormlike chains etc
<![if !supportLists]>· <![endif]>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
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).