Homework 4
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Homework 4
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 2
 School:
 California Institute of Technology
 Course:
 Aph 161  Physical Biology of the Cell
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APh161 The Physics of Biological Structure and Function Homework 4 Due Date Tuesday Feb 20 2007 An ounce of application is worth a ton of abstraction Booker T Washington Reading Read chap 9 of PBOC and write a referee report in the usual way Please remember as you are doing this that this is a huge help to us as we try to improve the book for its eventual publication We appreciate it very much and it is a chance for you to construct a concrete written argument 1 Nucleosome Formation and Assembly The goal of this problem is for you to reexamine the ideas developed in class concerning the assembly and accessibility of the nucleosome and to rederive the expression for the DNA accessibility using a discrete model a Repeat the derivation given in class and arrive at an expression for the free energy of formation of nucleosomes Make sure that you explain the qualitative features of the calculation and that you identify the numerical outcome of the analysis please report your energies in units of kB T In particular comment on the way in which you handle the elastic and interaction effects and rationalize the energy per length that you assign to each of these effects Also instead of pretending that the DNA wraps around the nucleosome fully two times use the more precise description involving 147 base pairs of wrapped DNA leading to 1 75 wraps around the histones A second refinement is to include the helical pitch of the DNA as it wraps around the nucleosome here just make an estimate to show that this refinement is not very important Hint to do this you will need to remember that the bending energy is of the form Ebend p kB T Z ds s 2 2 1 1 where s is the curvature In addition take a look at papers describing the structure of the nucleosome such as Nature 389 251 1997 Nature 423 145 2003 J Mol Bio 319 1097 2002 and make sure that you characterize the structural features of the nucleosome that you use in your model b In class we examined the experiments of Polach and Widom J
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