HOMEWORK # 3

BIOL/CHEM 5312

due Friday, February 20, 2015


van Holde et al. , Chapter 3, p.161-163, problems 3.1, 3.2ab, 3.3, 3.6, 3.8, 3.9

3.0 Using the Base-stacking energies of Table 3.10, determine the most stable dinucleotide triplet (a duplex of 3 base pairs).  What is the least stable triplet?

Notes:

3.1 use κε_o = 4π 8.85 x 10^-12 C² J^-1 m^-1 to evaluate D (lect 6, p17)

3.2 number the dipoles 1 and 2, r is the vector from the center of 1 to the center of 2
 Angles are determined by rotating one vector until it is parallel with another (in the same direction)

3.3 hint is in the book (Answer to 3.3b is -15.0)

3.6 use Table 1.7 to estimate separation of charges

3.8  use Table 3.15. In the Table in the problem, N should be called a base atom.  Those values are the surface areas for all atoms of a particular type.  (Recommendation: use a spread sheet to calculate)

3.9  In actual proteins |r| appears to be around 0.5-0.6 nm, but for this problem you can use |r| = 0.5 nm  To get the length of µ use the length of the CO bond and the length of the NHO hydrogen bond.  Both can be found in Ch. 1.  Assume the dipoles are aligned (θ = 0)  (My answers are -169 J/mol and -3.79 kJ/mol  The answer in my book is clearly wrong, since it gives the same value for each, and they certainly must differ by the ratio of the dielectric constants)