Physical Biochemistry - Additional Problems | CHEM 156, Assignments of Chemistry

Material Type: Assignment; Class: Physical Biochemistry; Subject: Chemistry; University: University of California - Los Angeles; Term: Spring 2001;

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Pre 2010

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Chem 156
Additional Problems
1. System A has A states, and an entropy of SA (in units of J/K). If there is a system B
with an entropy of SB = ( SA + 1 J/K ), then how many states does system B have?
2. You have a system of particles in which you have 3 possible energy levels:
.
2
5
,
2
3
,
2210
ω
ω
ω
hhh === EEE
(a) Calculate the probability that a particle has an energy of 5ħω/2.
(b) Suppose that you have one mole of particles. Calculated the total expected energy of the
system. How many particles would you expect to see in each state?
3. A new protein you discovered has two different conformations: one conformation, I, is
inactive, and cannot bind any ligand, B. The other conformation, A, can bind two ligands in a
cooperative fashion in its binding site. Here is a diagram that illustrates this point:
L-1 K1 K2
I A A·B A·B2
(a) Which equilibrium constant is larger, K1 or K2? Explain why.
(b) Calculate the mean free energy of this protein in the presence of ligand. Assume that GA,
the free energy of conformation A, is zero.
(c) Calculate the mean number of ligands bound to this protein.
4. When a molecule is in solution, it has two transport mechanisms: by diffusion, and by
random thermal motion. You want to compare the two mechanisms in riboclease (MW 13,683).
(a) Assume D = 1.1 × 10-6 cm2/sec at 20°C, C = 1 µM, and dC/dX = 0.1 mM/cm. Calculate
the velocity of molecule moving as a result of diffusion.
(b) Now calculate the root mean square speed of the molecule resulting from random thermal
motion. How does this compare with the speed of the molecule due to diffusion?
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Chem 156

Additional Problems

  1. System A has ΩA states, and an entropy of SA (in units of J/K). If there is a system B with an entropy of SB = ( SA + 1 J/K ), then how many states does system B have?
  2. You have a system of particles in which you have 3 possible energy levels:

h ω h ω h ω

E = E = E =

(a) Calculate the probability that a particle has an energy of 5 ħω /2.

(b) Suppose that you have one mole of particles. Calculated the total expected energy of the system. How many particles would you expect to see in each state?

  1. A new protein you discovered has two different conformations: one conformation, I , is inactive, and cannot bind any ligand, B. The other conformation, A , can bind two ligands in a cooperative fashion in its binding site. Here is a diagram that illustrates this point:

L-1^ K 1 K 2

I A A·B A·B 2

(a) Which equilibrium constant is larger, K 1 or K 2? Explain why.

(b) Calculate the mean free energy of this protein in the presence of ligand. Assume that GA , the free energy of conformation A , is zero.

(c) Calculate the mean number of ligands bound to this protein.

  1. When a molecule is in solution, it has two transport mechanisms: by diffusion, and by random thermal motion. You want to compare the two mechanisms in riboclease (MW 13,683).

(a) Assume D = 1.1 × 10-6^ cm^2 /sec at 20°C, C = 1 μM, and dC/dX = 0.1 mM/cm. Calculate the velocity of molecule moving as a result of diffusion.

(b) Now calculate the root mean square speed of the molecule resulting from random thermal motion. How does this compare with the speed of the molecule due to diffusion?

  1. You know that there are two known ways for a molecule to have a ratio, f / f 0 > 1: by shape, or by hydration. Let’s compare the two mechanisms.

(a) Calculate the ratio f / f 0 for a prolate ellipsoid with a/b = 2.

(b) Suppose there is a sphere with radius R with an identical f / f 0 ratio as the prolate ellipsoid in part (a). Assuming this increase in f / f 0 is due solely to hydration, how thick is the shell of water? What is the volume of the shell?

  1. This time, you have a dilute aqueous solution of CaSO 4. To model this solution, you decide to use Coulomb’s law (disregard screening effects), and calculate the chemical potential.

(a) Calculate Gel, Sel, and Hel when a Ca2+^ ion and a SO 4 2-^ ion are separated by a distance of 15 Ǻ in a medium of dielectric constant ε = 74.2, at 37ºC. Use the following data to

estimate T (^) P

∂ lnε

T, Celsius Diel. Const. 20 80. 25 78. 30 76. 35 75. 40 73. 45 71. 50 69.

(b) Compute the chemical potential for the solution for a solution of CaSO 4.

  1. You now make a 10mM aqueous solution of Na 3 PO 4. This time, you decide to include screening effects in your calculations, and apply the Debye-Hückel theory.

(a) Calculate I, the ionic strength.

(b) Calculate κ, the inverse of the Debye radius.

(c) Calculate γ ±, the mean activity coefficient.

(d) Calculate μ, the chemical potential for Na 3 PO 4.