Question

Chromatin is the complex of DNA and proteins (mostly histones) found in all eukaryotic cells. The fundamental repeating unit of chromatin is the nucleosome particle. The properties of the DNA and the protein in nucleosome particles were determined using a combination of velocity sedimentation, dynamic light scattering, and gel electrophoresis. Dynamic light scattering studies determined the diffusion coefficient of the nucleosome particle in solution at 293K to be 4.37x10^-7 cm^2/s. In the same solution, velocity sedimentation performed at 18,100 revolutions per minute obtained the following data: Time (minutes) Boundary Position r (cm) 0 4.460 80 4.593 160 4.713 240 4.844. Gel electrophoresis showed that the DNA molecule associated with a single nucleosome protein complex is 200 base pairs in length. a) What is the molecular weight of the nucleosome particle? Assume the solution has a density of 1.02 g/cm^3 and the specific volume of the nucleosome particle is 0.66 cm^3/g. b) Assuming the nucleosome particle is spherical, calculate its Stokes radius (assume the viscosity of the solution is 0.01 g cm^-1 s^-1). c) Each base pair in DNA is separated from the adjacent base pairs by about 3.4x10^-10 m. Based on this result and the result from part b, comment on how tightly packed the DNA is in the nucleosome. d) How are the proteins and DNA packed in the nucleosome? To answer this question, assume the eight proteins form an unhydrated spherical complex with a specific volume of 0.74 cm^3/g. Calculate the radius of this hypothetical protein sphere. e) Assume the 200 base pair DNA behaves as a random coil polymer. Calculate the root mean square (rms) end-to-end distance. Comparing the protein sphere radius with the rms end-to-end distance for the DNA, is most of the DNA packed outside or inside the protein core of the nucleosome? Explain.

          Chromatin is the complex of DNA and proteins (mostly histones) found in all eukaryotic cells. The fundamental repeating unit of chromatin is the nucleosome particle. The properties of the DNA and the protein in nucleosome particles were determined using a combination of velocity sedimentation, dynamic light scattering, and gel electrophoresis. Dynamic light scattering studies determined the diffusion coefficient of the nucleosome particle in solution at 293K to be 4.37x10^-7 cm^2/s. In the same solution, velocity sedimentation performed at 18,100 revolutions per minute obtained the following data: Time (minutes) Boundary Position r (cm) 0 4.460 80 4.593 160 4.713 240 4.844. Gel electrophoresis showed that the DNA molecule associated with a single nucleosome protein complex is 200 base pairs in length.

a) What is the molecular weight of the nucleosome particle? Assume the solution has a density of 1.02 g/cm^3 and the specific volume of the nucleosome particle is 0.66 cm^3/g.

b) Assuming the nucleosome particle is spherical, calculate its Stokes radius (assume the viscosity of the solution is 0.01 g cm^-1 s^-1).

c) Each base pair in DNA is separated from the adjacent base pairs by about 3.4x10^-10 m. Based on this result and the result from part b, comment on how tightly packed the DNA is in the nucleosome.

d) How are the proteins and DNA packed in the nucleosome? To answer this question, assume the eight proteins form an unhydrated spherical complex with a specific volume of 0.74 cm^3/g. Calculate the radius of this hypothetical protein sphere.

e) Assume the 200 base pair DNA behaves as a random coil polymer. Calculate the root mean square (rms) end-to-end distance. Comparing the protein sphere radius with the rms end-to-end distance for the DNA, is most of the DNA packed outside or inside the protein core of the nucleosome? Explain.

Added by Sharon W.

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