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Sedimentation etc

Sedimentation etc. Topic 3 Part 1 Biophysics. General Principles. f v. Sphere: f 0 = 6 ph R. F (like mg). Other particle: get r = f/ f 0 and f = r f 0. Example – prolate with a = 3 and b = 2. Sedimentation.

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Sedimentation etc

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  1. Sedimentation etc Topic 3 Part 1 Biophysics

  2. General Principles f v Sphere: f0 = 6phR F (like mg) Other particle: get r = f/ f0 and f = r f0 Example – prolate with a = 3 and b = 2

  3. Sedimentation 1- r is the buoyancy factor ~ 1- ro/r (if ro > r then it floats). s = sedimentation coefficient, [s] = Svedberg, 1 x 10-13 sec = 1 Svedberg. Density of medium, r = mo/V, V = volume. is specific volume, volume/mass of substance in solution (V/m)

  4. Determining sAnalytical Centrifuge This instrument scans absorption along the centrifuge cell as a function of time – giving concentration.

  5. Determining s vb = drb/dt = w2srb, where the subscript b signifies the boundary (so rb is the boundary between solvent and solution). • So plot ln(rb) vs t and get slope which is equal to w2s.

  6. Determining sDiffusion blurs boundary D = RT/NAf,

  7. More on s • Depends on temperature and viscosity so define for standard conditions • s depends on M and f (shape) so if know M can get f (shape information/stokes radius)

  8. Density Gradient used for separation

  9. Real data on hemoglobin free and bound to haptoglobin

  10. Electrophoresis Now have F = ZeE, fv = ZeE. Mobility, U = v/E = Ze/f Sphere: U = Ze/(6phR)

  11. Movement on a Gel • This is a gaussian centered around x = xo + mFt • With rms of , velocity = mF, • m = 1/(6phr) with r = radius and h = viscosity • D = mkBT = diffusion constant

  12. Running DNA on a Gel • Closed small plasmids give discrete bands • Long DNA tunnels and separation goes as 1/mass • Can get screening from lots of cations • 2-D electrophoresis good for large pieces of DNA • Genome project used Saenger method

  13. Running Plectonemic helices • L = T + W • For DNA at several Kbp, helices run by writhe and hence (for constant twist), L • Topoisomers for DNA of defined length give gaussian band due to different energies • Wang Paper http://www.cbs.dtu.dk/staff/dave/roanoke/supercoil.jpg

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