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Biophysics of macromolecules

Biophysics of macromolecules. Department of Biophysics, University of Pécs. Macromolecules are HUGE molecules. DNA strand released from bacteriophage. DNA double helix. Biological macromolecules are EXCITING molecules. Newly synthesized protein (silk fibroin). Structural model of

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Biophysics of macromolecules

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  1. Biophysics of macromolecules Department of Biophysics, University of Pécs

  2. Macromolecules are HUGE molecules DNA strand released from bacteriophage DNA double helix

  3. Biological macromolecules are EXCITING molecules Newly synthesized protein (silk fibroin) Structural model of hemoglobin

  4. Amount of macromolecules in the cell, by weight, is large Ions, small molecules (4%) Phospholipids (2%) 30 % other chemicals DNA (1%) RNA (6%) 70 % Water MACROMOLECULES Proteins 15%) Bacterial cell Polysaccharides (2%)

  5. Biophysics of macromolecules 1. Biological macromolecules - polymers 2. Polymerization 3. Equilibrium shape of polymers 4. Polymer mechanics 5. Studying biopolymers

  6. Biological macromolecules: biopolymers Polymers: Chains constructed of similar building blocks (monomers, subunits) Number of monomers: N>>1; Typically, N~102-104, But DNA: N~109-1010

  7. Polymer quantity • Equilibrium Growth (Log) Lag Time Formation of biopolymers: polymerization Covalent polymers: Enzyme-catalyzed process, from high-energy subunits Non-covalent polymers: Spontaneous, concentration-driven process Dynamic equilibrium

  8. 1. Linear • 2. Branched • 3. Circular 1 2 3 Shape of biopolymers The polymer chain is not rigid; due to its flexibility, it forms loose, random 3D network Basic flexibility mechanisms: Rotation around C-C bonds, Rigid segments connected with flexible (frictionless) joints (FJC), Torsion of bonds (WLC).

  9. r N R ri = elementary vector R = ”end-to-end” distance = correlation length N = number of elementary vectors Nl = L = contour length r 1 Polymer shape resembles random walk(Brownian motion) “Square-root law”: N.B.: Diffusion! <x2>=2D <x2> = mean squared displacement D = diffusion constant  = diffusion time (duration of observation)

  10. Biopolymer mechanics Elasticity of the entropic chain Entropic elasticity The polymer chain exhibits thermally driven bending motions configurational entropy increases (orientation entropy of elementary vectors). Correlation length Force (F) End-to-end distance (R) F = force l = correlation length (persistence length, measure of bending rigidity) kB = Boltzmann’s constant T = absolute temperature L = contour length R/L = relative extension

  11. Rigid chain Lp>>L Semiflexible chain Lp~L Flexible chain Lp<<L Biopolymer elasticity Microtubule Actin filament Titin molecule Lp = persistence length (measure of bending rigidity) L = contour length

  12. Laser Microscope objective Gradient force F F Refractile microbead EQUILIBRIUM Scattering force (light pressure) Mechanical investigation of biopolymers Grabbing single molecules with optical tweezers StarTrek Enterprise spaceship trapped by the tractor beam

  13. Tying a knot on a single biopolymer! (without releasing its ends!) Actin filament manipulation Arai et al. Nature 399, 446, 1999.

  14. Laser focus Laser #1 Laser #2 DNA molecule MCP CCD Fluor. Latex bead CCD Fluor. Exc. Illumination Moveable micropipette Stretching a DNA molecule with force-measuring optical tweezers Dual-beam optical tweezers setup Laser trap

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