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Biophysics of Macromolecules – Lecture Notes

Reader for the class ("Skript")

Schedule and Lecture notes "Biophysics of Macromolecules"

  • The schedule is preliminary, it will be refined as the semester proceeds. 
  • We will try to upload PDF files of the lecture slides (typically relatively shortly) before the lectures.
  • If you need the password for the files, send me an email.


Tuesday, April 25
  • Course introduction and overview
  • Fundamentals of molecular biology: Life, cells, evolution
  • Introduction to biological macromolecules: DNA
  • Lecture slides [PDF, with password]


Thursday, April 27
  • Introduction to biological macromolecules: RNA and proteins
  • Physical interactions of biological macromolecules
  • Molecular dynamics & beyond
  • Lecture slides [PDF, with password]
  • For your "edutainment": TV series Charité online (in German) [Link]


Tuesday, May 2
  • Introduction to biological macromolecules: DNA, continued
  • Chemical, structural and physical properties of DNA
  • Introduction to DNA nanotechnology
  • Lecture slides [PDF, with password]


Thursday, May 4
  • Reaction kinetics revised
  • Thermodynamics of DNA hybridization
  • Kinetics of DNA hybridization
  • Lecture slides [PDF, with password]

 

Tuesday, May 9

  • Traditional roles of RNA: mRNA, tRNA, rRNA
  • RNA "beyond the central dogma": Ribozymes, RNA interference, ribowitches
  • The RNA folding problem and the importance of electrostatics
  • Lecture slides [PDF, with password]

 

Thursday, May 11

  • Nucleic acid-ion interactions
  • Poisson-Boltzmann theory; derivation for infinitely charged plane
  • Comparison of PB theory to experiments; shortcomings of PB
  • Lecture slides [PDF, with password]


Tuesday, May 16


Thursday, May 18

  • DNA Folding in DNA origami
  • Intorduction to protein folding
  • Lecture slides [PDF, with password]


Tuesday, May 23

  • Protein folding: Anfinsen's hypothesis, Ramachandran plots, Levinthal's paradox, Dill's folding funnel
  • Simulating protein folding by molecular dynamics
  • Introduction to single-molecule force manipulation techniques
  • DNA as an isotropic elastic rod
  • Lecture slides [PDF, with password]


Thursday, May 25
Ascencion Day ("Himmelfahrt") - No class 
 

Tuesday, May 30

  • Isotropic elastic rod model
  • Worm-like chain model
  • Freely-jointed chain: root mean end-to-end distance 
  • Freely-jointed chain under external force 
  • Force-extension response of DNA
  • Lecture slides [PDF, with password]

 

Thursday, June 1

  • Stretching DNA: Entropic stretching modeled as a FJC and WLC, enthalpic stretching and the stretch modulus, overstretching
  • Stretching proteins: AFM force spectroscopy on titin Ig domains
  • Twisting DNA with magnetic tweezers
  • Lecture slides [PDF, with password]


Tuesday, June 6
Pentecost ("Pfingsten") - No class


Thursday, June 8

  • Introduction to the cytoskeleton molecules
  • Polymerization of actin and mictrotubules
  • Introduction to super-resolution microscopy
  • Lecture slides [PDF, with password]


Tuesday, June 13


Thursday, June 15
Corpus Christi ("Fronleichnam") -  No class 


Tuesday, June 20


Thursday, June 22

  • Force generation continued
  • Brownian ratchet model
  • Reaction-limited and diffusion-limited polymerization
  • Induced fit model
  • Lecture slides [PDF, with password]


Tuesday, June 27

  • Active Polymerization of Actin and Microtubules
  • Treadmilling
  • Dynamic Instability
  • Lecture slides [PDF, with password]


Thursday, June 29

  • Pointers on giving talks
  • Energy in biological systems
  • Enzyme-catalyzed reactions in biological systems 
  • Michaelis-Menten theory of enzymatic reactions
  • Michaelis-Menten at the single-molucule level
  • Lecture slides [PDF, with password]


Tuesday, July 4

  • Guest lecture Prof. Thorben Cordes (LMU Biology)
  • Protein conformational changes and ligand binding
  • Protein dynamics
  • FRET (Förster/Fluorescence resonance energy transfer)
  • Lecture slides [PDF, with password]

Thursday, July 6

  • Guest lecture Prof. Claudia Veigel (LMU Medicine)
  • Optical tweezers 
  • Molecular motors 
  • Lecture slides [PDF, with password]

Tuesday, July 11

  • Small-angle X-ray scattering (SAXS)
  • Polymer physics, excluded volume, and unfolded proteins & nucleic acids
  • Current applications of SAXS: An ASAXS-based molcular ruler; SAXS applied to DNA origami devices 
  • Lecture slides [PDF, with password]

Thursday, July 13

  • Guest lecture Prof. Karl Duderstadt (MPI Martinsried)


Tuesday, July 18
Student talks 

Thursday, July 20
Student talks 


Tuesday, July 25

  • Guest lecture Prof. Petra Schwille (MPI Martinsried) 

     

Thursday, July 27
Exam Review


MONDAY, July 31, 10:00 - 12:00
Final exam (N020, Kleiner Hörsaal der Physik)