Inhaltsbereich
Biophysics of Macromolecules – Lecture Notes
Literature
- Phillips, Kondev and Theriot "Physical Biology of the Cell"
- Jonathon Howard "Mechanics of Motor Proteins and the Cytoskeleton"
- Sackmann and Merkel "Lehrbuch der Biophysik" (in German) [http://www.biophy.de/]
- Alberts et al. "Molecular Biology of the Cell"
- Nelson "Biological Physics"
Reader for the class ("Skript")
- Very tentative version [PDF, with password]
Schedule and Lecture notes "Biophysics of Macromolecules
- If you need the password for the files, ask me in class or send me an email.
- Recordings of the lectures are available on LMUcast. Go to the "Recording" tab above and follow the link. You need an LMU account to access the recordings.
Tuesday, April 13
- Course introduction and overview
- Fundamentals of molecular biology: Life, cells, evolution
- Lecture slides [PDF, with password]
Thursday, April 15
- Cells and model organisms
- The central dogma of molecular biology
- Introduction to biological macromolecules: DNA, RNA, and proteins
- Lecture slides [PDF, with password]
Tuesday, April 20
- Protein Data Bank (PDB)
- Physical interactions of biological macromolecules
- Molecular dynamics simulations
- Comparison: MD vs. quantum simulations
- Lecture slides [PDF, with password]
Thursday, April 22
- Protein folding: Secondary structure, Ramachandran plots, Structural motifs
- Anfinsen's hypothesis, Levinthal's paradox, Dill's folding funnel
- Discussion of PS1
- Lecture slides [PDF, with password]
Tuesday, April 27
- Protein-ligand interactions
- Binding equilibrium
- Cooperativity and allostery: Hill model, MWC model, KNF model
- Inverted classroom" assignment:
- Watch David Baker explain the potential of proteins design [link]
- Watch Susan Lindquist explain protein misfolding diseases [link]
We will dicuss protein design and protein misfolding disease next Thursday. - Lecture slides [PDF, with password]
Thursday, April 29
- Protein-ligand interactions and cooperativity, cont.
- Derivation of the shift in equilibrium in the MWC model
- Discussion of PS2
- Lecture slides [PDF, with password]
Tuesday, May 4
- Selected topics protein folding: Chaperones, proline isomerization, disulfide bonds
- Protein design
- Misfolding diseases
- Lecture slides [PDF, with password]
Thursday, May 6
- Traditional roles of RNA: mRNA, tRNA, rRNA
- RNA "beyond the central dogma": Ribozymes, RNA interference, ribowitches
- "Inverted classroom" assignment: Watch Jennifer Doudna explain CRISPR/Cas [link]
We will dicuss CRISPR/Cas and the video next Tuesday. - Discussion of PS3
- Lecture slides [PDF, with password]
Tuesday, May 11
- CRISPR/Cas: a batecterial defense system turned powerful gene editing tool
- The RNA folding problem and the importance of electrostatics
- Nucleic acid-ion interactions
- Lecture slides [PDF, with password]
Thursday, May 13
Ascencion Day ("Himmelfahrt") - No class
Tuesday, May 18
- Recap: Nucleic acid-ion interactions and the ion atmosphere
- Small-angle X-ray scattering
- Poisson-Boltzmann theory: introduction and solution for infinite plane
- Poisson-Boltzmann for complex nucleic acids
- Lecture slides [PDF, with password]
Thursday, May 20
- Recap: Poisson-Boltzmann
- Comparison: experimental data and Poisson-Boltzmann predictions
- MD simulations for nucleic acid-ion interactions
- Discussion of PS4
- Introduction to single-molecule force manipulation techniques
- Lecture slides [PDF, with password]
Tuesday, May 25
Pentecost ("Pfingsten") - No class
Thursday, May 27
- Viruses: Basics, Baltimore classification, origin
- Case study: SARS-CoV-2
- Lecture slides [PDF, with password]
Tuesday, June 1
- Single-molecule force spectroscopy techniques
- Isotropic elastic rod (Kirchhoff rod) model
- Freely-joined chain and worm-like chain
- Freely-jointed chain: root mean end-to-end distance
- Freely-jointed chain under external force
- Lecture slides [PDF, with password]
Thursday, June 3
Feast of Corpus Christi ("Fronleichnam") - No class
Feast of Corpus Christi ("Fronleichnam") - No class
Tuesday, June 8
- 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
- Magnetic tweezers: Instrumentation and force-calibration
- Twisting DNA with magnetic tweezers
- Lecture slides [PDF, with password]
Thursday, June 10
- Recap: Twisting DNA
- Magnetic torque tweezers and single-molecule measurements
- DNA bending and twisting stiffness
- Discussion of PS5
- Lecture slides [PDF, with password]
Tuesday, June 15
- Radius of gyration and end-to-end distance for FJC
- Self-avoidance and the Flory exponent
- Experimental evidence for self-avoidance: SAXS measurements for unfolded proteins and nucleic acids
- Fluorescence measurements for DNA in 2D
- Lecture slides [PDF, with password]
Thursday, June 17
- AFM imaging
- Force sensing and imaging modes
- Sample preparation and resolution
- AFM imaging applications: intrinscally disordered proteins, long DNA, and nucleosome conformations
- Lecture slides [PDF, with password]
Tuesday, June 22
- Guest lecture Prof. Thorben Cordes (Department of Biology, LMU Munich)
- Förster Resonance Energy Transfer (FRET)
- Coformational dynamics of proteins
- Lecture slides [PDF, with password]
Thursday, June 24
- Potential topics for TED talks
- Pointers on giving scientific presentations
- Energy in biological systems
- Enzyme-catalyzed reactions in biological systems
- Michaelis-Menten theory of enzymatic reactions
- Lecture slides [PDF, with password]
Tuesday, June 29
- Michaelis-Menten theory of enzymatic reactions
- Michaelis-Menten: kcat/Km regime, point of half-maximal rate, saturation regime
- Lecture slides [PDF, with password]
Thursday, July 1
- Guest lecture Prof. Claudia Veigel (Medical school, LMU Munich)
- Optical tweezers
- Molecular motors and the cytoskeleton
- Mechano-chemical coupling of myosin motors
- Lecture slides [PDF, with password]
Lab tour, July 2
- Your chance to see magnetic tweezers, AFMs, our wetlab, etc. in real life.
- We will meet at 13:30 in the seminar room on the first floor of Amalienstrasse 54. Here is how to find us: [link].
- Please wear a FFP2 mask in the building.
Tuesday, July 6
- Diffusion limited enzymes
- Super-diffusive enzymes
- Michaelis-Menten at the single-molecule level
- Discussion PS7
- Life at low Reynolds number
- Lecture slides [PDF, with password]
Tuesday, July 8
- Student presentations "Biophysics TED Talks" - PART 1
- Schedule [PDF]
Thursday, July 13
- Student presentations "Biophysics TED Talks" - PART 2
- Schedule [PDF]
Tuesday, July 15
- Student presentation back-up date
- Presentation of possible master thesis projects
- Question & Answer session / exam preparation
- Lecture slides [PDF, with password]
FINAL EXAMS: Oral exams; dates to be announced