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. It is the same password as for the Zoom meetings.
- 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 21
- Course introduction and overview
- Fundamentals of molecular biology: Life, cells, evolution
- Lecture slides [PDF, with password]
Thursday, April 23
- 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 28
- Protein Data Bank (PDB)
- Physical interactions of biological macromolecules
- Molecular dynamics simulations
- Comparison: MD vs. quantum simulations
- Lecture slides [PDF, with password]
Thursday, April 30
- Protein folding: Secondary structure, Ramachandran plots, Structural motifs
- Anfinsen's hypothesis, Levinthal's paradox, Dill's folding funnel
- Lecture slides [PDF, with password]
Tuesday, May 05
- Protein-ligand interactions
- Binding equilibrium
- Cooperativity and allostery: Hill model, MWC model, KNF model
- Lecture slides [PDF, with password]
Thursday, May 07
- Protein-ligand interactions and cooperativity, cont.
- Derivation of the shift in equilibrium in the MWC model
- Selected topic protein folding: circular dichroisim, disulfide bridges, proline isomerization
- Lecture slides [PDF, with password]
Tuesday, May 12
- 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
- "Inverted classroom" assignment: Watch Jennifer Doudna explain CRISPR/Cas [link]
We will dicuss CRISPR/Cas and the video next Thursday. - Lecture slides [PDF, with password]
Thursday, May 14
- CRISPR/Cas: a batecterial defense system turned powerful gene editing tool
- Nucleic acid-ion interactions
- Small-angle X-ray scattering (SAXS)
- Lecture slides [PDF, with password]
Tuesday, May 19
- Nucleic acid-ion interactions, cont.
- Poisson-Boltzmann theory and PB equation
- Derivation Poisson-Boltzmann for infinite plane
- Introduction to viruses
- "Inverted classroom" assignment: Watch Britt Glaunsinger explain Coronaviruses [link]
- We will discuss Coronaviruses next Thursday in class.
- Questions to guide you in video and for the discussion [PDF] - Lecture slides [PDF, with password]
Thursday, May 21
Ascencion Day ("Himmelfahrt") - No class
Tuesday, May 26
- Recap: Poisson-Boltzmann
- Poisson-Boltzmann for complex nucleic acids
- Comparison: experimental data and Poisson-Boltzmann
- MD simulations for nucleic acid-ion interactions
- Introduction to single-molecule force manipulation techniques
- DNA as an isotropic elastic rod
- Lecture slides [PDF, with password]
Thursday, May 28
- Coronaviruses: Basic biology and the current pandemic
- Short answers to the questions guiding the discussion of "Coronavirus 101" by Britt Glaunsinger [PDF]
- Lecture slides [PDF, with password]
Tuesday, June 02
Pentecost ("Pfingsten") - No class
Thursday, June 4
- Recap: Single-molecule stretching experiments
- Isotropic rod model
- Worm-like chain
- Lecture slides [PDF, with password]
Tuesday, June 09
- Freely-jointed chain: root mean end-to-end distance
- Freely-jointed chain under external force
- Force-extension experiment for DNA
- Lecture slides [PDF, with password]
Thursday, June 11
Feast Corpus Christi ("Fronleichnam") - No class
Feast Corpus Christi ("Fronleichnam") - No class
Tuesday, June 16
- 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 18
- Recap: Twisting DNA and torsional stiffness
- Magnetic torque tweezers
- DNA bending and twisting stiffness
- Twist-stretch coupling
- Lecture slides [PDF, with password]
Tuesday, June 23
- 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 25
- Energy in biological systems
- Enzyme-catalyzed reactions in biological systems
- Michaelis-Menten theory of enzymatic reactions
- Lecture slides [PDF, with password]
Tuesday, June 30
- Pointers on giving scientific presentations
- Michaelis-Menten, revisted: kcat/Km regime, point of half-maximal rate, saturation regime
- Diffusion-limited enzymes
- Super-diffusive enzymes
- Michaelis-Menten at the single-molecule level
- Lecture slides [PDF, with password]
Thursday, July 2
- Disussion PS6
- AFM imaging
- Lecture slides [PDF, with password]
Tuesday, July 07
- DNA topology
- White's theorem: Lk = Tw + Wr
- Organization and processing of genomes
- Nucleosome structure and dynamics
- Lecture slides [PDF, with password]
Thursday, July 09
- Discussion PS7
- Life at low Reynolds number
- Diffusion coefficient, Einstein-Stokes relationship, Langevin equation
- Swimming bacteria: Scallop theorem, Purcell's swimmer, runs & tumbles
- Lecture slides [PDF, with password]
Tuesday, July 14
- Organization and processing of genomes, continued
- Phase transitions in biological systems
- Discussion: What the Drosten and coworkers viral load study can teach us about scientific publishing
- Lecture slides [PDF, with password]
Thursday, July 16
- Guest lecture by Prof. Thorben Cordes
- Time and length scales in biology
- Förster Resonance Energy Transfer (FRET)
- Protein Dynamics and ligand binding models
- Lecture slides [PDF, with password]
Tuesday, July 21
- Student presentations "Biophysics TED Talks"
- Schedule [PDF]
Thursday, July 23
- Student presentations "Biophysics TED Talks"
- Schedule [PDF]
Tuesday, July 28
- 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 during August 3-10, 2020
- See the "Overview" tab for details about how to sign up, the exam schedule, and exam results.