Structure of Life | - Cell architecture
- Organelles
- Mitochondria
- Cell membranes
- Protein synthesis: DNA -> mRNA -> amino acid chain -> protein folding
- The mechanism of a ribosome
- Difference between bacteria and eukaryotic cells
- Difference between plant cells and animal cells
- Dimensions of atoms, molecules, proteins, organelles, bacteria, human cells, neurons
- Lipid structure
- Detergents, Vesicles, Micelles, Membranes
- Phase transition in 2D in a lipidic membrane
- Critical Micellar Concentration
- Protein structure; Primary, Secondary, Tertiary, Quaternary structure
- Protein components: Alpha helix, Beta sheet, Unfolded
- Amino acid classes
- What is the Isoelectric point (pI)
- Hydrophobic effect
- Membrane protein vs. soluble protein
| - How to calculate the isoelectric point (pI)
- Lysosome
- Chloroplast
- Vacuole
- Golgi
- Endoplasmatic reticulum
- Cytoskeleton
- Waxes
- Caveolae
- Synapses
- Neurotransmitters
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Electrophoresis | - SDS-PAGE
- non-denaturing gels
- 2D gels
- How to make a gradient gel
- Isoelectric focussing
| - Linear and Gradient Gels
- Stacking vs. running gels
- DTT
- ME
- Amino acid side chain pK values
- DNA in gels
- Capillary electrophoresis
- Electroosmotic flow
- Northern, Southern and Western Blotting
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Chromatography | - Peak broadening mechanisms
- Refractometer mechanism
- Differential viscometer mechanism
- Amino acids that absorb light: Which ones, at which wavelengths?
- Ion exchange column principle mechanism
- IMAC column principle mechanism (Ni-NTA)
- Gel filtration column principle mechanism
| - Column principle: Theoretical plate, propagation speed on a column, peak width on a column, partitioning coefficient
- Light scattering mechanism
- FPLC
- Capacity factor of a column
- Reversed phase column
- Hydrophobic interaction column
- Affinity column
- Names and types of ion exchange column materials
- Names and types of gel filtration columns
- HPLC
- Perfusion chromatography
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Digitalization | - Raster vs. Vector graphics
- Histogram
- LUT
- Bayer pattern
- RGB vs. CMYK
- Metadata
- Lossy vs. Lossless compression
- pixels, voxels, bit-depth, number representation in a computer (integer vs. floats)
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Fourier | - Fourier transform equation (forwards and backwards)
- Friedel Symmetry
- Nyquist resolution
- Powerspectrum
- Real vs. reciprocal space and their units
- Cos&Sin representation vs. Amplitude&Phase representation (Argand diagram)
- Fourier equations:
- Convolution Theorem in Fourier space (important)
- Cross-Correlation Theorem in Fourier space (important)
- How to go from 2D images to a 3D reconstruction, using FT
- FT(rect, since, delta, Gaussian)
| - How are Fourier transforms stored in computer memory
- High-pass, Low-pass, Band-pass
- MotionCorr, drift correction of movies
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Energy Forms | - Molecules of the Respiratory Chain in Mitochondria
- F-ATPase structure and mechanism
- Experiment by the Kinosita group about direct observation of rotation
- Friction vs. Brownian motion
- Ratchet motor
- Proton Motive Force
- Energy of ATP, including Gibbs free energy due to concentration changes
- Protein folding forces and their binding energies
- Melting temperature of a protein
- Thermofluor & DSC
| - ATPsynthase differences between different organisms
- V-ATPases
- van't Hoff's relationship
- Proposed models for mechanisms of protein folding
- GroEL
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Mass spectrometry | - Principle of MS devices
- Electron ionisation, MALDI, Electro-spray ionisation
- Time of Flight, Reflectron Time of Flight, Quadrupole
- How to calculate the charge and mass of a particle from an ESI-TOF MS spectrum
- Peptide fingerprinting
- Protein sequencing with MS
| - FT-Ion Cyclotron Resonance
- CI, FAB, APCI
- Double-focusing magnetic sector
- Quadrupole ion trap
- Cross-linking MS
- Limited Proteolysis MS
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Hydrodynamic Methods | - Dynamic viscosity
- Ubbelohde viscometer
- Relative, specific and intrinsic viscosity
- Arrhenius type relationship for viscosity vs. temperature
- Newtonian vs. non-Newtonian fluids
| - Phase diagram of water
- Viscosity of DNA or random coil proteins
- LiquiGlide
- Ketchup
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Surface Effects | - Surface tension
- Contact angle of a drop on a surface
- Detergents, CMC
- Capillary force
- Lipid rafts
| - Names and types of detergents
- Langmuir Blodgett Trough
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Calorimetry | - Entropy, Enthalpy, Inner Energy, Gibbs free energy, Temperature, Entropy, pressure, volume
- Arrhenius effect, Arrhenius plot
- Exothermic vs. Endothermic reaction
- Enthalpy of a reaction
- Exothermic vs. Endothermic reaction
- Differential Scanning Calorimetry (DCS)
- Isothermal Titration Calorimetry (ITC)
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Spectroscopy | - Wave-Particle dualism
- Continuum of electromagnetic waves: Which radiation types are part of that?
- Other types of radiation?
- Beer-Lambert law
- Absorbance vs. Fluorescence
- Which amino acids show fluorescense?
- ORD
- Circular Dichroism (CD): What is it, how does it work, what does one measure?
- CD spectra of alpha-helical, beta-sheet and random-structure protein specimens
- FTIR: How does it work?
- Michelson-Moorley experiment
- Raman spectroscopy: What is it? How is it measured? What does it show about the sample?
- Stokes and Anti-Stokes shifts
- OCT (added only on June 19, 2025)
| - Human retina
- Absorption spectra of different biomolecules
- Bradford assay
- Thalidomide, Contergan
- CD spectra of DNA and RNA
- FTIR spectra of different substances
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Radiation Biophysics | - Bohr model, isotopes,
- Nuclear fission chain reaction principle
- Alpha, beta, gamma, neutron radiation, UV light and X-rays and other electromagnetic rays
- Radiation units: CPM, Curie, R, RAD, Gray, Sievert. What are they, what do they measure
- Typical amount of radiation per person per year in Switzerland in mS
- How many mS are threasholds for annual exposure, how many mS are dangerous if received in one exposure.
- Technetium-99m in medicine
- SPECT, PET principle
- Gamma knife principle
- Iodine 131 used in radiation therapy
- Protection effect of different materials against different types of radiation (alpha, beta, gamma, neutrons)
- Physical vs. biological half-life time.
| - Symptoms or radiation poisioning
- Chernobyl reactor principle and accident
- Other types of radiation used in medicine
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Electron Microscopy in Life Sciences | - Electron Source types
- SEM construction principle, operating mechanism, type of data recorded (surface)
- TEM construction principle, operating mechanism, type of data recorded (projection)
- Sample preparation principles for negative stain, for cryo-EM
- Electron/sample interaction
- Cryo-EM principle, workflow
- Frontiers in single particle cryo-EM: What are the limitations of current technology?
- Cryo-electron tomography principle
- How can sample movement during image recording be adressed?
- How can the noisy images still be used for a high-resolution reconstruction?
- How can the images be used to generate a 3D reconstruction of particles, or of a cell tissue slice?
- FSC, how is resolution measured?
| - Image formation
- Contrast transfer function (CTF)
- Effect of Defocus on the CTF
- RNA binding complex
- ABCG2 protein
- FOCUS software
- Microfluidic Cryo-EM grids
- Proteasome
- Tobacco Mosaic Virus (TMV)
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NMR spectroscopy, SPR | - Principle of NMR spectroscopy.
- How does the B-field relate to the proton resonance frequency?
- What is chemical shielding?
- How can a 1D NMR spectrum be interpreted?
- What is 2D NMR spectroscopy
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AFM | - STM vs. AFM, mechanism, principle of operation, what is measured and how?
- AFM: Construction principle, how can it operate on a sample that is in water?
- Typical resolution of STM and AFM
- Requirements for biological samples for imaging by AFM
- Conformational Landscape of a protein
- Typical sources of artifacts in STM and AFM
- Tapping mode vs. Contact (constant force or constant height) mode
- How can an energy landscape of a protein surface be determined from an AFM image
- High-speed AFM
| - Kavli prize
- Corynebacterium, S-layer
- Unzipping
- Aquaporin
- Photosynthesis
- Photosynthetic apparatus, photosynthesis molecules
- Supercomplexes in photosynthesis
- Myosin
- Affinity imaging with the AFM
- Unzipping with the AFM
- Force spectroscopy
- Tissue characterisation with the AFM
- Nanomechanical sensors
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X-ray diffraction | - XRD principle
- 3D protein crystal
- Methods to produce 3D protein crystals
- Ways to produce X-rays
- Synchrotrons
- Bragg's law
- Resolution in Fourier space
- What is the phase problem in X-ray diffraction
| - Equation for X-ray beam intensity
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Free Electron Laser | - SwissFEL: Setup, mechanism: How are X-rays generated?
- What is the specific about FEL radiation?
- Why did people think that is an advantage for structural biology? (Neutze et al.)
| - Intensities of different X-ray sources
- Parameters of SwissFEL beamlines
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Stahlberg lab setup and research | | - This will not be part of the exam
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