Biophysics 2 Theory Exam Notes 2023/2024

The Structure of Atoms

  • Thomson’s model of the atom.
  • Rutherford’s experiment
  • Rutherford’s model of the atom.
  • Bohr’s postulates and Bohr’s model.
  • Energy levels of the hydrogen atom according to Bohr’s model.
  • Explanation of the line spectra of atoms.
  • The Franck-Hertz experiment and its explanation.

Dual Nature of Light and Electrons

  • Electromagnetic waves
  • Dual nature of light.
  • Phenomena proving the wave nature of light.
  • Waves, characteristics of waves.
  • The Huygens-Fresnel principle.
  • Diffraction, interference, the double-slit experiment.
  • Light as a transverse wave, wave polarization.
  • Electromagnetic waves, the electromagnetic spectrum.
  • List of phenomena proving the wave nature of light.
  • De Broglie’s matter wave hypothesis and its experimental proof

The Quantum-Mechanical Model of the Atom

  • Orbitals, molecular orbitals
  • Wave properties of the electron: the wave function and electron states in the atom.
  • Atomic orbitals and their types.
  • Quantum numbers and their physical meaning (orbital angular momentum and spin).
  • The Pauli principle and Hund’s rule.
  • The Stern-Gerlach experiment and its interpretation.
  • The Einstein-de Haas experiment

The Laser

  • Spontaneous and stimulated emission, population inversion.
  • Energy levels in a laser, metastable state, lifetime of states.
  • The laser oscillator, resonance condition.
  • Physical properties of laser light.
  • Description of one of the laser types.
  • Comparison of continuous wave and pulsed lasers.
  • Medical and other applications of lasers

Absorption Spectroscopy

  • Energy levels of atoms and molecules, the Jablonski diagram.
  • Main spectroscopic methods and their grouping by the types of interactions and photon energy.
  • Light absorption in general, the Lambert-Beer law.
  • Transmittance, absorbance, absorption coefficient.
  • Absorption spectrum.
  • Structure, operation, and applications of absorption photometers

Fluorescence Spectroscopy

  • Energy transitions in atoms and molecules, explained through the Jablonski diagram.
  • Singlet and triplet states.
  • Concept and types of luminescence (fluorescence, phosphorescence).
  • The process of fluorescence, the Kasha rule.
  • Structure and function of the fluorimeter.
  • The concept of excitation and emission spectra, the method they are recorded.
  • The Stokes shift.
  • Fluorescence quantum efficiency and lifetime

Photophysics of Molecules. Biomedical Applications of Fluorescence

  • Molecular orbitals: sigma and pi bonds.
  • Energy levels of molecules.
  • Bioluminescence.
  • Green fluorescent protein (GFP).
  • Intrinsic and extrinsic fluorophores, fluorescent labels.
  • Direct and indirect immunofluorescence labeling

Infrared (IR) and Raman Spectroscopy

  • Energy-level system of molecules.
  • Vibrational motion of molecules, natural frequency.
  • Dipole moment for linear and non-linear molecules (e.g. HCH, CO2).
  • Vibrational modes of water.
  • Condition of resonance, absorption, the IR spectrum, and its interpretation.
  • Applications of IR spectroscopy.
  • Elastic and inelastic light scattering.
  • Recording and interpretation of Raman spectra.
  • Rayleigh peak, Stokes and anti-Stokes shift.
  • Applications of Raman spectroscopy.
  • Advantages and disadvantages of IR and Raman spectroscopy

Flow Cytometry

  • Components, operation, and applications of a flow cytometer (fluidic system, hydrodynamic focusing, optical system).
  • Detected parameters and their interpretation: light scattering and fluorescence emission.
  • Data representation and analysis: list mode, single- and multi-parametric representations and their interpretation.
  • Principles of cell sorting

X-rays

  • Physical properties of X-rays and their place within the electromagnetic spectrum (frequency, wavelength, neighboring radiation types).
  • Components and function of an X-ray tube.
  • Formation and production mechanism of characteristic and braking radiation, comparison of their spectra.
  • Explanation of the cutoff wavelength

X-ray Diffraction

  • The condition of the diffraction, objects that may be studied by X-ray diffraction.
  • The condition for the formation of interference maxima.
  • Laue and Bragg equations (graphical interpretation and calculation of the path difference).
  • The experimental procedure of X-ray diffraction studies.
  • The single-crystal and the powder method.
  • Biological applications

Diagnostic X-rays, CT

  • The nature of X-rays, energy, and wavelength range.
  • Mathematical description of X-ray absorption (equations, functions, attenuation coefficient, half-value layer).
  • Interactions responsible for absorption.
  • Detection of X-rays.
  • Factors influencing absorption.
  • Contrast materials: principles and examples.
  • Digital subtraction angiography.
  • Dual-energy X-ray absorptiometry (DEXA).
  • Computed tomography (CT): the scheme and operation of the instrument, principles of imaging and computing.
  • Voxels, CT number, Hounsfield units.
  • Windowing

Gas Laws. Phases of Water

  • The concept, types, and examples of a thermodynamic system.
  • Extensive and intensive quantities.
  • Properties of the ideal gas as a thermodynamic model system.
  • Gas laws (Boyle's law, Charles' law, Gay-Lussac's law) and their graphic representation.
  • The combined and ideal gas laws.
  • Characteristics of phase diagrams, the phase diagram of water.
  • Thermal expansion of liquids and solids

The First Law of Thermodynamics. Heat Capacity, Enthalpy

  • The zeroth law of thermodynamics.
  • Internal energy, the equipartition theorem, heat.
  • Equation and graphical interpretation of work.
  • The first law of thermodynamics, perpetual motion machines of the first kind.
  • Enthalpy

The Second Law of Thermodynamics. Entropy

  • Classical and statistical interpretation of entropy (micro- and macrostates, thermodynamic probability, Boltzmann-equation).
  • Different statements of the second law of thermodynamics (involving entropy change, direction of heat transfer, perpetual motion machines of the second kind).
  • Gibbs free energy, its change, and the direction of processes

Diffusion

  • Thermal motion of particles, the phenomenon of diffusion, its cause, and consequences.
  • Quantitative description of diffusion, Fick’s 1st law: matter flow rate, matter flow density, concentration gradient, and their relation.
  • Diffusion coefficient, Einstein-Stokes-formula.
  • Relation between the diffusion time and the mean displacement.
  • Classification of transport processes through the cell membrane according to the transport mechanism and energetic requirements

Osmosis

  • Semipermeable membrane.
  • The phenomenon of osmosis, its cause, and consequences.
  • Osmotic pressure and its interpretation using the hydrostatic pressure.
  • Van’t Hoff’s law.
  • Classification of solutions based on their osmotic pressure.
  • Biological relevance of osmosis: red blood cells in different osmotic pressure environments, treatment of edemas and inflamed areas, treatment of constipation, hemodialysis

Fluid Flow

  • Pascal’s law (physiological examples).
  • Laminar and turbulent flow, stationary flow.
  • Shear stress, velocity gradient, the definition of viscosity.
  • Ideal and real fluids (blood and synovial fluid).
  • Reynolds number.
  • Volumetric flow rate.
  • Continuity equation.
  • Static, hydrostatic, and dynamic pressure.
  • Bernoulli’s law.
  • Explanation of aneurysm development.
  • Venturi effect (Venturi mask).
  • Hagen-Poiseuille’s law (vasodilation)

Circulation. Work of the Heart

  • Structure of the circulatory system.
  • Blood pressure.
  • The changes of pressure, cross-sectional area, and flow speed along the systemic circulation.
  • Factors affecting the blood flow.
  • Blood viscosity.
  • Vascular resistance.
  • Structure and function of the heart.
  • Pressure and volume changes during the cardiac cycle, pressure-volume curve of the heart.
  • The work of the heart.
  • Frank-Starling law

Protein Structure, Protein Folding, Enzymes

  • Levels of protein structure, bond types providing their stability.
  • Anfinsen’s experiment and its interpretation.
  • Levinthal’s paradox.
  • The folding funnel theory and its thermodynamic background (change of free enthalpy).
  • Protein misfolding and its pathological consequences with examples.
  • Gibbs free energy change of enzyme-catalyzed reactions, effect of enzymes on the rate of reactions, graphic illustration

Sedimentation, Electrophoresis

  • Forces acting on the sedimented particle during centrifugation.
  • Types of sedimentation methods.
  • Density-gradient centrifugation.
  • Centrifuge types, preparative and analytical centrifugation.
  • Sedimentation constant.
  • Principle of electrophoretic methods.
  • Electrophoretic mobility.
  • 2D-electrophoresis, isoelectric focusing

Biological Membranes. Resting Membrane Potential

  • The structure of the cell membrane and its formation (hydrophobic-hydrophilic interaction), membrane models.
  • Membrane dynamics: lateral and transversal movements.
  • The concept of electric potential.
  • Electrochemical potential, ion channels, ion pumps.
  • Generation, maintenance, and measurement of the resting membrane potential.
  • The potassium-hypothesis of Bernstein.
  • Nernst-equation.
  • Donnan potential.
  • Goldman-Hodgkin-Katz equation

Sensory Receptors. Action Potential

  • Types of ion channels, function of K- and Na-channels.
  • Types of sensory receptors, modality, adequate stimulus.
  • Conditions of the generation of the action potential.
  • Phases of the action potential and the corresponding changes of the ion currents.
  • Refractory phases

Molecular Mechanisms of Biological Movement: Motor Proteins and Cytoskeletal Polymers

  • Cytoskeletal polymers and their types.
  • The process of polymerization.
  • Structural polarity and its consequences.
  • Motor proteins, types of motor proteins, their structural and functional characteristics.
  • Power stroke, working distance, stroke velocity, cycle time, duty ratio, processivity.
  • Cross-bridge, duty cycle of skeletal muscle myosin II (mechanical and biochemical aspects)

Molecular Mechanisms of Muscle Functioning

  • Structural properties and levels of organization of striated muscles.
  • Sarcomere, filament systems, and proteins.
  • What does the force generated by a sarcomere depend on?
  • Sliding filament model.
  • Steric blocking model and regulatory proteins (tropomyosin, troponin system)

Mechanical Properties of Muscles

  • Stimulus-contraction response of the striated muscle: twitch, wave summation, tetanus.
  • Length-dependence of the force developed by the sarcomere (its medical relevance in the functioning of heart muscles).
  • Dependence of force and power on the velocity of contraction.
  • Equilibrium of rigid bodies, torque.
  • The lever as a simple machine, conditions of equilibrium.
  • Characteristics of mechanically advantageous and disadvantageous levers.
  • Simple machines in the human body, examples of type 1, 2, and 3 levers

Mechanical Properties of Tissues

  • Spring constant, Hooke’s law.
  • Physical model of the perfect elastic body.
  • Mechanical stress, mechanical strain, elastic modulus, elastic energy.
  • Types of mechanical deformations.
  • Stress-strain characteristics of ideal and real elastic bodies, elastic and plastic region.
  • Ultimate mechanical stress and strain.
  • Properties of viscoelastic materials: creep, stress relaxation, hysteresis.
  • Biomechanical properties of bones.
  • Biomechanical properties of blood vessels: compliance, distensibility

Structure of the Atomic Nucleus

  • Discovery, composition, size of the atomic nucleus, characterization of nucleons.
  • Mass number, atomic number, and their indication in the chemical symbol.
  • Definition of the isotope, examples.
  • Characterization of the nuclear force.
  • Binding energy of the atomic nucleus, mass defect, mass-energy equivalency: E=mc2E=mc^2.
  • Stability of the atomic nucleus, binding energy per nucleon (graph).
  • Models of the atomic nucleus: the liquid drop model, the shell model, and magic nuclei

Radioactivity

  • Types of radioactive radiations: emitted particles, changes in atomic and mass numbers.
  • Natural and artificial isotopes and their fields of application.
  • Description of radioactive decay: decay law, activity, decay constant, mean lifetime, half-life (physical, biological, effective)

Interaction of Radioactive Radiations with Matter

  • Types and properties of radioactive radiations: penetration, absorption, scattering, energy, speed, ionization, LET.
  • Interactions of gamma-radiation: photoeffect, Compton-scattering, pair production.
  • Annihilation

Biological Effects of Radioactive Radiations

  • Stochastic and deterministic effects and their characteristics.
  • Dose quantities: absorbed dose, equivalent dose, effective dose.
  • Radiation protection: justification, dose limits, ALARA principle.
  • Models of radiation effect: target theory, water-activity model, dilution effect.
  • Physical, chemical, and biological factors influencing the radiation effect

Gamma-Camera, SPECT, PET

  • Radioactive isotopes used in diagnostics: types and applications.
  • Radiopharmacons.
  • Gamma-camera: parts, detection of gamma-photons. Collimators.
  • Single-photon emission computed tomography (SPECT): structure and function of the instrument.
  • Structure and operation of a PET instrument, isotopes used and their production.
  • Coincidence detection, image reconstruction.
  • Morphological and functional diagnostic imaging methods and the information acquired with the different methods

NMR Spectroscopy

  • The concept of spin, spin of atomic nuclei.
  • Examples of NMR-active and NMR-inactive nuclei.
  • Behavior of spins in external magnetic field.
  • Energy difference between spin states, resonance condition.
  • Parts of an NMR instrument, measurement process.
  • The NMR spectrum. Chemical shift.
  • Applications of NMR spectroscopy

Magnetic Resonance Imaging

  • Behavior of proton spins in an external magnetic field.
  • Precession, Larmor frequency.
  • The dependence of the energy difference between spin states on the strength of the magnetic field.
  • Effect of the RF wave, change of the magnetization vector.
  • Relaxation, detected signals.
  • Spin-spin and spin-lattice relaxation.
  • Meaning of spin density, T1- and T2-weighted images.
  • Identification of signal localization

Hearing

  • Sound as a wave. Physical quantities characterizing the sound.
  • The decibel scale.
  • Loudness, Fletcher curves.
  • Parts of the outer ear and their function.
  • Structure of the middle ear, mechanisms of amplification.
  • Structure of the inner ear. Békésy’s theory.
  • The structure of the organ of Corti, the molecular basis of hair cell function

Ultrasound

  • Definition of ultrasound, general and diagnostic frequency ranges.
  • Ultrasound generation and detection.
  • Ultrasound reflection (acoustic impedance, reflectivity).
  • Operation of a diagnostic ultrasound instrument (pulse-echo principle, distance determination).
  • Structure, function, and types of transducers, ultrasound focusing.
  • Imaging, ultrasound modes. Radial and lateral resolution.
  • Functional principle and application of Doppler ultrasound.
  • The interaction of ultrasound with tissues, therapeutic applications

Geometrical Optics

  • Reflection of light, the laws of reflection.
  • Image formation by a plane mirror.
  • Speed of light, refractive index.
  • Refraction of light, Snell’s law.
  • Total internal reflection.
  • Characteristics and types of optical lenses.
  • Focal length, diopter.
  • Image formation by converging lenses.
  • Image formation by diverging lenses.
  • The lens equation.
  • Magnification of lenses

Vision

  • Structure of the eye, refractive power of the interfaces.
  • Image formation of the eye, characteristics of the image.
  • Accommodation.
  • The color sensitivity curve.
  • Physical and biological resolving power of the eye and its explanation.
  • Vision defects and their correction.
  • Structure and types of photoreceptors and their comparison.
  • The molecular process of light sensing.
  • The mechanism of color vision

Light Microscopy, Fluorescence Microscopy

  • Classification and principles of microscopic techniques.
  • Light microscopy.
  • Role of refraction and diffraction in the image formation of the light microscope.
  • Requirements for image formation: magnification, resolution, contrast.
  • Resolution limit of the light microscope (Airy disk, Abbe’s principle, diffraction limit).
  • Numerical aperture.
  • Immersion media.
  • Structure and function of epifluorescence microscopes (light path, optical filters, dichroic mirrors)

Modern Microscopic Methods

  • Principle of confocal microscopy (conjugate focal plane).
  • Principle, advantages, and disadvantages of total internal reflection fluorescence (TIRF) microscopy.
  • Multiphoton microscopy.
  • Concept of superresolution, principles of STED and STORM microscopes

Mass Spectrometry

  • The concept and principles of mass spectrometry.
  • General set-up of a mass spectrometer.
  • The role of the vacuum system.
  • Options of sample introduction.
  • Characterization of the main ion sources: electron impact, electrospray, MALDI.
  • Separation of ions, main analyzer types: quadrupole, TOF.
  • Characteristics of the mass spectrum, information content, resolution.
  • Principles of tandem mass spectrometry, layouts, and operation.
  • Main medical applications of mass spectrometry, newborn screening