Biophysics 1

Data

Official data in SubjectManager for the following academic year: 2023-2024

Topic

The course addresses the physical basis of the structure and function of biological systems. The main topics include atomic and nuclear physics, thermodynamics, transport processes, molecular and supramolecular systems, bioelectric phenomena, and biological motion.

Lectures

• 1. Introduction - Dr. Lukács András Szilárd
• 2. Structure of atoms - Dr. Lukács András Szilárd
• 3. Dual nature of light and electrons. Electromagnetic waves - Dr. Lukács András Szilárd
• 4. The quantum mechanical atomic model. Orbitals, molecular orbitals - Dr. Lukács András Szilárd
• 5. Laser - Dr. Lukács András Szilárd
• 6. Absorption spectroscopy - Dr. Lukács András Szilárd
• 7. Fluorescence spectroscopy - Dr. Lukács András Szilárd
• 8. Photophysics of molecules. Biomedical applications of fluorescence - Dr. Lukács András Szilárd
• 9. Infrared and Raman spectroscopy - Dr. Lukács András Szilárd
• 10. Flow cytometry - Dr. Grama László
• 11. X-rays - Dr. Grama László
• 12. X-ray diffraction - Dr. Grama László
• 13. Diagnostic X-rays, CT - Dr. Grama László
• 14. Gas laws. Phases of water - Dr. Bugyi Beáta
• 15. The first law of thermodynamics. Heat capacity, entalpy - Dr. Lőrinczy Dénes
• 16. The second law of thermodynamics. Entropy - Dr. Lőrinczy Dénes
• 17. Protein structure and folding. Enzymes - Dr. Bódis Emőke
• 18. Diffusion - Dr. Bugyi Beáta
• 19. Osmosis - Dr. Bugyi Beáta
• 20. Fluid flow - Dr. Bugyi Beáta
• 21. Circulation. Work of the heart - Dr. Bódis Emőke
• 22. Sedimentation. Electrophoresis - Dr. Talián Csaba Gábor
• 23. Biological membranes. Resting membrane potential - Dr. Talián Csaba Gábor
• 24. Sensory receptors. Action potential - Dr. Talián Csaba Gábor
• 25. Molecular mechanisms of biological movement: motor proteins, cytoskeletal polymers - Dr. Bugyi Beáta
• 26. Molecular mechanisms of muscle functioning - Dr. Bugyi Beáta
• 27. Mechanical properties of muscles - Dr. Bugyi Beáta
• 28. Mechanical properties of tissues - Dr. Bugyi Beáta

Practices

• 1. Introduction. Laboratory safety training
• 2. Introduction. Laboratory safety training
• 3. Direct Current Measurements
• 4. Direct Current Measurements
• 5. Alternating Current Measurements
• 6. Alternating Current Measurements
• 7. Electrocardiography
• 8. Electrocardiography
• 9. Temperature Measurements
• 10. Temperature Measurements
• 11. Atomic Spectra
• 12. Atomic Spectra
• 13. The absorption spectrum of macromolecules
• 14. The absorption spectrum of macromolecules
• 15. Emission spectra of biological macromolecules
• 16. Emission spectra of biological macromolecules
• 17. Centrifugation
• 18. Centrifugation
• 19. Fluid flow and blood pressure measurement
• 20. Fluid flow and blood pressure measurement
• 21. Viscosity of fluids and surface tension
• 22. Viscosity of fluids and surface tension
• 23. Make-up lab, seminar
• 24. Make-up lab, seminar
• 25. Test writing
• 26. Test writing
• 27. Make-up lab, seminar
• 28. Make-up lab, seminar

Seminars

Reading material

Obligatory literature

Literature developed by the Department

1. Damjanovich Sándor, Fidy Judit, Szöllősi János (eds.): Medical Biophysics, Medicina, Budapest, 2009
2. Biophysics Laboratory Manual, Pécs University Press, Pécs
3. Online materials on departmental website https://aok.pte.hu/hu/egyseg/10)

Notes

Recommended literature

Conditions for acceptance of the semester

Maximum of 25 % absence allowed

Mid-term exams

There is a short test at the beginning of every practical lab in order to assess the preparation of the students. If the student fail two of these tests, every further failure would be counted as an absence.

Making up for missed classes

Missed practices can be made up during make-up opportunities provided by the department. During each make-up lab, only one missed practice can be executed.

Exam topics/questions

1. 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
2. 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
3. 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. Molecular orbitals: sigma and pi bonds. Energy levels of molecules
4. 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
5. Absorption specroscopy
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
6. 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
7. Photophysics of molecules. Biomedical applications of fluorescence
Bioluminescence. Green fluorescent protein (GFP). Intrinsic and extrinsic fluorophores, fluorescent labels. Direct and indirect immunfluorescence labeling. Fluorescence sensors (ions, pH, membrane potential). Förster resonance energy transfer (FRET): phenomenon, requirements and practical applications
8. 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
9. 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 multiparametric representations and their interpretation. Principles of cell sorting
10. 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
11. 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
12. 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
13. 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
14. The first law of thermodynamics. Heat capacity, enthalpy
The zeroth law of thermodynamics. Internal energy, the equipartition theorem, heat. Equation and grapical interpretation of work. The first law of thermodynamics, perpetual motion machines of the first kind. Enthalpy
15. 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
16. 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-catalysed reactions, effect of enzymes on the rate of reactions, graphic illustration
17. 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
18. 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
19. 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)
20. 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
21. 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
22. 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
23. 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
24. 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)
25. 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)
26. 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
27. 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

Examiners

• Dr. Bódis Emőke
• Dr. Bugyi Beáta
• Dr. Grama László
• Dr. Hild Gábor
• Dr. Huber Tamás
• Dr. Huberné Dr. Barkó Szilvia
• Dr. Kengyel András Miklós
• Dr. Lukács András Szilárd
• Dr. Nyitrai Miklós
• Dr. Szabó-Meleg Edina
• Dr. Szatmári Dávid Zoltán
• Dr. Talián Csaba Gábor
• Pécsi Ildikó

Instructor / tutor of practices and seminars

• Czimbalek Lívia Mária
• Dr. Bódis Emőke
• Dr. Bugyi Beáta
• Dr. Grama László
• Dr. Hild Gábor
• Dr. Huber Tamás
• Dr. Huberné Dr. Barkó Szilvia
• Dr. Kengyel András Miklós
• Dr. Lukács András Szilárd
• Dr. Szabó-Meleg Edina
• Dr. Szatmári Dávid Zoltán
• Dr. Szütsné Tóth Mónika Ágnes
• Dr. Takács-Kollár Veronika Tünde
• Dr. Talián Csaba Gábor
• Dr. Ujfalusi Zoltán
• Dr. Visegrády Balázs
• Karádi Kristóf Kálmán
• Leipoldné Dr. Vig Andrea Teréz
• Szeiliné Dr. Türmer Katalin Erzsébet