Biophysics: notes and exam prep for MU Sofia

I. Biothermodynamics4 topics

1. 1Basic concepts of thermodynamics, entropy, thermodynamic potentialsfreeSubject and basic concepts of thermodynamics. First and second principles of thermodynamics. Definition of entropy, thermodynamic probability and Boltzmann's formula about entropy. Thermodynamic potentials - definitions and properties.
2. 2Basics of non-equilibrium thermodynamics. Thermodynamics of living systemsfreeFree energy and entropy of closed and open systems. Steady states and thermodynamic equilibrium. Linear nonequilibrium thermodynamics - Onsager relations between fluxes and driving forces. Living organisms as open thermodynamic systems. Basic applications of thermodynamics to living systems.
3. 3BioenergeticsfreeEnergy sources and transformations in living organisms. Proton pump and ATP-synthase. Electrochemical gradient and chemiosmotic mechanism. Efficiency of the energy transfer from glucose to ATP. Bioenergetics and evolution.
4. 4Thermodynamics of biopolymersfreeTemperature stability and denaturation of proteins. Conformational unfolding transition "globule-coil". Protein misfolding. Denaturation and hybridization of nucleic acids. Thermal injuries.

II. Biological membranes6 topics

1. 5Biomembranes - functions, types, composition. Membrane lipidsfreeFunctions, types and chemical composition of the biological membranes. Membrane phospholipids, glycolipids and cholesterol. Saturated and unsaturated fatty acids - physiological significance.
2. 6Biomembranes - role of membrane proteins. Methods for investigation of biomembranesMembrane proteins and glycoproteins - localization, functions and structure. Methods for investigation of biomembranes.
3. 7Model membranes. Fluid-mosaic model of membrane. Lipid raftsFirst models of biological membranes. The fluid - mosaic model of the membrane structure. Definition of lipid rafts - classification. Role of the lipid rafts by the membrane fusion.
4. 8The erythrocyte membrane - characteristicsLocalization of the membrane proteins in the erythrocyte membrane. Molecular structure and functions of some peripheral proteins (membrane skeleton) and transmembrane glycoproteins. Erythrocyte membrane fragility - hemolysis, methods for investigation and importance in disease states (hemolytic anemias).
5. 9Model membranes - monolayer, BLM, liposomeHydrophobic effect and formation of lipid aggregates, order parameter. Model membranes - classification. Monolayer and BLM - nature and applications. Liposome - types, use in medicine.
6. 10Molecular mobility in membranes. Phase transitionsMobility of the membrane components - rotational, lateral and transversal diffusion (flip-flop). Solid-to-fluid phase transition in lipid bilayers. Lamellar and non-lamellar liquid crystalline phases.

From here on, topics open with Super.Super is €14.99 a month

III. Free radical processes and oxidative stress3 topics

1. 11Free radicals in living systemsFree radicals in biological systems - generation, types, basic reactions and properties. Reactive oxygen species (ROS). Methods for registration.
2. 12Lipid peroxidation of membrane lipidsNature of the lipid peroxidation, stages, termination of the oxidation chain reactions of lipids. Primary and secondary products of peroxidation.
3. 13Oxidative stress and antioxidant defenseConsequences of the membrane components oxidation. Molecular mechanisms of the oxidative stress caused by various physical and chemical factors. Antioxidant defense systems. Oxidation of pharmaceuticals.

IV. Membrane transport5 topics

1. 14Passive membrane transportNature and importance of membrane transport. Types of transport. Free diffusion of uncharged particles - first and second Fick's laws. The Stokes-Einstein equation.
2. 15Diffusion of ionsFree diffusion of ions - Nernst-Planck equation, dimensionless potential. Hindered diffusion across porous membranes.
3. 16Transport of water solutions across membranesOsmosis and filtration. Dialysis and hemodialysis. Water exchange across membranes and between blood and tissues.
4. 17Facilitated transportFacilitated diffusion. Ionophores - mobile carriers (valinomycin) and channel-forming carriers (gramicidin A). Principles of action, molecular structure and selectivity.
5. 18Active transportTypes of active transport. Role of ATP. Sodium-potassium, calcium and proton pumps - function, structure and mechanism of action.

V. Electrical properties of cells and tissues6 topics

1. 19Membrane potentialsEquilibrium (Nernst), diffusion and Donnan potentials - conditions and mechanisms of generation, dependencies on the ion concentrations and time.
2. 20Resting potentialResting potential - concepts of its formation. Goldmann equation. Resting potential components (diffusion and Donnan potentials, electrogenic Na-K pump).
3. 21Action potentialAction potential - mechanism of generation and propagation. Ion channels - structure, effects of toxins and drugs. Hodgkin-Huxley model.
4. 22Surface electric charge of cells. Electric double layer of charged membranesOrigin of the surface electric charge of cells. Electric double layer of charged membranes. Poisson - Boltzmann equation. Zeta potential.
5. 23Electrokinetic phenomena. ElectrophoresisElectrophoresis - nature. Electrophoretic mobility - dependence on pH and ionic strength of the medium. Types of electrophoresis.
6. 24Passive electrical properties of cells and tissuesElectrical conductivity of cells and tissues for direct (DC) and alternating (AC) current. Types of polarization of the tissues in electrical fields. Electroporation and electrofusion of cells. Impedance and dispersion of the dielectric permittivity. Applications in medicine.

VI. Biomechanics4 topics

1. 25Mechanics of tissuesfreeSubject and importance of biomechanics. Rheology of solid biomaterials. Viscoelastic properties of bones and muscles.
2. 26Mechanics of biological membranesMechanical properties of biomembranes and cells. Role of the cytoskeleton. Elastic moduli of lipid bilayers (bending, stretching, shear).
3. 27Mechanics of vascular and respiratory systemsfreePassive mechanical properties of blood vessels - Lame's equation, volume-pressure dependence, pulse wave. Mechanics of breathing. Role of lung surfactant.
4. 28Mechanical properties of bloodHemorheology - rheology characteristics of blood. Dependence of blood viscosity on the hematocrit, deformability and aggregation of red blood cells.

VII. Nanotechnologies in medicine2 topics

1. 29Nanotechnologies in medicine - drug nanocarriersBasic concepts and terminology. Characteristics of nanomaterials. Nanoparticles and nanocapsules as drug carriers. Targeting and controlled release of drugs. Interactions with cells.
2. 30Nanotechnologies in medicine - diagnostic methods, biomaterialsNanotechnologies in medical diagnostics. Early diagnostics in vitro. Nanoparticles in imaging diagnostics. Nanosensors - detection mechanisms and types. Nanotechnologies in tissue engineering and production of new biocompatible materials.