Biophysics Minimum Requirements (Medicine, Dentistry & Molecular Biology MSc) PDF

Biophysics minimum requirement questions (Medicine, Dentistry and Molecular Biology MSc) Required topics for the different programs are given below: Program...

Biophysics minimum requirement questions (Medicine, Dentistry and Molecular Biology MSc) Required topics for the different programs are given below: Program Molecular Topic Medicine Dentistry Biology 1 Basic physical definitions yes yes yes Atomic physics, electromagnetic yes yes yes 2 waves, X-ray 3 Absorption, luminescence, lasers yes yes yes Geometrical optics, microscopy, yes yes yes 4 electron microscopy 5 Nuclear physics, radioactivity yes yes yes Interaction of radiation with yes yes yes 6 material, detection of radiation Radiation biophysics, dosimetry, yes yes yes 7 biological effect of radiations Experimental and diagnostic use of isotopes, gamma camera, CT, PET, yes yes no 8 SPECT Basic principles and medical/biological applications of yes yes yes nuclear magnetic resonance 9 (NMR). 10 Sound, ultrasound yes yes yes 11 Thermodynamics yes yes no 12 Diffusion yes yes Yes Biological membranes and membrane transport. Electric yes yes yes 13 properties of membranes. yes yes no 14 Biophysics of the Sensory System 15 Biomechanics yes no no Fluid mechanics and biophysics of yes yes no 16 circulation 17 Biophysics of respiration yes no no Physical methods in biology and yes yes yes 18 medicine Minimum requirement questions, 2023/2024 Contents v2 ac = =  2 r , where v is velocity, r is the radius of the 1 Basic physical definitions........................................ 1 r path,  is angular velocity. 2 Atomic physics, electromagnetic waves, X-ray....... 2 3 Absorption, luminescence, lasers........................... 3 7. Define angular velocity in words and with a formula! 4 Geometrical optics, microscopy, electron Angular velocity () is the ratio of the angle (, usually measured in radians) traversed to the amount of time microscopy................................................................... 4 (t) it takes to traverse the angle: 5 Nuclear physics, radioactivity................................. 5  6 Interaction of radiation with material, detection of = t radiation....................................................................... 6 7 Radiation biophysics, dosimetry, biological effect 8. Define momentum in words and with a formula! of radiations................................................................. 6 Momentum (p) is the product of the mass (m) and the velocity (v) of an object: 8 Experimental and diagnostic use of isotopes, p = mv gamma camera, CT, PET, SPECT................................... 7 9 Basic principles and medical/biological applications 9. Define moment of inertia in words and with a of nuclear magnetic resonance (NMR)........................ 8 formula! Moment of inertia (I) serves the same purpose in circular 10 Sound, ultrasound................................................... 9 motion as mass in linear motion. It characterized the 11 Thermodynamics.................................................... 9 resistance of an object against angular acceleration, i.e. 12 Diffusion................................................................ 10 the change in angular velocity. Moment of inertia of a 13 Biological membranes and membrane transport. point-like object can be calculated by the following equation: Electric properties of membranes............................. 10 I = mr 2 , where m is the mass of the object, r is the 14 Biophysics of the Sensory System......................... 12 distance of the object from the axis of rotation. 15 Biomechanics........................................................ 13 16 Fluid mechanics, biophysics of circulation and 10. Define angular momentum! Angular momentum is analogous to momentum, it respiration.................................................................. 14 serves the same purpose in circular motion as 17 Physical methods in biology and medicine........... 14 momentum does in linear motion. By definition, the product of the angular velocity and the moment of inertia of an object is its angular momentum. 1 Basic physical definitions 11. Define the potential energy of an object in a homogenous gravitational field! 1. Define kinetic energy in words and with a formula, The potential energy of an object with mass m at a height and give its unit! of h in a homogenous gravitational field characterized by Kinetic energy is the amount of work an object with a a gravitational acceleration of g is given by the following mass of m moving at a speed of v can perform while its equation: speed is reduced to zero: 1 E pot = mgh Ekinetic = mv 2 2 The unit of kinetic energy is joule. 12. Define the potential energy of a charged object in an electrostatic field! 2. Define electron volt (eV)! The electrostatic potential energy of an object with Electron volt is a unit of energy. It is equivalent to the charge Q at position A in an electrostatic field is: amount of kinetic energy gained by a single electron E pot = QU A ,where UA is the electric potential at point A. when accelerated through a voltage difference of 1 V. 13. Define work in words and with a formula! 3. Define what force is! Work is the amount of energy transferred by a force. It Force is a vector quantity characterizing the capability to can be calculated according to the following formula: cause acceleration. W = Fs , where W is work, F is force and s is the displacement of the object in the direction of the force. 4. Define acceleration in words and with a formula! Acceleration is the rate of velocity change with time: 14. Define buoyant force in words and with a formula. dv , where a is acceleration, dv is the change in a= Buoyant force is an upward force exerted by a fluid (or dt gas) on an object immersed in it. Buoyant force is equal velocity in time t. to the weight of the fluid (or gas) that the body displaces (Archimedes principle). 5. Define Newton’s 2nd law in words and with a Fb =  f V ' g , where ρf is the density of the fluid, V’ is formula! The acceleration of an object (a) is given by the ratio of the submerged volume, g is gravity. the net (or resultant) force acting upon it (Fn) and the mass of the object (m): 15. Formulate the general form of the work-energy F theorem, and its special form for the electric and a= n homogenous gravitational fields! m m ( vB2 − v A2 ) = WAB , 1 6. Define centripetal acceleration in words and with a General form: Ekinetic , B − Ekinetic , A = formula! 2 Centripetal acceleration (ac) is the rate of change in the m is the mass, vB and vA are the speed of the object at direction of velocity with time: point A and B, respectively, WAB is the work done on the object between points A and B. Minimum requirement questions, 2023/2024, page 1  In an electric field: Ekinetic , B − Ekinetic , A = QU AB , Q is the Direction of the force can be determined by the right hand rule. The moving charged particle will be deflected charge of the object, UAB is electric potential difference perpendicularly to both the instantaneous velocity vector between points A and B and the magnetic field without any change in its kinetic In a homogenous gravitational field: energy. Ekinetic , B − Ekinetic , A = mghAB , hAB is the height difference between points A and B. 2 Atomic physics, electromagnetic 16. Define power in words and with a formula, and give its unit! waves, X-ray Power is the rate at which work is done, and it is 23. Give the energy and momentum of a photon with calculated according to the following formula: P = W , frequency f. t The energy of a photon with frequency f is hf, and its momentum is h f c = h  , where h and c are where P is power, W is the amount of work perform in J time t. The unit of power is watt ( W = ). Planck’s constant and the speed of light in vacuum, s respectively, and  is the wavelength of the photon. 17. Define the term and unit of voltage! The voltage between points A and B is the difference 24. Align in ascending order the following components between the electric potentials of points A and B. The of the electromagnetic spectrum according to their unit of voltage is volt (V). If the voltage between points A energy: microwaves, gamma, ultraviolet, visible and B is 1V (UB-UA=1V), the amount of work required to light, X-ray, infrared, radiowaves! move a charge of 1 coulomb from point A to B is 1 joule. radiowaves < microwaves < infrared < visible light < ultraviolet < X-ray, gamma 18. Define electric current and derive its unit from other SI units! 25. What is the definition of visible light? Electric current is the amount of charge transported The range of electromagnetic radiation observable by across a boundary per unit time. Its unit is ampere (A). the human eye (approximately 400-750 nm). coulomb A= second 26. Define the limiting frequency (fmax) of braking radiation at an accelerating voltage of U. 19. Define resistance and give its unit! eU f max = According to Ohm’s law resistance (R) of a piece of h conducting material is the ratio of the voltage applied where h is Planck's constant and e is the charge of an across the piece of material (U) and the current through electron. the material (I): U 27. List the three most important mechanisms R= I responsible for the absorption of  and X-rays! The unit of resistance is ohm (  = V ). - photoelectric effect A - Compton-effect 20. Define what electric dipole is, and describe how to - pair-production calculate its electric dipole moment! An electric dipole is a separated pair of positive 28. What is the major difference between the photoeffect -q -q charge (+q) and an equal amount of negative and the Compton effect? charge (-q). The electric dipole moment (p) is defined by All of the energy of the X-ray (or gamma) photon is used the following equation: to ionize the atom and set the electron in motion in p = q  r , where r is the separation distance between the photoelectric effect. On the contrary, only part of the photon energy is used for these processes in Compton charges. Electric dipole moment is a vector quantity effect, and the photon having lower energy is scattered. pointing from the negative charge towards the positive one. 29. What is the minimal energy of a -photon needed for 21. Give the magnitude and direction of the electric pair-production (not numerically)? Lorentz force acting on a particle of charge, Q in an The energy equivalent to the rest mass of an electron electric field, E. What is the consequence of the and a positron according to the Einstein mass-energy force on the charged particle? equivalence equation: E=(me+mp)c2, where me and mp are the rest masses of an electron and a positron, FL = EQ , where FL is the electric Lorentz force. respectively, c is the speed of light in vacuum and E is For positively charged particles the force is parallel, the minimal energy of a -photon inducing pair whereas for negatively charged particles it is antiparallel production. with the direction of the electric field. The particle will be accelerated in a linear fashion along the direction of the 30. Why is a heavy nucleus necessary for pair- force. production? The presence of a heavy nucleus is required by the law 22. Give the magnitude of the magnetic Lorentz force of conservation of momentum. acting on a particle of charge, Q which moves at a speed v in a magnetic field, B. What rule should be 31. What is annihilation? applied to obtain the direction of the force? What is The process in which an electron and a positron (or in the consequence of this force on the charged general a particle-antiparticle pair) collide with each particle? other and the total mass-energy of this particle system is FL = QvB sin  , where FL is the magnetic Lorentz converted to the energy of two gamma photons, is called annihilation. force,  is the angle enclosed by the velocity vector and the direction of the magnetic field. Minimum requirement questions, 2023/2024, page 2 32. Define interference. 42. What is the approximate coherence length of a laser Interference is the superposition of waves that results in and that of a classical light source? the generation of a new wave pattern. 1010 cm and a couple of cm, respectively 33. What is constructive and destructive interference? 43. Align in ascending order the following transitions Interference is constructive when the amplitude of the according to their energy difference: vibrational, resultant wave is greater than the amplitudes of the rotational and electronic! individual waves, and it is destructive when the rotational < vibrational < electronic amplitude of the resultant wave is less than that of the individual waves. 44. Write the Lambert-Beer law and interpret the variables in the formula! 34. What is the requirement for maximally constructive J and maximally destructive interference if two lg 0 =  cL = A or J = J 010−c L J propagating waves with identical wavelength J - intensity of light after passing through a material with interfere with each other? thickness L Maximally constructive interference takes place, if the Jo- incident intensity of light when it enters the sample path difference (s) between the waves is an integer A – absorbance (optical density or extinction) multiple of the wavelength (): s = l , where  - molar extinction coefficient l=0,1,2,3…. This happens when the crest of one of the c - concentration in mol/liter waves is superimposed on the crest of the other one. L - optical path length. Maximally destructive interference is generated, if  1 45. What does the molar extinction coefficient depend s =  l +   , i.e. when the crest of one of the on?  2 It depends on the type of the absorbing material, the waves is superimposed on the trough of the other one. wavelength of the light, temperature, the type of the solvent and the environment. 35. Give the condition for constructive interference for an electromagnetic wave with wavelength  46. How many fold does the intensity of light decreases if the absorbance (optical density, extinction) of a diffracted on a crystal with a grating constant of c! solution is 1? (angle of incidence is 90o) It decreases 10-fold. c cos=l , where l=0,1,2,3,...n, =angle of diffraction 47. What is the definition of the molar extinction 36. What is the definition of transverse and longitudinal coefficient? waves? It is the absorbance (optical density) of a solution with a In a transverse wave the displacement of oscillating concentration of 1M and an optical path length of 1 cm. particles is perpendicular to the direction of propagation of the wave. In a longitudinal wave the displacement is 48. At what wavelength are the characteristic absorption parallel to the direction of propagation. maxima of proteins and nucleic acids? proteins 280 nm, nucleic acids 260 nm 3 Absorption, luminescence, lasers 49. Which amino acids have reasonably high absorption? 37. What is monochromatic light? Tyr, Trp, Phe Light is monochromatic if its spectrum consists of a single wavelength only 50. What is the definition of a singlet and a triplet state? In a singlet and a triplet state the number of unpaired 38. What kind of special characteristics does laser light electrons is zero and two, respectively. In a singlet and have? a triplet state, the value of the resultant spin multiplicity - monochromatic is 1 and 3, respectively. - coherence in time and distance - small divergence 51. What are the possible ways of relaxation of an - high light density. excited electron in a molecule? (List at least 5 of them!) 39. List the types of interactions laser light can have - vibrational relaxation with tissues. - internal conversion - photothermal (laserthermy, coagulation, - intersystem crossing vaporization, carbonization) - fluorescence - fluorescence, photochemical reactions - phosphorescence - photodissociation - delayed fluorescence - multiphoton ionization - energy transfer to another molecule. 40. When is electromagnetic radiation coherent? 52. What is the definition of fluorescence lifetime? If it consists of photons capable of forming observable The time during which the number of excited molecules interference fringes. decreases to 1/e-times (37 %) of its initial value. 41. What basic phenomena is the generation of laser 53. What is a., scintillation, b., chemiluminescence, c., emission based on? photoluminescence? - population inversion is needed for light amplification to Processes where photon emission is elicited by occur, and it is only possible in systems with 3 or more a., ionizing radiation energy levels b., chemical reaction - stimulated emission is needed to give rise to coherent c., excitation by photons. monochromatic light. Minimum requirement questions, 2023/2024, page 3 54. How can fluorescence quantum efficiency (yield) be 64. What is the shortest resolvable distance in a light defined? microscope? (One definition is sufficient.) approximately 200 nm The fraction of excited molecules emitting a fluorescent photon, OR the number of fluorescence photons divided 65. How can the resolving power of a microscope be by the number of absorbed photons, OR the rate increased? constant of fluorescence divided by the rate constants of -by decreasing the wavelength of light all possible de-excitation processes. -by increasing the index of refraction of the material between the objective and the object 55. Why is the fluorescence quantum yield always -by increasing the half angle of the objective smaller than one? Because relaxation from the excited state can be 66. What is numerical aperture? accomplished not only by fluorescence emission. It is the product of the index of refraction of the material between the object and the objective (n), and the sine of 56. What is the lifetime range of fluorescence? the half angle of the objective (sin): n sin.  = 10-9 – 10-7s 67. Give the formula for the resolving power (f) of a 57. What is the lifetime range of phosphorescence? conventional light microscope!  = 10-6 – 10 s 1 2n sin  f = = , where: n = refractive index of the d  58. Why is phosphorescence lifetime longer than fluorescence lifetime? medium between the coverslip and the objective, = half Because phosphorescence is the result of spin- angle of the objective,  = wavelength of light, d = the forbidden transitions. minimum distance between two points at which they are resolvable. 59. Why is Förster type resonance energy transfer a sensitive method for distance measurements? 68. What is the function of the dichroic mirror in a Because its probability is proportional to the inverse sixth fluorescence microscope? power of the separation between the donor and the It reflects the excitation light, and is transparent for the acceptor. emitted photons, therefore it separates the excitation and emission light paths. 60. What can Förster-type resonance energy transfer be used for in biology? 69. What is the function of the excitation filter in a For measuring inter- and intramolecular distances. fluorescence microscope? It is transparent only in the wavelength range in which 61. List at least five parameters which can be the fluorescent dye can be excited, therefore it allows determined using fluorescent measurements! only those photons to reach the sample which can excite - DNA, RNA, protein and lipid content of a cell, or the the fluorescent molecule. quantity of any kind of material that we tagged with a fluorescent label. 70. What is the function of the emission filter in a - permeability of the cell membrane fluorescence microscope? - intracellular enzyme activities It is transparent only in the wavelength range in which - membrane potential the fluorescent dye emits photons, therefore only the - intracellular calcium level photons emitted by the fluorescent dye will reach the - intracellular pH detector. - presence and density of cell surface antigens and receptors 71. List at least three of the imaging aberrations in - mitochondrial potential and the number of optical systems! mitochondria per cell. -chromatic aberration -spherical aberration -astigmatism 4 Geometrical optics, microscopy, -coma -curvature of the field of the image electron microscopy -barrel-shaped and cushion-shaped distortion of the image 62. Define the index of refraction! The index of refraction (n) gives the speed of light (c) in 72. Give the equation for the relationship between the a given material according to the following equation: image distance (i), object distance (o) and the focal c0 distance (f)! c= , where c0 is the speed of light in vacuum. 1 1 1 n + = i o f 63. Write Snell’s law of refraction! A light beam is refracted when it travels from a material 73. Give the definition and SI unit of diopter! with a refractive index of n1 into a material with a D (diopter)=1/f, is the refractive power of the lens, where refractive index of n2 (n2n1). Refraction is described by f is the focal length of a given lens. the following equation: SI unit: 1/m. sin  c1 n2 = = , where  and  are the angles of 74. What were those two discoveries that made sin  c2 n1 construction of an electron microscope possible? incidence and refraction, respectively, c1 and c2 are the -an electron can be regarded as a wave, and its speeds of light in the two materials. wavelength is only a fraction of the wavelength of visible light -an electron beam can be focused with a magnetic field Minimum requirement questions, 2023/2024, page 4 75. List at least three signals that can be detected during powerful attractive forces whose magnitude exceeds an electron microscopic measurement! that of electrostatic forces. -back-scattered electrons -secondary electrons 85. On what kind of energy level does a nucleon reside -characteristic X-rays in a nucleus compared to the energy of a free -Auger electrons particle? -absorbed electrons A bound nucleon has negative potential energy -cathode luminescence compared to a free particle. -transmitted electrons 86. List the types of radioactive radiation and 76. What are the two types of electron microscopes? characterize the particles constituting them! transmission electron microscope (TEM) Alpha radiation consists of helium nuclei. Negative beta scanning electron microscope (SEM) radiation (-) is composed of electrons, whereas positive beta radiation (+) consists of positrons. Gamma 77. What is the principle of transmission electron radiation is an electromagnetic radiation consisting of microscopy? high energy photons. A thin, typically 100 nm thick, sample is illuminated with an electron beam. The sample scatters a fraction of the 87. What is the direction of changes in the atomic electrons, i.e. the sample usually does not absorb the number and the mass number of nuclei during alpha electrons. Using magnetic lenses an image is formed decay, both types of  decay, electron capture and from the electrons going across the sample. The image gamma decay? is characteristic of the electron scattering properties of the sample. change in change in atomic mass number number 78. What is the principle of scanning electron  decay −4 −2 microscopy?  (-) decay 0 +1 The sample is scanned by a thin electron beam. Secondary electrons induced by the electron beam are  (+) decay detected on a pixel-by-pixel basis. and electron 0 −1 capture  decay 0 0 5 Nuclear physics, radioactivity 88. Why is the spectrum of beta decay continuous? 79. Give the definition of isotopes! Besides an electron (or a positron) an antineutrino (or a Isotopes are the variants of a chemical element with a neutrino) is also emitted, and the energy released during given atomic number whose mass numbers are different. the decay is shared randomly between the two particles. 80. List the isotopes of hydrogen with their mass 89. What is electron capture and what does it produce? number and the constituents of their nuclei! Some nuclei are capable of capturing an electron residing on the K shell decreasing their atomic number by one. The vacancy generated this way on the K shell Mass Composition is filled by an electron from a higher shell. This transition number generates characteristic X-ray and/or an Auger electron. Hydrogen 1 1 proton Deuterium 2 1 proton+1 neutron 90. Give the equation describing the number of Tritium 3 1 proton+2 neutron undecayed nuclei as a function of time (i.e. the law of radioactive decay). 81. What is the mass defect of nuclei? N = N 0 e − t The mass defect equals the difference between the mass of a nucleus and the total mass of its constituents N0: number of radioactive nuclei at t=0, (Z: the number of protons and A-Z: the number of N: number of undecayed radioactive nuclei at the time of neutrons, where Z and A are the atomic number and the investigation, mass number of the nucleus, respectively): : decay constant, m = (Z mproton + [A-Z] mneutron) - matom t: time. where m is the mass defect, mproton, mneutron and matom are the masses of a free, unbound proton, a free, 91. What is the physical meaning of the radioactive unbound neutron and the given atomic nucleus, decay constant? respectively. Radioactive decay constant is equal to the inverse first power of the mean lifetime of a radioactive nucleus. 82. What is the relationship between the total binding energy (E) and the mass defect (m) of a given 92. What is the relationship between the radioactive nucleus? decay constant () and the half life (T)? E=mc2, according to Einstein's mass-energy ln 2 T= equivalence principle (c is the speed of light in vacuum).  ln 2: the natural logarithm of 2. 83. Describe how the binding energy per nucleon changes as a function of mass number. 93. Define biological half life. Binding energy per nucleon has a maximum at nuclei Biological half life is the time period during which half of with mass numbers 55-60 (i.e. Fe). the initial quantity of the radioactive isotope leaves the living system undecayed due to metabolism, secretion or 84. What are the properties of nuclear force (their range, excretion. strength and direction)? Nuclear forces have limited range, their effect is 94. Define effective half life. negligible at a distance of more than a single nucleon Effective half life gives the time during which the initial and they are independent of charge. They are very activity of a given type of radioactive nucleus decreases Minimum requirement questions, 2023/2024, page 5  to half of its original value either by physical decay or increased in succession along the length of the tube. metabolism. The energy of this collision is sufficient to free several or alternatively secondary electrons. In this way the number of electrons Effective half life gives the time period during which the increases at each dynode. number of the udecayed nuclei decreases to half of the original value either by physical decay or biological 105. What is the basic operation principle of ionization processes. detectors? One of the definitions is enough to asnwer the question. Electrons and positive ions produced by the ionization process are separated by the electric field of the 95. Describe the relationship between the effective (Teff), detector. The charged particles are attracted towards the physical (Tphys) and the biological (Tbiol) half the appropriate electrodes and generate electric lives! impulses. 1 1 1 = + 106. What is the principle of detection of radioactive Teff Tphys Tbiol radiation by a scintillation detector? In certain organic and inorganic substances the energy 96. Describe the relationship between the physical of radioactive particles is converted to luminous energy, (phys), the biological (biol) and the effective (eff) i.e. they generate visible light flashes. decay constants! eff = phys + biol 107. List the radioactive radiations in order of increasing penetrability! 