Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology

Page 1

Relation analysis questions:

A. The first statement is true, the second statement is true, and the second statement explains the first. (+ + +)
B. The first statement is true, the second statement is true, but the second statement does not explain the first.
(+ + −)
C. The first statement is true, the second statement is false. (+ −)
D. The first statement is false, the second statement is true. (− +)
E. The first statement is false, the second statement is false. (− −)

Multiple choice questions:

Two of the statements are true. 1 point for correctly circled statements, -0.5 point for incorrectly circled ones.
Max. 2 points, min. 0 point per question.

True and false questions:

1 point for a correct answer, -0.5 point for an incorrect answer.

1. Atomic physics

Relation analysis
Spin is an inherent property of the electron similar to mass and charge, because magnetic
moment is not coupled to the spin of the electron.

X rays and γ rays have overlapping frequencies, because both of them are generated by
electronic transitions.

The spectrum of braking radiation is continuous, because all electrons lose their kinetic
energy in one step.

True or false

- The frequency of characteristic X ray is characteristic of the material of the heated cathode
from which the electrons to be accelerated are released.

Definitions, short essays

spin, de Broglie wavelength, attenuation coefficient, annihilation

Essays

1.1. Frank-Hertz experiment

a. Describe briefly the experimental device the Frank-Hertz experiment can be carried
out with (electrodes, content of the chamber).
b. Explain why the collector current decreases to a minimum, if the kinetic energy of
electrons accelerated by the anode voltage is equal to the excitation energy of the gas
in the chamber.
c. Explain why the collector current vs. anode voltage plot shows several minima.

1.2. Generation of X rays

a. Explain why the spectrum of braking radiation is continuous.
b. Describe the sequence of events leading to the generation of a characteristic X ray
photon.
c. Explain the limiting frequency of braking radiation (the formula is not enough).

This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.
 Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology
Page 2

1.3. Attenuation of X rays

a. Plot the intensity of X ray as a function of the thickness of the absorbing material.
Label the axes of the graph. Indicate whether you used linear or logarithmic scale.
b. Write the equation describing the attenuation of X ray as a function of thickness.
Interpret the variables.
c. Describe briefly the mechanisms of the three most important processes leading to the
absorption of X ray.

2. Nuclear physics, radioactivity

Relation analysis

The biological and physical half-lives of a nucleus are linearly proportional to each other,
because an undecayed nucleus cannot leave the human body as a result of metabolism.

The energy distribution of ß− radiation is discrete because a neutron is emitted along with the
ß− particle during the decay.

All isotopes are radioactive, because neutron is negatively charged.

Multiple choice
Radioactive decay
A) The mass number decreases by 2 during α decay
B) The mass number does not change during β decay
C) The atomic number increases by 1 during β+ decay
D) The mass number increases by 1 during K electron capture
E) The atomic number increases by 1 during β– decay

Definitions, short essays

lifetime of a radioactive isotope, half life (effective, physical, biological), decay constant,

2.1. Radioactive decay

a. Plot in the SAME coordinate system the effective and the physical decay of a
radioactive isotope in a living system as a function of time. Indicate if you used
linear or logarithmic scales.
b. Write the equation describing the above graph. Interpret the variables.
c. Label the physical half life and physical lifetime of the radioactive isotope in the
above graph.
d. What is the relationship between the half life and the decay constant?
e. The half life of a radioactive isotope is 100 days. The initial number of radioactive
isotopes is 106. What will the number of this radioactive isotope be in 50 days, 100
days and 200 days?

2.2. Detection of ionizing radiation

a. Describe the sequence of events taking place after a particle of ionizing radiation
enters a scintillation counter.
b. Why a Geiger-Müller counter cannot be used to differentiate between different
types of radiations?
This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.
 Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology
Page 3

3. Physical methods in biology and medicine

Simple test
No and N1 denote the number of electrons in the ground state and the first excited state,
respectively. What can the N1/No ratio be in the case of population inversion?
A. 1
B. 0
C. 0.5
D. 10
E. 0.1

Relation analysis

In isoelectric focusing proteins accumulate in an environment where the pH of the

surrounding medium is equal to the isoelectric point of the protein, because the charge of a
protein is positive at a pH more acidic than its isoelectric point.

The spin of an electron results from the presence of an external magnetic field, because the
mass of an electron is much higher than that of a proton.

Förster-type fluorescence resonance energy transfer (FRET) can be detected between

molecules that are separated by as much as 1 μm, because FRET is a non-radiative process.
True and false
- Emission of fluorescence always takes place at a shorter wavelength than excitation.
- Electrophoretic mobility is linearly proportional to molecular weight.

Multiple choice

Imaging techniques…
A) The resolution power of positron emission tomography (PET) is inversely proportional
to the wavelength of the illuminating light.
B) Only positive β decaying isotopes can be used in SPECT.
C) PET is a functional imaging method.
D) SPECT gives the same type of information as a γ camera, but with 3D (three
dimensional) resolution.
E) Radioactive isotopes are not used in SPECT.

Definitions, short essays

interference, coherence, fluorescence lifetime, prohibited transition, Kasha rule, Stokes shift,
fluorescence quantum yield (efficiency), FRET efficiency, linearly polarized light, anisotropy,
radiopharmacon, spin-spin relaxation, spin-lattice relaxation, gating in flow cytometry,
fluorescence-activated cell sorting (FACS).

Essays

3.1. Lasers

This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.
 Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology
Page 4

a. Compare stimulated and spontaneous emission of radiation.

b. Explain why population inversion is necessary for lasing (simply describing what
population inversion is not sufficient).
c. Draw a three-level electronic energy system, and based on the figure describe how
population inversion and stimulated emission can be achieved. Indicate in the
figure between which energy levels stimulated emission and pumping takes place.
d. List at least 2 examples for the medical or biological application of lasers.

3.2. Sedimentation
a. What kind of sedimentation method can be used for the determination of the
density of a particle? Describe briefly how.
b. In a sedimentation equilibrium experiment why are all the particles not
concentrated at the bottom of the tube?

3.3. X ray diffraction

a. Explain how interference is generated according to the Laue interpretation of X ray
diffraction.
b. Explain how interference is generated according to the Bragg interpretation of X
ray diffraction.
c. What can X ray diffraction be used for in biology?

3.4 Fluorescence
a. Draw a Jablonski diagram. Label the energy levels and indicate the most important
transitions in the figure.
b. Draw the emission and absorption spectra of a molecule in the SAME coordinate
system. Label the axes of the graph. Explain why the two spectra are shifted
relative to each other.
c. What is FRET efficiency? What can FRET be used for in biology?

3.5. Nuclear magnetic resonance

a. Plot the splitting between the energies of the α and β spin states as a function of
magnetic field strength.
b. Describe the phenomena leading to spin-spin and spin-lattice relaxation.
c. Briefly describe how gradient fields are used in magnetic resonance imaging.

3.6. Describe the principles of positron emission tomography (nuclear event, detection)!
Compare the principle of image generation and information content of a PET with that of
a CT examination.

3.7. Describe the advantages of computer tomography compared to conventional X ray

imaging.

3.8. Describe how image generation is achieved in SPECT. Explain what the term
‘radiopharmacon’ means.

3.9. Describe how the DNA content of cells can be determined using flow cytometry (labeling
of cells, measurement, histogram).

3.10. What is the principle of operation of a confocal laser scanning microscope (CLSM)?

This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.
 Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology
Page 5

4. Radiation biophysics

Relation analysis
In the case of single-target single-hit dose response curve the irradiation dose of D37 damage
all target molecules, because at this dose the expected number of ionizations in the
radiosensitive volume of the target molecules is 1.

Short essays, definitions

direct action, indirect action, radical, Poisson distribution, dilution effect, absorbed dose,
exposure, KERMA, equivalent dose, quality factor, fractionation.

Essays

4.1.
a. Explain briefly the main difference between direct and indirect actions of radiation.
b. An enzyme is available in two forms: dry and in an aqueous solution. Which will be
damaged more after exposure to the same amount of radiation under the same
irradiation conditions? Why?
c. Why is a well-oxygenated tissue usually more radiation sensitive than a hypoxic one?

4.2
a. Plot the fraction of surviving objects as a function of dose, if the object contains one
target, and one hit is sufficient to inactivate the target. Mark D37 in the graph.
b. Explain why the expression describing the surviving fraction of cells contains two
terms (one linear and one quadratic function of D) according to the molecular model
of radiation sensitivity.

5. Thermodynamics

Definitions, short essays

first and second law of thermodynamics, Hess theorem, enthalpy, Helmholtz free energy,
Gibbs free energy, state variable, state function, relationship between the heat capacity at
constant pressure and at constant volume

6. Transport, water, diffusion, osmosis

Relation analysis

If the concentration of a solute in compartment A is higher than in compartment B, not a

single molecule will cross from compartment B to compartment A, because diffusion is
driven by the concentration gradient between the two compartments.

Essays

6.1.
a. Explain how diffusion can be interpreted from a statistical point of view.
b. Explain how diffusion can be interpreted using chemical potentials.

This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.
 Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology
Page 6

c. Write van’t Hoff’s law, interpret the variables.

d. There are two compartments:
A: 10 mM glucose in water, B: 1 mM glucose in water
Explain what happens if
• the membrane separating the two compartments is permeable to both water
and glucose
• the membrane separating the two compartments is permeable to water only
(semipermeable membrane).
(Hint: diffusion and osmosis can take place simultaneously depending on the
permeability of the membrane)
e. What are the manifestations of the high propensity of water to form H bonds in its
physico-chemical properties?

7. Biological membranes

Relation analysis
The cytoplasmic and extracellular leaflets of the cell membrane are hydrophobic and
hydrophilic, respectively, because transmembrane proteins have hydrophobic and hydrophilic
regions.

If the membrane potential is equal to the Nernst (equilibrium) potential of a given ion, the net
flux of the diffusible ion in question through a semipermeable membrane is zero because in
this case the electrochemical potential for the ion in question is the same on both sides of the
membrane.

Essays

7.1 Structure of membranes, membrane transport

a. Draw the schematic structure of a biological membrane. Include the following
components: phospholipids, cholesterol, transmembrane proteins, peripherial
membrane proteins. Mark the hydrophobic and hydrophilic part of the membrane.
b. Describe the Singer-Nicolson (fluid-mosaic) model of the cell membrane.
c. Describe how to measure the lateral diffusion of membrane proteins using FRAP
(fluorescence recovery after photobleaching).
d. Plot the rate of diffusion and the rate of facilitated diffusion as a function of the
concentration difference in the SAME coordinate system. Explain the difference
between the graphs.
e. What is facilitated diffusion?

7.2. Membrane potentials

a. What is the ionic background of the resting membrane potential?
b. Explain the development of Donnan potential.
c. What is the ionic background of action potential? How does it spread?
d. What kinds of positive and negative feedback mechanisms are operational in the
generation of an action potential?
e. How does the Na+/K+ ATPase work?
f. What is the contribution of the Na+/K+ ATPase to the maintenance of the resting
membrane potential? (Hint: there is more than one!)

This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.
 Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology
Page 7

7.3. Patch clamp

a. Explain what can be measured using the current clamp configuration of patch
clamp.
b. Explain what can be measured using the voltage clamp configuration of patch
clamp.

7.4. ECG
What is the integral vector and how is it related to the bipolar leads in ECG?

8. Biophysics of sensory systems

Relation analysis

Every kind of rod (red-, green-, blue-sensitive) contain the same type of prosthetic group, 11-
cis retinal, because the red-, green- and blue-sensitive rods contain different types of opsin.

Essays

8.1. Geometrical optics

a. Define what chromatic and spherical aberration is.
b. Construct the image of the objects (arrows) below produced by a thin lens. The
crosses label the focal points of the lens.

8.2. Optics and physiology of the human eye

a. Describe the optical background of short-sightedness and far-sightedness (where
the image is formed, what is the explanation, how can it be corrected using lenses).
b. Describe the signal transduction cascade induced by the absorption of a photon
leading to a membrane potential change of the photoreceptor. Start from the
absorption of the photon.
c. Describe the physiological background of color vision.

8.3. Hearing
a. What is the difference between longitudinal and transversal waves?
b. Is sound a longitudinal or transversal wave?
c. List the organs taking part in the perception of sound (start from the outer ear, end
with the activation of the acoustic nerve).
d. What is the molecular background of the sound-induced membrane potential
changes of the receptor cells in the organ of Corti?

This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.
 Publicly available exercises in biophysics released by the Department of Biophysics and Cell Biology
Page 8

9. Ultrasound

9.1
a. Describe how ultrasound can be produced using the inverse piezoelectric effect.
b. Describe what the basis of A-mode, B-mode and M-mode ultrasound detection is
(what is detected, how is it displayed).
c. Describe how the direction and speed of blood flow can be measured using
Doppler ultrasound.

10. Biocybernetics

10.1.
a. Calculate the redundancy of the coding system for amino acids (base triplets).
b. Describe negative and positive feed-back, and write a medical or biological
example for them.

This collection of exercises is not a question list for the exams, i.e. other questions from other topics will be in
the SCTs and the final exam, although some of these questions may also be included. The aim is to pinpoint the
most important parts of the material, and to give you an idea about the nature of the questions. To be used
together with the minimum requirement question list.