Schedule (1 unit are two 45 min periods held one after another in the same class) Introduction: What is biophysics and cell biophysics. A wide spectrum of biophysical approaches to fundamental problems in life sciences. Synergy of modern physics and biology in attempts to answer the question what is life. (1 unit)

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Oct 27, 2013 (3 years and 8 months ago)

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NAME OF THE COURSE

Biophysics

Code

99957

Year of study

Graduate level, first year

Course teacher

Davor Juretić

Credits (ECTS)

6

Associate teachers

Juraj Simunić

Bernarda Kežić

Type of instruction
(number of hours)

L

S

E

F

30


30


Status of the
course

Obligatory or Elective
depending on a Study
group

Percentage of
application of e
-
learning

0

COURSE DESCRIPTION

Course objectives

This course is primarily offered to Physics and Biology graduate students (the first
year of the MSc study curriculum)

and provides a modern view of molecular and
cellular biology as seen from the perspective of physics. The primary focus will be
on proteins as cellular workhorses, that cannot perform their work without physics
being involved, for instance, through proton
-
motive force.

This course will not
review experimental biophysical techniques which are covered by other courses.
Physicists will learn what sets apart biology from other fields covered by physics.
Biologists will learn what can be achieved by using phys
ical concepts and
quantitative tools. The goal is to merge two disciplines Physics and Biology into
unified conceptual framework.

Course enrolment
requirements and
entry competences
required for the
course

There are no formal requirements. However, for Physicists a basic knowledge from
biology and biochemistry would be useful. For Biologists the prerequisite is basic
knowledge of thermodynamics and calculus.

Learning outcomes
expected at the
level of the
course
(4 to 10 learning
outcomes)

By the end of the course, with all course requirements fulfilled, students should be
able to:

1)

Apply thermodynamic analysis to processes in cells
such as enzyme catalysis and operation of molecular motors

2)

Understand the
connection between free energy
storage and dissipation in cellular and extracellular environment

3)

Have a working knowledge how ion
-
motive force is
created and used by integral membrane proteins such as pumps and
channels

4)

Understand biophysical principles go
verning the
maintenance of resting potential and production of action potentials by
excitable cells

5)

Effectively communicate their thoughts and
findings about biophysical models connecting structure and function

6)

Perform balanced analysis of concepts present
ed
during this course with a focus on yet unsolved problems important in
biology and biomedicine


Course content
broken down in
detail by weekly
class schedule
(syllabus)

Schedule (1 unit are two 45 min periods held one after another in the same
class)


Introduction: What is biophysics and cell biophysics.
A wide spectrum of
biophysical approaches to fundamental problems in life sciences. Synergy of
modern physics and biology in attempts to answer the question what is life.

(1 unit)


Nanotechnology as an

ancient invention of biological evolution and
selection.

(1 unit)


How free energy is stored and used in biology. Beyond equilibrium
thermodynamics.

(2 units)


Common goal of thermodynamic and biological evolution. Entropic forces.

(1 unit)


Proteins, protein folding problem. Predicting structure and topology of
soluble and membrane proteins.

(2 units)


An example of interdisciplinary research: How peptide antibiotics connect
bioinformatics, biophysics, bioenergetics and biomedicine.

Hydropho
bic
moments and sequence moments. Difficulties in measuring and predicting
antibacterial activity and therapeutic index.

(1 unit)


Enzymes as molecular devices for coupling kinetics of product formation to
thermodynamics of irreversible processes.

Is any p
hysical
optimization/selection principle working in concert with biological evolution
and selection to get nearly perfect enzymes?

(1 unit)


Beyond single enzymes: membrane constituents. Topologically closed
membranes with integral membrane proteins as dev
ices for establishing
Nernst potentials, Donnan potentials, resting (difussion) potential.

(1 unit)


The Goldman
-
Hodgkin
-
Katz voltage equation. Action potentials.

(1 unit)


Voltage channels: structure, function and associated hereditary diseases.

(1 uni
t)


Putting it all together: How strong electrical field created by membrane
protein pumps prompts bacteria to commit suicide when exposed to peptide
antibiotics. The importance of entropy production to the emergence of self
-
replication during abiogenesis and
ultimately to the yet unsolved problem of
the emergence of life.

(1 unit)


A set of short student seminars.

(1 unit)

Format of
x

lectures


independent
assignments

instruction


seminars and workshops

x

exercises


on line
in entirety


partial e
-
learning


field work


multimedia


laboratory

x

work with mentor (to prepare seminar)








(
other
)

Student
responsibilities

Attend all lectures and exercises. Perform chosen student
project, including
seminar presentation about project findings with obligatory attendance of
other student presentations too. Communicate with course leader and course
assistants both in class and through e
-
mail about all points requiring
clarifications or

corrections. Such communication can be very beneficial to a
student also in the case when it leads to independent research project or
master thesis project.

Screening student
work
(name the
proportion of ECTS
credits for each
activity so that the
total
number of
ECTS credits is
equal to the ECTS
value of the course)

Class
attendance

2

Research

1

Practical training







Experimental
work


Report












(
O
ther)







Essay







Seminar
essay

1






(
O
ther)







Tests







Oral exam

1






(Other)







Written exam

1

Project












(Other)







Grading and
evaluating student
work in class and at
the final exam

Final oral and written exam 50%, homework
and exercises 20%, student seminars
or research projects 20%, in
-
class exams 10%

Required literature
(available in the
library and via other
media)

Title

Number of
copies in
the library

Availability via
other media

Meyer B. Jackson,
Molecular and
Cellular
Biophysics,

Cambridge University Press, Cambridge
2006.

1

Available to all
enrolled
students as the
pdf document

Rodney Cotterill,
Biophysics.

An Introduction
. John
Willey & Sons, New York 2006

1







Donald T. Haynie,
Biological Thermodynamics
,

Cambridge University Press, Cambridge 2008.

1







R. Glaser.
Biophysics.

Springer
-
Verlag. Berlin 2005

1







Davor Juretić, Biophysics_Introduction, Split, 2013,
39 pages of detailed lecture notes


Available to all
enrolled
students as the
pdf document



































Optional literature
(at the time of
submission of study
programme
proposal)

Phil Nelson,
Biological Physics


Energy,

Information, Life
, WH Freeman, NY, 2008.

Richard Leuchtag,
Voltage
-
Sensitive Ion Channels. Biophysics of Molecular
Excitability
, Spinger, The Netherlands, 2008.

Enrico di Cera,
Thermodynamics in Biology
, Oxford University Press, USA 2001.

Michel Daune,
Molecular Biophysics: Structures in Motion
, Oxford University Press,
1998

Kim Sneppen and Giovanni Zocchi,
Physics in Molecular Biology
,
Cambridge
University Press, Cambridge 2005.

Quality assurance
methods that
ensure the
acquisition of exit
competences

Exit competences will be ensured if the student passes all the requirements of this
course

Other (
as the
proposer wishes to
add)