Welcome to Biophysics

lecture 2011
Understanding biology using
simple ideas from
physics.
Your host:

Professor dr. SIMONA CAVALU
Biophysics and Medical physics


Office: P-ta 1 Decembrie 10, Faculty
of Medicine and Pharmacy.
[email protected]
Lecture topics
1. Basic concepts of biological thermodinamics.
2. Biomechanics biophysics of the muscle
contraction. Biophysical events specific to the
muscle contraction.
3. The eye and the vision. The optical system.
Optical defects and their correction.
4. The ear and hearing. The transmission and
measurement of sound. Defects of hearing.
5. Biomembranes. Transport through the
cell membrane. Active and passive
transport.
6. Neurobiophysics. Biopotentials. Ionic
channels. Measuring the ECG, EMG.
7. Optical fiber and lasers. Basic principle of
endoscopy. Lasers in medicine and
dentistry.
8. Ultrasonics. Generation and detection of
ultrasound. Doppler methods.
Physiological effects of ultrasound.

9. Ionising radiation. The nature of X-rays.
Interaction of X-rays with matter. X-rays
equipment.
10. Radioisotopes. Basics of nuclear
medicine.
11. Measuring and controlling radiation.
Dosimetry. Radiation protection.
12. Physical methods for structural
investigation of biomaterials.
Spectroscopy, microscopy and X rays
diffraction.

Need to know biology in
order to do biophysics!
Using physics to understand
biology!
Not biology to understand
physics!
What is Biophysics?

It is neither physics for biologists, nor physical methods
applied to biology

It is a modern, interdisciplinary field of science leading to new
approaches for our understanding of biological functions.
Paradigm: Biological system is not simply the sum of its
molecular components but is rather their functional integration
Mathematics +Physics +Biology + Chemistry
The idea is to help physics students to find their way to Biophysics and to help
biology students to overcome the activation energy barrier of mathematics and
physics and joint the field Biophysics.
Main goal
The goal of this course is to prepare physics students
to understand biological systems and to prepare
biology students to quantitatively understand the
physical laws underlying the many phenomena occurring
on the nanometer to micrometer scale in cells and
subcellular structures.
We will observe the overall structure of cells, learn the
principles underlying macromolecular structure,
interactions and reactions, and discover the molecular
and supramolecular devices which make a living cell
living.
Understanding the physics of biological systems
demands an understanding of some biochemistry
Divisions of Biophysics:

Molecular biophysics

Biomechanics

Membrane Biophysics

Bio-electrochemistry

Environmental Biophysics

Theoretical Biophysics
First Biophysicists


Heraclitus 5
th
century B.C. earliest mechanistic theories of
life processes, insight into dynamic.

Change is central to Universe.

Logos is the fundamental order of all on Nature changes of
objects with the flow of time


Plato argues against Heraclitus as follows:
How can that be a real thing which is never in the same state? ... for at the
moment that the observer approaches, then they become other ... so that
you cannot get any further in knowing their nature or state .... but if that
which knows and that which is known exist ever ... then I do not think they
can resemble a process or flux ....



Epicurus atom


Galen 2th century AD physician, most accomplished
medical researcher of the Roman period. His theories
dominated Western medicine for over millennium.



Leonardo da Vinci 16
th
century mechanical principals of
bird flight (to use for engineering design) - bionics
First Biophysicists
Giovanni Alfonso Borelli 17th century- related
animals to machines and utilized mathematics to
prove his theories.

De Motu Animalium comprehensive
biomechanical description of limbs mobility, birds
flight, swimming movement, heart function.
Borelli farther of biomechanics

Luigi Galvani / Alessandro Volta
Bio-electrochemistry

18
th
(1783)
Electric circuit = two different metals + frogs leg
Frog's leg = electrolyte and sensor
Metals = electrodes
If close the circuit dead leg will twitch.

Volta created first battery by substituting frog leg with electrolyte.

From frog leg to first battery.
Luigi Galvani / Alessandro Volta



First law of thermodynamic

Optical aspects of the human eye

Theory of hearing

Browns motion

Osmotic process

Nonequilibrium thermodynamics

Discovery of X-rays

Discovery of DNA structure

Information theory

Statistical physics of biopolymers

History of Biophysics:
Physics is about great laws
Some examples
Newtons three Laws
(Mechanics)


James Clerk Maxwell
1831-1879
Maxwells four Equations
(Electricity & Magnetism)


Schrodingers Eqn
(Quantum Mechanics)
Erwin Schrdinger 1887-1961
Isaac Newton, 1642-1727
Does Biology have any great
theories/laws?
Charles Darwin, Age 51, 1860,
On the Origin of Species
Evolution
-- Life evolved from simpler forms
--One of the best tested scientific theories
around
Evolution is a series of tricks/random events
Build complex beings from simpler parts
Often many ways of doing this
Our life form is just one.
Question biophysicists ask:
How do protein Fold?

How are Genes Turned On and Off?

How do Biomolecules assemble and interact?

What is molecular structure of cell membrane?

How do animals and plants respond to light and how do
animals respond to sound and smell?

How do cell move?

How does the nervous system work?
Question biophysicists ask:
How do protein Fold?
How three-directional structure determines function? Why do molecules and parts of
molecules assume the shapes they do? How do they fold into these shapes, and how
do they change their structure under changing conditions? The shapes molecules take
depend on the physical and chemical forces acting upon them and within them.

X-ray crystallography, nuclear magnetic resonance spectroscopy and scanning probe
microscopy, recombinant DNA, computation.
Question biophysicists ask:
How are Genes Turned On and Off?
The discovery of the double helical
structure of the DNA was a breakthrough for
many branches of biology, because it explained
how the structure of the molecule allows it to
function as a template for copying
genetic information. However, it was not
clear how DNA works in three dimensions
what sorts of three-dimensional
structures are superimposed on the double
helix and how these influence the interactions
of DNA with other molecules in its environment.

Binding of proteins to DNA determines when
and how genes are turned on and off and in
turn regulates both normal and abnormal
development.
Question biophysicists ask:
How do Biomolecules assemble and interact?
Most biological events involve interactions among assemblies of macromolecules
working together: replication of genes into proteins, binding of antigens by
antibodies, muscle contraction, transmission of nerve impulses and so forth.

In order to understand how these biological machines work, one must understand
the forces that drive them. The driving force for their self assembly and operation is
free energy. Each possible structure of an assembly of macromolecules has a
different free energy, which, in turn, determines how likely the assembly is to
assume that structure. These different energy states operate at different parts of
the biological cycle; they both drive the cycle and are driven by it. Free energy has
two components: enthalpy and entropy.
Question biophysicists ask:
What is molecular structure of cell membrane?
Embedded in lipid bi-layer are complex proteins that serve as molecular ports,
allowing certain kinds of molecules to cross the barrier, but not others. Both lipids
and proteins are able to move around within the bilayer. This combination of
hydrophobic and hydrophilic, structured and unstructured, raises a variety of
questions about the relationship between the structure of membranes and their
biological function.
Membranes compartmentalize cells and form barriers between different environments.
They also move molecules from one part of the cell to another by recognizing elements
of molecular structure that indicate where in the cell the molecule belongs. In addition,
membranes play a key role in energy transformations, taking light or chemical energy
and converting it into other forms that can be used by the cell.
Fluorescence microscopy of
endothelial cells using three
labels. Red lables the
mitochondria, green lables
the F-actine cytoskeleton
and blue lables the nucleus.

This is because biophysics is constantly evolving
extremely diverse and eclectic field. It has its roots in a
broad range of more traditional fields including
physiology (especially, electrophysiology), molecular and
cellular biology, biomedical imaging, physical chemistry,
physics and mathematics. It arose through recognition of
the important axiom that biology, no matter how
complex it may be, is subject to the laws of
physics and can be studied - indeed, ultimately must
be studied - through quantitative and theoretical
analysis.
Units