BIRUNI UNIVERSITY

BIOPHYSICS
FACULTY OF MEDICINE
1. Introduction to Biophysics
Lecturer: Demet ERDAĞ
Learning Goals

• Definition of biophysics
• Extensive content of biophysics
• Some biophysical words and terms and applying them to the
branches of biophysics
• How biophysics is classified
 What is Biophysics?

• A multidisciplinary science

• Physics of biology

• Uses of the principles, theories, and methods of physics to

understand biological systems.
 What does the physics of biology mean?

• Biophysics is the field that applies the theories and methods of

physics to understand how biological systems work.

• Physics is a science that deals with matter and energy.

• Biophysics, on the other hand, is an understanding of the functioning

of the laws of matter and energy on living systems.
 Brief History of Biophysics
• Biophysical age: 60-100 years

• Karl Pearson first uses the word "Biophysics"

(1882)

• In 1943, Erwin Schrödinger started with a

series of lectures in “biophysics.

• 1946, King college Medical Research council Karl Pearson

"biophysics research unit" was established.

• Fick, Poiseuille and Helmholz can be known

as the founders of biophysics in the 19th
century.

Erwin Schrödinger
 Biophysics content and disciplines
• "Biophysics involves everything that is interesting,
and excludes everything that is not interesting

Kenneth Stewart Cole.

• Biophysics deals with living organisms in an open, self-regulating,
producing, growing, heterogeneous and multi-stage manner;

• Data Analysis and Structure: Examine the forces between atoms that are
effective in determining the shapes of DNA and protein molecules.
• Computer algorithm development
• Molecules in Motion,
• Conducting research on leg movement mechanics or blood flow,
• Neuroscience,
• Bioengineering, Nanotechnologies, Biomaterials
1. Structure and conformation of biological molecules

• It deals with determining the structure, size and shape of biological

molecules.

• Proteins are molecules formed by the combination of 20 different amino

acids.

• Due to the different numbers and sequences of these amino acids, many
different proteins are synthesized.

• There are four different situations for biomolecules; these are primary,
secondary, tertiary and quaternary structures.
 2010 PJ Russell, iGenetics 3rd
ed.; all text material © 2014
by Steven M. Carr

• (a) The primary structure is the succession of amino acid residues, usually abbreviated by the 1- or 3-letter codes.

• (b) The secondary structure is the 3-D arrangement of the right-handed alpha helix (shown here), or alternative structures such as a beta-pleated
sheet.

• (c) The tertiary structure is the 3-D folding of the alpha helix (show as a purple ribbon), shaped by structures such as proline corners, disulfide
bridges between cysteine residues, and electrostic bonds.

• (d) Where more than one protein chain contributes to the protein, the quaternary structure is the arrangement of these subunits. In hemoglobin as
shown here, the quaternary structure comprises two alpha and two beta polypeptides, held together by elecrostatic bonds.
2. Structure-function relationship

• Determining the structure and shape of biomolecules is related to

which regions are important for the biological function of the
molecule.

• The regions that enable the development of function are called active
areas.
3. Conformational transitions
• Biophysicists use many techniques to measure conformational changes of
biomolecules.

• For example: Opening of the wings within the helix structure during DNA
molecule replication or reading

https://pt.slideshare.net/erindenn/the-structure-replication-of-dna-presentation-teacher-vers
4. Ligand binding and intermolecular bonds

• Small molecules make bonds with large molecules in subcellular biological

functions.

• The attached small molecules are called ligands.

• Deals with biophysics binding sites;

• Forces and energies in binding functions
• Interactions between multiple binding sites
• Attachment and biological function
• Bond formation rate and influencing factors
5. Diffusion and molecular transport
• This branch of biophysics studies the
movement of molecules inside,
outside, or across the cell
membrane.

• Diffusion is the transition of

molecules from a high density region
to a low density region.

• Diffusion provides a better

understanding of the activities
within the cell https://www4.uwsp.edu/physastr/kmenning/Phys204/Lect31.html
 6. Membrane biophysics

• All living things are made up of cells

• Membrane is a surface that separates the
inside and outside of the cell
• Cell membrane consists of lipid molecules
• cell membrane creates electropotential
difference to control ion flow
• Understanding the physics of membranes
and lipids gives information about the
different behavior of the cell membrane.

https://micro.magnet.fsu.edu/cells/plasmamembrane/plasmamembrane.html
 7. DNA and nucleic acid biophysics
• DNA composes genes and controls
physical inheritance

• Ribo Nucleic acid or RNA is a nucleic acid,

a polymer made up of nucleotides. Each
nucleotide consists of a nitrogenous base,
a ribose sugar, and a phosphate.

• RNA converts the genetic information

carried in DNA into protein.

• Inside the cell, RNA is usually single-

stranded, while DNA is usually double-
stranded.
Studies of Biophysics in DNA
• Conformational transitions in DNA (helix formation, twisting, opening)
• The binding of proteins to RNA and other molecules to DNA,
• Energy changes in conformational transitions, bonding conditions.
 8.Protein biophysics
Proteins take place in almost all biological
processes inside the cell:

• Catalyze or regulate biochemical reactions

• Allow molecules to move to another

location in the cell

• Biophysics studies the physical properties

of the folding, conformational change and
bonding of proteins.
https://slideplayer.com/slide/9296178/
9. Bioenergetics

• Examines the energy flow paths and

pathways in living systems.

• Bioenergetics deals with how organisms

and cells acquire energy to perform their
biological functions.(where does energy
come from, how is it stored, how is it
transformed into other forms)
 10. Thermodynamics
• Thermodynamic similar to bioenergetics
• The laws of thermodynamics explain how
energy behaves for physical and biological
systems.
• 0. Law: Thermal Equilibrium transitive
• 1. Law: Energy cannot be created from
nothing, cannot be destroyed
• 2. Law: Tells that the order of the system
will never increase over time for closed
systems
• 3. Law: Law of thermodynamics states that https://www.quora.com/What-are-the-first-2-laws-of-thermodynamics-How-are-they-used
the entropy of a system approaches a
constant value as the temperature
approaches absolute zero.
11. Statistical mathematics

• Statistical averages can be used to determine thermodynamic

quantities such as temperature, pressure, and amounts of energy
released or absorbed.
12.Kinetic
• It gives the information how fast the reaction will occur.
 Allosterics
• Allosteric regulation (or allosteric
control) is the regulation of
an enzyme by binding an effector
molecule at a site other than the
enzyme's active site.

• The best example is the binding of

oxygen to the hemoglobin molecule.
 Biophysical Techniques and Applications
• Learning Goals
1. Description of biophysical techniques,
2. What can be learned through biophysical techniques
3. To learn its use for medicine and other application areas
 Biophysical Techniques and Applications
1. Ultracentrifuge
• Centrifuge is a machine that rotates the sample around a circle and creates a force on the
sample in a circular motion.

• Ultracentrifuges are designed to rotate at high speeds.

• They allow more force to be applied than gravity.

• Centrifuges work according to the sedimentation principle.

• It activates the substances in the liquid by applying force and allows the particles to go
down with the effect of gravity.

• It is used for separating molecules of different sizes.

• In particular, ultrascentrifuges are used to obtain DNA samples.

2.Electrophoresis
• It is a kind of sedimentation technique.

• By applying the electric field strength to electrically charged

particles, the structure, size and shape of biological molecules
are determined.

• The negatively charged DNA molecule is allowed to migrate

towards the positive direction of the electric field in the
aqueous environment.

• The best known type is gel electrophoresis.

• Small molecules travel faster on the gel than large ones.

 3. Size exclusion chromatography
• It is based on sedimentation
technique.

• Molecules are separated

according to their size.

• Large molecules dissociate faster

than small molecules.
4. Spectroscopy
• It takes place by measuring the
changes caused by electromagnetic
radiation sent on the target tissue.
• Spectroscopy techniques provide
information about the identity,
conformational transitions, bonding
and kinetics of biological molecules.
• The measurements taken are
expressed graphically depending on
the wavelength or frequency.

ϑ=c/λ
ϑ is frequency, c light speed, λ wavelength
5. Absorption Spectroscopy
• In Absorption Spectroscopy, light
with a certain wavelength is sent
on the sample and the absorbed
light intensity is measured.

• It is used to determine the

density of the molecule in
solution.

• It also gives information whether

the molecule is bound to the
ligand.
6. Fluorescence Spectroscopy

• Fluorescence is the opposite of absorption.

• Determine ligand binding and conformational

changes for characterization of molecules.

• In absorption spectroscopy, the transmitted light

is converted into kinetic energy within the
molecule or atom.

• Electrons absorbed in fluorescence spectroscopy

rise to a higher energy level, either high or
excited

• The electrons then fall to the energy level they

should be and light is emitted at this time.
7.Mass Spectrometer
• It is used for the analysis of mass and molecular weights of charged
molecules in the magnetic field.
8.Nuclear Magnetic Resonance Spectroscopy

• In NMR, light touches the atomic nucleus in a strong magnetic field.

9. Electron Microscope

• In the electron microscope,

accelerated electrons are
used.
• Image formation is achieved
by dropping electrons on a
fluorescent coated material.
• Scanning Electron Microscopy
(SEM)
• Transmission Electron
Microscope (TEM)
10. Atomic Force Microscope
• It gives real and three dimensional information of objects.
11. Optical Tweezers
• The force created by laser beams in the size of pico Newton enables
microscopic particles in the size of molecules or atoms (virus, DNA,
bacteria) to be held.
12. Voltage Clamping Tecnique

• It is an
electrophysiology
technique.
• It enables
measurement and
characterization of
electrical currents in
excitable cells.
13. Current Clamping
• Similar with voltage clamping.
• It measures the potential difference around the cell membrane by
keeping the current between the inside and outside of the cell
membrane constant.
14. Patch Clamping
• It is the technique in which the electrode is applied to the cell.
• It provides electrical isolation of the cell part.
References
• Biophysics, A Physiological Approach PATRICK F. DILLON

• Biophysics Demystified, Daniel Goldfarb.

• Biyofizik, Prof. Dr. Ferit Pehlivan, Pelikan Yayınevi

• Biyofizik: Nörobiyofizik, Prof. Dr. Ferhan Esen, Prof. Dr. Hamza Esen,
Nobel Tıp Kitabevi.
• derdag@biruni.edu.tr