Biophysics

LECTURE / WEEK 1-6 / MODULE-BASED

TOPIC OUTLINE  first used the term Biophysics in 1882

1 Biophysics: An Introduction  The Grammar of Science
- “a branch of science is therefore needed
2 Biophysical Topics: Molecular and dealing with the application of the laws of
Subcellular Biophysics inorganic phenomena, or Physics, to the
development of organic forms.”
What is Biophysics?  He proposes that the new branch of science be
called bio-physics.
The physics of biology. It tries to understand how the
laws of matter and energy are at work in living Erwin Schrödinger
systems. Biophysics uses of the principles, theories,  won the 1933 Nobel Prize in Physics for his
and methods of physics to understand biology. work on quantum mechanics
 Then in February 1943, Schrödinger gave
ACADEMIC DISCIPLINE his now famous lecture series titled “What Is
Life?”.
– branch of knowledge that is taught and researched  A year later the lecture series was published
at the college or university level. Disciplines are as the book, What Is Life? The Physical
defined (in part) and recognized by the academic Aspects of the Living Cell.
journals in which research is published, and the  The lecture series and book had a major
learned societies and academic departments or impact on several notable scientists of the
faculties to which their practitioners belong. time. Only a few years later, in 1946, the
Medical Research Council of King’s College
SCIENTIFIC FIELD in London established the Biophysics
Research Unit of King’s College.
-widely recognized category of specialized expertise
within science, and typically embodies its own  Their goal was to hire physicists and put
terminology and nomenclature. Such a field will them to work on questions of biological
usually be represented by one or more scientific significance
journals, where peer reviewed research is published.
Maurice Wilkins and Rosalind Franklin
A natural science – one that seeks to elucidate the  were among those who joined the unit to become
rules that govern the natural world using empirical biophysicists
and scientific methods.  There at King’s College they used X-ray
▪ A biological science – concerned with the study diffraction to investigate the structure of DNA.
of living organisms, including their structure,
function, growth, evolution, distribution, and James Watson and Francis Crick
taxonomy.  made one of the most far-reaching discoveries of
▪ A branch of physics – concerned with the study our time when they used Rosalind Franklin’s X-
of matter and its motion through space and time, ray diffraction data to discover the double helix
along with related concepts such as energy and force. structure of DNA.

INTERDISCIPLINARY FIELD Biophysical Society (1957)

 was founded, to encourage growth and
– field of science that overlaps with other sciences. It dissemination of knowledge in biophysics.
is an interdisciplinary science. Biophysics relates to  Since then, interest in biophysics has only
all levels of biological organization, from molecular increased.
processes to ecological phenomena that includes  By the early 1980s numerous universities
other biological sub-areas like biochemistry, offered graduate degrees in biophysics, but
physiology, cytology, morphology, genetics, only a few, if any, colleges offered
systematics and ecology. undergraduate degrees.
 Today over 60 colleges and universities
offer undergraduate degrees in biophysics,
BRIEF HISTORY OF BIOPHYSICS and the Biophysical Society has over 9000
members.
Karl Pearson

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Figure 1-2 shows a timeline of science and various levels of complexity, from single molecules to
biophysics to put the age of biophysics in supramolecular] structures, viruses and small living
systems.
perspective
BIOPHYSICAL TECHNIQUES
Methods used for gaining information about biological
systems on an atomic or molecular level. Methods to
characterize molecular structure, the measurement of
molecular properties, and the observation of molecular
behavior. These biophysical techniques provide
information about the electronic structure, size, shape,
dynamics, polarity, and modes of interaction of biological
molecules. Some of the most exciting techniques provide
images of cells, subcellular structures, and even individual
molecules.

1. Biophotonics – combination of biology and photonics,

with photonics being the science and technology of
generation, manipulation, and detection of photons,
A. Biophysical topics based on relative size quantum units of light. Biophotonics can also be described
of subject as the "development and application of optical techniques,
1. Molecular and subcellular biophysics particularly imaging, to the study of biological molecules,
2. Physiological and anatomical biophysics cells and tissue". One of the main benefits of using optical
3. Environmental biophysics techniques which make up biophotonics is that they
preserve the integrity of the biological cells being
examined.
B. Biophysical techniques and applications

4. General biophysical techniques 2. Calcium imaging – various optical techniques for

5. Imaging biophysics recording the location and concentration of calcium.
6. Medical biophysics Typically, this is done in cell and tissue samples using
either genetically encoded or chemically derived
BRANCHES OF BIOPHYSICS fluorescent calcium indicating dyes.

ASTROBIOPHYSICS
3. Calorimetry
field of intersection between astrophysics and biophysics
a. Isothermal Titration Calorimetry (ITC) – measures
concerned with the influence of the astrophysical
the heat effects caused by interactions.
phenomena upon life on planet Earth or some other planet
4. Chromatography – various techniques from this field
in general.
are used for the purification and analysis of biological
molecules
MEDICAL BIOPHYSICS 5. Circular Dichroism – method to measure chirality of a
sample using circularly polarized light. This technique is
interdisciplinary field that applies methods and concepts commonly used to determine protein structure.
from physics to medicine or healthcare, ranging from 6. Computational chemistry – use of numerical methods
radiology to microscopy and nanomedicine. to probe the structure and dynamical equilibrium in
biological systems.
MEMBRANE BIOPHYSICS 7. Cryobiology- studies the effects of low temperatures
on the physiology of living things
study of biological membranes using physical, 8. Dual Polarization Interferometry – analytical
computational, mathematical, and biophysical methods. technique used to measure the real-time conformation
and activity of a wide range of biomolecules and their
MOLECULAR BIOPHYSICS interactions.
9. Electrophysiology – studies electrical properties of cell
interdisciplinary field that applies methods and concepts membranes and provide functional data, often related to
from physics, chemistry, engineering, mathematics and systematic changes in structure.
biology to understand biomolecular systems and explain a. Patch clamping – provides temporal and electrical
biological function in terms of molecular structure, information of a cell, or a portion of membrane. Typically,
structural organization, and dynamic behavior at

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this provides data on electrogenic processes, such ion

channel or transporter activity.
10. Electron microscopy – used to gain high-resolution The most common branches of biophysics are those dealing
images of subcellular structures and proteins. with molecules and subcellular function where biology,
11. Fluorescence spectroscopy – for detecting structural chemistry and physics are encountered. This division of
rearrangements, as well as interactions of biomolecules. biophysics is sometimes also called biochemical physics,
12. Force spectroscopy – probes the mechanical physical biochemistry, or biophysical chemistry. Within
properties of individual molecules or macromolecular this division of biophysics we find the following topics.
assemblies using small flexible cantilevers, focused laser
light, or magnetic fields.
13. Gel electrophoresis – determines the mass, the A. The Structure and Conformation of Biological
charge and the interactions of biological molecules Molecules
14. Imaging – scientific imaging of biological materials,
usually by some form of microscopy, or sometimes  This branch of biophysics deals with
indirectly such as in x-ray crystallography or by determining the structure, size, and shape of
computer imaging; at a wide range of magnifications to see biological molecules.
macromolecules, cells, tissues, or organisms
15. Mass spectrometry – technique that gives the  A biomolecule or biological molecule is a
molecular mass with great accuracy. loosely used term for molecules and ions
16. Microscale Thermophoresis (MST) – method to present in organisms that are essential to one or
measure binding affinities, enzymatic activities, changes more typically biological processes, such as cell
in molecule conformation and changes in size, charge or division, morphogenesis, or development
hydration entropy. (Biological process are the processes vital for a
17. Microscopy – used in many ways, for example, to living organism to live, and that shape its
enable the use of laser instruments for scanning and capacities for interacting with its environment.)
transmission.
a. Atomic force microscopy  Most biomolecules are organic compounds and
18. Neuroimaging just four elements (C, O, H, N).
19. Neutron spin echo spectroscopy
20. Nuclear Magnetic Resonance Spectroscopy – method Biomolecules include
for measuring the local environment of atomic nuclei a. large macromolecules (or polyanions) such as
within a sample. Can be used to derive both structural and proteins, carbohydrates, lipids, and nucleic acids
kinetic information on proteins and small molecules.  Commonly created by polymerization of small
21. Optical tweezers and Magnetic tweezers – allow for subunits (monomers)
the manipulation of single molecules, providing  Composed of thousands of atoms and more
information about DNA and its interaction with proteins  Most common macromolecules in biochemistry
and molecular motors, such as Helicase and RNA are biopolymers and large non-polymeric.
polymerase.
22. NMR spectroscopy – provides information about the
exact structure of biological molecules, as well as on
dynamics
23. Single molecule spectroscopy – is a technique that is
sensitive enough to detect single molecules and often
incorporates fluorescence detection.
24. Small angle X-ray scattering (SAXS) – technique
that gives a rough low-resolution molecular structure.
25. Spectrophotometry – measurement of the
transmission of light through different solutions or
substances at different wavelengths of light.
a. Colorimetry
26. Spectroscopy and Circular dichroism – method for
detecting chiral groups in molecules, especially to
determine the secondary structure of proteins
27. Ultracentrifugation – gives information on the shape
and mass of molecules b. small molecules such as primary metabolites,
28. X-ray crystallography – method to determine the secondary metabolites, and natural products.
exact structure of molecules with atomic resolution.  A low molecular weight organic compound that
may regulate a biological process, with a size
on the order of 1 nm. Many drugs are small
Biophysical Topics: Molecular and molecules.
Subcellular Biophysics

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 Many biological molecules are polymers. A sheet, can fold back on itself (sometimes over and
polymer is a large molecule made by over) and form a globular shape.
connecting together many smaller molecules.
 Each of the smaller molecules is called a residue 4. Quaternary structure refers to the case where
(or monomer). The residues making up a polymer two or more tertiary shapes attach to one
may be identical, like links in a typical chain another to form an even larger molecule or
where the links are all ovals. complex.
 The residues may also be a set of related but
not identical molecules.  Not all biomolecules exhibit all four levels of
 Biopolymers (biological polymers) - where the structure. Small molecules (for example, simple
residues have something in common but are sugars or amino acids) typically exhibit only
not identical. Polymers are produced by living primary and secondary structures.
organisms.  Biopolymers most commonly exhibit all levels
up to tertiary structure, and sometimes exhibit
Example: Proteins are made by linking together smaller quaternary structure.
molecules called amino acids. Each of the residues making
up a protein is an amino acid and there are about 20 or so
different amino acids found in proteins. Various amounts of
these 20 or so amino acids can be linked together in various
sequences to make different proteins.

Four Levels of Structure

1. Primary structure specifies the atoms or
groups of atoms making up a molecule and the
order in which they are connected to one another.
In polymers, typically indicate only which
residues we find and in what order we find them.

2. Secondary structure refers to the initial, simple,

three-dimensional structure of a molecule. For
example, a molecule, or part of a molecule, may
take the shape of a helix or a shape similar to a
pleated sheet.

3. Tertiary structure refers to the fact that a

secondary structure, such as a helix or pleated

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 The structure and conformation of biological

molecules, as a branch of biophysics, also
includes analyzing the forces and energy
required for a molecule to maintain a
particular shape.
 With this information, biophysicists develop
geometric and mathematical models to predict the
secondary and tertiary structure of a molecule,
given its primary structure.
 Conformational transition is just a fancy term
for a change in shape. In biochemistry, a
conformational change is a change in the shape of
a macromolecule, often induced by
environmental factors (transition of possible
shapes).
 Biomolecules often change their shape as part
of their function. Factors that may induce such
changes include temperature, pH, voltage, light
in chromophores, ion concentration,
phosphorylation, or the binding of a ligand.
B. Structure Function Relationships
 Transitions between these states occur on a
 Closely related to determining the structure and variety of length scales (tenths of Å to nm) and
shape of biomolecules is determining which parts time scales (ns to s).
of a molecule are involved in its biological
function and determining how changes to its
structure or shape affect its biological function.
 When a one particular part of a molecule or Biophysical techniques used to study macromolecular
complex is involved in carrying out its function, conformational change:
that part is referred to as the active site of the  Crystallography, NMR, electron paramagnetic
molecule. resonance (EPR) using spin label techniques,
 It is also possible for a molecule or complex to circular dichroism (CD), hydrogen exchange, and
have more than one active site. In biology, the FRET
active site is the region of an enzyme (one type
of protein) where substrate molecules bind and Examples:
undergo a chemical reaction. a. Figure: Example of Conformational change (Mass
 The active site consists of residues that form Changes)
temporary bonds with the substrate (binding
site) and residues that catalyse a reaction of that
substrate (catalytic site).

C. Conformation of Biological Molecules

 Conformation in biophysics it almost always

means shape or structure (three-dimensional
arrangement of atoms in a biological molecule). b. The DNA double helix must temporarily unwind in order
 The determination of the three-dimensional for the genetic instructions to be read or in order for the
structure of a biological molecule is the DNA to replicate itself for the next generation.
starting point in the understanding of
molecular mechanisms involved in its complex Biophysicists use a variety of techniques to measure
biochemical reactions. conformational changes in biomolecules, to measure the
energy associated with them and to determine the

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relationship between the various conformations and their are roughly equal in size and bind together to form a larger
biological function. complex (quaternary structure). Each individual molecule
in the complex is called a subunit.
It is also possible to induce conformational changes in the Example: Hemoglobin - a large complex protein that
laboratory. Induced conformational transitions can be used carries oxygen from our lungs, through our blood, to the
to develop medical treatments and diagnostics. These cells in our body. Hemoglobin is made up of four subunit
induced changes may or may not happen in nature. proteins that bind together. Hemoglobin consists of protein
subunits (the "globin" molecules).

c. Spike protein attaches to the receptor on the target cell,

ACE2, and is the dominant target of the immune system. In other cases of molecular binding, a smaller molecule
binds to a larger molecule. A ligand is a smaller molecule
Spike proteins of SARS-CoV-2 are known to exhibit or atom that binds to a larger molecule. The smaller
open and closed conformations. In the closed molecule may be integral to the biological purpose of the
conformation the receptor binding site is hidden, larger molecule, or it may simply serve to activate or
whereas it is exposed in the open conformation. This has deactivate the larger molecule in carrying out its purpose.
also been seen in purified SARS-CoV-2 spike proteins, but
the relevance of these different conformations in the The term ligand to mean specifically the case where a
context of an intact virus has been unknown. smaller molecular (or atom) binds to a much larger
molecule. We will use the more generic terms molecular
binding, subunit binding, or simply binding to refer to cases
where the size difference between the two molecules is not
significant.

Example: When hemoglobin carries oxygen from the lungs

to all of the cells in our body, oxygen molecules bind to the
hemoglobin in the lungs. Later, the oxygen is released from
the hemoglobin, so it can be used inside our body’s cells.
When oxygen binds to hemoglobin, the oxygen is
considered a ligand. A single oxygen molecule reversibly
binds to each heme within each of the four protein chains.
The binding of O2 to the heme changes the whole structure
of hemoglobin. There are two major conformations of
hemoglobin in T state and R state known as states of
hemoglobin.

Biophysicists studying ligand binding and other

intermolecular binding seek to measure and understand.
a. The forces and energy involved in binding
b. The interaction between multiple binding sites
c. How changes to the molecules affect binding
d. The relationship between binding and conformational
transitions
e. The relationship between binding and biological
function
f. The competition between different ligands that can
bind to the same molecule
g. The rate at which binding occurs and the factors that
D. Ligand Binding and Intermolecular Binding affect binding rates.
A common theme in subcellular biological function is the
binding together of molecules. Sometimes the molecules

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Characteristics of Simple Diffusion

E. Diffusion and Molecular Transport  Occurs across a semipermeable membrane
 how molecules move around within cells and  Requires a concentration gradient across the
how molecules move from outside a cell to inside cell membrane
the cell and vice versa.  It is a passive transport mechanism thus require
 In fluids, molecules are continually moving, no energy expenditure by the cell
randomly colliding, and jostling about.  Does not need a carrier transport protein
 Diffusion is the process of molecules spreading  Happens by random motion
out, as a result of this random motion.  Cannot be inhibited by an inhibitor molecule
 By spreading out, we mean that the random because of the absence of carrier proteins
motion will cause molecules to move from a  Non-specific to any particle
region of higher concentration (where they are  A comparably slow process than other forms of
closer together) to one of lower concentration diffusion
(where they are further apart). The physics of
diffusion can be described mathematically and Practical Examples of Simple Diffusion
can be used to better understand and predict  Gas exchange in plants with the help of stomata
biological activity in cells. Diffusion is the  Absorption of nutrients such as carbohydrates,
primary means of molecules moving around minerals, and vitamins in the small intestine
within a cell.
2. Facilitated Diffusion - occurring in living cells where
the molecules move from the region of their higher
concentration to the region of lower concentration
guided by a helper protein molecule. The helper protein
is usually an integral membrane protein that forms a pore or
channel in the cell membrane. Facilitated diffusion is a
passive transport mechanism and thus requires no energy
expenditure by the cell.

Facilitated diffusion is a spontaneous process in which

charged ions or molecules are transported across the
Type of Diffusion lipid-based cell membrane via a carrier transmembrane
1. Simple Diffusion - defined as the movement of protein molecule. It is a selective process, which means
substances like ions, atoms, and molecules from an area the membrane allows only selective molecules and ions
of their higher concentration to lower concentration to pass through it, denying passage to others.
without the involvement of any other molecules like a
carrier protein. Characteristics of Facilitated Diffusion
 Occurs due to the random motion of molecules
It is a natural phenomenon where the particles move along (Brownian motion)
a concentration gradient in a solution through a  Requires a biological membrane for transport
semipermeable membrane to attain equilibrium on both  Requires a carrier protein, thus also known as
sides. Simple diffusion occurs because the particles carrier-mediated diffusion
undergoing this process are always in a state of random  Does not require energy expenditure and use of
motion. high energy phosphate molecules – ATP
(Adenosine triphosphate) or GTP (Guanosine-5′-

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triphosphate) hydrolysis and thus it is a type of certain molecules to the outer surfaces of such lipid vesicles
passive transport mechanism to help the vesicles bind to
 Transports large charged ions, small
molecules, proteins, and other solutes
 It is a selective process thus allowing the passage
of selective molecules across the membrane

Biological Example of Facilitated Diffusion

 Transport of glucose across the cell membrane specific sites in the body.
with the help of carrier proteins called glucose  In this way we can create targeted delivery
transporter systems to deliver drugs or chemicals to a
 Passage of water across the lipid bilayer of the specific location in the body (for example, to the
cell membrane using specific transmembrane site of a tumor).
channel proteins called aquaporins  By understanding the physics of lipid
 Selective transport of ions and solutes in and conformational transitions, we can control these
out of the cell using membrane proteins called conformational transitions, and thus control
ion channels the ability of the lipid vesicles to contain the
drug or chemical inside them.
Factors affecting the motion of molecules will limit the  Once the drug-filled lipid vesicles are in the
rate of diffusion, these include: bloodstream, we can apply a stimulus like heat or
a. Temperature – Higher temperature mild radiation to a specific part of the body to
increases the random motion of molecules and thus cause the lipid vesicles to release the drugs at that
higher is the rate of diffusion place.
b. Concentration – Higher the concentration
gradient between the regions undergoing diffusion, more G. DNA and Nucleic Acid Biophysics
is the rate of diffusion  studies the physics of DNA and RNA.
c. Distance – The rate of diffusion is faster in  DNA stands for deoxyribonucleic acid, while
smaller distances RNA is ribonucleic acid.
d. Size of the molecules – Smaller the size of the  Although DNA and RNA both carry genetic
molecule, faster is the rate of diffusion and vice versa. information, there are quite a few differences
between them.
F. Membrane Biophysics
 All living things are made up of cells.  While there is some evidence DNA may have
 The membrane is what defines the boundary occurred first, most scientists believe RNA
between a cell and the outside world. Internally evolved before DNA. RNA has a simpler
(inside the cell) membranes define and separate structure and is needed for DNA to function.
various parts of the cell from one another. The
main components that make up all cell  Also, RNA on its own can act as a catalyst for
membranes are lipids, proteins, and certain chemical reactions. The real question is
carbohydrates. why DNA evolved if RNA existed.
 Membranes limit and control the movement of
molecules into and out of the cell and from one
region of the cell to another.  The most likely answer for this is that having a
 Membranes are also able to create electrical double-stranded molecule helps protect the
potential across their surface, by controlling the genetic code from damage.
flow of ions into and out of the cell.
 Cell membranes are typically made of a double
 If one strand is broken, the other strand can serve
layer of lipid molecules.
as a template for repair.
 Lipids and membranes can help us to better
understand and predict how cells will behave
under various conditions.  Proteins surrounding DNA also confer
additional protection against enzymatic attack.
Lipid vesicles are small hollow spheres of artificial
membrane that can be made from various types of lipids.
A lipid vesicle is like a cell with nothing inside it, just the
membrane alone.

It is possible to also place drugs or chemical agents

inside lipid vesicles. Additionally, there are ways to attach

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 DNA (deoxyribonucleic acid) is the biochemical

that makes up our genes and controls our physical
heredity. The secondary structure of DNA is a
double helix, like two spiral staircases wrapped
around each other. The double helix itself can
bend and twist to form a helix as well.
 This helix of a helix is called a superhelix.
 The process of forming a superhelix in DNA is
known as supercoiling.
 Supercoiling of the double helix is a tertiary
structure in DNA.
 A quaternary structure in DNA occurs when the
DNA superhelix wraps itself around protein H. Protein Biophysics
complexes known as histones (see Fig. 2-4).  Proteins are involved in nearly every
biological process within the cell.
 Examples include catalyzing biochemical
reactions, regulating (turning on and off)
biochemical processes, and transporting
molecules across cell membranes, from cell to
cell and from one part of a cell to another.
 Proteins are also involved in cell motility (self-
induced movement of the cell).
 In order to carry out these functions, proteins
typically must fold into very specific shapes, bind
with other molecules, or undergo one or more
conformational transitions. Since proteins do all
of these things as part of their normal function,
understanding the physics of protein folding,
conformational transitions, and binding is
crucial to understanding and possibly
controlling their role in biological processes.
Protein folding is the process by which a protein
structure assumes its functional shape or conformation.

All protein molecules are heterogeneous unbranched

chains of amino acids. By coiling and folding into a
specific three-dimensional shape they are able to perform
their biological function. (Protein folding is a process by
which a polypeptide chain folds to become a biologically
active protein in its native 3D structure)

Four stages of Protein Folding

The folding of a protein is a complex process, involving
four stages, that gives rise to various 3D protein

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structures essential for diverse functions in the human misfolding. Huntington's disease and Parkinson's
body. disease
Cystic fibrosis (CF) is a fatal disease caused by
The structure of a protein is hierarchically arranged, misfolding of the cystic fibrosis transmembrane
from a primary to quaternary structure. The wide conductance regulator (CFTR) protein.
variation in amino acid sequences accounts for the I. Bioenergetics
different conformations in protein structure. This branch of biophysics studies the physics of energy
 Primary structure refers to the linear sequence flow in living systems. Bioenergetics is concerned with all
of amino-acid residues in the polypeptide levels and branches of biophysics, from the environment,
chain. to the organism, to the cell, and to the molecules within the
 Secondary structure is generated by formation cell. At the core of bioenergetics is the study of how
of hydrogen bonds between atoms in the organisms and cells obtain the energy they need to carry
polypeptide backbone, which folds the chains out biological processes. This includes where the energy
into either alpha helices or beta-sheets. comes from, how the energy is stored, how the energy is
 Tertiary structure is formed by the folding of converted into various forms, and where and how excess or
the secondary structure sheets or helices into unusable energy is released. While every branch of
one another. biophysics needs to be concerned with energy, some
 The tertiary structure of protein is the geometric biophysicists specialize in understanding the energetics of
shape of the protein. It usually has a any biological process, whether the process is protein
polypeptide chain as a backbone, with one or folding, DNA unwinding, respiration, or energy flow in the
more secondary structures. The tertiary environment.
structure is determined by the interactions and Ultimately, most life forms get their energy from the sun.
bonding of the amino acid side chains in the Plants use photosynthesis to capture sunlight, and
protein. herbivores eat the plants to obtain energy. Carnivores eat
 Quaternary structure results from folded the herbivores, and eventual
amino-acid chains in tertiary structures
interacting further with each other to give rise to Example:
a functional protein such as hemoglobin or DNA Cellular processes such as the building and breaking down
polymerase. of complex molecules occur through stepwise chemical
reactions. Some of these chemical reactions are
spontaneous and release energy, whereas others require
Protein folding is a very sensitive process that is energy to proceed. Just as living things must continually
influenced by several external factors including electric consume food to replenish their energy supplies, cells must
and magnetic fields, temperature, pH, chemicals, space continually produce more energy to replenish that used by
limitation and molecular crowding. These factors the many energy-requiring chemical reactions that
influence the ability of proteins to fold into their correct constantly take place. Together, all of the chemical
functional forms. reactions that take place inside cells, including those that
consume or generate energy, are referred to as the cell’s
Example: metabolism.
Protein folding in water. Consider the metabolism of sugar. This is a classic
The hydrophobic effect constrains the apolar residues of a example of one of the many cellular processes that use and
protein to escape water. These apolar residues converge to produce energy. Living things consume sugars as a major
form an apolar core of the protein, leaving more polar energy source, because sugar molecules have a great deal
residues at the surface where they can form hydrogen bonds of energy stored within their bonds. For the most part,
with water molecules (upper panel). The enthalpic photosynthesizing organisms like plants produce these
contribution to the folding reaction is illustrated in the sugars. During photosynthesis, plants use energy (originally
lower panel (electrostatic interaction between the positive from sunlight) to convert carbon dioxide gas (CO2) into
N-terminus in blue and the negative C-terminus in red). sugar molecules (like glucose: C6H12O6). They consume
Apolar surfaces (white) disappear from the surface when carbon dioxide and produce oxygen as a waste product.
the protein folds. This reaction is summarized as

Because this process involves synthesizing an energy-

storing molecule, it requires energy input to proceed.
During the light reactions of photosynthesis, energy is
Diseases related to incorrect protein folding provided by a molecule called adenosine triphosphate
Misfolded proteins denature easily and lose their structure (ATP), which is the primary energy currency of all cells.
and function. Incorrect protein folding can lead to many Just as the dollar is used as currency to buy goods, cells use
human diseases. molecules of ATP as energy currency to perform
Alzheimer's disease is an example of a immediate work. In contrast, energy-storage molecules
neurodegenerative condition caused by protein such as glucose are consumed only to be broken down to

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use their energy. The reaction that harvests the energy of a

sugar molecule in cells requiring oxygen to survive can be
summarized by the reverse reaction to photosynthesis. In
this reaction, oxygen is consumed and carbon dioxide is
released as a waste product. The reaction is summarized as:

J. Thermodynamics
Very closely related to bioenergetics is the study of
thermodynamics. The laws of thermodynamics describe
how energy behaves in physical systems, biological or
otherwise. The first law of thermodynamics states that
energy cannot be created or destroyed. (Energy exists in
many different forms. According to the first law of
thermodynamics, energy may be transferred from place to
place or transformed into different forms, but it cannot be
created or destroyed.) The second law of thermodynamics
states that in a closed system the orderliness of the
system can never increase but can only decrease over
time. At first glance, because living things are so complex
and highly organized and because they have the ability to
stay organized, it would appear that living things may
somehow violate the laws of thermodynamics, particularly
the second law. But living things are not closed systems.
They interact with their environment. Yet as recently as the
1940s many scientists continued to consider the possibility
that living things do not behave according to the laws of
physics. However, decades of exhaustive thermodynamic
and physical studies of living things only confirm that
organisms follow the same laws of physics found in the
nonliving universe.

Shown are some examples of energy transferred and

transformed from one system to another and from one form
to another. The food we consume provides our cells with
the energy required to carry out bodily functions, just as
light energy provides plants with the means to create the
chemical energy they need. (credit “ice cream”:
modification of work by D. Sharon Pruitt; credit “kids”:
modification of work by Max from Providence; credit
“leaf”: modification of work by Cory Zanker)

Example:
The measure of randomness or disorder within a system as
entropy. High entropy means high disorder and low
energy. Molecules and chemical reactions have varying
entropy as well. For example, entropy increases as
molecules at a high concentration in one place diffuse
and spread out. The second law of thermodynamics says
that energy will always be lost as heat in energy
transfers or transformations. Living things are highly
ordered, requiring constant energy input to be maintained in
a state of low entropy.

Shaniah Azel G. 11
Biophysics
LECTURE / WEEK 1-6 / MODULE-BASED

Four elements of biomolecule

 Carbon
 Nitrogen
 Oxygen
 Hydrogen

A biological sub-area related to Biophysics that deals with

the function of living organisms and their parts is

 Physiology

Arrange the timeline of Science and Biophysics according

to its age.

 Pythagorean Theorem, Newton’s 2nd Law of

Motion, Birth of Biophysics

Methods used for gaining information about biological

systems on an atomic or molecular level is known as

 biological techniques

Who is the physicist that marked the birth of Biophysics?

 Karl Pearson/ Erwin Schrodinger

Which scope in molecular biophysic is/are NOT

considered?

 Application of optical techniques to the study of

biological molecules, cells and tissue.
 Determines the mass, the charge and the
interactions of biological molecules
 Researching the effects of radioactivity on the
Quiz Question environment
 Dynamics of reptiles
Two common and convenient ways to classify the various
branches of biophysics are by The movement of particles in diffusion is always from high
 technique used and by application. concentration towards to low concentration.
 size of what is studied and by whether  True
mathematics is used.
 size of what is studied and by technique being A branch of biophysics that deals with the study of
utilized. interdisciplinary field that applies methods and concepts
 technique used and by percentage of physics, from physics to medicine or healthcare, ranging from
chemistry, biology, and mathematics used. radiology to microscopy and nanomedicine.

What is Biophysics? Check all that apply.  Medical biophysics

 It is an interdisciplinary science involving What are the characteristics of facilitated diffusion? Check
physics, chemistry, biology and mathematics. all that apply
 The physics of biology.
 It tries to understand the application of the  It is a selective process of diffusion.
laws of matter and energy to living forms.  Requires a carrier protein.
 Transports large charged ions, small
Biophysical Society was founded in year molecules, proteins, and other solutes.

 1957 Does not need a carrier transport protein.

Slow process compare to other form of diffusion.

Shaniah Azel G. 12
Biophysics
LECTURE / WEEK 1-6 / MODULE-BASED

Occurs across a semipermeable membrane.  True

 False (Not all)
Identify the two Biophysicists of Medical Research Council  False (can exhibit two)
of King’s College in London who investigated the structure
of DNA using X-ray diffraction. Biophysicists seek to measure and understand the force and
energy involved in the interaction of biomolecules.
 Rosalind Franklin & Maurice Wilkins
 True
A biological sub-area related to Biophysics that deals with  False (in binding of biomolecules only)
the structure and function of plant and animal cells is  False ( development of biomolecules)
 Cytology
One particular part or region of a molecule or complex
Factors affecting diffusion. Check all that apply. involved in carrying out its function.
 distance
 Concentration of the particles  active site
 Temperature
Bonding needed to form secondary protein structure.
What are the characteristics of simple diffusion? Check all  hydrogen bonds
that apply
Active site is also known as _____.
 Slow process compare to other form of
diffusion.  substrate site
 Transports large charged ions, small molecules, A smaller molecule or atom that binds to a larger molecule.
proteins, and other solutes.  monomer
 Occurs across a semipermeable membrane.
 Requires a carrier protein. Each individual molecule in the complex.
 Does not need a carrier transport protein.  subunit
 It is a selective process of diffusion.
What is ligand in hemoglobin molecule once binding
Name different techniques to study biological systems on occur?
an atomic or molecular level. List all that apply  oxygen

 X-ray crystallography Another name of monomer

 Mass spectrometry  residue
 Electron microscopy
 Calorimetry There are two hemoglobin molecules. How many oxygen
 Microscopy molecules can bind to these number of hemoglobin
 Cryobiology molecules?
Molecular structure affects its biological function.  four

 False (may not affects) It means biomolecular shape.

 False ( does not affect)  conformation
 True
Hemoglobin is part of what type of blood cell.
Quaternary protein structure consists of more than one  red blood cells
amino acid chain.
A change in shape of biomolecule.
 False (more than one peptide)  conformational transition
 True
 False (complex structure) Other name of macromolecules aside from polyanions.
 polymers
Biophysicists use a variety of techniques to measure
conformational changes in biomolecules. The product formed by peptide bond.
 Amide/ Amino acids
 False (specific Techniques)
 True Other name of quaternary structure.
 False (few techniques)  Oligomers

All biomolecules exhibit all four levels of structure. The molecules and ions in living organisms are commonly
called as

Shaniah Azel G. 13
Biophysics
LECTURE / WEEK 1-6 / MODULE-BASED

 biomolecules

Branch of biophysics having combine concepts of biology,

chemistry and physics in studying molecules and
subcellular function is also called
 all of these
 biophysical chemistry
 biochemical physics
 physical biochemistry

A smaller molecule or atom that binds to a larger molecule.

 Ligand

Shaniah Azel J. Gaodgaod

Gaodgaod, Shaniah Azel J.
BS Biology-2B

Shaniah Azel G. 14