Republic of the Philippines

Leyte Normal University

Paterno Street, Tacloban
City

COLLEGE OF ARTS AND

SCIENCES

Study Outline 1
(Introduction to Biophyscis)

Second Semester, A.Y. 2022-2023

Submitted to:

Mr. Jefferson Flores

Submitted by:

John Paul C. Macato Av31

February 2023
 CHAPTER 1
INTRODUCTION
BIOPHYSICS -

 The physics of biology

 Tries to understand how energy and matter is at work in a living system

 Utilizes the principles, theories, and methods of physics to understand biology.

 Physics applies mathematical principles to the explanation of the physical world and can be used
to study the behavior of biological systems and organisms.

 contributes to the investigation of some of the most significant mysteries in the field of biology.

Prerequisites for Biophysics

 In order  to understand some complex concepts, this discipline of science necessitates some basic
understanding in not only biology but also in physics, chemistry, and mathematics.

 having taken at least any physics or chemistry course at the college level (or advanced high school level).

Basic Knowledge Example:

Take for example the newton second law of motion which is force is equal to mass times acceleration
where F (force) and a (acceleration) are both vector quantities.

F = ma

This implies that if a force F is applied to a mass object, the result will be an acceleration of the
mass object at a rate of acceleration. Additionally, it also states that that the acceleration rate for
every given force F applying on a mass (m) object will be precisely equal to the rate at which the
product (mass x acceleration) equals the force.

Note:

 If we apply the same force to an object with more mass, the acceleration must be reduced.

 A less massive object will accelerate more quickly when the same force is applied to it.
Let’s say:

An object with a mass of 2 kilograms is driven to a force of 12 newtons (N) (kg). At a speed of
6 meters per second (or 6 m/s2), the object will accelerate.

( Note that : For as long as we keep applying that force, the object will move at a rate of 6
meters per second (or 6 m/s) per second, increasing every second).

 However, applying the same force of 12 N to a heavier object, let's say one weighing 24 kg,
the acceleration of that object will be significantly slower, at only 1.2 m/s2.

Applying the same force to two objects with different masses will result in the more massive object
accelerating much slower compared to the less massive object, which will accelerate much faster.

Another Basic Example:

 Every living organism is dependent on millions of constant chemical reactions. Every biological
process required for a living thing to survive depends on it.

CO2 + H2O → sugar + O2

the chemical equation signifies that the reaction between carbon dioxide and water can produce both sugar
and oxygen.

 this reaction should have been written with a double arrow, CO2 + H2O ↔ sugar + O2 because it can
occur in both direction.

 From left to right reaction, the process of photosynthesis occur when carbon dioxide and water combine
to create sugar and oxygen.

 From right to left reaction, cellular respiration happens when glucose plus oxygen forms carbon dioxide
plus water and releases energy in a form of ATP.
 A Snippet of Biophysics History

 The field of biophysics is relatively modern (young branch of science).

 It emerged in the early to mid-20th Century as a distinct subfield. The field of biophysics is merely
60 to 100 years old.

 It is slightly older than genetic engineering and computer science, but far younger than physics,
mathematics, chemistry, or biology.

 Karl Pearson first coined the term "biophysics" in 1892. The term is frequently used to denote the
study of physical and chemical quantities in biological systems
.
 After the publication of the book What is Life?  in 1944 by Austrian physicist Erwin Schrödinger,
biophysics became more and more well-known.

 A few years later, the King's College Biophysics Research Unit was established by the Medical Research
Council of King's College in London.

 Among those who entered the unit to become biophysicists were the scientists Rosalind Franklin and
Maurice Wilkins.

 As a result, scientists like James Watson and Francis Crick inspired to turn their attention to biophysics.
They made major discoveries on genetic molecules with the help of Rosalind Franklin’s X-ray diffraction
data to discover the double helix structure of DNA.

Biophysics History Timeline

 Topics of biophysics into two broad classifications subdivided up into six categories.

 Biophysical topics based on relative size of subject:

1. Molecular and subcellular biophysics

2. Physiological and anatomical biophysics

3. Environmental biophysics

 Biophysical techniques and applications

1. General biophysical techniques

2. Imaging biophysics

3. Medical biophysics

As per the two major categories just presented, the topics found in biophysics are briefly described in the next
two chapters.
 CHAPTER 2

Biophysical Topics

- overview of the various topics of biophysics according to the following three major divisions :

 molecular and subcellular biophysics

 physiological and anatomical biophysics

 Environmental biophysics.

OBJECTIVES:

 Gain an understanding of the broad scope of biophysics.

 acquire some vocabulary of biophysics, learning the most commonly used Terms and how they apply to the
branches of biophysics.

 learn to classify the topics of biophysics into the three major divisions of Molecular and subcellular biophysics.

 physiological and anatomical biophysics.

 Environmental biophysics

 learn how the topic areas of biophysics are interrelated.

MOLECULAR AND SUBMOLECULAR BIOPHYSICS

 The branches of biophysics that deal with molecules and subcellular activity are the most prevalent.

 Also known as physical biochemistry, biochemical physics, or biophysical chemistry.

 where physics, chemistry, and biology all come together.

 aims to explain the structure, dynamics, and composition of molecules—from molecular to

submolecular level in order to understand how biological processes work.
I. The Structure and Conformation of Biological Molecules

 The subfield of biophysics focused with identifying  the composition, properties, and structure of biological
molecules.

 Polymer is a large molecule formed by joining several smaller molecules.

 (Biopolymers) ex. proteins are made by linking together smaller molecules called amino acids.

 These roughly 20 amino acids can be combined together in diverse quantities and sequences to generate a
wide range of different proteins.

 four levels of structure in biological molecules: primary, secondary, tertiary, and quaternary.
 The atoms or groups of atoms that make up a molecule are identified by the primary structure, along
with the connections between them.

 The initial, straight, three-dimensional structure of a molecule is referred to as secondary structure.

 Tertiary structure refers to the fact that a secondary structure, such as a helix or pleated sheet, can
fold back on itself and form a globular shape.

 Quaternary structure is when two or more tertiary shapes combine to produce a bigger molecule or complex

II. Structure Function Relationships

 Identifying the form and structure of biomolecules is figuring out which components of a molecule are
responsible for its biological activity.

 figuring out how modifications to its shape or structure affect its biological function.

 One specific component of a molecule or complex, known as the active site, is responsible for carrying out its
function.

 Additionally, a molecule or complex may contain many active sites.

III. Conformational Transitions

 change in shape.

 In the field of biophysics, the word "conformation" usually always refers to shape, more precisely the three-
dimensional arrangement of atoms in a molecule.

 To quantify conformational dynamics, biophysicists employ a range of modifications in biomolecules, to

quantify the energy involved, and to establish a link between the various conformations and their
biological function.

 Biomolecules frequently alter their shape in order to perform certain functions

.
IV. Ligand Binding and Intermolecular Binding

 Approximately equal in size molecules join to form a larger complex (quaternary structure).

 A subunit is a single molecule that makes up the complex.

 Ex. Four component proteins that link to one another form the hemoglobin molecule

 A smaller molecule or atom that binds to a larger molecule is known as a ligand.

 When two or more molecules bind together, the term "ligand" may occasionally be used (not just a smaller
molecule binding to a larger one).

Biophysicists studying ligand binding and other intermolecular binding seek to measure and understand;

 The forces and energy involved in binding

 The interaction between multiple binding sites

 How changes to the molecules affect binding

 The relationship between binding and conformational transitions

 The relationship between binding and biological function

 The competition between different ligands that can bind to the same molecule

 The rate at which binding occurs and the factors that affect binding rates
 2

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V. Diffusion and Molecular Transport

 This branch of biophysics studies how molecules move around within cells and how
molecules move from outside a cell to inside the cell and vice versa.

 Diffusion is the process of molecules spreading out, as a result of this random motion.

 The physics of diffusion can be described mathematically and can be used to better
understand and predict biological activity in cells.

 Diffusion is the primary means of molecules moving around within a cell.

VI. Membrane Biophysics

 The membrane is what defines the bound- ary between a cell and the outside world.

 Cell membranes are typically made of a double layer of lipid molecules.

 Lipid molecules have a string-like shape with a “head” at one end.

 Membranes limit and control the movement of molecules into and out of the
cell and from one region of the cell to another.

 Lipid vesicles are small hollow spheres of artificial membrane that can be made from
various types of lipids.

 By understanding the physics of lipid conformational transitions, we can control these

conformational transitions, and thus control the ability of the lipid vesicles to contain the
drug or chemical inside them.

VII. DNA and Nucleic Acid Biophysics

 This branch of biophysics studies the physics of DNA and RNA.

 DNA (deoxyribonucleic acid) is the biochemical that makes up our genes

and controls our physical heredity.

 A closely related nucleic acid is RNA (ribonucleic acid), which serves many purposes
within the cell.

DNA biophysics includes studying;

 Conformational transitions in DNA, including winding, unwinding, bending,

stretching, and supercoiling

 Binding of proteins, RNA, and other molecules to DNA

 Energy changes associated with conformational transitions and binding and their effect on
function
VIII. Protein Biophysics

 Proteins are involved in nearly every biological process within the cell.

 Ex. catalyzing biochemical reactions, regulating (turning on and off) biochemical processes, and
transporting molecules across cell membranes,

 Proteins are also involved in cell motility (self-induced movement of the cell).

 proteins typically must fold into very specific shapes, bind with other molecules, or undergo
one or more conformational transitions.

 understanding the phys- ics of protein folding, conformational transitions, and binding is crucial to
understanding and possibly controlling their role in biological processes.

IX. Bioenergetics

 This branch of biophysics studies the physics of energy flow in living systems.

 concerned with all levels and branches of biophysics, from the environment, to the organism, to the cell,
and to the molecules within the cell.

 study of how organisms and cells obtain the energy they need to carry out biological processes.
X. Thermodynamics

 The first law of thermodynamics states that energy 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

 organisms follow the same laws of physics found in the nonliving universe.

 describe how energy behaves in physical systems,

XI. Statistical Mechanics

 the application of probability and statistics to large populations of molecules.

 statistical mechanics allows to interpret the things that can measure in terms of what specific molecules
are doing.

 A model to determine the behaviour of molecules is a mathematical description of how the molecules
move, how much energy they have, how they change shape, and so on.

XII. Kinetics

 This branch of biophysics deals with measuring the rate or speed of biological processes such as
biochemical reactions, conformational transitions, and binding or unbinding of biomolecules .

 Kinetics tells us how fast it will occur.

 Living systems often regulate their biological processes by modulating the rate at which they happen.

 When an organism needs to modulate the rate at which a process happens, typically this is done
in one of two ways: either by providing the energy needed to get over a speed bump (high-energy
intermediate) or by providing an alternative path.

 studying kinetics also develop models to describe the molecular mechanism of a process

XIII. Molecular Machines

 Living things are full of machines and motors.

 Ex. our muscles use our bones as levers to redirect and in some cases magnify or decrease the forces
they apply.

 our muscles use our bones as levers to redirect and in some cases magnify or decrease the forces they
 apply.
Other examples, besides muscle contraction, of organisms generating a mechanical force or
motion include ;

 Cilia. These are hairlike projections on the surface of some cells that move, allowing the cell to swim.

 Flagella. These are longer, whiplike structures that stick out from the body of some cells and move
to propel the cell forward.

 Pseudopodia. Some cells move by temporarily pushing out on their mem- brane at one or more
locations, changing the shape of the cell and causing the cell to crawl along.

 Secretions. Cells that manufacture proteins or other substances to be used elsewhere in the body.

 Separation of chromosomes (DNA) during cell division. When a cell is getting ready to divide, it first
duplicates its chromosomes.
Allosterics

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