Biophysical Topics: Molecular and Subcellular Biophysics

Module 2
Biophysical Topics: Molecular and Subcellular Biophysics

Learning Objectives:
You should be able to
➢ Learn different topics under the scope of molecular and subcellular biophysics
➢ Describe and understand essential concepts related to these extent
➢ Acquire commonly used terms in molecular and subcellular biophysics
➢ Apply the concepts in distinct biophysics settings
➢ Learn how the topic areas of biophysics are interrelated.

Molecular and Subcellular Biophysics

The most common branches of biophysics are those dealing with molecules and subcellular
function where biology, chemistry and physics are encountered. This division of biophysics is sometimes
also called biochemical physics, physical biochemistry, or biophysical chemistry. Within this division of
biophysics we find the following topics.

The topics include here are as follows: (SET A)

A. The Structure and Conformation of Biological Molecules

This branch of biophysics deals with determining the structure, size, and shape of biological
molecules.
A biomolecule or biological molecule is a loosely used term for molecules and ions present
in organisms that are essential to one or more typically biological processes, such as cell
division, morphogenesis, or development (Biological process are the processes vital for a
living organism to live, and that shape its capacities for interacting with its environment.) Most
biomolecules are organic compounds and just four elements (C, O, H, N).
Biomolecules include
a. large macromolecules (or polyanions) such as proteins, carbohydrates, lipids, and nucleic acids.
- Commonly created by polymerization of small
subunits (monomers)
- Composed of thousands of atoms and more
- Most common macromolecules in biochemistry are
biopolymers and large non-polymeric.
(See Figure Biomolecules Chart)
b. small molecules such as
primary metabolites, secondary metabolites,
and natural products.
- 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 molecules.

Figure: Hierarchical Structure of Biomolecule

 Biophysical Topics: Molecular and Subcellular Biophysics

Many biological molecules are polymers. A polymer is a large molecule

made by connecting together many smaller molecules. Each of the smaller
molecules is called a residue (or monomer). The residues making up a polymer may
be identical, like links in a typical chain where the links are all ovals. The residues
may also be a set of related but not identical molecules.
Biopolymers (biological polymers) - where the residues have something in
common but are not identical. Polymers are produced by living organisms.

Example:
Proteins are made by linking together smaller 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.
Figure: Biomolecules Chart

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.
 Biophysical Topics: Molecular and Subcellular Biophysics

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 sheet, can
fold back on itself (sometimes over and over) and form a globular shape.
4. Quaternary structure refers to the case where two or more tertiary shapes attach to one another to
form an even larger molecule or complex.

Not all biomolecules exhibit all four levels of structure. Small molecules (for example, simple
sugars or amino acids) typically exhibit only primary and secondary structures. Biopolymers most
commonly exhibit all levels up to tertiary structure, and sometimes exhibit quaternary structure.

Figure: The four levels of

structure in biological molecules
are illustrated here using the
example of a protein but apply as
well to other molecules and
subcellular complexes.
 Biophysical Topics: Molecular and Subcellular Biophysics

B. Structure Function Relationships

Closely related to determining the structure and shape of biomolecules is determining
which parts 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 complex is
involved in carrying out its function, that part is referred to as the active site of the molecule. It is also
possible for a molecule or complex to have more than one active site.
In biology, the active site is the region of an enzyme (one type of protein) where
substrate molecules bind and undergo a chemical reaction. The active site consists of residues that form
temporary bonds with the substrate (binding site) and residues that catalyse a reaction of that substrate
(catalytic site).

Figure: Enzyme Action

C. Conformation of Biological Molecules

Conformation in biophysics it almost always means shape or structure (three-dimensional
arrangement of atoms in a biological molecule). The determination of the three-dimensional structure of
a biological molecule is the starting point in the understanding of molecular mechanisms involved in its
complex biochemical reactions.
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. Transitions between these states occur on a
variety of length scales (tenths of Å to nm) and time scales (ns to s).
Biophysical techniques used to study macromolecular conformational change:
Crystallography, NMR, electron paramagnetic resonance (EPR) using spin label techniques, circular
dichroism (CD), hydrogen exchange, and FRET
 Biophysical Topics: Molecular and Subcellular Biophysics

Examples:
a. Figure: Example of Conformational
change (Mass Changes)

b. The DNA double helix must temporarily unwind in order for the genetic instructions to be read or in
order for the DNA to replicate itself for the next generation. Biophysicists use a variety of techniques to
measure conformational changes in biomolecules, to measure the energy associated with them and to
determine the relationship between
the various conformations and their
biological function. It is also possible
to induce conformational changes in
the laboratory. Induced
conformational transitions can be
used to develop medical treatments
and diagnostics.
These induced changes may or may
not happen in nature.

c. Spike protein attaches to the receptor on the target cell, ACE2, and is the dominant target of the
immune system.

Spike proteins of SARS-CoV-2 are known to exhibit open and closed conformations. In the closed
conformation the receptor binding site is hidden, whereas it is exposed in the open conformation. This
has also been seen in purified SARS-CoV-2 spike proteins, but the relevance of these different
conformations in the context of an intact virus has been unknown.
 Biophysical Topics: Molecular and Subcellular Biophysics

Spike Conformations of SARS-CoV-2

 Biophysical Topics: Molecular and Subcellular Biophysics

Module 2: Set A
The Structure and Conformation of Biological Molecules

A. Picture Perfect:
A.1. Identify the images below using the four levels of Protein structure:

1. ______________________ 2. _____________________ 3._____________________

4. ______________________ 5. ____________________ 6. ___________________________

B.2. Label each part B.3. Learn By Drawing: Draw the complex form of B.2.

C. Application in Real Life Situations. Find/Identify at least 3 situations under the scope of conformation
of Biological Molecules that can be expressed in a single statement.