QUANTITATIVE

VIEWS OF MODERN
BIOLOGY
Unit 3
Why Biology Data is most meaningful against the backdrop of a
concept or theory

by the Goal: to develop kinds of models that can be put forth

for modern biological data

numbers? Motion of inanimate objects moving in a space can be

explained by fitting some mathematical equations
easily
Biological systems are highly complex
Difficult to consider all the systems functioning
together just to make one type of cell
Millions of such cells make one organs
Multiple organs make an organisms
Imagine the total number of cells in a human !!! And the
complexities involved
 Model High complexity of biological systems
Too difficult to be comprehended by simple equations

Building alone
Need for model building.
Approach A model is a small but accurate scale replica of the
original system that is built by abstraction and
simplifying the highly complex characteristics into an
average ones.
Multiple models can be made out of a system.
To explain a particular characteristic of the system,
select only the relevant properties of the system
explaining those characteristics.
Some of the key model systems are: DNA, protein, cell
membrane, microbes..
 Organisms are constructed from
four major classes of
macromolecules
Proteins, carbohydrates, lipids and
nucleic acids
Proteins structural elements,
catalyze necessary reactions
Lipids form membranes, separate
cell from rest of the space and
compartmentalize cell organelles
Carbohydrates energy storage,
create specific surface of the cell
membranes
Nucleic acids genetic material,
perform critical functions of having
instructions to generate other kind
of macro molecules and to
replicate themselves
 Nucleic acids and proteins are polymers with different
language of monomers
Nucleic acids built up from alphabets of 4 letters A, G, C
and T
DNA letters are read as three letter words called as
codons
Each possible codon codes for one amino acid (some
redundancy and exceptions like stop codons)
Proteins are made up of alphabets of 20 distinct amino
acids
In proteins groups of amino acid letters form words giving
rise to secondary structure in proteins alpha helix, beta
strands.
Complete sentence in protein is fully folded protein that
could either be an enzyme or a structural protein etc.
Nucleic
acids to
Amino
acids
 Model DNA is one of the most important molecules
carrier of genetic information

Building in Polarity to each strand of the helical polymeric

Biology:
molecule: two ends of the strand are structurally and
chemically distinct, called 5 and 3 ends

DNA Heterogeneity along the length

Five different projections of the DNA can be
considered depending on the context.
1. Sequence of base pairs
2. Binding site (for a protein)
3. Charged rod - Net distribution of charge
4. Bending elasticity
5. Freely jointed polymer arranged in a random walk
 Model
Building in
Biology:
DNA
 Model Proteins are considered as linear sequence of amino acids
Perform most of the important biological functions in a

Building in cell.
Detailed atomic structure more complex than DNA

Biology : because of the 20 fundamental units involved (rather than

4 in DNA).

Proteins Proteins can be represented as:

1. Simple linear sequence of amino acids
2. Based on nature of amino acids (hydrophobic H or
hydrophilic P)
3. Three dimensional folded structure at different levels
4. Lattice models amino acids occupy regular array of
positions in space.
5. Binding platform for ligands
6. Two-state system (active or inactive) that causes
modifications in the structure of protein
 Model
Building in
Biology :
Proteins
 Idealization
of
membranes

Membranes can be thought of

1. Springy elastic sheets
2. Random surfaces
3. Arrays of electrical elements
4. Selective barriers
Idealization of
a Living Cell-
Bacteria
E.coli.

For Model Building we can think of it as:

1. Organism carrying protein receptors on its surface
2. Or how it swims through water using flagella (hydrodynamics)
3. Path it follows in the water (random walk)
4. Responses to changing condition changes in gene expression
 Biological Much of the important modeling of biological systems
has been in the form of visual schematics which

cartoons illustrate the most essential features in a given

biological process and how they interact.

select those Conceptual model building

Example in case: Structure of Mitochondria that can be
features of depicted in many ways based on the Electron

the problem
micrograph structure
You can find: 2D, 3D or detailed mitochondrial

thought to membrane view depending on the context and

relevance

be essential
 Applying The idea of a simple spring motion can be used to
explain some of the biological processes

idea of Potential energy for almost any system subjected to

small displacements from equilibrium is well

springs to approximated by a quadratic function of the

displacement.

biological Mathematically written as, Energy = (kx2)

model k is the spring constant or stiffness depends on the

material properties.

building Hookes law, F = -kx

Restoring force that is proportional to how far the
spring is displaced from its equilibrium position.
Spring models can explain many concepts in Biology
 Some other key physics concepts that can be used in biological models

Simple Harmonic oscillator

Ideal gas and ideal solution models
Two-level systems and Ising model
Random walks, entropy and macromolecular structure
Poisson-Boltzmann model of charges in solution
Elastic theory
Newtonian fluid model, Navier Stokes equation
Diffusion
Rate equations of chemical kinetics