Unit-I

Basic Cell Biology

Introduction: Living Organisms, Cells and their type, Cell theory, Cell Principle, Cell Structure
and Function, Central Dogma of molecular Biology, Structure and types of DNA, and RNA,
DNA replication, Transcription, Translation and structures of proteins, Cell growth, Cell
Division and differentiation.

INTRODUCTION

The living beings are comprised of a cell or number of cells. Cell biology is an
integrative science including biochemistry, biophysics, molecular biology, microscopy, genetics,
physiology, computer science and developmental biology and thereby reveals the size, shape,
location and movements of cell components. The cell (Gr., kytos: cell; L., cella: hollow space) is
the basic unit of organization or structure of all living matter and a fundamental unit of life. The
cell is the smallest unit that can still carry on all life processes.

CELL:

A cell can be defined as the smallest unit of life. It is the structural, functional and biological unit
of all living beings. A cell can replicate itself independently and are thus referred to as
the building blocks of life. Each cell contains a cytoplasm which is enclosed by a membrane and
contains several biomolecules like proteins, nucleic acids, etc.

Discovery of cell:

The cell was first discovered and named by Robert Hooke in 1665. He remarked that it looked
strangely similar to cellula or small rooms which monks inhabited, thus depriving the name.
However what Hooke actually saw was the dead cell walls of plant cells (cork) as it appeared
under the microscope. Hooke’s description of these cells was published in Micrographia. The
cell walls observed by Hooke gave no indication of the nucleus and other organelles found in
most living cells. The first man to witness a live cell under a microscope was Anton van
Leeuwenhoek, who in 1674 described the algae Spirogyra. Van Leeuwenhoek probably also saw
bacteria.
 Diagram of cell

Types of Organisms

Unicellular Organisms: - Unicellular organisms are known as singled-celled organisms. They

are made up of a single cell. E.g. Ameoba, Acetabularia, Chlamydomonas.

i. A single is capable of independent existence

ii. Able to perform all the essential function of life

Multicellular Organisms: - Organisms that consist of more than one cell are known as
multicellular organisms.

i. A higher animal or plant contains billions of cells.

Difference between the unicellular and multicellular:

Types of Cells
Cells are similar to small factories with different laborers and departments that work all the time
to make life possible. Various kinds of cells perform different functions like protein synthesis
and energy production. There are two major kinds of living organisms based on their cellular
structure namely: prokaryotes and eukaryotes.

 Prokaryotes are made up of cell with no nucleus. They all are single-celled microorganisms
including archaea, bacteria and photosynthetic blue-green algae which are also known
as cyanobacteria. ‘Group of prokaryotes’ is known as Monera. Prokaryotes were probably
anaerobic and heterotrophic. This group includes eubacteria (Lactococcus lactis),
 archaebacteria (Methanosarcina), green bacteria, purple bacteria, virus, prochlorophyta,
cyanophyta and Mycoplasma; on the basis of detailed analysis of the DNA sequences froma
variety of prokaryotic organisms has revealed two distinct types: the bacteria and the
archaea. They make up a huge part of the earth’s biomass and are quite adaptable as they
have been found 7 miles deep in the ocean and 40 miles up in the atmosphere.
Morphologically, prokaryotic cells are the most primitive cells.

 Eukaryotes consist of cells with a nucleus. This large category involves all plants, fungi
(such as molds, yeast, and mushrooms), protozoa (Plasmodium falciparum and parasite that
cause malaria) and animals. The plasma membrane is responsible for monitoring the
transport of nutrients and electrolytes in and out of the cell and also responsible for cell to
cell communication.

Cellular life is entirely dependent on the various chemical processes for survival. These chemical
reactions mainly occur in a watery solution within the cell known as cytoplasm.

Differnece Between Prokaryotic and Eukaryotc Cell

BASIS FOR
PROKARYOTIC CELLS EUKARYOTIC CELLS
COMPARISON

Size 0.5-3um 2-100um

BASIS FOR
PROKARYOTIC CELLS EUKARYOTIC CELLS
COMPARISON

Kind of Cell Single-cell Multicellular

Cell Wall Cell wall present, comprise of Usually cell wall absent, if present
peptidoglycan or mucopeptide (plant cells and fungus), comprises
(polysaccharide). of cellulose (polysaccharide).

Presence of Well-defined nucleus is absent, A well-defined nucleus is present

Nucleus rather 'nucleoid' is present which is enclosed within nuclear
an open region containing DNA. memebrane.

Shape of DNA Circular, double-stranded DNA. Linear, double-stranded DNA.

Mitochondria Absent Present

Ribosome 70S 80S

Golgi Apparatus Absent Present

Endoplasmic Absent Present

Reticulum

Mode of Asexual Most commonly sexual

Reproduction

Cell Divison Binary Fission, Mitosis

(conjugation, transformation,
transduction)

Lysosomes and Absent Present

Peroxisomes

Chloroplast (Absent) scattered in the cytoplasm. Present in plants, algae.

BASIS FOR
PROKARYOTIC CELLS EUKARYOTIC CELLS
COMPARISON

Transcription and Occurs together. Transcription occurs in nucleus

Translation and translation in cytosol.

Organelles Organelles are not membrane Organelles are membrane bound

bound, if present any. and are specific in function.

Replication Single origin of replication. Multiple origins of replication.

Number of Only one (not true called as a More than one.

Chromosomes plasmid).

Examples Archaea, Bacteria. Plants and Animals.

The Function and Characteristics of Cells

 The cell interior is organized into different special compartments or organelles surrounded by
a separate membrane.
 The nucleus (major organelle) holds genetic information necessary for reproduction and cell
growth.
 Every cell has one nucleus and other types of organelles exist in multiple copies in the
cytoplasm.
 Mitochondria, a double membrane-bound organelle is mainly responsible for the energy
transactions vital for survival of the cell.
 Lysosomes digest unwanted materials in the cell.
 Endoplasmic reticulum plays a significant role in the internal organization of the cell by
synthesizing selective molecules and processing, directing and sorting them to their
appropriate locations
 CELL THEORY

In the 1830’s, Matthias Schleiden who was a botanist & Theodore Schwann who was a
zoologist, stated that all living things were made of cells. In 1855, Rudolf Virchow stated that
cells only arise from pre-existing cells. Virchow’s idea contradicted the idea of spontaneous
generation.

The combined work of Schleiden, Schwann & Virchow is known as the Cell Theory.

Schwann Schleiden Virchow

Principles of the Cell Theory

i. All living things are made of one or more cells.

ii. Cells are the basic unit of structure & function in organisms.
iii. Cells come only from the reproduction of existing cells

Modern interpretation- The generally accepted parts of modern cell theory

include:

1. All known living things are made up of one or more cells

2. All living cells arise from pre-existing cells by division.
3. The cell is the fundamental unit of structure and function in all living
organisms.
4. The activity of an organism depends on the total activity of independent
cells.
5. Energy flow (metabolism and biochemistry) occurs within cells.
6. Cells contain DNA which is found specifically in the chromosome
and RNA found in the cell nucleus and cytoplasm.
7. All cells are basically the same in chemical composition in organisms of
similar species.
 STRUCTURE AND TYPES OF DNA

DNA is the largest macromolecule that represents the genetic material of the cell.
Chemically, DNA is a double helix of two antiparallel polynucleotide chains.
Each polynucleotide chain is a linear mixed polymer of four deoxyribotides i.e.
deoxyadenylate, deoxyguanylate, deoxycytidylate and thymidylate.

Watson-Crick Model of DNA: In 1953, J.D. Watson (an American biologist)

and F.H.C. Crick (a British Physicist) proposed the three-dimensional model of
physiological DNA (i. e B-DNA) on the basis of X-ray diffraction data of DNA
obtained by Franklin and Wilkins. For this epoch-making discovery, Watson,
Crick and Wilkins got Nobel Prize in medicine in 1962. Term DNA was given by
Zaccharis.

The important features of Watson – Crick Model or double helix model of

DNA are as follows:

1. The DNA molecule consists of two polynucleotide chains or strands that

spirally twisted around each other and coiled around a common axis to form a
right-handed double-helix.

2. The two strands are antiparallel i.e. they ran in opposite directions so that the 3′
end of one chain facing the 5′ end of the other.

3. The sugar-phosphate backbones remain on the outside, while the core of the
helix contains the purine and pyrimidine bases.

. The two strands are held together by hydrogen bonds between the purine and
pyrimidine bases of the opposite strands.

5. Adenine (A) always pairs with thymine (T) by two hydrogen bonds and
guanine (G) always pairs with cytosine (C) by three hydrogen bonds. This
complimentarily is known as the base pairing rule. Thus, the two stands are
complementary to one another.

6. The base sequence along a polynucleotide chain is variable and a specific

sequence of bases carries the genetic information.
7. The base compositions of DNA obey Chargaff s rules (E.E. Chargaff, 1950)
according to which A=T and G=C; as a corollary ∑ purines (A+G) = 2
pyrimidines (C+T); also (A+C) = (G+T). It also states that ratio of (A+T) and
(G+C) is constant for a species (range 0.4 to 1.9)

8. The diameter of DNA is 20nm or 20 A. Adjacent bases are separated 0.34 nm

or by 3.4 A along the axis. The length of a complete turn of helix is 3.4 nm or 34
A i.e. there are 10bp per turn. (B- DNA-Watson rick DNA)

9. The DNA helix has a shallow groove called minor groove (-1,2nm) and a deep
groove called major groove (- 2.2nm) across.
Some other characteristics of DNA:

1. The amount of DNA per nucleus is constant in all the somatic cells of a given
species.

2. The total amount of DNA in a haploid genome is a characteristic of each

organism and is known as C-value.

3. Only a small fraction of DNA is functional in eukaryotes.

4. DNA is the chemical basis of heredity and is organized into genes or cistrons.

5. DNA replicates to form DNAs and transcribes to form RNAs.

6. DNA replication occurs in the S-phase of cell cycle.

7. DNA replication is semi conservative in which two daughter DNA molecules

formed; each receives one of parental strand and one new strand.

8. One strand of DNA directs the synthesis called template strand, or antisense or
non-coding strand. The other strand is called coding or non template of sense
strand which has the same sequence as the RNA transcript except for T in place of
U.

9. DNA has many repeated base sequences, some of which ire mobile.

10. DNA can easily undergo denaturation (melting) and renaturation with any
change in pH, temperature and salt concentration. DNA with a high G+ G content
are more resistant to thermal melting than A + T rich molecules.

11. DNA can be synthesized in vitro (in the laboratory).

12. DNA can be measured by the unit picogram (lpg= 10 g)

Biological Importance or Function of DNA:

1. Hereditary material: The genetic information stored in the nucleotide

sequence of DNA helps in synthesis of specific proteins or polypeptides and
transmit the information to daughter cells or offspring’s. Thus, DNA is called as
molecular blueprint or thread of life.
2. Autocatalytic role DNA: DNA undergoes replication (self-duplication) in the
S-phase of cell cycle. During the process each DNA strand of a double helix can
act as template for the synthesis of daughter strand.

3. Heterocatalytic role: During transcription any one strand of DNA acts as

template for the synthesis of RNA. This is called the heterocatalytic role of RNA.

4. Variations: DNA undergoes recombination its meiosis and occasional

mutation (changes in nucleotide sequences) which creates variations in population
and ultimately contributes to evolution.

5. DNA controls cellular metabolism, growth, and differentiation.

6. DNA finger printing (-DNA typing or profiling): Each individual carries

specific short nucleotide repeats which are called as minisatellites or VNTRs
(Variable Number of Tandem Repeats). The VNTRs of two individuals are
variable and forms the basis of DNA fingerprinting This technique is used to
identify criminals, determine paternity, verification of immigrant etc.

7. Recombinant DNA technology (Genetic engineering): It involves the

artificial cleaving and rejoining DNA sequences from two or more organisms to
create recombinant DNA. This technology is employed for production of
genetically modified organisms (GMOs), genetically modified foods (GMFs),
vaccines, hormones, enzymes, clones etc. It is also used for construction of probes
(short polynucleotide chain attached to a radioactive or fluorescent marker) for
diagnosis of diseases und curing hereditary diseases by replacing a faulty gene
with a normal gene (gene therapy), formation of clones etc.

STRUCTURE AND TYPES OF RNA

RNA or ribonucleic acid is a polymer of nucleotides that is made up of a ribose

sugar, a phosphate, and bases such as adenine, guanine, cytosine, and uracil. It
plays a crucial role in gene expression by acting as the intermediate between the
genetic information encoded by DNA and protein

Types of RNA

In both prokaryotes and eukaryotes, there are three main types of RNA –
messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
These 3 types of RNA are discussed below.
1. Messenger RNA (mRNA): mRNA accounts for just 5% of the total RNA in
the cell. mRNA is the most heterogeneous of the 3 types of RNA in terms of both
base sequence and size. It carries complimentary genetic code copied, from DNA
during transcription, in the form of triplets of nucleotides called codons.

Each codon specifies a particular amino acid, though one amino acid may be
coded for by many different codons. Although there are 64 possible codons or
triplet bases in the genetic code, only 20 of them represent amino acids. There are
also 3 stop codons, which indicate that ribosomes should cease protein generation
by translation.

As part of post-transcriptional processing in eukaryotes, the 5’ end of mRNA is

capped with a guanosine triphosphate nucleotide, which helps in mRNA
recognition during translation or protein synthesis. Similarly, the 3’ end of an
mRNA has a poly-A tail or multiple adenylate residues added to it, which
prevents enzymatic degradation of mRNA. Both the 5’ and 3’ end of an mRNA
imparts stability to the mRNA.

2. Ribosomal RNA (rRNA): rRNAs are found in the ribosomes and account for
80% of the total RNA present in the cell. rRNAs combine with proteins and
enzymes in the cytoplasm to form ribosomes, which act as the site of protein
synthesis. These complex structures travel along the mRNA molecule during
translation and facilitate the assembly of amino acids to form a polypeptide chain.
They interact with tRNAs and other molecules that are crucial to protein
synthesis.

Ribosomes are of two type – 70S in case of prokaryotes and 80 S in case of

Eukaryotes. RNA of eukaryotes are of four type-28S,18S,5.8S and 5S.Prokaryotic
ribosomes have three types of RNA-23S,16S and 5S.
Functions-

1. rRna bind protein molecule and give rise to ribosome.

2. 3’ end of 18S rRNA has nucleotide complementary to

those of cap region of mRNA.
3. 5S rRNA and surrounding protein complex provide
binding site for tRNA.

3. Transfer RNA (tRNA)

tRNA is the smallest of the 3 types of RNA, possessing around 75-95 nucleotides.
tRNAs are an essential component of translation, where their main function is the
transfer of amino acids during protein synthesis. Therefore, they are called
transfer RNAs.

Each of the 20 amino acids has a specific tRNA that binds with it and transfers it
to the growing polypeptide chain. tRNAs also act as adapters in the translation of
the genetic sequence of mRNA into proteins. Thus, they are also called adapter
molecules.

tRNAs have a clover leaf structure which is stabilized by strong hydrogen bonds
between the nucleotides. They normally contain some unusual bases in addition to
the usual 4, which are formed by methylation of the usual bases. Methyl guanine
and methylcytosine are two examples of methylated bases.
Functions- 1 tRNA ment for transferring to ribosomes for the synthesis of
polypeptides.

2. There different tRNAfor different amino acids.

Other types of RNA

Beyond the primary role of RNA in protein synthesis, several varieties of RNA
exist that are involved in post-transcriptional modification, DNA replication, and
gene regulation. Some forms of RNA are only found in particular forms of life,
such as in eukaryotes or bacteria.

Small Nuclear RNA (snRNA)

snRNA is involved in the processing of pre-messenger RNA (pre-mRNA) into

mature mRNA. They are very short, with an average length of only 150
nucleotides.

Regulatory RNAs

A number of types of RNA are involved in regulation of gene expression,

including micro RNA (miRNA), small interfering RNA (siRNA) and antisense
RNA (aRNA).

miRNA (21-22 nt) is found in eukaryotes, and acts through RNA interference
(RNAi). miRNA can break down mRNA that it is complementary to, with the aid
of enzymes. This can block the mRNA from being translated, or accelerate its
degradation.

siRNA (20-25 nt) are often produced by breakdown of viral RNA, though there
are also endogenous sources of siRNAs. They act similarly to miRNA. An mRNA
may contain regulatory elements itself, such as riboswitches, in the 5' untranslated
region or 3' untranslated region; these cis-regulatory elements regulate the activity
of that mRNA.

Transfer-messenger RNA (tmRNA)

Found in many bacteria and plastids. tmRNA tag the proteins encoded by mRNAs
that lack stop codons for degradation, and prevents the ribosome from stalling due
to the missing stop codon.

Ribozymes (RNA enzymes)

RNAs are now known to adopt complex tertiary structures and act as biological
catalysts. Such RNA enzymes are known as ribozymes, and they exhibit many of
the features of a classical enzyme, such as an active site, a binding site for a
substrate and a binding site for a cofactor, such as a metal ion.

One of the first ribozymes to be discovered was RNase P, a ribonuclease that is

involved in generating tRNA molecules from larger, precursor RNAs. RNase P is
composed of both RNA and protein; however, the RNA moiety alone is the
catalyst.

Double-stranded RNA (dsRNA)

This type of RNA has two strands bound together, as with double stranded DNA.
dsRNA forms the genetic material of some viruses.

CENTRAL DOGMA

Central Dogma- It is the flow of information from DNA to mRNA and then
decoding the information present in mRNA in the formation of polypeptide chain
or protein
 DNA REPLICATION

Introduction: The basic mechanisms of DNA replication are similar across

organisms. In this article, we'll focus on DNA replication as it takes place in the
bacterium E. coli, but the mechanisms of replication are similar in humans and
other eukaryotes.

Key points:

 DNA replication is semiconservative. Each strand in the double helix acts

as a template for synthesis of a new, complementary strand.
 New DNA is made by enzymes called DNA polymerases, which require a
template and a primer (starter) and synthesize DNA in the 5' to 3'
direction.
 During DNA replication, one new strand (the leading strand) is made as a
continuous piece. The other (the lagging strand) is made in small pieces.
 DNA replication requires other enzymes in addition to DNA polymerase,
including DNA primase, DNA helicase, DNA ligase, and topoisomerase.

The basic idea

DNA replication is semiconservative, meaning that each strand in the DNA

double helix acts as a template for the synthesis of a new, complementary strand.

This process takes us from one starting molecule to two "daughter" molecules,
with each newly formed double helix containing one new and one old strand.

1. DNA double helix.

2. Hydrogen bonds break and helix opens.
3. Each strand of DNA acts as a template for synthesis of a new,
complementary strand.
4. Replication produces two identical DNA double helices, each with one
new and one old strand.
Schematic of Watson and Crick's basic model of DNA replication

In a sense, that's all there is to DNA replication! But what's actually most
interesting about this process is how it's carried out in a cell.

Cells need to copy their DNA very quickly, and with very few errors (or risk
problem such as cancer). To do so, they use a variety of enzymes and proteins,
which work together to make sure DNA replication is performed smoothly and
accurately.

DNA polymerase: One of the key molecules in DNA replication is the

enzyme DNA polymerase. DNA polymerases are responsible for synthesizing
DNA: they add nucleotides one by one to the growing DNA chain, incorporating
only those that are complementary to the template.

Here are some key features of DNA polymerases:

 They always need a template

 They can only add nucleotides to the 3' end of a DNA strand
 They can't start making a DNA chain from scratch, but require a pre-
existing chain or short stretch of nucleotides called a primer
 They proofread, or check their work, removing the vast majority of
"wrong" nucleotides that are accidentally added to the chain

The addition of nucleotides requires energy. This energy comes from the
nucleotides themselves, which have three phosphates attached to them (much like
the energy-carrying molecule ATP). When the bond between phosphates is
broken, the energy released is used to form a bond between the incoming
nucleotide and the growing chain.
DNA polymerization reaction

The diagram shows a template DNA strand paired up with a new DNA strand that
is currently being synthesized. The bases of the new strand and the template form
complementary pairs held together by hydrogen bonds. The two strands are
antiparallel. Their sequences are:

New strand: 5' ACTG... 3' Template strand: 3' TGACAT 5'

At the end of the new strand, a 3' hydroxyl group is exposed on the final
nucleotide of the strand. This hydroxyl group will undergo a chemical reaction
with a phosphate group in an incoming nucleotide, resulting in the formation of a
new bond (and the addition of the nucleotide to the end of the chain). Specifically,
the next nucleotide exposed on the template is an A. The nucleotide
complementary to an A is a T, so when a T pairs with the A on the template
strand, it will undergo a reaction with the 3' hydroxyl at the end of the chain and
be added on.

The nucleotide consists of a sugar with a chain of three phosphates, a base, and a
hydroxyl attached. The 3' hydroxyl exposed at the end of the growing strand will
form a bond to the innermost phosphate in the chain of the new nucleotide, a
reaction that release a two-phosphate unit called pyrophosphate. The
pyrophosphate will be further cleaved into two individual phosphate ions. The
result of the reaction is the addition of the T nucleotide to the growing strand of
DNA. The 3' hydroxyl of the T nucleotide is now exposed at the end of the chain.
This hydroxyl can participate in a new reaction with the phosphate of the next
nucleotide to be added to the chain.

In prokaryotes such as E. coli, there are two main DNA polymerases involved in
DNA replication: DNA pol III (the major DNA-maker), and DNA pol I, which
plays a crucial supporting role we'll examine later.

Starting DNA replication: How do DNA polymerases and other replication

factors know where to begin? Replication always starts at specific locations on the
DNA, which are called origins of replication and are recognized by their
sequence.

E. coli, like most bacteria, has a single origin of replication on its chromosome.
The origin is about 245245245 base pairs long and has mostly A/T base pairs
(which are held together by fewer hydrogen bonds than G/C base pairs), making
the DNA strands easier to separate.

Specialized proteins recognize the origin, bind to this site, and open up the DNA.
As the DNA opens, two Y-shaped structures called replication forks are formed,
together making up what's called a replication bubble. The replication forks will
move in opposite directions as replication proceeds.
Bacterial chromosome. The double-stranded DNA of the circular bacteria
chromosome is opened at the origin of replication, forming a replication bubble.
Each end of the bubble is a replication fork, a Y-shaped junction where double-
stranded DNA is separated into two single strands. New DNA complementary to
each single strand is synthesized at each replication fork. The two forks move in
opposite directions around the circumference of the bacterial chromosome,
creating a larger and larger replication bubble that grows at both ends.

How does replication actually get going at the forks? Helicase is the first
replication enzyme to load on at the origin of replication^33start superscript, 3,
end superscript. Helicase's job is to move the replication forks forward by
"unwinding" the DNA (breaking the hydrogen bonds between the nitrogenous
base pairs).

Proteins called single-strand binding proteins coat the separated strands of DNA
near the replication fork, keeping them from coming back together into a double
helix.

Primers and primase: DNA polymerases can only add nucleotides to the 3' end
of an existing DNA strand. (They use the free -OH group found at the 3' end as a
"hook," adding a nucleotide to this group in the polymerization reaction.) How,
then, does DNA polymerase add the first nucleotide at a new replication fork?

Alone, it can't! The problem is solved with the help of an enzyme called primase.
Primase makes an RNA primer, or short stretch of nucleic acid complementary to
the templat that provides a 3' end for DNA polymerase to work on. A typical
primer is about five to ten nucleotides long. The primer primes DNA synthesis,
i.e., gets it started.

Once the RNA primer is in place, DNA polymerase "extends" it, adding
nucleotides one by one to make a new DNA strand that's complementary to the
template strand.

Leading and lagging strands: In E. coli, the DNA polymerase that handles most
of the synthesis is DNA polymerase III. There are two molecules of DNA
polymerase III at a replication fork, each of them hard at work on one of the two
new DNA strands.

DNA polymerases can only make DNA in the 5' to 3' direction, and this poses a
problem during replication. A DNA double helix is always anti-parallel; in other
words, one strand runs in the 5' to 3' direction, while the other runs in the 3' to 5'
direction. This makes it necessary for the two new strands, which are also
antiparallel to their templates, to be made in slightly different ways.

One new strand, which runs 5' to 3' towards the replication fork, is the easy one.
This strand is made continuously, because the DNA polymerase is moving in the
same direction as the replication fork. This continuously synthesized strand is
called the leading strand.

The other new strand, which runs 5' to 3' away from the fork, is trickier. This
strand is made in fragments because, as the fork moves forward, the DNA
polymerase (which is moving away from the fork) must come off and reattach on
the newly exposed DNA. This tricky strand, which is made in fragments, is called
the lagging strand.

The small fragments are called Okazaki fragments, named for the Japanese
scientist who discovered them. The leading strand can be extended from one
primer alone, whereas the lagging strand needs a new primer for each of the short
Okazaki fragments.

The maintenance and clean-up crew

Some other proteins and enzymes, in addition the main ones above, are needed to
keep DNA replication running smoothly. One is a protein called the sliding
clamp, which holds DNA polymerase III molecules in place as they synthesize
DNA. The sliding clamp is a ring-shaped protein and keeps the DNA polymerase
of the lagging strand from floating off when it re-starts at a new Okazaki
fragment^44start superscript, 4, end superscript.

Topoisomerase also plays an important maintenance role during DNA

replication. This enzyme prevents the DNA double helix ahead of the replication
fork from getting too tightly wound as the DNA is opened up. It acts by making
temporary nicks in the helix to release the tension, then sealing the nicks to avoid
permanent damage.

Finally, there is a little clean-up work to do if we want DNA that doesn't contain
any RNA or gaps. The RNA primers are removed and replaced by DNA through
the activity of DNA polymerase I, the other polymerase involved in replication.
The nicks that remain after the primers are replaced get sealed by the
enzyme DNA ligase.

Summary of DNA replication in E. coli

Let's zoom out and see how the enzymes and proteins involved in replication
work together to synthesize new DNA.

Illustration shows the replication fork. Helicase unwinds the helix, and single-
strand binding proteins prevent the helix from re-forming. Topoisomerase
prevents the DNA from getting too tightly coiled ahead of the replication fork.
DNA primase forms an RNA primer, and DNA polymerase extends the DNA
strand from the RNA primer. DNA synthesis occurs only in the 5' to 3' direction.
On the leading strand, DNA synthesis occurs continuously. On the lagging strand,
DNA synthesis restarts many times as the helix unwinds, resulting in many short
fragments called “Okazaki fragments.” DNA ligase joins the Okazaki fragments
together into a single DNA molecule.

 Helicase opens up the DNA at the replication fork.

  Single-strand binding proteins coat the DNA around the replication fork
to prevent rewinding of the DNA.
 Topoisomerase works at the region ahead of the replication fork to
prevent supercoiling.
 Primase synthesizes RNA primers complementary to the DNA strand.
 DNA polymerase III extends the primers, adding on to the 3' end, to
make the bulk of the new DNA.
 RNA primers are removed and replaced with DNA by DNA polymerase
I.
 The gaps between DNA fragments are sealed by DNA ligase.

DNA replication in eukaryotes

The basics of DNA replication are similar between bacteria and eukaryotes such
as humans, but there are also some differences:

 Eukaryotes usually have multiple linear chromosomes, each with multiple

origins of replication. Humans can have up to 100,100,100,
comma000000000 origins of replication^55start superscript, 5, end
superscript!
 Most of the E. coli enzymes have counterparts in eukaryotic DNA
replication, but a single enzyme in E. coli may be represented by multiple
enzymes in eukaryotes. For instance, there are five human DNA
polymerases with important roles in replication^55start superscript, 5, end
superscript.
 Most eukaryotic chromosomes are linear. Because of the way the lagging
strand is made, some DNA is lost from the ends of linear chromosomes
(the telomeres) in each round of replication.

TRANSCRIPTION

Overview of transcription: In transcription, the DNA sequence of a gene is

transcribed (copied out) to make an RNA molecule.

Key points:

 Transcription is the first step in gene expression. It involves copying a

gene's DNA sequence to make an RNA molecule.
  Transcription is performed by enzymes called RNA polymerases, which
link nucleotides to form an RNA strand (using a DNA strand as a
template).
 Transcription has three stages: initiation, elongation, and termination.
 In eukaryotes, RNA molecules must be processed after transcription: they
are spliced and have a 5' cap and poly-A tail put on their ends.
 Transcription is controlled separately for each gene in your genome.

Overview of transcription: In biology, transcription is the process of copying

out the DNA sequence of a gene in the similar alphabet of RNA. Transcription is
the first step in gene expression, in which information from a gene is used to
construct a functional product such as a protein. The goal of transcription is to
make a RNA copy of a gene's DNA sequence. For a protein-coding gene, the
RNA copy, or transcript, carries the information needed to build a polypeptide
(protein or protein subunit). Eukaryotic transcripts need to go through some
processing steps before translation into proteins.

In transcription, a region of DNA opens up. One strand, the template strand,
serves as a template for synthesis of a complementary RNA transcript. The other
strand, the coding strand, is identical to the RNA transcript in sequence, except
that it has uracil (U) bases in place of thymine (T) bases.

Example:

Coding strand: 5'-ATGATCTCGTAA-3' Template strand: 3'-

TACTAGAGCATT-5' RNA transcript: 5'-AUGAUCUCGUAA-3'
For a protein-coding gene, the RNA transcript contains the information needed to
synthesize a polypeptide (protein or protein subunit) with a particular amino acid
sequence. In this case:

RNA transcript (acting as messenger RNA): 5'-AUGAUCUCGUAA-3'

Polypeptide: Met-Ile-Ser-STOP

RNA polymerase: The main enzyme involved in transcription is RNA

polymerase, which uses a single-stranded DNA template to synthesize a
complementary strand of RNA. Specifically, RNA polymerase builds an RNA
strand in the 5' to 3' direction, adding each new nucleotide to the 3' end of the
strand.

RNA polymerase synthesizes an RNA strand complementary to a template DNA

strand. It synthesizes the RNA strand in the 5' to 3' direction, while reading the
template DNA strand in the 3' to 5' direction. The template DNA strand and RNA
strand are antiparallel.

RNA transcript: 5'-UGGUAGU...-3' (dots indicate where nucleotides are still

being added at 3' end) DNA template: 3'-ACCATCAGTC-5'

Stages of transcription: Transcription of a gene takes place in three stages:

initiation, elongation, and termination. Here, we will briefly see how these steps
happen in bacteria. You can learn more about the details of each stage (and about
how eukaryotic transcription is different) in the stages of transcription article.

1. Initiation. RNA polymerase binds to a sequence of DNA called

the promoter, found near the beginning of a gene. Each gene (or group of
co-transcribed genes, in bacteria) has its own promoter. Once bound, RNA
 polymerase separates the DNA strands, providing the single-stranded
template needed for transcription.

The promoter region comes before (and slightly overlaps with) the transcribed
region whose transcription it specifies. It contains recognition sites for RNA
polymerase or its helper proteins to bind to. The DNA opens up in the promoter
region so that RNA polymerase can begin transcription.

2. Elongation. One strand of DNA, the template strand, acts as a template

for RNA polymerase. As it "reads" this template one base at a time, the
polymerase builds an RNA molecule out of complementary nucleotides,
making a chain that grows from 5' to 3'. The RNA transcript carries the
same information as the non-template (coding) strand of DNA, but it
contains the base uracil (U) instead of thymine (T).
RNA polymerase synthesizes an RNA transcript complementary to the DNA
template strand in the 5' to 3' direction. It moves forward along the template
strand in the 3' to 5' direction, opening the DNA double helix as it goes. The
synthesized RNA only remains bound to the template strand for a short while,
then exits the polymerase as a dangling string, allowing the DNA to close back up
and form a double helix.

In this example, the sequences of the coding strand, template strand, and RNA
transcript are:

Coding strand: 5' - ATGATCTCGTAA-3'

Template strand: 3'-TACTAGAGCATT-5'

RNA: 5'-AUGAUC...-3' (the dots indicate where nucleotides are still being added
to the RNA strand at its 3' end)

Termination. Sequences called terminators signal that the RNA transcript is

complete. Once they are transcribed, they cause the transcript to be released from
the RNA polymerase. An example of a termination mechanism involving
formation of a hairpin in the RNA is shown below.
The terminator DNA encodes a region of RNA that forms a hairpin structure
followed by a string of U nucleotides. The hairpin structure in the transcript
causes the RNA polymerase to stall. The U nucleotides that come after the hairpin
form weak bonds with the A nucleotides of the DNA template, allowing the
transcript to separate from the template and ending transcription.

Eukaryotic RNA modifications: In bacteria, RNA transcripts can act

as messenger RNAs (mRNAs) right away. In eukaryotes, the transcript of a
protein-coding gene is called a pre-mRNA and must go through extra processing
before it can direct translation.

 Eukaryotic pre-mRNAs must have their ends modified, by addition of a 5'

cap (at the beginning) and 3' poly-A tail (at the end).
 Many eukaryotic pre-mRNAs undergo splicing. In this process, parts of
the pre-mRNA (called introns) are chopped out, and the remaining pieces
(called exons) are stuck back together.

Top of image: Diagram of a pre-mRNA with a 5' cap and 3' poly-A tail. The 5'
cap is on the 5' end of the pre-mRNA and is a modified G nucleotide. The poly-A
tail is on the 3' end of the pre-mRNA and consists of a long string of A
nucleotides (only a few of which are shown).

The pre-mRNA still contains both exons and introns. Along the length of the
mRNA, there is an alternating pattern of exons and introns: Exon 1 - Intron 1 -
Exon 2 - Intron 2 - Exon 3. Each consists of a stretch of RNA nucleotides.

During splicing, the introns are removed from the pre-mRNA, and the exons are
stuck together to form a mature mRNA.

Bottom of image: Mature mRNA that does not contain the intron sequences (Exon
1 - Exon 2 - Exon 3 only).

End modifications increase the stability of the mRNA, while splicing gives the
mRNA its correct sequence. (If the introns are not removed, they'll be translated
along with the exons, producing a "gibberish" polypeptide.)

To learn more about pre-mRNA modifications in eukaryotes, check out the article
on pre-mRNA processing.

TRANSLATION

Overview of translation: How the nucleotide sequence of an mRNA is translated

into the amino acid sequence of a polypeptide (protein).

The genetic code: During translation, a cell “reads” the information in a

messenger RNA (mRNA) and uses it to build a protein. Actually, to be a little
more techical, an mRNA doesn’t always encode—provide instructions for—a
whole protein. Instead, what we can confidently say is that it always encodes
a polypeptide, or chain of amino acids.
Genetic code table. Each three-letter sequence of mRNA nucleotides corresponds
to a specific amino acid, or to a stop codon. UGA, UAA, and UAG are stop
codons. AUG is the codon for methionine, and is also the start codon.

In an mRNA, the instructions for building a polypeptide are RNA nucleotides

(As, Us, Cs, and Gs) read in groups of three. These groups of three are
called codons.

There are 616161 codons for amino acids, and each of them is "read" to specify a
certain amino acid out of the 202020 commonly found in proteins. One codon,
AUG, specifies the amino acid methionine and also acts as a start codon to signal
the start of protein construction.

There are three more codons that do not specify amino acids. These stop codons,
UAA, UAG, and UGA, tell the cell when a polypeptide is complete. All together,
this collection of codon-amino acid relationships is called the genetic code,
because it lets cells “decode” an mRNA into a chain of amino acids.
Each mRNA contains a series of codons (nucleotide triplets) that each specifies an
amino acid. The correspondence between mRNA codons and amino acids is
called the genetic code.

Hh35' AUG - Methionine ACG - Threonine GAG - Glutamate CUU - Leucine

CGG - Arginine AGC - Serine UAG - Stop 3'

Overview of translation

How is an mRNA "read" to make a polypeptide? Two types of molecules with

key roles in translation are tRNAs and ribosomes.

Transfer RNAs, or tRNAs, are molecular "bridges" that connect mRNA codons
to the amino acids they encode. One end of each tRNA has a sequence of three
nucleotides called an anticodon, which can bind to specific mRNA codons. The
other end of the tRNA carries the amino acid specified by the codons.

There are many different types of tRNAs. Each type reads one or a few codons
and brings the right amino acid matching those codons.

Ribosomes are composed of a small and large subunit and have three sites where
tRNAs can bind to an mRNA (the A, P, and E sites). Each tRNA carries’ a
specific amino acid and binds to an mRNA codon that is complementary to its
anticodon.

Ribosomes are the structures where polypeptides (proteins) are built. They are
made up of protein and RNA (ribosomal RNA, or rRNA). Each ribosome has
two subunits, a large one and a small one, which come together around an
mRNA—kind of like the two halves of a hamburger bun coming together around
the patty.

The ribosome provides a set of handy slots where tRNAs can find their matching
codons on the mRNA template and deliver their amino acids. These slots are
called the A, P, and E sites. Not only that, but the ribosome also acts as an
enzyme, catalyzing the chemical reaction that links amino acids together to make
a chain.

Want to learn more about the structure and function of tRNAs and ribosomes?
Check out the tRNA and ribosomes article!

Steps of translation

Your cells are making new proteins every second of the day. And each of those
proteins must contain the right set of amino acids, linked together in just the right
order. That may sound like a challenging task, but luckily, your cells (along with
those of other animals, plants, and bacteria) are up to the job.

To see how cells make proteins, let's divide translation into three stages: initiation
(starting off), elongation (adding on to the protein chain), and termination
(finishing up).

Getting started: Initiation

In initiation, the ribosome assembles around the mRNA to be read and the first
tRNA (carrying the amino acid methionine, which matches the start codon,
AUG). This setup, called the initiation complex, is needed in order for translation
to get started.

Extending the chain: Elongation

Elongation is the stage where the amino acid chain gets longer. In elongation, the
mRNA is read one codon at a time, and the amino acid matching each codon is
added to a growing protein chain.

Each time a new codon is exposed:

 A matching tRNA binds to the codon

 The existing amino acid chain (polypeptide) is linked onto the amino acid
of the tRNA via a chemical reaction
  The mRNA is shifted one codon over in the ribosome, exposing a new
codon for reading

Elongation has three stages:

1) The anticodon of an incoming tRNA pairs with the mRNA codon exposed in
the A site.

2) A peptide bond is formed between the new amino acid (in the A site) and the
previously-added amino acid (in the P site), transferring the polypeptide from the
P site to the A site.

3) The ribosome moves one codon down on the mRNA. The tRNA in the A site
(carrying the polypeptide) shifts to the P site. The tRNA in the P site shifts to the
E site and exits the ribosome.

During elongation, tRNAs move through the A, P, and E sites of the ribosome, as
shown above. This process repeats many times as new codons are read and new
amino acids are added to the chain.
Termination is the stage in which the finished polypeptide chain is released. It
begins when a stop codon (UAG, UAA, or UGA) enters the ribosome, triggering
a series of events that separate the chain from its tRNA and allow it to drift out of
the ribosome.

After termination, the polypeptide may still need to fold into the right 3D shape,
undergo processing (such as the removal of amino acids), get shipped to the right
place in the cell, or combine with other polypeptides before it can do its job as a
functional protein

PROTEIN

Proteins are ubiquitous organic nitrogenous components of high molecular weight occurring in
all living organisms – plants, animals and bacteria. These macromolecules contain carbon,
hydrogen, oxygen, nitrogen, frequently sulphur and sometimes phosphorus and iron. These are
the major building material of cells and take part in controlling different activities of living
systems. Proteins are made-up of amino acids that are covalently linked together by peptide
bonds (–CO–NH–) formed by the condensation of an amino group (-NH2) of one amino acid
and carboxyl group (-COOH) of another (as shown in the figure below).

Figure: Amino group (–NH2) of one amino acid and carboxyl group (–COOH) of another
amino acid join to form a peptide bond.

There are some 20 different kinds of amino acids arranged in a definite sequences and number in
different protein molecules. Simple proteins consist of only amino acids, whereas complex
proteins have other substances like lipids and carbohydrates also.
Proteins are classified into seven types on the basis of their biological functions.

S.
Class Example Functions
No.
Help in catalyzing
i) Enzymes Ribonuclease, Trypsin chemical reactions in
living cells.
Haemoglobin, Serum Involved in the transport
ii) Transport proteins albumin, Myoglobin, of molecules and ions
Lipoprotein across the membranes.
Gliadin (wheat), Provide the essential
Nutrient and
iii) Ovalbumin (egg), Casein components by storing
storage proteins
(milk), Ferritin them in the body.
Coordinate movements
Contractile or Actin, Myosin, Tubulin,
iv) such as movements of
motile proteins Dynein
chromosomes in mitosis.
Keratin, Fibroin,
Essential components of
v) Structural proteins Collagen, Elastin,
various cells and tissues.
Proteoglycans
Antibodies, Fibrinogen, Help in protection
Thrombin, Dotulinus against harmful agents
vi) Defense proteins
toxin, Diphtheria toxin, such as bacteria and
Snake venoms Ricin virus.
Insulin, Growth
Regulatory Control of growth and
vii) hormone, Corticotropin,
proteins differentiation.
Repressors

Table: Classification of proteins according to biological functions.

The polypeptides which form proteins after being synthesized on ribosomes in

linear chains are biologically inactive. But within a few seconds after their
synthesis, the folding of polypeptide chain occurs in specific forms to give
functionally active proteins which have many levels of organization. These levels
are expressed as primary, secondary, tertiary and quaternary structures

Primary structure: The simplest level of protein structure, primary structure,

is simply the sequence of amino acids in a polypeptide chain. For example, the
hormone insulin has two polypeptide chains, A and B, shown in diagram below.
(The insulin molecule shown here is cow insulin, although its structure is similar
to that of human insulin.) Each chain has its own set of amino acids, assembled in
a particular order. For instance, the sequence of the A chain starts with glycine at
the N-terminus and ends with asparagine at the C-terminus, and is different from
the sequence of the B chain.
Image of insulin. Insulin consists of an A chain and a B chain. They are connected
to one another by disulfide bonds (sulfur-sulfur bonds between cysteines). The A
chain also contains an internal disulfide bond. The amino acids that make up each
chain of insulin are represented as connected circles, each with the three-letter
abbreviation of the amino acid's name.

The sequence of a protein is determined by the DNA of the gene that encodes the
protein (or that encodes a portion of the protein, for multi-subunit proteins). A
change in the gene's DNA sequence may lead to a change in the amino acid
sequence of the protein. Even changing just one amino acid in a protein’s
sequence can affect the protein’s overall structure and function.

Hemoglobin molecule is made up of two α chains and two β chains, each

consisting of about 150 amino acids, for a total of about 600 amino acids in the
whole protein. The difference between a normal hemoglobin molecule and a
sickle cell molecule is just 2 amino acids out of the approximately 600.

Secondary structure: The next level of protein structure, secondary structure,

refers to local folded structures that form within a polypeptide due to interactions
between atoms of the backbone. (The backbone just refers to the polypeptide
chain apart from the R groups – so all we mean here is that secondary structure
does not involve R group atoms.) The most common types of secondary structures
are the α helix and the β pleated sheet. Both structures are held in shape by
hydrogen bonds, which form between the carbonyl O of one amino acid and the
amino H of another.
Images showing hydrogen bonding patterns in beta pleated sheets and alpha
helices.

In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the
amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl
of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This
pattern of bonding pulls the polypeptide chain into a helical structure that
resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids.
The R groups of the amino acids stick outward from the α helix, where they are
free to interact^33start superscript, 3, end superscript.

In a β pleated sheet, two or more segments of a polypeptide chain line up next to

each other, forming a sheet-like structure held together by hydrogen bonds. The
hydrogen bonds form between carbonyl and amino groups of backbone, while the
R groups extend above and below the plane of the sheet^33start superscript, 3,
end superscript. The strands of a β pleated sheet may be parallel, pointing in the
same direction (meaning that their N- and C-termini match up), or antiparallel,
pointing in opposite directions (meaning that the N-terminus of one strand is
positioned next to the C-terminus of the other).

Certain amino acids are more or less likely to be found in α-helices or β pleated
sheets. For instance, the amino acid proline is sometimes called a “helix breaker”
because its unusual R group (which bonds to the amino group to form a ring)
creates a bend in the chain and is not compatible with helix formation^44start
superscript, 4, end superscript. Proline is typically found in bends, unstructured
regions between secondary structures. Similarly, amino acids such as tryptophan,
tyrosine, and phenylalanine, which have large ring structures in their R groups,
are often found in β pleated sheets, perhaps because the β pleated sheet structure
provides plenty of space for the side chains^44start superscript, 4, end superscript.

Many proteins contain both α helices and β pleated sheets, though some contain
just one type of secondary structure (or do not form either type).

Tertiary structure: The overall three-dimensional structure of a polypeptide is

called its tertiary structure. The tertiary structure is primarily due to interactions
between the R groups of the amino acids that make up the protein.

R group interactions that contribute to tertiary structure include hydrogen

bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces
– basically, the whole gamut of non-covalent bonds. For example, R groups with
like charges repel one another, while those with opposite charges can form an
ionic bond. Similarly, polar R groups can form hydrogen bonds and other dipole-
dipole interactions. Also important to tertiary structure are hydrophobic
interactions, in which amino acids with nonpolar, hydrophobic R groups cluster
together on the inside of the protein, leaving hydrophilic amino acids on the
outside to interact with surrounding water molecules.

Finally, there’s one special type of covalent bond that can contribute to tertiary
structure: the disulfide bond. Disulfide bonds, covalent linkages between the
sulfur-containing side chains of cysteines, are much stronger than the other types
of bonds that contribute to tertiary structure. They act like molecular "safety
pins," keeping parts of the polypeptide firmly attached to one another.
Image of a hypothetical polypeptide chain, depicting different types of side chain
interactions that can contribute to tertiary structure. These include hydrophobic
interactions, ionic bonds, hydrogen bonds, and disulfide bridge formation.

Quaternary structure: Many proteins are made up of a single polypeptide chain

and have only three levels of structure (the ones we’ve just discussed). However,
some proteins are made up of multiple polypeptide chains, also known as
subunits. When these subunits come together, they give the protein
its quaternary structure.

We’ve already encountered one example of a protein with quaternary structure:

hemoglobin. As mentioned earlier, hemoglobin carries oxygen in the blood and is
made up of four subunits, two each of the α and β types. Another example is DNA
polymerase, an enzyme that synthesizes new strands of DNA and is composed of
ten subunits^55start superscript, 5, end superscript.

In general, the same types of interactions that contribute to tertiary structure

(mostly weak interactions, such as hydrogen bonding and London dispersion
forces) also hold the subunits together to give quaternary structure.
 CELL DIVISION

In higher eukaryotes life starts with the formation of a fertilized egg cell of approximately 100
m in diameter. Our bodies are made up of billions and trillions of cells with a greater mass. Cell
division is a process by which cells produce new cells. Cell division differs
in prokaryotes (bacteria) and eukaryotes (protists, fungi, plants, & animals). As more and more
cells are added as a result of successive divisions the developing embryos undergo a process of
differentiation and adult structures are organized. During this period, the rate of cell division and
the number of dividing cells change so that there are fewer cells dividing in a fully formed
organism than during the course of development. In an adult organism there are tissues where no
cells are dividing and are mitotically inactive, while there are other tissues wherein new cells are
continuously being made while old cells are dying. Some tissues must be repaired often such as
the lining of gut, white blood cells, and skin cells with a short lifespan. There are also some
tissues like bone marrow or germinal tissues or meristematic regions in plants where continuous
cell division takes place. Some differentiated cell types divide rarely such as red blood cells,
skeletal muscle cells and nerve cells. The mammal nerve cells and muscle cells do not divide at
all after birth. The cells divide by two specific methods known as ‘mitosis’ and ‘meiosis’ which
we will study in details.

Reasons for Cell Division:

 Cell growth
 Repair & replacement of damaged cell parts or old cells.
 Reproduction of the species

Keeping Cells Identical by Copying DNA:

 Since the instructions for making cell parts are encoded in the DNA, each new cell must
get a complete set of the DNA molecules.
 This requires that the DNA be copied (replicated, duplicated) before cell division.
 Each new daughter cell will then have an identical copy of the DNA.

Chromosomes & their Structure:

 The plans for making cells are coded in DNA

  DNA, deoxyribose nucleic acid, is a long thin molecule that stores genetic information
 DNA in a human cell is estimated to consist of six billion pairs of nucleotides
 DNA is organized into giant molecules called chromosomes
 Chromosomes are made of protein & a long, single, tightly-coiled DNA molecule visible
only when the cell divides

Figure:

 When a cell is not dividing the DNA is less visible & is called chromatin
 DNA in eukaryotic cells wraps tightly around proteins called histones to help pack the
DNA during cell division

Figure: Eukaryotic histone complex - DNA wrapped around twice

  Non-histone proteins help control the activity of specific DNA genes
 Kinetochore proteins bind to centromere and attach chromosome to the spindle in mitosis
 Centromeres hold duplicated chromosomes together before they are separated in mitosis
 Telomeres are the ends of chromosomes which are important in cell aging
 When DNA makes copies of itself before cell division, each half of the chromosome is
called a sister chromatid held together by a centromere.

 DNA of prokaryotes (bacteria) is one, circular chromosome attached to the inside of the
cell membrane.

Chromosome Numbers:

 Humans somatic or body cells have 23 pairs of chromosomes or 46

chromosomes (diploid or 2n number)
 The two chromatids of a chromosome pair are called homologues (have genes for the
same trait at the same location)

Homologs

 Human reproductive cells or gametes (sperms & eggs) have one set or 23
chromosomes (haploid or ‘n’ number)
 Every organism has a specific chromosome number

 Fertilization, joining of the egg & sperm, restores the diploid chromosome number in the
zygote (fertilized egg cell)
 Sex chromosomes, either X or Y, determine the sex of the organism.
 Two X chromosomes, XX, will be female (♀) and XY will be male (♂).
 All other chromosomes, except X & Y, are called autosomes
  Chromosomes from a cell may be arranged in pairs by size starting with the longest pair
and ending with the sex chromosomes to make a karyotype
 A human karyotype has 22 pairs of autosomes and 1 pair of sex chromosomes (23 total)

Genes:

 A section of DNA which codes for a protein is called a gene

 Each gene codes for one protein
 Humans have approximately 50,000 genes or 2000 per chromosome
 About 95% of the DNA in chromosome is "junk" that does not code for any proteins

Cell Cycle:

A growing cell undergoes through phases or a cell cycle during its life before dividing to form
new cells. The cell cycle represents a complex series of stage by which cellular material is
divided equally between daughter cells.

Figure: The Cell Cycle. Time intervals are relative; actual time varies with the cell type and
species.

Cell division is only the final phase. Before, the cell divides by mitosis, its main molecular
components have already been duplicated. In this respect, cell division can be considered as the
final separation of the already duplicated molecular units. The cell cycle includes two main
periods:
 a) Interphase: “Resting” stage of the cell and cell makes material needed for the cell
growth. It is the period of non-apparent division; and
b) Cell division: The period of division. Includes mitosis (nuclear division) and cytokinesis
(division of the cytoplasm).

Cell Division – Prokaryotic and Eukaryotic

 Cell division in Prokaryotes

 Prokaryotes such as bacteria do not have a nucleus

 Prokaryotes divide into two identical new cells by the process of binary fission
 Binary fission is an asexual method of reproduction
 In binary fission, the chromosome, attached to cell membrane, makes a copy of itself and
the cell grows to about twice its normal size
 Next, a cell wall forms between the chromosomes & the parent cell splits into 2
new identical daughter cells (clones)
Figure: Showing bacterial cell dividing by binary fission.

CELL DIVISION IN EUKARYOTES

In eukaryotes, division generally takes place by mitosis or meiosis.

Eukaryotes have a nucleus in their each cell containing the same information/
directions as well as the membrane-bound organelles which must be copied
exactly so the two new cells formed from division will be exactly alike.
The original parent cell & 2 new daughter cells must have identical chromosomes.
DNA is copied in the S phase of the cell cycle & organelles, found in the
cytoplasm, are copied in the growth phases. Both the nucleus (mitosis) and
the cytoplasm (cytokinesis) must be divided during cell division in eukaryotes.

Mitosis Stages

Mitosis is the process of cell division that forms two genetically identical nuclei
from on parent cell nucleus. It is used for:

 Asexual reproduction (e.g. Paramecium)

 Growth (increasing cell number)
 Repair and Maintenance (replace damaged cells with identical
replacements)

Although we traditionally break down mitosis into a series of stages and sub-
stages, it is actually a continuous process. In the micrographs opposite, you can
see that mitosis is not necessarily synchronised and looks much messier than the
clean, idealised textbook diagrams!

Interphase - Not strictly a stage of mitosis, this is where the cell prepares to
divide by growing, storing energy, replicating organelles and replicating DNA

Prophase - The chromosomes supercoil and become visible under a light

microscope. The chromosomes assume their classic 'X' shape - two
sister chromatids joined in the middle at the centromere. Other key events are:

 Nuclear Envelope breaks down;

 Centriole divides in two, travels to opposite poles of the cell to form the
spindle.

Metaphase - An easy stage to identify, Metaphase is characterized by the

chromosomes lining up, single file, along the middle (the equator) of the cell. At
this point, each chromosome becomes attached to the spindle at its centromere.

Anaphase - Another easily recognizable stage! Anaphase sees the chromosomes

split at the centromere, separating the sister chromatids:

 The sister chromatids are pulled apart to opposite poles of the cell
 At this point, each chromatid becomes an individual chromosome -
identical to the original parent chromosome
 Spindle fibres shorten, pulling each chromatid by the centromere - this
causes the chromatids to look like Vs

Telophase - a simple stage to recognize - you will see two nuclei starting to form
in early telophase; in late telophase you will no longer be able to see the
chromosomes, just two complete nuclei at opposite ends of the cell.
 Figure: The stages of mitosis and cytokinesis in an animal cell

Sexual Reproduction – Meiosis

 Reduces the number of chromosomes in new cells to half the number in the original cell
 New cells have a single copy of chromosomes (23 total) but are not identical to each
other or the original parent cell
 Used for making gametes (sperm and eggs) with the haploid or n number
 In meiosis, cells divide twice after a single DNA duplication
 Meiosis I separates homologs & the Meiosis II separates sister chromatids
 Meiosis I stages are Prophase I, Metaphase I, Anaphase I, & Telophase I
 Meiosis II stages are Prophase II, Metaphase II, Anaphase II, & Telophase II
 Produces 4 haploid cells or gametes
 When a sperm fertilizes an egg to form a zygote, the diploid number of chromosomes is
restored (23 + 23 = 46)
 Egg cells or ova (ovum, singular) are larger, non-motile cells
 Gametogenesis is meiosis producing eggs & occurs in the female's ovaries
 Meiosis I:

1) The cell that undergoes Meiosis I is a primary spermatocyte or oocyte

2) Prophase I:
o Chromosomes coil tightly & are visible
o Nuclear membrane & nucleolus disintegrate
o Spindle forms
o Synapsis (joining) of homologous chromosomes occurs making tetrads
o Kinetochore fiber forms on each chromosome
o Chromosomes in tetrad exchange fragments by a process called crossing over

3) Metaphase I:
o Tetrads become aligned in the center of the cell attached to spindle fibers
4) Anaphase I:
o Homologous chromosomes separate
5) Telophase I:
o May not occur in all species
o Cytokinesis occurs producing 2 cells
o In females, 2nd cell in females is called the 1st Polar Body
o 1st Polar Body dies due to uneven splitting of the cytoplasm
 Prophase II:
o Cells called Secondary Spermatocytes or oocytes
o DNA is not copied before cell divides
o Chromatids attach to spindle fiber
 Metaphase II:
o Chromosomes become aligned in the center of the cell attached to spindle fibers
 Anaphase II:
o Sister chromatids separate randomly
o Called independent assortment
 Telophase I:
o Cytokinesis occurs producing 4 cells in males called spermatids
o Spermatids mature & form flagellum to become sperm
o Cytokinesis in females produces a 2nd Polar Body that dies and an ootid
o Ootids mature to become ovum or egg
Asexual & Sexual reproduction:

 Evolution is the slow process of change in living populations over time

 Variations are differences that occur due to crossing-over among members of a sexually
reproducing population
 Variations are important to the survival of individuals in a population (some must survive
to reproduce)
 Asexually reproducing organisms rarely show variations because the organisms have
identical genes

 Comparison of Mitosis and Meiosis

S. Mitosis Meiosis
No.
1. The cell divides only once. There are two cell divisions, the first
and the second meiotic divisions.
2. Mitosis takes place in the somatic Meiosis takes place in the germ
cells of the body. cells.
3. Occurs in both sexually as well as Occurs only in sexually reproducing
asexually reproducing organisms. organisms.
4. DNA replication takes place DNA replication takes place during
during interphase I. interphase I but not interphase II.
5. The DNA replicates once for one The DNA replicates once for two
cell division. cell divisions.
6. The duration of prophase is short, Prophase is comparatively longer
usually of a few hours. and may take days.
7. Prophase is comparatively simple Prophase is complicated and is
divided into leptotene, zygotene,
pachytene, diplotene and diakinesis.
8. The cell divides only once and the There are two cell divisions but the
chromosomes also divide only chromosomes divide only once.
once.
9. There is no synapsis. Synapsis of homologous
chromosomes takes place during
prophase.
10. The two chromatids of a Chromatids of two homologous
chromosome do not exchange chromosomes exchange segments
segments during prophase. during crossing-over.
11. Each chromosome consists of two The two homologous chromosomes
chromatids united by a form bivalents or tetrads. Each
centromere. bivalent has four chromatids and
two centromeres.
12. The arms of the prophase The arms of the chromatids are
chromatids are close to one separated widely in prophase II.
another.
13. Chromosomes are already When prophase I commences the
duplicated at the beginning of chromosomes appear single
prophase. (although DNA replication has taken
place in interphase I).
14. In the metaphasic plate all the In metaphase I the centromeres are
centromeres line up in the same lined up in two planes which are
plane. parallel to one other.
15. The metaphasic plate is made up The metaphasic plate is made up of
of chromosome pairs. paired chromosome pairs.
16. Division of centromeres takes There is no centromeric division
place during anaphase. during anaphase I. Centromeres
divide only during anaphase II.
17. The chromosomes separate Short chromosomes separate early;
simultaneously during anaphase. separation of long chromosomes is
delayed.
18. Spindle fibres disappear Spindle fibres do not disappear
completely in telophase. completely during telophase I.
19. Nucleoli reappear at telophase. Nucleoli do not reappear in
telophase I.
 20. The chromosome number remains The chromosomal number is
constant at the end of mitosis. reduced from the diploid to the
haploid.
21. The genetic constitution of the The genetic constitution of the
daughter cells is identical to that of daughter cells differs from that of
the parent cells. the parent cell. The chromosomes of
daughter cells usually contain a
mixture of maternal and paternal
genes.

Cellular differentiation is the process where a cell changes from one cell type to
another. Usually, the cell changes to a more specialized type. Differentiation
occurs numerous times during the development of a multicellular organism as it
changes from a simple zygote to a complex system of tissues and cell types.
Differentiation continues in adulthood as adult stem cells divide and create fully
differentiated daughter cells during tissue repair and during normal cell turnover.
Some differentiation occurs in response to antigen exposure. Differentiation
dramatically changes a cell's size, shape, membrane potential, metabolic activity,
and responsiveness to signals. These changes are largely due to highly controlled
modifications in gene expression and are the study of epigenetics. With a few
exceptions, cellular differentiation almost never involves a change in
the DNA sequence itself. Thus, different cells can have very different physical
characteristics despite having the same genome.
 Unit-II

Molecular aspects of life

Gene regulation, Operon, Lac operon, Trp operon.

Aging, apoptosis, stem cell Biology, Degeneracy in biological system and Tissue engineering.

Biosensors -Chemoreceptors, hot and cold receptors, baro receptors, sensors for smell, sound,
vision, osmolality and taste.

Immunology- Human immune system, Types of Immunity: innate immunity, adaptive

immunity, self and non-self, antigen-antibody reactions.

GENE REGULATION
Gene regulation refers to the mechanisms that act to induce or repress the expression of a gene.

The operon model of prokaryotic gene regulation was proposed by Fancois Jacob and Jacques
Monod. Groups of genes coding for related proteins are arranged in units known as operons. An
operon consists of an operator, promoter, regulator, and structural genes.
The lac operon: Regulation of genes for lactose utilization. lac repressor, catabolite activator
protein, and cAMP.
Key points:

 The lac operon of E. coli contains genes involved in lactose metabolism. It's expressed
only when lactose is present and glucose is absent.
 Two regulators turn the operon "on" and "off" in response to lactose and glucose levels:
the lac repressor and catabolite activator protein (CAP).
 The lac repressor acts as a lactose sensor. It normally blocks transcription of the operon,
but stops acting as a repressor when lactose is present. The lac repressor senses lactose
indirectly, through its isomer allolactose.
 Catabolite activator protein (CAP) acts as a glucose sensor. It activates transcription of
the operon, but only when glucose levels are low. CAP senses glucose indirectly, through
the "hunger signal" molecule cAMP.

Introduction

Lactose: it's what's for dinner! While that may not sound delicious to us (lactose is the main
sugar in milk, and you probably don't want to eat it plain), lactose can be an excellent meal for E.
coli bacteria. However, they'll only gobble up lactose when other, better sugars – like glucose –
are unavailable.

With that for context, what exactly is the lac operon? The lac operon is an operon, or group of
genes with a single promoter (transcribed as a single mRNA). The genes in the operon encode
proteins that allow the bacteria to use lactose as an energy source.

What makes the lac operon turn on?

E. coli bacteria can break down lactose, but it's not their favorite fuel. If glucose is around, they
would much rather use that. Glucose requires fewer steps and less energy to break down than
lactose. However, if lactose is the only sugar available, the E. coli will go right ahead and use it
as an energy source.

To use lactose, the bacteria must express the lac operon genes, which encode key enzymes for
lactose uptake and metabolism. To be as efficient as possible, E. coli should express
the lac operon only when two conditions are met:

 Lactose is available, and

 Glucose is not available

How are levels of lactose and glucose detected, and how do changes in levels affect lac operon
transcription? Two regulatory proteins are involved:

 One, the lac repressor, acts as a lactose sensor.

 The other, catabolite activator protein (CAP), acts as a glucose sensor.

These proteins bind to the DNA of the lac operon and regulate its transcription based on lactose
and glucose levels. Let's take a look at how this works.
Structure of the lac operon

The lac operon contains three genes: lacZ, lacY, and lacA. These genes are transcribed as a
single mRNA, under control of one promoter.

Genes in the lac operon specify proteins that help the cell utilize lactose. lacZ encodes an
enzyme that splits lactose into monosaccharides (single-unit sugars) that can be fed into
glycolysis. Similarly, lacY encodes a membrane-embedded transporter that helps bring lactose
into the cell.

In addition to the three genes, the lac operon also contains a number of regulatory DNA
sequences. These are regions of DNA to which particular regulatory proteins can bind,
controlling transcription of the operon.

Structure of the lac operon. The DNA of the lac operon contains (in order from left to right):
CAP binding site, promoter (RNA polymerase binding site), operator (which overlaps with
promoter), lacZ gene, lacY gene, and lacA gene. The activator protein CAP, when bound to a
molecule called cAMP (discussed later), binds to the CAP binding site and promotes RNA
polymerase binding to the promoter. The lac repressor protein binds to the operator and blocks
RNA polymerase from binding to the promoter and transcribing the operon.

 The promoter is the binding site for RNA polymerase, the enzyme that performs
transcription.
 The operator is a negative regulatory site bound by the lac repressor protein. The
operator overlaps with the promoter, and when the lac repressor is bound, RNA
polymerase cannot bind to the promoter and start transcription.
 The CAP binding site is a positive regulatory site that is bound by catabolite activator
protein (CAP). When CAP is bound to this site, it promotes transcription by helping RNA
polymerase bind to the promoter.
Let's take a closer look at the lac repressor and CAP and their roles in regulation of
the lac operon.

The lac repressor

The lac repressor is a protein that represses (inhibits) transcription of the lac operon. It does this
by binding to the operator, which partially overlaps with the promoter. When bound,
the lac repressor gets in RNA polymerase's way and keeps it from transcribing the operon.

When lactose is not available, the lac repressor binds tightly to the operator, preventing
transcription by RNA polymerase. However, when lactose is present, the lac repressor loses its
ability to bind DNA. It floats off the operator, clearing the way for RNA polymerase to
transcribe the operon.

Upper panel: No lactose. When lactose is absent, the lac repressor binds tightly to the operator. It
gets in RNA polymerase's way, preventing transcription.
Lower panel: With lactose. Allolactose (rearranged lactose) binds to the lac repressor and makes
it let go of the operator. RNA polymerase can now transcribe the operon.

This change in the lac repressor is caused by the small molecule allolactose, an isomer
(rearranged version) of lactose. When lactose is available, some molecules will be converted to
allolactose inside the cell. Allolactose binds to the lac repressor and makes it change shape so it
can no longer bind DNA.

Allolactose is an example of an inducer, a small molecule that triggers expression of a gene or

operon. The lac operon is considered an inducible operon because it is usually turned off
(repressed), but can be turned on in the presence of the inducer allolactose.

The trp operon

How the trp repressor controls expression gene expression. Feedback inhibition & attenuation.

Key points:

 The trp operon, found in E. coli bacteria, is a group of genes that encode biosynthetic
enzymes for the amino acid tryptophan.
 The trp operon is expressed (turned "on") when tryptophan levels are low and repressed
(turned "off") when they are high.
 The trp operon is regulated by the trp repressor. When bound to tryptophan,
the trp repressor blocks expression of the operon.
 Tryptophan biosynthesis is also regulated by attenuation (a mechanism based on
coupling of transcription and translation).

What is the trp operon?

Bacteria such as Escherichia coli (a friendly inhabitant of our gut) need amino acids to survive—
because, like us, they need to build proteins. One of the amino acids they need is tryptophan.

If tryptophan is available in the environment, E. coli will take it up and use it to build proteins.
However, E. coli can also make their own tryptophan using enzymes that are encoded by five
genes. These five genes are located next to each other in what is called the trp operon.

If tryptophan is present in the environment, then E. coli bacteria don't need to synthesize it, so
transcription of the genes in the trp operon is switched "off." When tryptophan availability is
low, on the other hand, the operon is switched "on," the genes are transcribed, biosynthetic
enzymes are made, and more tryptophan is produced.

Structure of the trp operon

The trp operon includes five genes that encode enzymes needed for tryptophan biosynthesis,
along with a promoter (RNA polymerase binding site) and an operator (binding site for a
repressor protein). The genes of the trpoperon are transcribed as a single mRNA.

From left to right, the operon contains a promoter (where RNA polymerase binds), and within
the right end of the promoter, an operator (where a repressor binds). There are some additional
regulatory sequences, not labeled in this diagram, and then five coding sequences: trpE,
trpD, trpC, trpB, and trpA.

The operon is transcribed to produce a single mRNA that contains the coding sequences of all
five of the genes.

The coding sequences in the mRNA are translated separately, each one producing a protein.
These proteins are enzymes (or enzyme subunits) needed for tryptophan biosynthesis.

Turning the operon "on" and "off"

What does the operator do? This stretch of DNA is recognized by a regulatory protein known as
the trp repressor. When the repressor binds to the DNA of the operator, it keeps the operon from
being transcribed by physically getting in the way of RNA polymerase, the transcription enzyme.

The trp repressor does not always bind to DNA. Instead, it binds and blocks transcription only
when tryptophan is present. When tryptophan is around, it attaches to the repressor molecules
and changes their shape so they become active. A small molecule like trytophan, which switches
a repressor into its active state, is called a corepressor.

High tryptophan: The tryptophan binds to the trprepressor and causes it to change shape,
converting into its active (DNA-binding) form. The trprepressor with the bound tryptophan
attaches to the operator, blocking RNA polymerase from binding to the promoter and preventing
transcription of the operon.

When there is little tryptophan in the cell, on the other hand, the trp repressor is inactive
(because no tryptophan is available to bind to and activate it). It does not attach to the DNA or
block transcription, and this allows the trpoperon to be transcribed by RNA polymerase.

Low tryptophan: trp repressor is not bound to tryptophan (since there is no tryptophan) and is
thus in its inactive state (does not bind to the DNA of the operator). This allows RNA
polymerase to bind to the promoter and transcribe the operon.
In this system, the trp repressor acts as both a sensor and a switch. It senses whether tryptophan
is already present at high levels, and if so, it switches the operon to the "off" position, preventing
unnecessary biosynthetic enzymes from being made.

AGING

Ageing or aging (see spelling differences) is the process of becoming older. The term refers
especially to human beings, many animals, and fungi, whereas for example bacteria, perennial
plants and some simple animals are potentially biologically immortal. In the broader sense,
ageing can refer to single cells within an organism which have ceased dividing (cellular
senescence) or to the population of a species (population ageing).

APOPTOSIS

Apoptosis is a form of programmed cell death that occurs in multicellular organisms.

Biochemical events lead to characteristic cell changes (morphology) and death. These changes
include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, chromosomal
DNA fragmentation, and global[vague] mRNA decay. The average adult human loses between 50
and 70 billion cells each day due to apoptosis. For an average human child between the ages of 8
to 14 year old approximately 20 to 30 billion cells die per day.

In contrast to necrosis, which is a form of traumatic cell death that results from acute cellular
injury, apoptosis is a highly regulated and controlled process that confers advantages during an
organism's lifecycle. For example, the separation of fingers and toes in a developing
human embryo occurs because cells between the digits undergo apoptosis. Unlike necrosis,
apoptosis produces cell fragments called apoptotic bodies that phagocytic cells are able to engulf
and remove before the contents of the cell can spill out onto surrounding cells and cause damage
to them.

Because apoptosis cannot stop once it has begun, it is a highly regulated process. Apoptosis can
be initiated through one of two pathways. In the intrinsic pathway the cell kills itself because it
senses cell stress, while in the extrinsic pathway the cell kills itself because of signals from other
cells. Weak external signals may also activate the intrinsic pathway of apoptosis. Both pathways
induce cell death by activating caspases, which are proteases, or enzymes that degrade proteins.
The two pathways both activate initiator caspases, which then activate executioner caspases,
which then kill the cell by degrading proteins indiscriminately.

Research on apoptosis has increased substantially since the early 1990s. In addition to its
importance as a biological phenomenon, defective apoptotic processes have been implicated in a
wide variety of diseases. Excessive apoptosis causes atrophy, whereas an insufficient amount
results in uncontrolled cell proliferation, such as cancer. Some factors like Fas receptors and
caspases promote apoptosis, while some members of the Bcl-2 family of proteins inhibit
apoptosis.

STEM CELLS
In our body, we have a variety of fully differentiated cells. Most of them are specific for
individual organs. The cells for replacement of these losses come from the cells known as stem
cells found in most of the tissues/ organs of the body, although some organs like heart and
pancreas possess few or no stem cells. In different parts of an animal’s body, stem cells occur
along with other specialized cells, and are characterized by two special attributes, self-renewal
and differentiation. Actually in most cases, stem cells can regulate the production of either more
stem cells or more differentiated cells, whenever the equilibrium between stem cells and
differentiated cells, is disturbed due to injury or stress environment. Thus an important
component of stem cell concept is the requirement that the stem cell should be able to form more
stem cells, in addition to producing differentiated cells of one or more specific types. In view of
these attributes, stem cells can be used to provide for the replacement of those tissues that are
damaged by age, trauma, or disease.

 Origin and Functions of Stem Cells

Stem cells are generally totipotent/ pluripotent (capable of differentiating into many types of
cells). However, stem cells derived from specific tissues can also be unipotent and will
differentiate into the specific type required to replenish the cells of the tissue to which these stem
cells belong. For instance intestinal stem cells continuously regenerate the lining of the gut, skin
stem cells make skin and hematopoietic stem cells give rise to a range of blood cells. Stem cells
thus repair every day wear and tear in different organs of our body. However there are organs in
our body, which retains few or no stem cells in an adult, and therefore, the cells in these organs
can not renew the damaged tissues. Embryonic stem cells are, however, extraordinary, since
they are totipotent and can give rise to essentially all cell types in the body.

It has also been shown that even the adult central nervous system, which was believed for long
time not to contain any dividing cells, harbour stem cells, so that neurogenesis is now known to
continue throughout the life of a human being, at least in certain parts of the brain.

In contrast to the stem cells, which are generally pluripotent, the progenitor cells refer to
partially committed cells with more restricted potential than the stem cells. Similarly precursor
cells are those which ate further restricted in their potential and represents the penultimate stage
in the developmental pathway of any specialized cell type.

 Asymmetric division of stem cells

Stem cells undergo two types of divisions

(1) Symmetric cell division to expand their number during development, and

(2) Asymmetric cell division to self renew themselves and to give rise to more differentiated
progeny.
In asymmetric cell division for generating differentiated cells, two different strategies may be
followed.

In invariant asymmetric cell division, each stem cell gives rise to one daughter stem cell and
another daughter cell that undergoes differentiation (e.g. Drosophila ovary for production of
eggs).

In populational asymmetric cell division, on the other hand, a stem cell divides to give two
daughter cells which may be either both stem cells or committed progenitor cells, or else like
invariant asymmetric division, one daughter cell may be stem cell (self renewal) and the other a
progenitor (due to differentiation).
Figure: Two models of asymmetric division of stem cells. (a) In individual cell level
invariant asymmetry, stem cell divides to give a stem cell (S) and a progenitor cell (P); stem
cells phenotype depends on reciprocal signaling and progenitor cells differentiate in
response to extrinsic cues, (b) In population level asymmetry, a stem cell follows one of
three pathways producing either only stem cells or only progenitor cells or both;
extracellular matrix (ECM) or adjoining cells provide the extrinsic signals for
differentiation (thick arrows indicate signals).

At steady state, on an average, each stem cell division give rise to one stem cell and one
committed progenitor cell, but this asymmetry is achieved at the population level of individual
cell division. This populational asymmetry facilitates response to variable physiological needs,
as and when increased production of blood cells or epidermal cells is required due to injury.

Asymmetric cell division is believed to be achieved either by the unequal segregation of cell fate
determinants or by the influence of micro environment of the dividing cell. The structural
proteins, including the components of cytoskeleton help in unequal partitioning of cell fate
determinants. There are a numbers of factors, which make up the micro environment or niche
from the division of a cell.

 Types of Stem Cells

The stem cells can be broadly classified into

(1) Adult stem cells – derived from mature organs in the adult individual;

(2) Fetal stem cells – derived from the developing fetus; and

(3) Embryonic stem cells – derived from the totipotent cells of early embryo.

Depending upon the source of their origin, stem cells from the adult organs or the corresponding
parts of the fetus are further classified in the following types:

1) Hematopoietic stem cells (HSCs)

These are found in bone marrow and are a continuous source of progenitors of red cells,
platelets, monocytes, granulocytes and lymphocytes.

2) Mesenchymal stem cells or Marrow stromal cells (MSCs)

These are also isolated from bone marrow and, in culture can differentiate into osteoblasts,
chondrocytes, adipocytes, and even myoblasts.

3) Neural stem cells

These are isolated from the central nervous system (CNS) and have the potential to differentiate
into neurons, astrocytes and oligodendrocytes.

There are other kinds of stem cells, depending upon the source and some of the different types of
human stem cells that have already been isolated and cultured are listed below in the given table.

S.
Stem Cell Type Source Daughter Tissues
No.
1. Embryonic (ESC) Embryo or fetus All types
2. Hematopoietic (HSC) Adult bone marrow Blood cells; brain
3. Mesenchymal (MSC) Adult bone marrow Muscle; bone; cartilage
4. Neuronal (NSC) Fetal brain Neurons; glia; blood

Table: Different types of human stem cells isolated (upto March, 2001).

DEGENERACY IN BIOLOGICAL SYSTEM

Within biological systems, degeneracy occurs when structurally dissimilar

components/modules/pathways can perform similar functions (i.e. are effectively
interchangeable) under certain conditions, but perform distinct functions in other
conditions. Degeneracy is thus a relational property that requires comparing the behavior of two
or more components. In particular, if degeneracy is present in a pair of components then there
will exist conditions where the pair will appear functionally redundant but other conditions
where they will appear functionally distinct.

Note that this use of the term has practically no relevance to the questionably meaningful
concept of evolutionarily degenerate populations that have lost ancestral functions.

Biological Examples of degeneracy are found in the genetic code, when many
different nucleotide sequences encode the same polypeptide; in protein folding, when different
polypeptides fold to be structurally and functionally equivalent; in protein functions, when
overlapping binding functions and similar catalytic specificities are observed; in metabolism,
when multiple, parallel biosynthetic and catabolic pathways may coexist. More generally,
degeneracy is observed in proteins of every functional class (e.g. enzymatic, structural, or
regulatory), protein complex assemblies, ontogenesis, the nervous system, cell
signalling (crosstalk) and numerous other biological contexts reviewed in.

Contribution to robustness
Degeneracy contributes to the robustness of biological traits through several mechanisms.
Degenerate components compensate for one another under conditions where they are
functionally redundant, thus providing robustness against component or pathway failure.
Because degenerate components are somewhat different, they tend to harbor unique sensitivities
so that a targeted attack such as a specific inhibitor is less likely to present a risk to all
components at once. There are numerous biological examples where degeneracy contributes to
robustness in this way. For instance, gene families can encode for diverse proteins with many
distinctive roles yet sometimes these proteins can compensate for each other during lost or
suppressed gene expression, as seen in the developmental roles of the adhesins gene family
in Saccharomyces. Nutrients can be metabolized by distinct metabolic pathways that are
effectively interchangeable for certain metabolites even though the total effects of each pathway
are not identical In cancer, therapies targeting the EGF receptor are thwarted by the co-
activation of alternate receptor tyrosine kinases (RTK) that have partial functional overlap with
the EGF receptor (and are therefore degenerate), but are not targeted by the same specific EGF
receptor inhibitor. Other examples from various levels of biological organization can be found
in.

Theoretical relationships between biological properties that are important to evolution. For a
review of evidence that supports these relationships, see.

Several theoretical developments have outlined links between degeneracy and important
biological measurements related to robustness, complexity, and evolvability. These include:

 Theoretical arguments supported by simulations have proposed that degeneracy can lead
to distributed forms of robustness in protein interaction networks. Those authors suggest
that similar phenomena is likely to arise in other biological networks and potentially may
contribute to the resilience of ecosystems as well.
 Tononi et al. have found evidence that degeneracy is inseparable from the existence of
hierarchical complexity in neural populations. They argue that the link between
degeneracy and complexity is likely to be much more general.
  Fairly abstract simulations have supported the hypothesis that degeneracy fundamentally
alters the propensity for a genetic system to access novel heritable phenotypes and that
degeneracy could therefore be a precondition for open-ended evolution.
 The three hypotheses above have been integrated in where they propose that degeneracy
plays a central role in the open-ended evolution of biological complexity. In the same
article, it was argued that the absence of degeneracy within many designed (abiotic)
complex systems may help to explain why robustness appears to be in conflict with
flexibility and adaptability, as seen in software, systems engineering, and artificial life.

BIOSENSOR

A biosensor is an analytical device, used for the detection of a chemical substance that combines
a biological component with a physicochemical detector. The sensitive biological element, e.g.
tissue, microorganisms, organelles, cell receptors, enzymes, antibodies, nucleic acids, etc., is a
biologically derived material or biomimetic component that interacts, binds, or recognizes with
the analyte under study. The biologically sensitive elements can also be created by biological
engineering. The transducer or the detector element, which transforms one signal into another
one, works in a physicochemical way: optical, piezoelectric,
electrochemical, electrochemiluminescence etc., resulting from the interaction of the analyte
with the biological element, to easily measure and quantify. The biosensor reader device with the
associated electronics or signal processors that are primarily responsible for the display of the
results in a user-friendly way.[3] This sometimes accounts for the most expensive part of the
sensor device, however it is possible to generate a user friendly display that includes transducer
and sensitive element (holographic sensor). The readers are usually custom-designed and
manufactured to suit the different working principles of biosensors.

A chemoreceptor, also known as chemosensor, is a specialized sensory receptor cell

which transduces (converts) a chemical substance (endogenous or induced) and generates a
biological signal. This signal may be in the form of an action potential if the chemoreceptor is a
neuron (nerve cell), or in the form of a neurotransmitter that can activate a nearby nerve fiber if
the chemosensor is a specialized sensory receptor cell, such as the taste receptor in a taste bud or
in an internal peripheral chemoreceptor such as the carotid body (ex, in chemotherapy). In more
general terms, a chemosensor detects toxic or hazardous chemicals in the internal or external
environment of the human body (ex. chemotherapy) and transmits that information to the central
nervous system, (and rarely the peripheral nervous system), in order to expel the biologically
active toxins from the blood, and prevent further consumption of alcohol and/or other acutely
toxic recreational intoxicants.

Plant chemoreceptors
Plants have various mechanisms to perceive danger in their environment. Plants are able to
detect pathogens and microbes through surface level receptor kinases (PRK). Additionally,
receptor-like proteins (RLPs) containing ligand binding receptor domains capture pathogen-
associated molecular patterns (PAMPS) and damage-associated molecular patterns (DAMPS)
which consequently initiates the plant's innate immunity for a defense response.[5]

Plant receptor kinases are also used for growth and hormone induction among other important
biochemical processes. These reactions are triggered by a series of signaling pathways which are
initiated by plant chemically sensitive receptors. Plant hormone receptors can either be
integrated in plant cells or situate outside the cell, in order to facilitate chemical structure and
composition. There are 5 major categories of hormones that are unique to plants which once
bound to the receptor, will trigger a response in target cells. These include auxin, abscisic
acid, gibberellin, cytokinin, and ethylene. Once bound, hormones can induce, inhibit, or maintain
function of the target response.

There are two main classes of chemoreceptor: direct and distance.

 Examples of distance chemoreceptors are:

o olfactory receptor neurons in the olfactory system: Olfaction involves the ability
to detect chemicals in the gaseous state. In vertebrates, the olfactory system
detects odors and pheromones in the nasal cavity. Within the olfactory system
there are two anatomically distinct organs: the main olfactory epithelium (MOE)
and the vomeronasal organ (VNO). It was initially thought that the MOE is
responsible for the detection of odorants, while the VNO detects pheromones. The
current view, however, is that both systems can detect odorants and
pheromones.[8] Olfaction in invertebrates differs from olfaction in vertebrates. For
example, in insects, olfactory sensilla are present on their antennae.
 Examples of direct chemoreceptors include:
o Taste receptors in the gustatory system: The primary use of gustation as a type of
chemoreception is for the detection of tasteants. Aqueous chemical compounds
come into contact with chemoreceptors in the mouth, such as taste buds on the
tongue, and trigger responses. These chemical compounds can either trigger an
appetitive response for nutrients, or a defensive response against toxins depending
on which receptors fire. Fish and crustaceans, who are constantly in an aqueous
environment, use their gustatory system to identify certain chemicals in the
mixture for the purpose of localization and ingestion of food.
o Insects use contact chemoreception to recognize certain chemicals such as
cuticular hydrocarbons and chemicals specific to host plants. Contact
chemoreception is more commonly seen in insects but is also involved in the
mating behavior of some vertebrates. The contact chemoreceptor is specific to one
type of chemical.

A thermoreceptor is a non-specialised sense receptor, or more accurately the receptive portion

of a sensory neuron, that codes absolute and relative changes in temperature, primarily within the
innocuous range. In the mammalian peripheral nervous system, warmth receptors are thought to
be unmyelinated C-fibres (low conduction velocity), while those responding to cold have both C-
fibers and thinly myelinated A delta fibers (faster conduction velocity).[1] The adequate stimulus
for a warm receptor is warming, which results in an increase in their action potential discharge
rate. Cooling results in a decrease in warm receptor discharge rate. For cold receptors their firing
rate increases during cooling and decreases during warming. Some cold receptors also respond
with a brief action potential discharge to high temperatures, i.e. typically above 45°C, and this is
known as a paradoxical response to heat. The mechanism responsible for this behavior has not
been determined.

In humans, temperature sensation enters the spinal cord along the axons of Lissauer's tract that
synapse on second order neurons in grey matter of the dorsal horn, one or two vertebral levels
up. The axons of these second order neurons then decussate, joining the spinothalamic tract as
they ascend to neurons in the ventral posterolateral nucleus of the thalamus.

In mammals, temperature receptors innervate various tissues including the skin (as cutaneous
receptors), cornea and urinary bladder. Neurons from the pre-optic and hypothalamic regions of
the brain that respond to small changes in temperature have also been described, providing
information on core temperature. The hypothalamus is involved in thermoregulation, the
thermoreceptors allowing feed-forward responses to a predicted change in core body temperature
in response to changing environmental conditions.

Thermoreceptors have been classically described as having 'free' non-specialized endings; the
mechanism of activation in response to temperature changes is not completely understood.

Cold-sensitive thermoreceptors give rise to the sensations of cooling, cold and freshness. In the
cornea cold receptors are thought to respond with an increase in firing rate to cooling produced
by evaporation of lacrimal fluid 'tears' and thereby to elicit a blink reflex.

Warm and cold receptors play a part in sensing innocuous environmental temperature.
Temperatures likely to damage an organism are sensed by sub-categories of nociceptors that may
respond to noxious cold, noxious heat or more than one noxious stimulus modality (i.e., they are
polymodal). The nerve endings of sensory neurons that respond preferentially to cooling are
found in moderate density in the skin but also occur in relatively high spatial density in
the cornea, tongue, bladder, and facial skin. The speculation is that lingual cold receptors deliver
information that modulates the sense of taste; i.e. some foods taste good when cold, while others
do not.

This area of research has recently received considerable attention with the identification and
cloning of the Transient Receptor Potential (TRP) family of proteins. The transduction of
temperature in cold receptors is mediated in part by the TRPM8 channel. This channel passes a
mixed inward cationic (predominantly carried by Na+ ions although the channel is also
permeable to Ca2+) current of a magnitude that is inversely proportional to temperature. The
channel is sensitive over a temperature range spanning about 10-35°C. TRPM8 can also be
activated by the binding of an extracellular ligand. Menthol can activate the TRPM8 channel in
this way. Since the TRPM8 is expressed in neurons whose physiological role is to signal cooling,
menthol applied to various bodily surfaces evokes a sensation of cooling. The feeling of
freshness associated with the activation of cold receptors by menthol, particularly those in facial
areas with axons in the trigeminal (V) nerve, accounts for its use in numerous toiletries including
toothpaste, shaving lotions, facial creams and the like.

Another molecular component of cold transduction is the temperature dependence of so-called

leak channels which pass an outward current carried by potassium ions. Some leak channels
derive from the family of two-pore (2P) domain potassium channels. Amongst the various
members of the 2P-domain channels, some close quite promptly at temperatures less than about
28°C (e.g. TRAAK, TREK). Temperature also modulates the activity of the Na +/K+-ATPase.
The Na+/K+-ATPase is a P-type pump that extrudes 3Na+ ions in exchange for 2K+ ions for each
hydrolytic cleavage of ATP. This results in a net movement of positive charge out of the cell, i.e.
a hyperpolarizing current. The magnitude of this current is proportional to the rate of pump
activity.

It has been suggested that it is the constellation of various thermally sensitive proteins together in
a neuron that gives rise to a cold receptor. This emergent property of the neuron is thought to
comprise, the expression of the aforementioned proteins as well as various voltage-sensitive
channels including the hyperpolarization-activated, cyclic nucleotide-gated (HCN) channel and
the rapidly activating and inactivating transient potassium channel (IK A).

Baroreceptors (or archaically, pressoreceptors) are sensors located in the carotid sinus (at the
bifurcation of external and internal carotids) and in the aortic arch. They sense the blood
pressure and relay the information to the brain, so that a proper blood pressure can be
maintained.

Baroreceptors are a type of mechanoreceptor sensory neuron that are excited by a stretch of the
blood vessel. Thus, increases in the pressure of blood vessel triggers increased action
potential generation rates and provides information to the central nervous system. This sensory
information is used primarily in autonomic reflexes that in turn influence the heart cardiac
output and vascular smooth muscle to influence total peripheral resistance. Baroreceptors act
immediately as part of a negative feedback system called the baroreflex. As soon as there is a
change from the usual mean arterial blood pressure, returning the pressure toward a normal level.
These reflexes help regulate short-term blood pressure. The solitary nucleus in the medulla
oblongata of the brain recognizes changes in the firing rate of action potentials from the
baroreceptors, and influences cardiac output and systemic vascular resistance.

Baroreceptors can be divided into two categories based on the type of blood vessel in which they
are located: high-pressure arterial baroreceptors and low-pressure baroreceptors (also known as
cardiopulmonary or volume receptor.

Olfaction is a chemoreception that forms the sense of smell. Olfaction has many purposes, such
as the detection of hazards, pheromones, and food. It integrates with other senses to form the
sense of flavor.

Olfaction occurs when odorants bind to specific sites on olfactory receptors located in the nasal
cavity. Glomeruli aggregate signals from these receptors and transmit them to the olfactory bulb,
where the sensory input will start to interact with parts of the brain responsible for smell
identification, memory, and emotion.

Often, land organisms will have separate olfaction systems for smell and taste (orthonasal
smell and retronasal smell), but water-dwelling organisms usually have only one system

Human Immune System

Overview: The immune system is a complex system that is responsible for protecting us against
infections and foreign substances. There are three lines of defense: the first is to keep invaders
out (through skin, mucus membranes, etc.), the second line of defense consists of non-specific
ways to defend against pathogens that have broken through the first line of defense (such as with
inflammatory response and fever). The third line of defense is mounted against specific
pathogens that are causing disease (B cells produce antibodies against bacteria or viruses in the
extracellular fluid, while T cells kill cells that have become infected). The immune system is
closely tied to the lymphatic system, with B and T lymphocytes being found primarily within
lymph nodes. Tonsils and the thymus gland are also considered lymph organs and are involved in
immunity. We often don't realize how effective the immune system is until it fails or
malfunctions, such as when the lymphocytes are attacked by HIV in an AIDS patient.

Lymphatic System: The human lymphatic system and the immune system are terms that are
used interchangeably to refer to the body's ability to defend against pathogens. The lymphatic
system is comprised of three interrelated functions: (1) Removal of excess fluids, lymph, from
body tissues, (2) Absorption of fatty acids and subsequent transport of fat, chyle, to the
circulatory system and (3) Formation of white blood cells (WBCs), and initiation of immunity
through the formation of antibodies, lending specific resistance to pathogens.

Organs, Tissues and Cells of the Immune System: The immune system consists of a network
of lymphatic organs, tissues, and cells. These structures are supported by the reticuloendothelial
system: loose connective tissue with a network of reticular fibers. Phagocytic cells, including
monocytes and macrophages, are located in the reticular connective tissue. When micro-
organisms invade the body, or the body encounters antigens (such as pollen), antigens are
transported to the lymph. Lymph is carried through the lymph vessels to regional lymph nodes.
In the lymph nodes, the macrophages and dendritic cells phagocytose the antigens, process them,
and present the antigens to lymphocytes, which can then start producing antibodies or serve as
memory cells. The function of memory cells is to recognize specific antigens in the future.

Primary Lymphatic Organs: The primary lymphatic organs are the red bone marrow and the
thymus. They and are the site of production and maturation of lymphocytes, the type of white
blood cell that carries out the most important work of the immune system.
Fig. Organs of immune system

Secondary Lymphatic Organs: The secondary lymphatic organs also play an important role in
the immune system as they are places where lymphocytes find and bind with antigens this is
followed by the proliferation and activation of lymphocytes. The secondary organs include the
spleen, lymph nodes, tonsils, Peyer’s patches, and the appendix.

 The spleen: The spleen is a ductless, vertebrate gland that is closely associated with the
circulatory system, where it functions in the destruction of old red blood cells in holding
a reservoir of blood located in the upper left region of the abdominal cavity, is divided
into partial compartments.
 Lymph Nodes: are small oval shaped structures located along the lymphatic vessels.
They are about 1-25 mm in diameter. Lymph nodes act as filters, with an internal
honeycomb of connective tissue filled with lymphocytes that collect and destroy bacteria
and viruses.
 Tonsils: are often the first organs to encounter pathogens and antigens that come into the
body by mouth or nose. There are 3 pairs of tonsils in a ring about the pharynx.
 Peyer’s patches: located in the wall of the intestine and the appendix, attached to the
cecum of the large intestine, intercept pathogens that come into the body through the
intestinal tract.

Leukocytes: The primary cells of the immune system are the leukocytes or white blood cells
(WBC). Most leukocytes are much larger then red blood cells, but they are not nearly as
numerous. A microliter of whole blood contains about 5 million red blood cells but only about
7000 leukocytes.
Leukocytes can be distinguished from one another in stained tissue samples by the shape and
size of the nucleus, the staining characteristics of the cytoplasm and the cytoplasmic inclusions,
and the regularity of the cell border.

Leukocytes are are divided into six basic types Eosinophils, basophils, neutrophills, monocytes,
lymphocytes, and dendritic cells.

Human Immune System:

One functional group of leukocytes is the phagocytes, WBC that engulf and ingest their
targets by Phagocytosis: This group includes the neutrophils, macrophages, monocytes (which
are macrophage precursors), and Eosinophils.

A second functional group is the cytotoxic cells, so named because they kill the cells they
attack: This group includes Eosinophils and some types of lymphocytes.
Eosinophils: Eosinophils fight parasites and contribute to allergic reactions. They are easily
recognized by the bright pink staining granules in their cytoplasm. They account for only 1-3%
of all leukocytes. The life span of a typical eosinophil in the blood is about 6-12 hours.
Eosinophils are known to attach to large parasites and release substances from their granules that
damage or kill the parasite.

Basophiles: Basophills release histamine and other chemicals. Basophils are rare in circulation
but are easily recognized in a stained blood smear by the large, dark blue granules in their
cytoplasm. They also release mediators that contribute to inflammation. The granules contain
histamine, heparin(an anticoagulant), cytokines, and other chemicals involved in allergic and

immune responses. Illustration of a cell during Phagocytosis.

Neutrophils: Neutrophils "eat" bacteria and release cytokines. Neutrophils are the most
abundant WBC, 50-70% of the total. They are easily identified by a segmented nucleus. They are
phagocytic cells that typically ingest and kill bacteria. In addition to ingesting bacteria and
foreign particles, neutrophils release a variety of cytokines.

Monocytes: Monocytes are the precursor cells of tissue macrophages. Monocytes are not that
common in the blood 1-6% of WBC. Once out of the blood, monocytes enlarge and differentiate
into macrophages. Some tissue macrophages patrol the tissues, creeping along by amoeboid
motion. Others find a location and remain fixed in place. Macrophages are the primary
scavengers within tissues. Macrophages also remove larger particles, such as old RBC and dead
neutrophils. Macrophages play an important role in the development of acquired immunity.

Lymphocytes: Lymphocytes are the key cells that mediate the acquired immune response of the
body. Only about 5% of lymphocytes are found in circulation. They constitute 20-30% of all
WBC. Most lymphocytes are found in lymphoid tissues, where they are more likely to encounter
invaders. By one estimate, the adult body contains a trillion lymphocytes at any one time.

Dendritic Cells: Dendritic cells activate lymphocytes. They are antigen-presenting cells
characterized by long, thin processes that resemble neuronal dendrites. Dendritic cells are found
in the skin called Langerhans cells and also in various organs. When dendritic cells recognize
and capture antigens, they migrate to secondary lymphoid tissues, where they present the
antigens to lymphocytes.

INNATE IMMUNITY (Defenses against Infection): First line of defense Physical and
chemical barriers are the body's first line of defense.

1. Physical or Mechanical barriers

• Skin: one of the bodies’ first line of defenses against bacteria and other harmful organisms is
the skin. Millions of microorganisms live harmlessly on the skin and in the air around us.
Sebaceous glands in the skin produce sweat and sebum, which, combined help to protect the
skin.. The skin itself can also become infected by bacteria, viruses, fungi or tiny parasites. Some
examples of these are: boils, impetigo; ringworm, athlete’s foot; cold sore.

 Mucus membranes: Another very important first line of defense is our mucus
membranes. The mucous membranes line various body cavities that are exposed to the
external environment and internal organs. Mucus membranes serve different functions,
however, their more important job is to secrete mucus that traps bacteria and other
foreign debris that irritates the lining of the respiratory tract.

2. Chemical Defenses: Tears, saliva Tears and saliva contain lysozyme, an antiseptic enzyme
that attacks cell walls of bacteria and breaks them down.

• Stomach acids Glands in the stomach lining produce hydrochloric acid. This acid kills most
invading organisms that are swallowed and take up residence there.

Non-specific responses to infection - 2nd line of defense: We are born with built in
nonspecific defenses that all respond in the same way to invading pathogens. The outermost
defense our body has is our skin. The sebaceous glands produce sweat and sebum, which contain
ANTISEPTIC properties which protect. This bacteria-killing substance called LYZOSOME is
also found in tears and saliva. Acidic urine in the urinary tract and friendly bacteria in the genital
tract prevent the multiplying of harmful organisms in these areas. Most invading organisms in
the stomach are killed by gland production of hydrochloric acid. These are a few examples of
how the outer defenses protect us.
All outer defenses work together as the body's first line of defense.

Inflammatory response: Any break in the skin will allow bacteria to enter the body. These
foreign microbes will cause swelling and reddening at the site of injury. This reaction by the
body is called an inflammatory reaction or inflammatory response.

• Swelling, redness, heat, and pain Inflammation is characterized by the following quintet:
swelling (tumor), redness (rubor), heat (calor), pain (dolor) and dysfunction of the organs
involved (functio laesa).

When an injury occurs, a capillary and several tissue cells are apt to rupture, releasing histamine
and kinins. These cause the capillaries to dilate, become more permeable, and leak fluid into
these tissues. Dilation and fluid leaking into the tissues causes swelling, redness, and heat. The
swelling and kinins stimulate nerve endings, causing pain.

• Phagocytosis: neutrophills and macrophages:

In the event of a break in the skin, neutrophills, monocytes (and macrophages) arrive and attempt
to engulf and destroy the invaders. Phagocytosis is receptor-mediated event, which ensures that
only unwanted particles are ingested.

Complement System: Complement protein attacking a cell membrane. The complement system
is a biochemical cascade of the immune system that helps clear pathogens from an organism, and
promote healing. It is derived from many small plasma proteins that work together to form the
primary end result of cytolysis by disrupting the target cell's plasma membrane

Interferon in response to viral infection Interferon (IFNs): are naturally occurring

glycoprotein’s involved in non-specific immune responses

When a cell has been infected by a virus the virus will then cause the cell to make viral nucleic
acid. This nucleic acid acts as a signal and it causes the cell to realize that it has been infected
with a virus. So the cell will start making and sending out interferons. The IFN's that the cell
sends out go to nearby healthy cells and warns them of a virus. The healthy cells then start
intracellular changes that help the cells to be more resistant to the virus.

ADAPTIVE IMMUNITY (Specific Defense--third line of defense):This part of the immune

system directly targets invading microbes. Our specific immune defenses respond to antigens.
An antigen is a protein (or polysaccharide) molecule, typically on the cell membrane, that the
body recognizes as nonself. They are found on microbes, foreign cells, or on cancer cells.
Normally our immune system does not respond to our own antigens (if it does, then this is an
autoimmune disease). Lymphocytes Specific immunity is dependent upon two types of
lymphocytes, the B cells and the T cells. Their names are based on where in the body they
mature.

B cells mature in the bone marrow, and T cells mature in the thymus gland. In comparison, both
B and T cells can recognize and target antigen-bearing cells, although they go about this in
different ways. B and T cell lymphocytes are capable of recognizing an antigen because they
have specific receptor molecules on their surface which exactly fit individual antigens (like a
lock and a key). Any B or T cell can only respond to one type of antigen.

B Cells Produce Antibodies B cell lymphocytes are responsible for antibody-mediated immunity
(humoral immunity). They produce antibodies, which are proteins that bind with and neutralize
specific antigens.

a) Antibodies do not directly kill bacteria, but mark them for destruction. When antibodies
bind to viruses they can prevent the viruses from infecting cells.
b) When antibodies bind to toxins they can neutralize the toxin (why we get immunized
against the tetanus toxin).
c) Humoral immunity works best fighting against target viruses, bacteria, and foreign
molecules that are soluble in blood and lymph before the bacteria or viruses have entered
into cells (extracellular bacteria and extracellular viruses).

B cells produce two different types of cells:

• plasma cells • memory cells

Plasma cells: As B cells mature during embryonic development, they develop surface receptors
that allow them to recognize specific antigens.

The foreign antigen can be presented to the B cell directly, but usually macrophages and T cell
lymphocytes (helper T cells) interact with B cells.

i. Upon such an encounter, the B cell's receptors will bind to the antigen. The appropriate B
cell is turned on or stimulated. It then grows bigger, and rapidly multiplies into a large
homogenous group (clone). Most of these cells are plasma cells, which actively secrete
antibody that will bind with the original stimulating antigen .
ii. While most of the B cells remain in the lymphatic system, the antibodies are secreted into
the lymph fluid which then enters into the blood plasma to circulate throughout the body.
Although the clone cells only live a few days, their antibodies remain and circulate in the
blood and lymph, gradually decreasing in number.
iii. Memory B: cells At the time of activation some of the clones become memory B cells.
These cells are long lived and have recorded the information about the foreign antigen so
antibodies can be made more quickly, and in greater amount, in case a second exposure
should occur.

Antibody Structure and Function

There are different classes of antibodies, or immunoglobulins (Ig), such as IgA, IgG, IgE, and
IgM. They can attach to the surface of a microbe and make it more easily phagocytized by
neutrophils, monocytes and macrophages. Anything that simplifies phagocytosis is called an
opsonin. The process of antibodies attaching to invaders can be termed 'opsonization.'

Acquired Immunity: Antigen-specific Responses Acquired immunity responses are antigen-

specific responses in which the body recognizes a foreign substance and selectively reacts to it.
This is mediated primarily by lymphocytes. Acquired immunity overlaps with the process of
innate immunity.

Acquired immunity can be subdivided into active immunity and passive immunity.

Active Immunity: occurs when the body is exposed to a pathogen and produces its own
antibodies. Active immunity can occur naturally, when a pathogen invades the body, or
artificially, like when we are given vaccinations containing disabled or killed pathogens. The
body does require prior exposure to an antigen to develop an active immunity.

Passive Immunity: occurs when we acquire antibodies made by another human or animal.
Passive immunity is passive because it requires no response from the person's immune system. In
passive immunity you are not presenting the body with foreign antigens.

The transfer of antibodies from mother to fetus across the placenta is one example. Injections
containing antibodies are another.
ANTIGEN –ANTIBODY REACTIONS

Antigen-antibody interaction, or antigen-antibody reaction, is a specific chemical interaction

between antibodies produced by B cells of the white blood cells and antigens during immune
reaction. It is the fundamental reaction in the body by which the body is protected from complex
foreign molecules, such as pathogens and their chemical toxins. In the blood, the antigens are
specifically and with high affinity bound by antibodies to form an antigen-antibody complex.
The immune complex is then transported to cellular systems where it can be destroyed or
deactivated.

Important antigen-antibody reactions are: 1. Precipitation Reactions 2. Immunodiffusion 3.

Agglutination Reactions 4. Complement Fixation Reactions 5. Radioimmunoassay 6. Enzyme-
Linked Immunosorbent Assay 7. Fluorescent Antibody Technique.

1. Precipitation Reactions:

The reaction of soluble antigens with IgG or IgM antibodies to form a large interlocking
aggregates (lattices) is called precipitation reaction. The precipitates formed by antibodies are
known as precipitins.

The precipitation reactions occur in two stages: (i) Rapid interactions within a second
between antigen and antibodies and formation of complex.

(ii) Slow rate of reaction completing even within a few minutes or hours and forming lattices
from antigen-antibody complexes.

When the antibodies and antigens are in proper ratio, precipitation reactions normally occur.
When there is excess amount of either of two, no visible precipitate is formed.

One can produce the optimal ratio of these two by putting antigens and antibody adjacent to each
other and waiting for their diffusion together. In precipitation test, a precipitation ring appears
which display the creation of optimal ratio. This zone is known as the zone of equivalence

Fig. Precipitation ring test

2. Immunodiffusion Test (IDT):

Immunodiffusion tests are performed in a gelled agar medium. One of the IDTs is Ouchterlony
test (Fig. 22.22). In Ouchterlony test wells are cut, into which a purified antiserum (a serum
containing antibodies) is added, and to each surrounding well, soluble form of test antigens are
added.

Thereafter, a line of visible precipitate is formed between the wells where after diffusion optimal
ratio of antigen-antibody is formed. Through the Ouchterlony test, the presence of antibodies in
the serum against more than one antigen at a time can be demonstrated. Through this test,
identical, partially identical and different types of antigens can also be found out.

3. Agglutination Reactions:
Agglutination is the process of linking together of antigens by antibodies and formation of
visible aggregates. Agglutination reactions involve particulate antigens i.e. soluble antigens
adhering to particles. Agglutination reactions are very sensitive, readable and available in several
varieties.

It is of two types, direct and indirect agglutination tests:

1. Direct Agglutination Test: Direct agglutination test diagnoses antibodies against a large
number of cellular antigens such as RBCs, bacteria and fungi. This test is carried out in plastic
microtiter plates that have several small shallow wells. Each well acts as small test tube (Fig.
22.24).

Previously this test was done in test tubes. However, each well contains an equal amount of par-
ticulate antigen (e.g. RBCs) but the amount of antibodies in the serum is serially diluted in suc-
cessive wells so that their concentration may be half of the previous well.

If one starts with more antibodies, more dilutions will be required to lower the amount to a point
at which agglutination does not occur. This is the measure of titer or concentration of serum
antibody.

In a positive reaction, agglutination occurs, and sufficient antibodies are present in the serum to
link the antigen together. This results in formation of antibody-antigen mat which sinks to
bottom of well (A). However, in the negative reaction, agglutination does not occur and
insufficient antibodies are present to cause the linking of antigens.

The particulate antigens roll down the sloping sides of the well, and form a pellet at the bottom.
In this example the antigen titer is only 80 since the well with a 1: 80 concentration is the most
dilute concentration that gives a positive reaction. It may also be demonstrated that before
illness, blood of persons does not have any antibody, whereas titer develops significantly with
the progress of disease. This change in titer is called servotiter.
2. Indirect (Passive) Agglutination Tests:

This type of diagnostic tests are very rapid particularly for the detection of streptococci. If the
antigens are adsorbed onto particles (e.g. RBCs, latex beads, bentomile clay), soluble antigens
can respond to agglutination test. Antibody reacts with the soluble antigen adhering to the
particles. Therefore, the particles agglutinate with each other as these do in the direct
agglutination tests.

3. Haemagglutination:

Haemagglutination is the phenomenon of clumping of RBCs. When the RBCs are agglutinated
by certain viruses such as those causing mumps, measles, influenza, etc. it is called viral
haemagglutination. In the serum of a person, certain antibodies act against the antigens (of these
viruses), the antibodies neutralize them after reaction. The haemagglutination test is widely used
for the diagnosis of a number of viruses including those as above.

4. Complement Fixation Reactions:

A group of 20 or more serum protein is collectively known as complement. During reaction, the
complement binds to antigen-antibody complex and is used up or fixed. This process of
complement fixation may be used to measure even very small amount of antibody that does not
produce a visible reaction such as precipitation or agglutination. Therefore, it is necessary to use
indicator system.

This method is used in diagnosis of diseases such as leptospirosis, mycoplasmal pneumonia, Q

fever, polio, rubella, histoplasmosis, coccidiodomycosis and streptococcal infections. The test
requires patient’s serum, test antigen, complement from guinea pig and antibodies of sheep
RBCs to determine whether sheep RBCs may be lysed by guinea pig complement.

The test is accomplished in the following two stages:

Stage 1:

The patient’s serum is heated at 56°C for 30 minutes so that the complement should be
inactivated. The heated serum is diluted and then added to known amount of specific antigen and
complement (Fig. 22.24). The test antigen may correspond to the diseases.

For example, if a patient is suffering from a disease caused by streptococci the test antigen would
be the streptococcal antigen. If the patient’s serum contains antibodies against streptococci, the
test antigen will form complement sequence. This mixture is again incubated for about 30
minutes. At this point, no antigen-antibody reaction occurs.

Stage 2:
In stage 2, the complement fixed by antigen-antibody reaction is detected by an indication
system. This system consists of sheep RBCs containing specific antibodies attached to their
surfaces.

When these are added to complement, haemolysis of RBCs occurs that impart changes in colour
of the mixture. This shows that the complements have not been fixed during the first stage;
therefore, these become available to cause haemolysis (Fig. 22.25). This indicates that the patient
has no streptococcal pneumonia.

However, if the guinea pig complements are destroyed, they will not be able to cause the lysis of
RBCs. On the other hand, if the complements are fixed (by antigen- antibody reaction) during
the first stage, these will not be available to cause haemolysis during the second stage. This
indicates that the patient has the infection of streptococci.

5. Radioimmunoassay (RIA):

It is such a technique which is highly sensitive and can measure even the less concentration (i.e.
0.001 µg/ml) of antigen or antibody. In 1960, for the first time this technique was developed by
S.A. Berson and R. Yalow when they were engaged in determining the concentration of insulin
and anti-insulin complexes in diabetics. Thereafter, Berson died, and significance of this
technique was realized. In 1977, Yalow was awarded a Nobel Prize.
There are two methods of measuring RIA: the liquid phase and the solid phase RIAs.

1. Liquid Phase RIA:

The liquid phase RIA is based on competitive binding of radiolabeled antigen and un-labelled
antigen, to a high affinity antibody. The antigen labelled with 125I is mixed with such a
concentration of antibody that can just saturate the antibody. Therefore, the increasing amount of
antigen (un-labelled) of unknown concentration is added. The two types of antigens now
compete for available sites of the antibody.

The antibody does not differentiate the labelled antigen from the un-labelled one. Upon gradually
increasing concentration of un-labelled antigen, the labelled antigen could be displaced from the
binding sites available on antibody. The labelled antigens are made free in the solution. The
amount of labelled antigen in solution is measured, and the concentration of un-labelled antigen
can be determined.

2. Solid Phase RIA:

In solid phase RIA, either antigen or antibody is immobilized on a solid phase matrix. It is
simple and easy in handling as compared to liquid phase RIA.

6. Enzyme-Linked Immunosorbent Assay (ELISA):

The principle of ELISA is similar to RIA, but differs slightly. In RIA radiolabelled antigen is
used, whereas in ELISA enzyme is used that reacts with a colourless substrate and develops a
coloured reaction product. There is a large number of enzymes such as alkaline phosphatase,
horse radish peroxidase, and p-nitro-phenyl phosphatase which are employed in ELISA. As
compared to RIA, this assay is both cheaper and safer.

On the basis of known concentration of antigen or antibody a standard curve is prepared from
which the unknown concentration of sample is measured. A microliter plate with numerous
shallow wells is used in this method. It is very useful in testing for AIDS antibodies. However,
now-a days a number of ELISA kits have been developed and are in current use.

1. Indirect ELISA:

It is used to measure antibody. Known antigen is coated on the plastic lining of the wells of
microtiter plate which is made up of polystyrene latex. To test for the presence of antibodies
against this antigen in the patient, his blood serum is added to the wells (Fig. 22.26A). If the
patient’s serum contains antibody specific to antigen, the antibody will bind to the absorbed
antigen otherwise not.

After incubation the wells are washed and the enzyme, labelled with antihuman gamma globulin
(anti-Hgg), is added to the wells. Anti-Hgg can react with antigen antibody complex. The
mixture of wells is washed to remove the excess of unbound labelled anti- Hgg.

Finally the correct substrate for the enzyme is added which is hydrolysed by the enzyme and
develops a colour. Varying concentrations of antibody in serum shows changes in the intensity of
colour. This method is very useful in detection of antibodies to HIV, Salmonella, Yersinia,
Brucella, Treponema and streptococci.

2. Double Antibody Sandwich ELISA:

This method detects antigen. In this case antibody (antiserum) is immobilised on the surface of
wells of microtiter plate (Fig. 22.26B). A test antigen is added to each well and allowed to react
with the bound antibody. It is incubated during this period. If antigen combines specifically with
antibody absorbed to wells, the antigen will be retained even after washing and unbound antigen
would be made free.

Thereafter, a second enzyme-linked antibody (e.g. alkaline phosphatase tagged to antibody) is

added to react with bound antigen. It is again incubated for a few seconds, the enzyme labelled
antibody reacts with the antigen-antibody complex already formed in the wells and results in the
development of a “sandwich’.

The mixture in wells is washed again to remove the excess of labelled enzyme. A chromogenic
substrate e.g. nitro-phenyl phosphate is added which reacts with enzyme and develop yellow
colour.

The reaction can be stopped simply by changing the pH or denaturing the enzyme. The change in
colour is measured visually or spectrophotometrically. Change in colour shows the presence of
desired antigen in the sample. This technique is useful in detection of toxins of Vibrio cholerae,
E. coli, Staphylococcus enterotoxin-A and antigens of rotavirus.
7. Fluorescent Antibody (FA) Technique: The FA technique is used to detect the
microorganisms present in clinical specimens, and specific antibodies present in serum. If the
antibodies bind to cell or tissues, it can be observed by tagging the antibody with a fluorescent
dye such as fluorescein isothiocyanate and rhodamine.

Both the dyes can conjugate the FC region of antibody without affecting the specificity and make
the antibody fluorescent when exposed to UV light. Fluorescein absorbs blue light (490 nm) and
emits yellow green fluorescence (517 nm). Similarly, rhodamine absorbs the yellow green light
(515 nm) and emits deep red fluorescence (546 nm). The FA technique is very useful in testing
for rabies within a few hours with 100% accuracy.

There are two methods of FA test, direct FA test and indirect FA test. Direct FA test is used to
identify the microorganisms present in clinical specimen. The specimen containing antigen is
fixed onto a slide and, thereafter, fluorescein-labelled antibodies are added on the specimen. It is
incubated for a few minutes.

The slide is washed to remove unbound antibody and observed under the UV microscope for
yellow-green fluorescence. The indirect FA test is useful for the detection of specific antibodies
in serum formed by a microorganism.
 Unit-III

Cancer- Biology and nature of cancer, metastasis, stem Cells and cancer.

Drug design, biosafety, bioresources.

Cloud Computing
Techniques used in Biophysics and Biochemistry.
Cloud computing means on demand delivery of IT resources via the internet with pay-as-you-go
Introductory Bioinformatics,
pricing. It provides Engineers
a solution designs encouraged
of IT infrastructure in lowbycost.
examples in Biology. Engineering aspects of
some Nobel prizes in Chemistry, physiology and Medicine.
Why Cloud Computing?

CANCER

What is cancer: Cancer cells grow and divide at an abnormally rapid rate, are poorly
differentiated, and have abnormal membranes, cytoskeletal proteins, and morphology. The
abnormality in cells can be progressive with a slow transition from normal cells to benign tumors
to malignant tumors.

Cancer is a broad term. It describes the disease that results when cellular changes cause the
uncontrolled growth and division of cells. Some types of cancer cause rapid cell growth, while
others cause cells to grow and divide at a slower rate. Certain forms of cancer result in visible
growths called tumors, while others, such as leukemia, do not. Most of the body's cells have
specific functions and fixed lifespans. While it may sound like a bad thing, cell death is part of a
natural and beneficial phenomenon called apoptosis.A cell receives instructions to die so that the
body can replace it with a newer cell that functions better. Cancerous cells lack the components
that instruct them to stop dividing and to die. As a result, they build up in the body, using oxygen
and nutrients that would usually nourish other cells. Cancerous cells can form tumors, impair the
immune system and cause other changes that prevent the body from functioning regularly.
Cancerous cells may appear in one area, then spread via the lymph nodes. These are clusters of
immune cells located throughout the body.
How Cancer Cell Different From Normal Cell: Cancer cells vary greatly from normal cells.
There are many differences between them.

1. Growth: Cancer cells continue to grow after enough cells are present. This
overgrowth forms a cluster of cells, causing the formation of a tumor. Normal
cells stop growing when enough cells are present
2. Communication: Cancer cells do not respond to the signals from other cells
warning overgrowth. Normal cells, in turn, respond to these signals and stop
growing
3. Cell Repair: Cancer cells don’t repair themselves when they are old or damaged.
Normal cells do repair themselves or may even die off if they are not healthy.

TYPES

There are many different types of tumors and a variety of names for them. Their names usually
reflect their shape, the origin of the cell, and the type of tissue they appear in.

In general, tumors are divided into three groups:

 Benign: These are not cancerous and cannot spread. A benign tumor will remain in its
current form. They do not generally return after being removed.
 Premalignant: A premalignant tumor is not yet cancerous but appears to be developing
the properties of cancer.
 Malignant: Malignant tumors are cancerous. They can grow, spread, and get worse.

There is sometimes no clear dividing line between cancerous, precancerous and non-cancerous
tumors. In some cases, putting a tumor in a category can be an estimation, especially if the tumor
is in the middle of the spectrum or changing rapidly. Some benign tumors can eventually become
premalignant, and then malignant.

1. Benign: Most benign tumors are not harmful to human health. However, even
though they are not cancerous, some may press against nerves or blood vessels
and cause pain or other negative effects. Benign tumors of endocrine tissues may
result in the excessive production of some hormones. Examples of benign tumors
include:

Adenomas are tumours that arise from glandular epithelial tissue, the thin membrane that covers
glands, organs, and other structures in the body. A polyp in the colon is a type of adenoma. Other
examples : parathyroid adenoma, eosinophilic adenoma, basophilic adenoma, bile duct adenoma,
chromophobe adenoma, fibroadenoma, hepatic adenoma. Adenomas do not start as cancers.
However, they can change and become cancerous, taking the form of adenocarcinomas.
Fibroids, or fibromas are benign tumors that can grow on the fibrous or connective tissue of any
organ. Uterine fibroids are common and can cause vaginal bleeding, pelvic pain or discomfort,
and urinary incontinence. They can be "soft" or "hard" depending on the proportion of fibers to
cells. There are many types of fibroma, including angiofibroma, dermatofibroma, and ossifying
and non-ossifying fibroma. Some fibromas can cause symptoms and may require surgical
removal. In rare cases, fibroids can change and eventually become cancerous. They are then
called fibrosarcomas.

Hemangiomas are benign tumors that consist of excessive blood cells. They can sometimes be
seen on the surface of the skin and are known as strawberry marks. The majority of
hemangiomas appear at birth and gradually go away after some months or years. Hemangiomas
do not usually require any treatment. If they affect the ability of an individual to eat, hear, or see,
the doctor may recommend treatment with corticosteroids. If the patient is over 10 years of age,
they are more commonly removed using laser surgery.

Lipomas are the most common form of soft-tissue tumor. They consist of fat cells. Most of them
are very small, painless, soft to the touch, and generally movable. They are more common
among people aged over 40 years. Experts disagree on whether lipomas can change and become
cancerous. There is a range of lipomas, including: angiolipoma, myelolipoma, fibrolipoma,
spindle cell lipoma, hibernoma, atypical lipoma

2. Premalignant: This type of tumor requires close monitoring. Examples of

premalignant growths include

Actinic keratosis: Also known as senile keratosis or solar keratosis, this is a premalignant growth
consisting of patches of skin that turn crusty, scaly, and thick. Fair-skinned people are more at
risk of developing these types of growths, especially those who are overexposed to sunlight.
Actinic keratoses are seen as potentially premalignant, because around 20 percent of them
progress to squamous cell carcinoma. Doctors usually recommend treating them because of this.
Continuous exposure to the sun increases the risk of malignancy.

Cervical dysplasia: This is a change in the normal cells lining the cervix. The growth can be
premalignant and is at risk of developing into cervical cancer. Cervical dysplasia is diagnosed
with a PAP smear. It is most common in women aged 25 to 35 years and may be removed with
freezing techniques or by removing the cone of tissue from the cervix.

Metaplasia of the lung: These growths occur in the tubes that carry air from the windpipe into the
lung, or the bronchi. The bronchi are lined with glandular cells, which can change and become
squamous cells. Metaplasia of the lung is most commonly caused by smoking.

Leukoplakia: Thick, white patches can form on the gums, the bottom of the mouth, the insides of
the cheeks, and, less commonly, on the tongue. They cannot be scraped off easily. Experts
believe smoking or chewing tobacco is the main cause. Although Leukoplakia is rarely
dangerous, a small percentage can eventually become cancerous. Many mouth cancers occur
near areas of leukoplakia. The condition usually clears up when people quit smoking. Quitting
both alcohol and tobacco together has better results. The patches can be removed using a laser, a
scalpel, or a cold probe that freezes the cancer cells.

3. Malignant: Malignant tumors divide and spread rapidly, colonizing new areas.
Malignant tumors are cancerous tumors that can potentially result in death. Unlike
benign tumors, malignant ones grow quickly, and can spread to new territory in a
process known as metastasis. The abnormal cells that form a malignant tumor
multiply at a faster rate. The cancer cells that metastasize are the same as the
original ones. If a lung cancer spreads to the liver, the cancer cells now growing
in the liver are still lung cancer cells. They have, however, acquired the ability to
invade other organs.

Different types of malignant tumor are made up of specific types of cancer cells, including:

 Carcinoma: These tumors are formed from epithelial cells. For example, carcinomas can
occur in the stomach, prostate, pancreas, lung, liver, colon, or breast. Many of the most
common tumors are carcinomas, especially among older adults.
 Sarcoma: These tumors start in connective tissue, such as cartilage, bones, fat, and
nerves. They originate in the cells outside the bone marrow. The majority of sarcomas are
malignant.
 Germ cell tumor: These are tumors made from the cells that give life, sperm and egg
cells. Germ cell tumors most commonly occur in the ovaries or testicles. The majority of
testicular tumors start from germ cells. Less commonly, germ cell tumors may also
appear in the brain, abdomen or chest.
 Blastoma: Tumors formed from embryonic tissue or developing cells are known as
blastomas and are more common in children than adults. Examples include
medulloblastoma and glioblastoma, types of brain tumor, retinoblastoma, a tumor in the
retina of the eye, osteoblastoma, a type of bone tumor, and neuroblastoma, a tumor of the
nervous system found in children.

Treatments

Innovative research has fueled the development of new medications and treatment technologies.
Doctors usually prescribe treatments based on the type of cancer, its stage at diagnosis, and the
person's overall health. Below are examples of approaches to cancer treatment:
 Chemotherapy aims to kill cancerous cells with medications that target rapidly dividing cells.
The drugs can also help shrink tumors, but the side effects can be severe.

 Hormone therapy involves taking medications that change how certain hormones work or
interfere with the body's ability to produce them. When hormones play a significant role, as
with prostate and breast cancers, this is a common approach.

 Immunotherapy uses medications and other treatments to boost the immune system and
encourage it to fight cancerous cells. Two examples of these treatments are checkpoint
inhibitors and adoptive cell transfer.

 Precision medicine, or personalized medicine, is a newer, developing approach. It involves

using genetic testing to determine the best treatments for a person's particular presentation of
cancer. Researchers have yet to show that it can effectively treat all types of cancer, however.

 Radiation therapy uses high-dose radiation to kill cancerous cells. Also, a doctor may
recommend using radiation to shrink a tumor before surgery or reduce tumor-related symptoms.

 Stem cell transplant can be especially beneficial for people with blood-related cancers, such as
leukemia or lymphoma. It involves removing cells, such as red or white blood cells, that
chemotherapy or radiation has destroyed. Lab technicians then strengthen the cells and put them
back into the body.

 Surgery is often a part of a treatment plan when a person has a cancerous tumor. Also, a
surgeon may remove lymph nodes to reduce or prevent the disease's spread.

 Targeted therapies perform functions within cancerous cells to prevent them from multiplying.
They can also boost the immune system. Two examples of these therapies are small-molecule
drugs and monoclonal antibodies.
Doctors will often employ more than one type of treatment to maximize effectiveness.

Metastasis is a pathogenic agent's spread from an initial or primary site to a different or

secondary site within the host's body; it is typically spoken of as such spread by
a cancerous tumor. The newly pathological sites, then, are metastases (mets). It is generally
distinguished from cancer invasion, which is the direct extension and penetration by cancer cells
into neighboring tissues.
Cancer occurs after cells are genetically altered to proliferate rapidly and indefinitely. This
uncontrolled proliferation by mitosisproduces a primary heterogeneic tumour. The cells which
constitute the tumor eventually undergo metaplasia, followed by dysplasia then anaplasia,
resulting in a malignant phenotype. This malignancy allows for invasion into the circulation,
followed by invasion to a second site for tumorigenesis.

Some cancer cells known as circulating tumor cells acquire the ability to penetrate the walls
of lymphatic or blood vessels, after which they are able to circulate through the bloodstream to
other sites and tissues in the body. This process is known (respectively)
as lymphatic or hematogenous spread. After the tumor cells come to rest at another site, they re-
penetrate the vessel or walls and continue to multiply, eventually forming another clinically
detectable tumor. This new tumor is known as a metastatic (or secondary) tumor. Metastasis is
one of the hallmarks of cancer, distinguishing it from benign tumors. Most cancers can
metastasize, although in varying degrees. Basal cell carcinoma for example rarely metastasizes.
When tumor cells metastasize, the new tumor is called a secondary or metastatic tumor, and its
cells are similar to those in the original or primary tumor. This means that if breast
cancer metastasizes to the lungs, the secondary tumor is made up of abnormal breast cells, not of
abnormal lung cells. The tumor in the lung is then called metastatic breast cancer, not lung
cancer. Metastasis is a key element in cancer staging systems such as the TNM staging system,
where it represents the "M". In overall stage grouping, metastasis places a cancer in Stage IV.
The possibilities of curative treatment are greatly reduced, or often entirely removed, when a
cancer has metastasized.

DRUG DESIGN AND BIOSAFETY

Drugs are chemical or biological substances that have some kind

of physiological or biochemical effect on our bodies. They may be single compounds or a
mixture of different compounds. Their effects are intended to be beneficial but can cause harmful
side effects in some people. All drugs interact with specific ‘targets’ in the body, with the aim of
modifying their activity and often resulting in a therapeutic effect. For example, pain relief. Drug
targets are usually proteins but are in some cases small regions of DNA or RNA. Drugs work
either by stimulating or blocking the activity of their targets.

Drug design, often referred to as rational drug design or simply rational design, is
the inventive process of finding new medications based on the knowledge of a biological target.
The drug is most commonly an organic small molecule that activates or inhibits the function of
a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the
most basic sense, drug design involves the design of molecules that are complementary
in shape and charge to the biomolecular target with which they interact and therefore will bind to
it. Drug design frequently but not necessarily relies on computer modeling techniques. This type
of modeling is sometimes referred to as computer-aided drug design. Finally, drug design that
relies on the knowledge of the three-dimensional structure of the biomolecular target is known
as structure-based drug design. In addition to small
molecules, biopharmaceuticals including peptides and especially therapeutic antibodies are an
increasingly important class of drugs and computational methods for improving the affinity,
selectivity, and stability of these protein-based therapeutics have also been developed.

The phrase "drug design" is to some extent a misnomer. A more accurate term is ligand design
(i.e., design of a molecule that will bind tightly to its target). Although design techniques for
prediction of binding affinity are reasonably successful, there are many other properties, such
as bioavailability, metabolic half-life, side effects, etc., that first must be optimized before a
ligand can become a safe and efficacious drug. These other characteristics are often difficult to
predict with rational design techniques. Nevertheless, due to high attrition rates, especially
during clinical phases of drug development, more attention is being focused early in the drug
design process on selecting candidate drugs whose physicochemical properties are predicted to
result in fewer complications during development and hence more likely to lead to an approved,
marketed drug. Furthermore, in vitro experiments complemented with computation methods are
increasingly used in early drug discovery to select compounds with more
favorable ADME (absorption, distribution, metabolism, and excretion)
and toxicological profiles.

Drug targets: A biomolecular target (most commonly a protein or nucleic acid) is a key
molecule involved in a particular metabolic or signaling pathway that is associated with a
specific disease condition or pathology or to the infectivity or survival of a microbial pathogen.
Potential drug targets are not necessarily disease causing but must by definition be disease
modifying. In some cases, small molecules will be designed to enhance or inhibit the target
function in the specific disease modifying pathway. Small molecules (for example
receptor agonists, antagonists, inverse agonists, or modulators; enzyme activators or inhibitors;
or ion channel openers or blockers) will be designed that are complementary to the binding
site of target. Small molecules (drugs) can be designed so as not to affect any other important
"off-target" molecules (often referred to as antitargets) since drug interactions with off-target
molecules may lead to undesirable side effects. Due to similarities in binding sites, closely
related targets identified through sequence homology have the highest chance of cross reactivity
and hence highest side effect potential. Most commonly, drugs are organic small
molecules produced through chemical synthesis, but biopolymer-based drugs (also known
as biopharmaceuticals) produced through biological processes are becoming increasingly more
common. In addition, mRNA-based gene silencing technologies may have therapeutic
applications.

Computer-aided drug design: The most fundamental goal in drug design is to predict whether a
given molecule will bind to a target and if so how strongly. Molecular mechanics or molecular
dynamics is most often used to estimate the strength of the intermolecular interaction between
the small molecule and its biological target. These methods are also used to predict
the conformation of the small molecule and to model conformational changes in the target that
may occur when the small molecule binds to it. Semi-empirical, ab initio quantum chemistry
methods, or density functional theory are often used to provide optimized parameters for the
molecular mechanics calculations and also provide an estimate of the electronic properties
(electrostatic potential, polarizability, etc.) of the drug candidate that will influence binding
affinity.

Molecular mechanics methods may also be used to provide semi-quantitative prediction of the
binding affinity. Also, knowledge-based scoring function may be used to provide binding affinity
estimates. These methods use linear regression, machine learning, neural nets or other statistical
techniques to derive predictive binding affinity equations by fitting experimental affinities to
computationally derived interaction energies between the small molecule and the target.
Ideally, the computational method will be able to predict affinity before a compound is
synthesized and hence in theory only one compound needs to be synthesized, saving enormous
time and cost. The reality is that present computational methods are imperfect and provide, at
best, only qualitatively accurate estimates of affinity. In practice it still takes several iterations of
design, synthesis, and testing before an optimal drug is discovered. Computational methods have
accelerated discovery by reducing the number of iterations required and have often provided
novel structures.

Drug design with the help of computers may be used at any of the following stages of drug
discovery:

1. hit identification using virtual screening (structure- or ligand-based design)

2. hit-to-lead optimization of affinity and selectivity (structure-based design, QSAR, etc.)
3. lead optimization of other pharmaceutical properties while maintaining affinity

In order to overcome the insufficient prediction of binding affinity calculated by recent scoring
functions, the protein-ligand interaction and compound 3D structure information are used for
analysis. For structure-based drug design, several post-screening analyses focusing on protein-
ligand interaction have been developed for improving enrichment and effectively mining
potential candidates:

 Consensus scoring
o Selecting candidates by voting of multiple scoring functions
o May lose the relationship between protein-ligand structural information and
scoring criterion
 Cluster analysis
o Represent and cluster candidates according to protein-ligand 3D information
o Needs meaningful representation of protein-ligand interactions.

Types: There are two major types of drug design. The first is referred to as ligand-based drug
design and the second, structure-based drug design.

Ligand-based: Ligand-based drug design (or indirect drug design) relies on knowledge of
other molecules that bind to the biological target of interest. These other molecules may be used
to derive a pharmacophore model that defines the minimum necessary structural characteristics a
molecule must possess in order to bind to the target. In other words, a model of the biological
target may be built based on the knowledge of what binds to it, and this model in turn may be
used to design new molecular entities that interact with the target. Alternatively, a quantitative
structure-activity relationship (QSAR), in which a correlation between calculated properties of
molecules and their experimentally determined biological activity, may be derived. These QSAR
relationships in turn may be used to predict the activity of new analogs.

Structure-based: Structure-based drug design (or direct drug design) relies on knowledge of
the three dimensional structure of the biological target obtained through methods such as x-ray
crystallography or NMR spectroscopy. If an experimental structure of a target is not available, it
may be possible to create a homology model of the target based on the experimental structure of
a related protein. Using the structure of the biological target, candidate drugs that are predicted to
bind with high affinity and selectivity to the target may be designed using interactive graphics
and the intuition of a medicinal chemist. Alternatively various automated computational
procedures may be used to suggest new drug candidates. Current methods for structure-based
drug design can be divided roughly into three main categories. The first method is identification
of new ligands for a given receptor by searching large databases of 3D structures of small
molecules to find those fitting the binding pocket of the receptor using fast
approximate docking programs. This method is known as virtual screening. A second category is
de novo design of new ligands. In this method, ligand molecules are built up within the
constraints of the binding pocket by assembling small pieces in a stepwise manner. These pieces
can be either individual atoms or molecular fragments. The key advantage of such a method is
that novel structures, not contained in any database, can be suggested. A third method is the
optimization of known ligands by evaluating proposed analogs within the binding cavity.

Binding site identification: Binding site identification is the first step in structure based design.
If the structure of the target or a sufficiently similar homolog is determined in the presence of a
bound ligand, then the ligand should be observable in the structure in which case location of the
binding site is trivial. However, there may be unoccupied allosteric binding sites that may be of
interest. Furthermore, it may be that only apoprotein (protein without ligand) structures are
available and the reliable identification of unoccupied sites that have the potential to bind ligands
with high affinity is non-trivial. In brief, binding site identification usually relies on
identification of concave surfaces on the protein that can accommodate drug sized molecules that
also possess appropriate "hot spots" (hydrophobic surfaces, hydrogen bonding sites, etc.) that
drive ligand binding.

Scoring functions: Structure-based drug design attempts to use the structure of proteins as a
basis for designing new ligands by applying the principles of molecular
recognition. Selective high affinity binding to the target is generally desirable since it leads to
more efficacious drugs with fewer side effects. Thus, one of the most important principles for
designing or obtaining potential new ligands is to predict the binding affinity of a certain ligand
to its target (and known antitargets) and use the predicted affinity as a criterion for selection.

One early general-purposed empirical scoring function to describe the binding energy of ligands
to receptors was developed by Böhm.

Biosafety: For the release of biopharmaceutical drugs onto the market, products must be shown
to be safe. Regulatory bodies such as the US Food & Drug Administrators (FDA) and the
Medicines and Healthcare Regulatory Agency (MHRA) require products are tested for
compliance before release. This involves a number of stringent tests to provide proof that a
product is free of contamination and does not pose a risk to patient health. Failure to perform
comprehensive and effective biosafety testing can result in the recall of products from the
market, reduced confidence in products or have an adverse impact upon patient health.

Biosafety is the prevention of large-scale loss of biological integrity, focusing both

on ecology and human health. These prevention mechanisms include conduction of regular
reviews of the biosafety in laboratory settings, as well as strict guidelines to follow. Biosafety is
used to protect from harmful incidents. Many laboratories handling biohazards employ an
ongoing risk management assessment and enforcement process for biosafety. Failures to follow
such protocols can lead to increased risk of exposure to biohazards or pathogens. Human
error and poor technique contribute to unnecessary exposure and compromise the best safeguards
set into place for protection.
The international Cartagena Protocol on Biosafety deals primarily with the agricultural definition
but many advocacy groups seek to expand it to include post-genetic threats: new molecules,
artificial life forms, and even robots which may compete directly in the natural food chain.

Biosafety in agriculture, chemistry, medicine, exobiology and beyond will likely require the
application of the precautionary principle, and a new definition focused on the biological nature
of the threatened organism rather than the nature of the threat.

When biological warfare or new, currently hypothetical, threats (i.e., robots, new artificial
bacteria) are considered, biosafety precautions are generally not sufficient. (link to incident
report, i.e. such as problems with CDC research labs in 2014)The new field
of biosecurity addresses these complex threats.

Biosafety level refers to the stringency of biocontainment precautions deemed necessary by

the Centers for Disease Control and Prevention(CDC) for laboratory work with infectious
materials.

Typically, institutions that experiment with or create potentially harmful biological material will
have a committee or board of supervisors that is in charge of the institution's biosafety. They
create and monitor the biosafety standards that must be met by labs in order to prevent the
accidental release of potentially destructive biological material. (note that in the US, several
groups are involved, and efforts are being made to improve processes for government run labs,
but there is no unifying regulatory authority for all labs.

Biosafety is related to several fields:

 In ecology (referring to imported life forms from beyond ecoregion borders),

 In agriculture (reducing the risk of alien viral or transgenic genes, genetic engineering or
prions such as BSE/"MadCow", reducing the risk of food bacterial contamination)
 In medicine (referring to organs or tissues from biological origin, or genetic therapy
products, virus; levels of lab containment protocols measured as 1, 2, 3, 4 in rising order
of danger),
 In chemistry (i.e., nitrates in water, PCB levels affecting fertility)
  In exobiology (i.e., NASA's policy for containing alien microbes that may exist on space
samples. See planetary protection and interplanetary contamination), and
 In synthetic biology (referring to the risks associated with this type of lab practice)

BIORESOURCES

Bio resources are no fossil biogenic resources which can be used by humans for multiple
purposes: to produce food, substantial products, and/or energy carriers.

Categories of bio resources

1. Primary bio resources: Primary bio resources are generated for a specific application-
oriented purpose in forestry, agri- or aquaculture to enable the production of food,
substantial products, or eventually energy, examples are
wood, grain, potato, bamboo, algae.
2. Secondary bio resources: These may be generated during primary processing, in further
industrial processing as by-products or residues, but also during maintenance of large
green areas. Typical regarding properties are following characteristics: they
accrue genuine from virgin materials, they contain mainly a low amount of impurities,
and they are produced in large quantities.
3. Tertiary bio resources: These are also parts from virgin materials, which were separated
along the processing chain. But compared to secondary bio resources they are residues
which occur rather in small amounts at the generation place and/or are not genuine.
Also uncontrolled modifications, e.g. degradation during storage, may have taken place.
They have generally a lower value than secondary bio resources.
4. Quaternary bio resources... Occur after a product is used and can be distinguished
according to the time frames of their generation after start of utilization into short-, mid- ,
and long-term categories.

Value of bio resources

Direct value – Agriculture, Medicine, Bio products

Indirect value – Ecosystem services (nutrient cycling, pollina4on,

Primary bio resources from agriculture have traditionally special value for food & feed and from
forestry for pulp & paper, particle boards and construction wood production. As “side effect”
they are from large value regarding their welfare and cultural function.

Biomass will be a scare resource in future, because the area for growing of primary bio resources
is the limiting factor. The efficient utilization of secondary, tertiary and quaternary bio resources
is therefore absolutely necessary.

Today waste & wastewater based secondary, tertiary and quaternary bio resources are often
either not collected at all, disposed or inefficiently treated. This has to change! Manifold
products are possible to make from the waste & wastewater based bio resources ranging e.g.
from compost & biogas over mineral fertilizers & bioethanol & lactic acid up to specific
chemicals and much more. Some are produced already in technical scale, but mostly the research
& demonstration is actually pre-dominant. The design of multi-product cascades and bio
refineries is from special interest for the future to use bio resources as complete as possible.

TECHNIQUES USED IN BIOPHYSICS AND BIOCHEMISTRY

Biophysics : interdisciplinary science that uses the methods of physics to

study biological systems

Nature of biophysics.

Biophysics is

 An academic discipline – branch of knowledge that is taught and researched at the

college or university level. Disciplines are defined (in part), and recognized by the
academic journals in which research is published, and the learned societies and academic
departments or faculties to which their practitioners belong.
 A scientific field (a branch of science) – widely recognized category of specialized
expertise within science, and typically embodies its own terminology and nomenclature.
 Such a field will usually be represented by one or more scientific journals, where peer
reviewed research is published.
o A natural science – one that seeks to elucidate the rules that govern
the natural world using empirical and scientific methods.
 A biological science – concerned with the study of living organisms,
including their structure, function, growth, evolution, distribution,
and taxonomy.
 A branch of physics – concerned with the study of matter and
its motion through space and time, along with related concepts such
as energy and force.
 An interdisciplinary field – field of science that overlaps with other sciences

Biophysical techniques – methods used for gaining information about biological systems on an
atomic or molecular level. They overlap with methods from many other branches of science.

 Biophotonics – combination of biology and photonics, with photonics being the science and
technology of generation, manipulation, and detection of photons, quantum units of light.
Biophotonics can also be described as the "development and application of optical
techniques, particularly imaging, to the study of biological molecules, cells and tissue". One
of the main benefits of using optical techniques which make up biophotonics is that they
preserve the integrity of the biological cells being examined.
 Calcium imaging – various optical techniques for recording the location and concentration of
calcium. Typically this is done in cell and tissue samples using either genetically encoded or
chemically derived fluorescent calcium indicating dyes.
 Calorimetry –
o Isothermal Titration Calorimetry (ITC) – measures the heat effects caused by
interactions.
 Chromatography – various techniques from this field are used for the purification and
analysis of biological molecules
 Circular Dichroism – method to measure chirality of a sample using circularly polarized
light. This technique is commonly used to determine protein structure.
 Computational chemistry – use of numerical methods to probe the structure and dynamical
equilibrium in biological systems.
 Cryobiology –
 Dual Polarisation Interferometry – analytical technique used to measure the real-time
conformation and activity of a wide range of biomolecules and their interactions.
 Electrophysiology – studies electrical properties of cell membranes and provide functional
data, often related to systematic changes in structure.
o Patch clamping – provides temporal and electrical information of a cell, or a portion of
membrane. Typically this provides data on electrogenic processes, such ion
channel or transporter activity.
 Electron microscopy – used to gain high-resolution images of subcellular structures and
proteins.
 Fluorescence spectroscopy – for detecting structural rearrangements, as well as interactions
of biomolecules. See also, Fluorescence.
 Force spectroscopy – probes the mechanical properties of individual molecules or
macromolecular assemblies using small flexible cantilevers, focused laser light, or magnetic
fields.
 Gel electrophoresis – determines the mass, the charge and the interactions of biological
molecules
 Imaging – scientific imaging of biological materials, usually by some form of microscopy, or
sometimes indirectly such as in x-ray crystallography or by computer imaging; at a wide
range of magnifications to see macromolecules, cells, tissues, or organisms
 Mass spectrometry – technique that gives the molecular mass with great accuracy.
 Microscale Thermophoresis (MST) – method to measure binding affinities, enzymatic
activities, changes in molecule conformation and changes in size, charge or hydration
entropy.
 Microscopy – used in many ways, for example, to enable the use of laser instruments for
scanning and transmission.
o Atomic force microscopy –
 Neuroimaging –
 Neutron spin echo spectroscopy –
 Nuclear Magnetic Resonance Spectroscopy – method for measuring the local environment of
atomic nuclei within a sample. Can be used to derive both structural and kinetic information
on proteins and small molecules.
 Optical tweezers and Magnetic tweezers – allow for the manipulation of single molecules,
providing information about DNA and its interaction with proteins and molecular motors,
such as Helicase and RNA polymerase.
 NMR spectroscopy – provides information about the exact structure of biological molecules,
as well as on dynamics
 Single molecule spectroscopy – is a technique that is sensitive enough to detect single
molecules and often incorporates fluorescence detection.
 Small angle X-ray scattering (SAXS) – technique that gives a rough low resolution
molecular structure.
 Spectrophotometry – measurement of the transmission of light through different solutions or
substances at different wavelengths of light.
o Colorimetry –
 Spectroscopy and Circular dichroism – method for detecting chiral groups in molecules,
especially to determine the secondary structure of proteins
 Ultracentrifugation – gives information on the shape and mass of molecules
 X-ray crystallography – method to determine the exact structure of molecules with atomic
resolution

Biochemistry is the application of chemistry to the study of biological processes at the

cellular and molecular level. It emerged as a distinct discipline around the beginning of the
 20th century when scientists combined chemistry, physiology and biology to investigate the
chemistry of living systems.

Biochemistry is both a life science and a chemical science - it explores the chemistry of
living organisms and the molecular basis for the changes occurring in living cells.

It uses the methods of chemistry, physics, molecular biology and immunology to study the
structure and behaviour of the complex molecules found in biological material and the ways
these molecules interact to form cells, tissues and whole organisms.

Techniques used in Biochemistry

• Centrifugation
• Microscopy
• Recombinant DNA and genetic analysis
• Immunochemical Techniques
• Protein structure, purification, characterization and function analysis
• Mass spectrometric Techniques
• Electrophoretic techniques
• Chromatographic Techniques
• Spectroscopic techniques
• Radioisotopes techniques
• Cell membrane receptor and cell signaling
• Drug discovery and development

BIOINFORMATICS

Bioinformatics is an interdisciplinary field that develops and improves on methods for storing,
retrieving, organizing and analysing biological data. A major activity in bioinformatics is to
develop software tools to generate useful biological knowledge.

Bioinformatics has become an important part of many areas of biology. In experimental

molecular biology, bioinformatics techniques such as image and signal processing allow
extraction of useful results from large amounts of raw data. In the field of genetics and genomics,
it aids in sequencing and annotating genomes and their observed mutations. It plays a role in the
textual mining of biological literature and the development of biological and gene ontologies to
organize and query biological data. It plays a role in the analysis of gene and protein expression
and regulation. Bioinformatics tools aid in the comparison of genetic and genomic data and more
generally in the understanding of evolutionary aspects of molecular biology. At a more
integrative level, it helps analyse and catalogue the biological pathways and networks that are an
important part of systems biology. In structural biology, it aids in the simulation and modeling of
DNA, RNA, and protein structures as well as molecular interactions. Researchers affiliated with
our program conduct research in systems biology, genomics, and proteomics.

Systems Biology: Systems biology is an emerging approach applied to biomedical and biological
scientific research. Systems biology is a biology-based inter-disciplinary field of study that
focuses on complex interactions within biological systems, using a more holistic perspective
(holism instead of the more traditional reductionism) approach to biological and biomedical
research. Particularly from year 2000 onwards, the concept has been used widely in the
biosciences in a variety of contexts. One of the outreaching aims of systems biology is to model
and discover emergent properties, properties of cells, tissues and organisms functioning as a
system whose theoretical description is only possible using techniques which fall under the remit
of systems biology.

Genomics: Genomics is a discipline in genetics that applies recombinant DNA, DNA

sequencing methods, and bioinformatics to sequence, assemble, and analyse the function and
structure of genomes (the complete set of DNA within a single cell of an organism). The field
includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic
mapping. The field also includes studies of intragenomic phenomena such as heterosis, epistasis,
pleiotropy and other interactions between loci and alleles within the genome. In contrast, the
investigation of the roles and functions of single genes is a primary focus of molecular biology or
genetics and is a common topic of modern medical and biological research. Research of single
genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and
functional information analysis is to elucidate its effect on, place in, and response to the entire
genome’s networks.
Metagenomics: Metagenomics is the study of metagenomes, genetic material recovered directly
from environmental samples. The broad field may also be referred to as environmental
genomics, ecogenomics or community genomics. While traditional microbiology and microbial
genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene
sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in
a natural sample. Such work revealed that the vast majority of microbial biodiversity had been
missed by cultivation-based methods. Recent studies use “shotgun” Sanger sequencing or
massively parallel pyrosequencing to get largely unbiased samples of all genes from all the
members of the sampled communities. Because of its ability to reveal the previously hidden
diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial
world that has the potential to revolutionize understanding of the entire living world.

Population Genomics: Population genomics is the study of allele frequency distribution and
change under the influence of the four main evolutionary processes: natural selection, genetic
drift, mutation and gene flow on a genome-wide level. It also takes into account the factors of
recombination, population subdivision and population structure. It attempts to explain such
phenomena as adaptation and speciation.

Proteomics: Proteomics is the large-scale study of proteins, particularly their structures and
functions. Proteins are vital parts of living organisms, as they are the main components of the
physiological metabolic pathways of cells. Proteomics, formed on the basis of the research and
development of the Human Genome Project, is also an emerging scientific research, involving
exploration of the proteome from the overall level of intracellular protein composition, structure,
and its own unique activity patterns. It is an important component of functional genomics.

Engineers designs encouraged by examples in Biology

Biological engineering, or bioengineering/bio-engineering, is the application of principles of
biology and the tools of engineering to create usable, tangible, economically viable
products. Biological engineering employs knowledge and expertise from a number of pure and
applied sciences, such as mass and heat transfer, kinetics, biocatalysts,
biomechanics, bioinformatics, separation and purification processes, bioreactor design, surface
science, fluid mechanics, thermodynamics, and polymer science. It is used in the design of
medical devices, diagnostic equipment, biocompatible materials, renewable bioenergy,
ecological engineering, agricultural engineering, and other areas that improve the living
standards of societies. Examples of bioengineering research include bacteria engineered to
produce chemicals, new medical imaging technology, portable and rapid disease diagnostic
devices, prosthetics, biopharmaceuticals, and tissue-engineered organs. Bioengineering overlaps
substantially with biotechnology and the biomedical sciences in a way analogous to how various
other forms of engineering and technology relate to various other sciences (for
example, aerospace engineering and other space technology to kinetics and astrophysics).

In general, biological engineers (or biomedical engineers) attempt to either mimic biological
systems to create products or modify and control biological systems so that they can replace,
augment, sustain, or predict chemical and mechanical processes. Bioengineers can apply their
expertise to other applications of engineering and biotechnology, including genetic modification
of plants and microorganisms, bioprocess engineering, and biocatalysis. Working with doctors,
clinicians and researchers, bioengineers use traditional engineering principles and techniques and
apply them to real-world biological and medical problems

Bio-inspired technologies

Biomimetics could in principle be applied in many fields. Because of the diversity and
complexity of biological systems, the number of features that might be imitated is large.
Biomimetic applications are at various stages of development from technologies that might
become commercially usable to prototypes. Murray's law, which in conventional form
determined the optimum diameter of blood vessels, has been re-derived to provide simple
equations for the pipe or tube diameter which gives a minimum mass engineering system. [14]

Locomotion: Aircraft wing design and flight techniques are being inspired by birds and
bats. Biorobots based on the physiology and methods of locomotion of
animals include BionicKangaroo which moves like a kangaroo, saving energy from one jump
and transferring it to its next jump. Kamigami Robots, a children's toy, mimic cockroach
locomotion to run quickly and efficiently over indoor and outdoor surfaces.

Construction and architecture: Researchers studied the termite's ability to maintain virtually
constant temperature and humidity in their termite mounds in Africa despite outside temperatures
that vary from 1.5 °C to 40 °C (35 °F to 104 °F). Researchers initially scanned a termite mound
and created 3-D images of the mound structure, which revealed construction that could influence
human building design. The Eastgate Centre, a mid-rise office complex
in Harare, Zimbabwe, stays cool without air conditioning and uses only 10% of the energy of a
conventional building of the same size.

In structural engineering, the Swiss Federal Institute of Technology (EPFL) has incorporated
biomimetic characteristics in an adaptive deployable "tensegrity" bridge. The bridge can carry
out self-diagnosis and self-repair. The arrangement of leaves on a plant has been adapted for
better solar power collection.

Analysis of the elastic deformation happening when a pollinisator lands on the sheath-like perch
part of the flower Strelitzia reginae (known as Bird-of-Paradise flower) has inspired architects
and scientists from the University of Freiburg and University of Stuttgart for the creation of
hingeless shading systems that can react to their environment. These bio-inspired products is sold
under the name Flectofin.
Other hingeless bioinspired system includes Flectofold. Flectofold has been inspired from the
trapping system developed by the carnivorous plant Aldrovanda vesiculosa.

Structural materials: There is a great need for new structural materials that are light weight but
offer exceptional combinations of stiffness, strength, and toughness.

Such materials would need to be manufactured into bulk materials with complex shapes at high
volume and low cost and would serve a variety of fields such as construction, transportation,
energy storage and conversion. In a classic design problem, strength and toughness are more
likely to be mutually exclusive i.e., strong materials are brittle and tough materials are weak.
However, natural materials with complex and hierarchical material gradients that span
from nano- to macro-scales are both strong and tough. Generally, most natural materials utilize
limited chemical components but complex material architectures that give rise to exceptional
mechanical properties. Understanding the highly diverse and multi functional biological
materials and discovering approaches to replicate such structures will lead to advanced and more
efficient technologies. Bone, nacre (abalone shell), teeth, the dactyl clubs of stomatopod shrimps
and bamboo are great examples of damage tolerant materials. The exceptional resistance
to fracture of bone is due to complex deformation and toughening mechanisms that operate at
spanning different size scales - nanoscale structure of protein molecules to macroscopic
physiological scale.

Nacre exhibits similar mechanical properties however with rather simpler structure. Nacre shows
a brick and mortar like structure with thick mineral layer (0.2∼0.9-μm) of closely packed
aragonite structures and thin organic matrix (∼20-nm). While thin films and micrometer sized
samples that mimic these structures are already produced, successful production of bulk
biomimetic structural materials is yet to be realized. However, numerous processing techniques
have been proposed for producing nacre like materials.

Biomorphic mineralization is a technique that produces materials with morphologies and

structures resembling those of natural living organisms by using bio-structures as templates for
mineralization. Compared to other methods of material production, biomorphic mineralization is
facile, environmentally benign and economic.

Freeze casting (Ice templating), an inexpensive method to mimic natural layered structures was
employed by researchers at Lawrence Berkeley National Laboratory to create alumina-Al-Si and
IT HAP-epoxy layered composites that match the mechanical properties of bone with an
equivalent mineral/ organic content. Various further studies also employed similar methods to
produce high strength and high toughness composites involving a variety of constituent phases.

Recent studies demonstrated production of cohesive and self supporting macroscopic tissue
constructs that mimic living tissues by printing tens of thousands of heterologous picoliter
droplets in software-defined, 3D millimeter-scale geometries. Efforts are also taken up to mimic
the design of nacre in artificial composite materials using fused deposition modelling and the
helicoidal structures of stomatopod clubs in the fabrication of high performance carbon fiber-
epoxy composites.
 Various established and novel additive manufacturing technologies like PolyJet printing, direct
ink writing, 3D magnetic printing, multi-material magnetically assisted 3D printing and
magnetically-assisted slip casting have also been utilized to mimic the complex micro-scale
architectures of natural materials and provide huge scope for future research.

Spider web silk is as strong as the Kevlar used in bulletproof vests. Engineers could in principle
use such a material, if it could be reengineered to have a long enough life, for parachute lines,
suspension bridge cables, artificial ligaments for medicine, and other purposes.The self-
sharpening teeth of many animals have been copied to make better cutting tools. New ceramics
that exhibit giant electret hysteresis have also been realized.

Self healing materials: In general in biological systems, self healing occurs via chemical
signals released at the site of fracture which initiate a systemic response that transport repairing
agents to the fracture site thereby promoting autonomic healing. To demonstrate the use of
micro-vascular networks for autonomic healing, researchers developed a microvascular coating–
substrate architecture that mimics human skin. Bio-inspired self-healing structural color
hydrogels that maintain the stability of an inverse opal structure and its resultant structural colors
were developed. A self-repairing membrane inspired by rapid self-sealing processes in plants
was developed for inflatable light weight structures such as rubber boats or Tensairity®
constructions. The researchers applied a thin soft cellular polyurethane foam coating on the
inside of a fabric substrate, which closes the crack if the membrane is punctured with a
spike. Self-healing materials, polymers and composite materials capable of mending cracks have
been produced based on biological materials.

Surfaces: Surfaces that recreate properties of shark skin are intended to enable more efficient
movement through water. Efforts have been made to produce fabric that emulates shark
skin.[14][46]

Surface tension biomimetics are being researched for technologies such

as hydrophobic or hydrophilic coatings and microactuators.

Wet adhesion: Some amphibians, such as tree and torrent frogs and arboreal salamanders, are
able to attach to and move over wet or even flooded environments without falling. This kind of
organisms have toe pads which are permanently wetted by mucus secreted from glands that open
into the channels between epidermal cells. They attach to mating surfaces by wet adhesion and
they are capable of climbing on wet rocks even when water is flowing over the surface.
Tire treads have also been inspired by the toe pads of tree frogs.

Marine mussels can stick easily and efficiently to surfaces underwater under the harsh conditions
of the ocean. Mussels use strong filaments to adhere to rocks in the inter-tidal zones of wave-
swept beaches, preventing them from being swept away in strong sea currents. Mussel foot
proteins attach the filaments to rocks, boats and practically any surface in nature including other
mussels. These proteins contain a mix of amino acid residues which has been adapted
specifically for adhesive purposes. Researchers from the University of California Santa Barbara
borrowed and simplified chemistries that the mussel foot uses to overcome this engineering
challenge of wet adhesion to create copolyampholytes, and one-component adhesive systems
 with potential for employment in nanofabrication protocols. Other research has proposed
adhesive glue from mussels.

Dry adhesion: Leg attachment pads of several animals, including many insects
(e.g. beetles and flies), spiders and lizards (e.g. geckos), are capable of attaching to a variety of
surfaces and are used for locomotion, even on vertical walls or across ceilings. Attachment
systems in these organisms have similar structures at their terminal elements of contact, known
as setae. Such biological examples have offered inspiration in order to produce climbing
robots, boots and tape. Synthetic setae have also been developed for the production of dry
adhesives.

Inspiration from fruits and plants: For instance, the chiral self-assembly of cellulose inspired
by the Pollia condensata berry has been exploited to make optically active films. Such films are
made from cellulose which is a biodegradable and biobased resource obtained from wood or
cotton. The structural colours can potentially be everlasting and have more vibrant colour than
the ones obtained from chemical absorption of light. Pollia condensata is not the only fruit
showing a structural coloured skin, other berries such as Margaritaria nobilis does. These fruits
show iridescent colors in the blue-green region of the visible spectrum which gives the fruit a
strong metallic and shiny visual appearance. The structural colours come from the organisation
of cellulose chains in the fruit's epicarp, a part of the fruit skin. Each cell of the epicarp is made
of a multilayered envelope that behaves like a Bragg reflector. However, the light which is
reflected from the skin of these fruits is not polarised unlike the one arising from man-made
replicates obtained from the self-assembly of cellulose nanocrystals into helicoids, which only
reflect left-handed circularly polarised light.

The fruit of Elaeocarpus angustifolius also show structural colour that come arises from the
presence of specialised cells called iridosomes which have layered structures.[61] Similar
iridosomes have also been found in Delarbrea michieana fruits.

In plants, multi layer structures can be found either at the surface of the leaves (on top of the
epidermis), such as in Selaginella willdenowii or within specialized intra-cellular organelles, the
so-called iridoplasts, which are located inside the cells of the upper epidermis. For instance, the
rain forest plants Begonia pavonina have iridoplasts located inside the epidermal cells.

Structural colours have also been found in several algae, such as in the red alga Chondrus
crispus (Irish Moss).
ENGINEERING ASPECTS OF SOME NOBEL PRIZES IN CHEMISTRY,
PHYSIOLOGY AND MEDICINE

IN CHEMISTRY

1. Jacques Dubochet, Joachim Frank and Richard Henderson got

novel prize in 2017 “for developing cryo-electron microscopy for
the high-resolution structure determination of biomolecules in
solution”.

Work

Fundamental processes of life are governed by a number of complicated molecules. The electron
microscope, which uses electron beams instead of light, expands the possibilities to image these
molecules. However, many biological molecules depend on water, which evaporates in the
vacuum of an electron microscope. In the early 1980s Jean Dubochet succeeded in cooling the
water so rapidly that it solidified around the molecules without the formation of distorting ice
crystals. Electron microscope images provide knowledge that is important for the development
of pharmaceuticals, among other things.

2. Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L.

Feringa ” got novel prize in 2016 for the design and synthesis of
molecular machines”

Work

We can imagine that the components of the smallest machines could be molecules. For a
machine to function, its parts must be able to move relative to each other. Fraser Stoddart has
contributed to the development of molecular machines, for example by developing a "rotaxane"
in 1991. A ring-shaped molecule was threaded over another molecule that functions like an axle.
In the future, molecular machines could be used for new materials, sensors, and energy storage
systems.
 3. Eric Betzig, Stefan W. Hell and William E. Moerner “ got novel
prize in 2014 for the development of super-resolved fluorescence
microscopy”

Work

In normal microscopes the wavelength of light sets a limit to the level of detail possible.
However this limitation can be circumvented by methods that make use of fluorescence, a
phenomenon in which certain substances become luminous after having been exposed to light.
Around 2000, Eric Betzig and William E. Moerner helped create a method in which fluorescence
in individual molecules is steered by light. An image of very high resolution is achieved by
combining images in which different molecules are activated. This makes it possible to track
processes occurring inside living cells.

4. Kurt Wüthrich ” got noval prize in 2002 for his development of

nuclear magnetic resonance spectroscopy for determining the
three-dimensional structure of biological macromolecules in
solution”

Work

The protons and neutrons in an atomic nucleus act like tiny, spinning magnets. This causes atoms
and molecules to adopt certain positions in a magnetic field. This alignment, however, can be
disrupted by radio waves with specific frequencies that vary for different atoms. These resonance
frequencies are also affected by the atoms' chemical environment. Thus, the phenomenon can be
exploited to determine the compositions and structures of different molecules. In the 1980s, Kurt
Wüthrich developed a method for mapping the structure of large biological molecules.

5. Richard R. Ernst ” got novel prize in1991 for his contributions to

the development of the methodology of high resolution nuclear
magnetic resonance (NMR) spectroscopy”
Work

Protons and neutrons in the atomic nucleus behave like small spinning magnets. Accordingly,
atoms and molecules assume a certain orientation in a magnetic field. This can be dislodged,
however, by radio waves of certain frequencies that are characteristic for different atoms. Known
as resonance frequencies, these are also affected by the atoms' chemical surroundings. As a
result, the phenomenon can be utilized to determine the composition and structure of various
molecules. To accomplish this, Richard Ernst developed highly sensitive and high resolution
methods in the 1960s and 1970s.

6. Ilya Prigogine “ got novel prize in1977 for his contributions to

non-equilibrium thermodynamics, particularly the theory of
dissipative structures”

Work

Thermodynamics is about heat and its transformation into other forms of energy - basically
involving statistical descriptions of atomic and molecular movements. Irreversible
thermodynamic processes go in only one direction, usually toward more disorder. However,
during the 1960s Ilya Prigogine developed a theory about dissipative structures, which maintains
that long before a state of equilibrium is reached in irreversible processes, orderly and stable
systems can arise from more disordered systems. The result has been applied in a great many
areas.

7. Lars Onsager “ got novel prize in1968 for the discovery of the
reciprocal relations bearing his name, which are fundamental for
the thermodynamics of irreversible processes”

Work

Thermodynamics is about heat and its conversion into other forms of energy - basically
involving statistical descriptions of atomic and molecular movements. Irreversible
thermodynamic processes go in only one direction and not in the reverse. Lars Onsager analyzed
mathematical equations for various irreversible thermodynamic processes and in 1931 found the
connection that led him to formulate equations that came to be known as reciprocal relations.
This allowed a complete description of irreversible processes.