BIOTECHNOLOGY

PRINCIPLES AND PROCESSES

9.1 Principles of Biotechnology

9.2 Tools of Recombinant DNA Technology
9.3 Processes of Recombinant DNA Technology

BIOTECHNOLOGY: PRINCIPLES AND PROCESSES

• Two core techniques that enabled birth of modern biotechnology:

o Genetic engineering: Techniques to alter the chemistry of genetic material

(DNA and RNA) to introduce into host organisms and thus change the
phenotype of the host organism.
o Maintenance of sterile (microbial contamination-free) ambient chemical
engineering processes to enable growth of only the desired microbe/
eukaryotic cell in large quantity

Conceptual development of the principle of genetic engineering:

• Asexual reproduction preserves the genetic identity of species.

• Sexual reproduction creates variation and creates unique combinations of
genetic makeup.
• Traditional hybridization procedures used in plant and animal breeding lead
to inclusion of undesirable genes along with desired genes.
• The techniques of genetic engineering which includes creation of
recombinant DNA, use of gene cloning and gene transfer, overcome this
limitation and allows us to isolate and introduce only one or a set of
desirable genes without introducing undesirable genes into target organism
• Three basic steps in genetically modifying an organism –
o Identification of DNA with desirable gene
o Introduction of the identified DNA into the host.
o Maintenance of introduced DNA in the host and transfer of the DNA to its
progeny.
 TOOLS OF RECOMBINANT DNA TECHNOLOGY

Restriction Enzymes:

• In the year 1963 two enzymes discovered from Escherichia coli which
restrict the growth of bacteriophage in it.
o One of these added methyl groups to DNA.
o Other cut the phage DNA. (restriction endonuclease)
• The first restriction endonuclease discovered is Hind II.
• Hind II always cut DNA molecule at particular point by recognizing a
specific sequence of six base pairs. This is called recognition sequence for
Hind II.
• Till date around 900 restriction enzymes isolated from 200 strains of
bacteria each of which recognize different recognition sequences.
• Restriction enzyme belongs to nucleases.
• There are two kind of nucleases:
o Exonuclease
o Endonuclease
• Exonuclease removes nucleotides from the free ends of the DNA.
• Endonucleases make cuts at specific positions within the DNA.
• Each restriction endonuclease recognizes a specific palindromic nucleotide
sequences in the DNA.
• Palindromes are the group of letters that read same both forward and
backward, e.g.“MALAYALAM”.
• The palindrome in DNA is a sequence of base pairs that reads same on the
two strands when orientation of reading is kept same
• The restriction enzyme cut the strand of DNA little away from the centre of
the palindrome sites,but between the same two bases on the opposite strand.
This leaves single stranded portions at the ends. There are overhanging
stretches called sticky ends on each strand.
• This stickiness of the ends facilitates the action of the enzyme DNA ligases.
• The foreign DNA and the host DNA cut by the same restriction endonuclease,
the resultant DNA fragments have the same kind of ‘sticky-ends’ and these can
be joined together using DNA ligases.

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Convention for naming restriction endonuclease:

• The first letter of the name comes from the genus.

• Second two letters come from the species of the prokaryotic cell from
which the enzyme isolated
• The fourth letter is in capital form derived from the Strain of microbes.
• The Roman letter followed is the order of discovery
• Best example: EcoRI comes from Escherichia coli RY 13
Separation and isolation of DNA fragments:

• The cutting of DNA by restriction endonucleases results in the fragments of

DNA.
• These fragments are separated by a technique called gel electrophoresis.
• Since the DNA fragments are negatively charged, they can be separated by
forcing them to move towards anode under an electric field through a
medium/matrix.
• Most commonly used matrix is agarose, a natural polymer extracted from
sea weed.
• DNA fragments separate according to their size through sieving effect
provided by the agarose gel. Hence the smaller the fragment size, farther it
moves.
• The separated fragments are visualized by staining them with Ethidium
bromide followed by exposure to UV radiation.
• The separated bands of DNA are cut out from the agarose gel and
extracted from the gel piece. This step is called elution

Cloning vector

• The plasmid and bacteriophages have the ability to replicate within

Features of cloning vector

Origin of replication:

• This is the sequence where the replication starts called ori gene.
• The alien DNA linked with vector also replicates.
• Controls the copy number of the linked DNA.

Selectable marker:

• It is required to identify recombinant from the non-recombinant.

• Helps in identifying and eliminating non-transformants and selectively
permitting the growth of the transformants.
• Transformation is a procedure through which a piece of foreign DNA is
introduced in a host bacterium.
• Normally, the gene coding resistance to antibiotics such as ampicilin.
Tetracycline,chloramphenicol or kanamycins etc are considered as useful
selectable markers for E.coli.
• Thr normal E.coli cells do not carry resistance against any of antibiotics.

Cloning sites:

• In order to link the alien DNA, the vector needs to have very few,
preferably single, recognition sites (palindromic site)for the commonly used
restriction endonuclease.
• Commonly used vector is pBR322, for E.coli.
• The ligation of foreign DNA is carried out at a restriction site present in
one of the two antibiotic resistance genes.
• If a foreign DNA ligated or inserted at the Bam H I site of tetracycline
resistance gene in the vector pBR322, the recombinant plasmid will lose
tetracycline resistance. (insertional inactivation)
• The recombinant can be identified from the non-recombinant in following
steps:
o All are grown in ampicilin medium
o One replica of above plate grown in ampicilin medium (control)
o Other replica grown in the medium containing both tetracycline and
ampicilin.
o The colonies grows in plate-I but failed to grow in plate-II are
identified as recombinants.
Alternative selectable marker:

• In E.coli a plasmid called PUK-18 is used as selectable marker, which is

better than pBR322.
• The foreign DNA is introduced within the coding sequence of an enzyme β-
galactosidase, which convert X-Gal (chromatogenic substrate) into Galactose
and 5-bromo+4 chloro indigo (blue color)
• The non-recombinant produce enzyme and give blue colored colonies.
• The recombinant unable to produce β-galactosidase and does not produce
blue colored colonies after addition of chromatogenic substrate i.e. X-Gal.
• This inactivation of insertion of foreign DNA called insertional inactivation.

Vectors for cloning genes in plants and animals:

• Agrobacterium tumefaciens, a pathogenic bacterium of several dicot plants.

• This bacterium contains a plasmid called Ti-plasmid.(tumor inducing)
• In natural condition the A.tumifaciens transfer the T-DNA into the plant
which transform normal plant cells into a tumor and direct these tumor cells
to produce the chemical required by the pathogen.
• Retroviruses in animals have the ability to transform normal cells into
cancerous cells.
• The dis-armed retroviruses are being used to transfer gene into animals.
• In Ti-plasmid the T-DNA is replaced by the gene of interest, still
A.tumifaciens able to transfer the gene into the plant without causing tumor
in plants.

Competent Host (for transformation with recombinant DNA)

• DNA is a hydrophilic molecule; it cannot pass through cell membranes.

• In order to force bacteria to take-up the plasmid, the bacterial cells must
first be made ‘competent’ to take up DNA.
• The bacterial cell is treated with divalent cations such as calcium, which
increases the efficiency of DNA up take by the bacteria.
• Recombinant DNA and the bacterial cells are incubated in ice, followed by
placing them briefly at 42oC (heat shock) and then putting them back in ice.
• By microinjection the recombinant DNA directly injected into the nucleus
of the animal cell.
• Plant cells are bombarded with high velocity micro-particles of gold or
tungsten coated with DNA in amethod known as biolistics or gene gun.

PROCESS OF RECOMBINANT TECHNOLOGY

• Isolation of DNA ,
• Fragmentation of DNA by restriction endonuclease.
• Isolation of desired DNA fragment by gel electrophoresis.
• Ligation of DNA fragment with a vector by DNA ligase
• Transferring the recombinant DNA into the host
• Culturing the host cells in a medium at large scale in a bioreactor.
• Extraction of desired product by downstream processing

Isolation of the Genetic material (DNA)

• Bacterial cell wall digested by Lysozyme.

• Plant cell wall is digested by cellulase and pectinase.
• Fungal cell wall is digested by chitinase.
• RNA of the cellular content is digested by ribonuclease.
• Proteins are removed by Proteases.
• Purified DNA ultimately precipitated out after addition of chilled
ethanol.

Amplification of Gene of Interest using PCR:

• PCR stands for Polymerase chain reaction:
• Multiple copy of gene of interest can be synthesized in vitro.
• PCR includes following steps:
 Denaturation:
• Double stranded DNA made single stranded.
• It is done by heating the DNA at 94oC.
• Each single stranded DNA is called Template strand

Annealing:
• Two sets of primer (small oligonucleotide chain that
are complementary to the DNA at 3’ end of the DNA
template) added to the medium.
• This is done at around 50oC.

Extension:
• Deoxyribonucleotides triphosphates are added in the medium.
• Taq polymerase catalyses the polymerization reaction using
nucleotides extending from the primer towards 5’ end of the
template.
• Taq polymerase is a thermostable polymerase isolated from a
bacterium called Thermus aquaticus.
• It catalyses polymerization reaction at 74oC.
Obtaining the Foreign Gene product or Recombinant produ

• The protein encoding gene is expressed in a heterogeneous host is called a

recombinant protein.
• The host is cultured in a continuous culture system provided in bioreactor.
• A bioreactor provides optimum growth conditions (temperature, pH,

Downstream processing

• After biosynthesis inside the bioreactor, the product has to be subjected

through a series of processes before it is ready for marketing.
• The process includes separation and purification, which are collectively
referred as downstream processing.
• The product has to be formulated in suitable preservatives.
• Such formulation has to undergo through clinical trials as in case of drugs.