Biotechnology : Principles and Processes
Intoduction
Biotechnology deals with techniques of using live organisms or enzymes from organisms to produce products and processes useful to humans
In this sense, making curd, bread or wine, which are all microbe-mediated processes, could also be thought as a form of biotechnology
Introduction
However, it is used in a restricted sense today, to refer to such of those processes which use genetically modified organisms to achieve the same on a larger scale
Further, many other processes/techniques are also included under biotechnology
For example, in vitro fertilisation leading to a ‘test-tube’ baby, synthesising a gene and using it, developing a DNA vaccine or correcting a defective gene, are all part of biotechnology
The European Federation of Biotechnology (EFB) has given a definition of biotechnology that encompasses both traditional view and modern molecular biotechnology
Principles of Biotechnology
(i) Genetic engineering : Techniques to alter the chemistry of genetic material (DNA and RNA), to introduce these into host organisms and thus change the phenotype of the host organism
(ii) Bioprocess engineering : Maintenance of sterile (microbial contamination-free) ambience in chemical engineering processes to enable growth of only the desired microbe/eukaryotic cell in large quantities for the manufacture of biotechnological products like antibiotics, vaccines, enzymes, etc
Let us now understand the conceptual development of the principles of genetic engineering
You probably appreciate the advantages of sexual reproduction over asexual reproduction
The former provides opportunities for variations and formulation of unique combinations of genetic setup, some of which may be beneficial to the organism as well as the population
Asexual reproduction preserves the genetic information, while sexual reproduction permits variation
Traditional hybridisation procedures used in plant and animal breeding, very often lead to inclusion and multiplication of undesirable genes along with the desired genes
The techniques of genetic engineering which include 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 the target organism
Do you know the likely fate of a piece of DNA, which is somehow transferred into an alien organism? Most likely, this piece of DNA would not be able to multiply itself in the progeny cells of the organism
But, when it gets integrated into the genome of the recipient, it may multiply and be inherited along with the host DNA
This is because the alien piece of DNA has become part of a chromosome, which has the ability to replicate
In a chromosome there is a specific DNA sequence called the origin of replication, which is responsible for initiating replication
Therefore, for the multiplication of any alien piece of DNA in an organism it needs to be a part of a chromosome(s) which has a specific sequence known as ‘origin of replication’
Thus, an alien DNA is linked with the origin of replication, so that, this alien piece of DNA can replicate and multiply itself in the host organism
This can also be called as cloning or making multiple identical copies of any template DNA
Let us now focus on the first instance of the construction of an artificial recombinant DNA molecule
The construction of the first recombinant DNA emerged from the possibility of linking a gene encoding antibiotic resistance with a native plasmid (autonomously replicating circular extra-chromosomal DNA) of Salmonella typhimurium
Stanley Cohen and Herbert Boyer accomplished this in 1972 by isolating the antibiotic resistance gene by cutting out a piece of DNA from a plasmid which was responsible for conferring antibiotic resistance
The cutting of DNA at specific locations became possible with the discovery of the so-called ‘molecular scissors’– restriction enzymes
The cut piece of DNA was then linked with the plasmid DNA
These plasmid DNA act as vectors to transfer the piece of DNA attached to it
You probably know that mosquito acts as an insect vector to transfer the malarial parasite into human body
In the same way, a plasmid can be used as vector to deliver an alien piece of DNA into the host organism
The linking of antibiotic resistance gene with the plasmid vector became possible with the enzyme DNA ligase, which acts on cut DNA molecules and joins their ends
This makes a new combination of circular autonomously replicating DNA created in vitro and is known as recombinant DNA
When this DNA is transferred into Escherichia coli, a bacterium closely related to Salmonella, it could replicate using the new host’s DNA polymerase enzyme and make multiple copies
The ability to multiply copies of antibiotic resistance gene in E. coli was called cloning of antibiotic resistance gene in E. coli
You can hence infer that there are three basic steps in genetically modifying an organism —
(i) identification of DNA with desirable genes;
(ii) introduction of the identified DNA into the host;
(iii) maintenance of introduced DNA in the host and transfer of the DNA to its progeny
Tools of Recombinant DNA Technology
Now we know from the foregoing discussion that genetic engineering or recombinant DNA technology can be accomplished only if we have the key tools, i.e., restriction enzymes, polymerase enzymes, ligases, vectors and the host organism
Let us try to understand some of these in detail
Restriction Enzymes
In the year 1963, the two enzymes responsible for restricting the growth of bacteriophage in Escherichia coli were isolated
One of these added methyl groups to DNA, while the other cut DNA
The later was called restriction endonuclease
The first restriction endonuclease–Hind II, whose functioning depended on a specific DNA nucleotide sequence was isolated and characterised five years later
It was found that Hind II always cut DNA molecules at a particular point by recognising a specific sequence of six base pairs
This specific base sequence is known as the recognition sequence for Hind II
Besides Hind II, today we know more than 900 restriction enzymes that have been isolated from over 230 strains of bacteria each of which recognise different recognition sequences
The convention for naming these enzymes is the first letter of the name comes from the genus and the second two letters come from the species of the prokaryotic cell from which they were isolated, e.g., EcoRI comes from Escherichia coli RY 13
In EcoRI, the letter ‘R’ is derived from the name of strain
Roman numbers following the names indicate the order in which the enzymes were isolated from that strain of bacteria
Restriction enzymes belong to a larger class of enzymes called nucleases
These are of two kinds; exonucleases and endonucleases
Exonucleases remove nucleotides from the ends of the DNA whereas, endonucleases make cuts at specific positions within the DNA
Each restriction endonuclease functions by ‘inspecting’ the length of a DNA sequence
Each restriction endonuclease recognises a specific palindromic nucleotide sequences in the DNA
Do you know what palindromes are? These are groups of letters that form the same words when read both forward and backward, e.g., “MALAYALAM”
As against a word-palindrome where the same word is read in both directions, the palindrome in DNA is a sequence of base pairs that reads same on the two strands when orientation of reading is kept the same
For example, the following sequences reads the same on the two strands in 5’$\rarr$ 3’ direction
This is also true if read in the 3’$\rarr$ 5’ direction Restriction enzymes cut the strand of DNA a little away from the centre of the palindrome sites, but between the same two bases on the opposite strands
This leaves single stranded portions at the ends
These are named so because they form hydrogen bonds with their complementary cut counterparts
This stickiness of the ends facilitates the action of the enzyme DNA ligase
Restriction endonucleases are used in genetic engineering to form ‘recombinant’ molecules of DNA, which are composed of DNA from different sources/genomes
When cut by the same restriction enzyme, the resultant DNA fragments have the same kind of ‘sticky-ends’ and, these can be joined together (end-to-end) using DNA ligases (Figure 9.2)
You may have realised that normally, unless one cuts the vector and the source DNA with the same restriction enzyme, the recombinant vector molecule cannot be created
Separation and isolation of DNA fragments : The cutting of DNA by restriction endonucleases results in the fragments of DNA
These fragments can be separated by a technique known as gel electrophoresis
Since DNA fragments are negatively charged molecules they can be separated by forcing them to move towards the anode under an electric field through a medium/matrix
Nowadays the most commonly used matrix is agarose which is a natural polymer extracted from sea weeds
The DNA fragments separate (resolve) according to their size through sieving effect provided by the agarose gel
Hence, the smaller the fragment size, the farther it moves
Look at the Figure 9.3 and guess at which end of the gel the sample was loaded
The separated DNA fragments can be visualised only after staining the DNA with a compound known as ethidium bromide followed by exposure to UV radiation (you cannot see pure DNA fragments in the visible light and without staining)
You can see bright orange coloured bands of DNA in a ethidium bromide stained gel exposed to UV light (Figure 9.3)
The separated bands of DNA are cut out from the agarose gel and extracted from the gel piece
This step is known as elution
The DNA fragments purified in this way are used in constructing recombinant DNA by joining them with cloning vectors