biotechnology and bioinformatics Notes

Biotechnology and bioinformatics

Approaching the topic

  • Understanding the concepts
  • Application of these concepts 



  • They are small, have fast growth rate and metabolically diverse. These features made them significant in food industry, chemical industry and medical
  • They can be used to make food essentials like bread, cheese, yoghurt, beer and wine and antibiotics, hormones, bio-chemicals as medicine essentials.
  • The genes of these microorganisms can be altered to increase their performance or to obtain certain desirable

Pathway engineering

  • It is method to alter or modify the genetic makeup of the microorganism for to derive the products for human
  • This method can be used to obtain metabolites of interest without interfering with the normal bacterial growth and
    Why microorganism?
    • They have fast growth rate, high yielding capacity and easy to handle.
    • Are dependent on glucose for their carbon source, which is easily accessible.


  • The process of large scale culture of microorganism to produce metabolites of interest using fermenters.
    Figure 13.1 A fermenter
    • A fermenter is a large steel vessel in fitted with an impeller to prevent sedimentation of the medium i.nside
    • A sterile nutrient medium and an inoculum of desired microorganisms are filled in the vessel.
    • If the metabolic process is aerobic then gas through air bubbles is released which is determined by pressure gauge which lets it out if exceeds the limit.
    • Metabolic process inside the vessel releases heat as one of the waste products and therefore a cooling jacket filled with cool water surrounds the
    • Temperature, oxygen and pH probes are fitted to monitor the respective conditions.
    • The mentioned conditions must be maintained in order to continue the process efficiently.
  • There are two types of fermentation; fed-batch and continuous fermentation.
    • Fed-batch fermentation: In this, a fixed amount of nutrients and substrates are added at a time and no further addition is done during the incubation period. The products are extracted when reach the higher concentrations. It is used for obtaining secondary metabolites.
    • Continuous fermentation: The nutrients are added constantly and the products are harvested at the same rate.

Fed-batch production of penicillin (an antibiotic)

  • Penicillium chrysogenum is the mould used for the production of penicillin.
  • Firstly, this mould is kept in liquid medium with the glucose supply through which its gets energy and produce primary metabolite called pyruvic acid.
  • Once the concentration of the biomass by Penicillium reached a certain level, it is transferred to a batch fermenter where glucose is missing. But it has the medium containing corn steep liquor, yeast extract, lactose, pH buffers and minerals.
  • Fermenter vessel is also maintained with the temperature of 24ᵒC, pH of 6.5 and good oxygen supply as required.
  • While the Penicillium starves due to no glucose, it makes penicillin (a kind of self-defence) as a secondary metabolite. Penicillin is extracted by filtering, washing and drying processes.

Continuous-batch fermentation of citric acid

  • Citric acid is a flavour enhancer and can be used as a preservative. It is obtained by fermentation of mould Aspergillus niger.
  • High sugar concentration, acidic pH, temperature of about 30ᵒC, and high dissolved oxygen are required to maintain the optimal conditions required.
  • It is then filtered and precipitated out using calcium hydroxide.

Biogas production

  • Anaerobic microbes work in the production of biogas by breaking down organic matter such as manure, plant matter and household organic
  • Biogas is a mixture of many gases; methane (50-75%), CO2 (25-45%), Nitrogen (0-10%), water (2-7%) and H2S (0-3%).
  • The two groups of bacteria named; eubacteria and archaeabacteria work together. Eubacteria convert organic waste into acetate, CO2 and hydrogen. Then the archaeabacteria works on the products of eubacteria to produce
  • The reactions follow;

𝐶𝑂2 + 4𝐻2 → 𝐶𝐻4 + 2𝐻2𝑂


  • Series of events take place is: Liquefaction (hydrolysis of long chain compounds), acidification, acetic acid formation and at last methanogenesis.
    Figure 13.2 Fictional diagram of biogasformation

Gram staining

  • It is a method of differentiating two groups of bacteria named; gram-negative and gram-positive bacteria. These two groups are different based on their structure of cell wall. 
  • Gram-positive bacteria have thick layer of and important material peptidoglycan while gram-negative bacteria have thin layer of Also gram-negative bacteria have an outer layer of lipopolysaccharide and carbohydrates.
  • Gram staining includes certain chemicals to act on these two kinds in order to differentiate them.

Biotechnology in agriculture

Genetically modified crops

  • The technique of biotechnology makes it possible to have genetically modified crops (GM crops).
  • When a new gene is introduced in a species that offers production of the proteins that were not the part of its proteome earlier is called transgene and the organism possessing this gene is called transgenic.
  • This transfer of gene is done between the species in which, one is having the feature that could be very useful if shown by the
  • Genetically modification in crops may offer certain benefits like increased crop yields, resistance to unfavourable environmental factors
  • Examples include;
    • Soybean crops if introduced with glyphosate (a herbicide) resistant gene then it will stay unharmed by glyphosate herbicide and the weeds will be
      • Agrobacterium tumefaciens is a pathogenic bacterium that is used as a vector to transfer the desired gene into the plants. It attacks the plant and causes tumour due to its Ti plasmid (tumour inducing plasmid). This circular plasmid is altered by the ligation of new desired gene and these bacteria cells are cultured with some soybean cells.
      • Each cell in the culture is grown into new plant with glyphosate resistant gene.
  • Hepatitis B vaccine can be made by tobacco plants. Here TMV (tobacco mosaic virus) is used as vector to transfer the desired gene. TMV if altered with the gene that induces antibodies in the plant and transferred to the plant then after few days vaccine can be collected from tobacco
  • Golden rice were made using the genes daffodil plants and a bacterium with an intention to produce β-carotene which is a precursor of Vitamin-A.
  • An Amflora potato is made which produces 100% amylopectin compared to 80% in normal
  • Corn has been introduced with the CRY gene taken from Bacillus thuringiensis. It now can produces toxin which can harm corn

Means to transfer desired genes

Physical methods

  • Electroporation: Recipient cell undergoes electrical impulses which cause pores in their cell membranes which enables DNA to enter the cell and the
  • Biolistics: DNA is coated on the micro-particles of gold or tungsten and fired in a plant cell to make it transformed. This method is not used on animals because animal cells have to cell wall.
  • Microinjection: DNA is injected directly into the protoplast with a

Chemical methods

  • Transfection: A solution containing DNA with calcium-phosphate ions and the recipient cell is prepared. The cell engulfs the DNA wrapped with calcium- phosphate ions which tend to neutralise it in order to be taken by the
  • Lipofection: Liposomes (which are artificially prepared lipid with an aqueous interior). The DNA is put into the aqueous part and liposome is fused with the lipid bilayer making DNA to cross the membrane and enter the

Environmental protection


  • It is the process of using organisms, especially microorganisms to eradicate pollutants. Microorganisms have the right enzyme to break the pollutants and the products released would be neutral to the
  • They perform the breakdown of these pollutants as a part of their
  • Examples include:
    • Marinobacter acts on a hydrocarbon pollutant benzene and can turn it into simple CO2.
    • A species of Pseudomonas called Pseudomonas aeruginosa with the help of a molecule named rhamnolipid (a surfactant) can eradicate crude oil from the water bodies.
    • A bacterium named Geobacter sulfurreducens could be helpful in eradication of uranium. It makes soluble uranium to insoluble and therefore it would be settled which can be collected.
    • Mercury pollution can also be eradicated with the help of Pseudomonas. Mercury can leach into soil or water where a bacterium named Desulfovibrio desulfuricans adds a methyl group to it and makes it even more harmful. Pseudomonas acts on it and convert it into simple elemental mercuric form.


  • A biofilm is a film of aggregates of microorganism that sticks to the surface due to cooperation between individual
  • A certain biofilm may be composed of protozoan, algae, fungi and bacteria altogether. They kept united and hold together themselves and with the surface by secreting extracellular polymeric
  • Likewise as an example, dental plague may contain as many of 500 taxa of

Emergent properties

  • These are the properties shown by biofilms as a consequence of the unity of many different types of
  • These properties can be particularly mentioned as;
    • Complex structure
      The microorganism when found a surface comes closer through the means of that surface and when combined, they release ESP-extra cellular matrix which bond them even
    • Quorum sensing
      It is a system of behaviours of microorganisms to function in a cooperative They work in a way that even the gene expression can be affected by the population density.
    • At first, a small population called inducers tend to make EPS and signal some more to be inducers. Once the inducers run high the whole population is stimulated to transcribe their gene to produce EPS to make a strong
    • Likewise is the activity of Pseudomonas aeruginosa (causes lung infection). They use quorum sensing to form a biofilm in the lungs and when this biofilm turn aggressive they become resistant to immune
  • Resistance to anti-microbials agents
    • The biofilm covered around with EPS offer resistance to many anti-microbial
    • Viruses (more specifically bacteriophages) may be used to eradicate biofilm of a particular species of


  1. Trickle filter beds
    1. Biofilms are used in sewage treatment plants. A trickle filter bed is aerobic bacteria laid on surface of filter media (may be rock or plastic).
    2. The sewage water is sprayed on it and aerobic bacteria oxidise the organic matter into CO2.
    3. The treated water along with CO2 is collected in an under drainage system.
  2. Cleaning of water bodies
    1. Biofilm can be formed on the roots of the rafts in the water body. They helps in removing nitrogen and phosphorus (which are already absorbed by rafts’ roots), also copper, zinc, lead and other solids out of the water.


Genetic markers

  • These are the genetic variations in the DNA sequences if any disease is
  • They may contribute to the disease by involving in the coding sequence or may not be involve in any coding sequence but still can influence the
  • These markers could be single nucleotide polymorphs – SNPs (snips) or tandem Though mostly SNPs.
  • The marker alleles are found more frequently in people affected with any
  • These markers can tell the susceptibility to a certain disease but that disease may or may not occur in

DNA microarray

  • It is a small surface having a collection of DNA probes attached to it which can be used to identify the genetic
  • Process to identify marker follows:
    • Isolation of mRNA from a collected sample or blood or
    • Translation of mRNA into cDNA using reverse transcriptase (RT). The process is called reverse
    • cDNA is then labelled with fluorescent labels and hybridized with the known DNA probes of the
    • Excess cDNA is rinsed off (which do not get hybridized). The microarray is then put under the scanner and fluorescence is measured. The intensity of fluorescence would indicate the amount of expressed
    • More the intensity means more number of cDNA gets attached. And the gene in the probe has matched with the gene in the
  • Analysis of DNA microarray

 Polymerase chain reaction (PCR)

  • It is the most prominent tool in biotechnology to amplify any strand of DNA. Thereby found its place in detecting markers as
  • It can be used to diagnose many infecting viruses including H1N1 flu virus, influenza A and B, SARS Covid-19
  • The process follows:
    • Nasal secretions are collected, nucleotides, DNA polymerase enzyme as a primer.
    • The DNA strand extracted from the nasal secretions and denaturalised by heating.
    • The DNA is cooled and hybridization starts with the primer. Further nucleotides add up by DNA polymerase to complete the complementary strand.
    • Fluorescent is to be added already, so that the number of copies made the fluorescence would be increased and virus would be diagnosed.

ELISA – Enzyme-Linked Immunosorbent Assay

  • It is also a diagnostic tool, may be used to diagnose HIV and to test the presence of drug in blood and
  • It works on the condition that, there must be prior immune response to certain pathogen entered the body to cause any particular

Protein tracking in the body

  • Tracking experiments are done using a reporting element like green fluorescent protein (GFP) or radioactive probes to track the location or interaction of the protein molecule rolling inside the
  • Luminescent probes could also be used for tracking purposes. One of the examples of doing is tracking with
    • Quantum rods (a luminescent probe) were used in this experiment. Transferrin protein was attached with the quantum rod and let it flow in the blood stream. Transferrin receptors are present most prominently in cancer cells and therefore transferrin from quantum rod binds with its receptor.
    • The observation was, only the target cells took up the rods and thus have greater luminescence.

Gene therapy – using viral vectors

  • In this technique the viral vector could be retrovirus or
  • The process follows;
    • Disabling of the virus (genetically) to make it non-virulent.
    • Incorporation of the desired cloned gene into the virus to be delivered to the humans cells.
    • Removal of the cells that contain defective gene and then culturing them with the virus so that to transfer normal gene into the genome of the patient.
    • The genetically altered cells are reintroduced back into the body of the patient.
    • This technique may cure cystic fibrosis, haemophilia, adenosine deaminase deficiency, to name a few.

Treatment of SCID using gene therapy

SCID – Severe Combined Immunodeficiency

Patients with SCID lack a functional immune system. They seemed to have altered the ADA gene which produces an enzyme adenosine deaminase. This enzyme is responsible for immune response.

This is how a gene therapy was performed to cure:

Removal of the defected lymphocytes and then culture it with the retroviral cells containing normal ADA producing gene.

The normal gene is then incorporates into the cells and they are then reintroduced.


  • The idea of biopharming was that, if the edible vaccines could be produced (like vaccine in crop) then the antigens would be produced which could stimulate the release of antibiotics and thus provided
  • Genetically modified animals or transgenic animals are also the means of They are made to get the desired product along with the benefits they already provide.
  • Biopharming of anti-thrombin is done using goats. This could be helpful for haemophilic patients as they genetically lost their capacity to control out blood flow from any



  • It is the collection of articles, images, quantitative and qualitative information etc. stored in
  • Bioinformatics is prominent in genomics. It uses information technology and computer to help us understand biological
  • There are some major databases like:
    • GenBank, it has the collection of all publicly available DNA sequences.
    • Ensembl, it has genomic information about humans and other vertebrates.
    • Swiss-Prot, database of protein sequences.
    • Protein Data Bank (PDB), three-dimensional structure databases.
    • KEGG (Kyoto Encyclopedia of Gene and Genomes), databases having information about enzymes and reactions used in metabolic pathways.
    • EMBL (The European Molecular Biology Laboratory), nucleotide sequences database.

EST – Expressed sequence tag

  • It is a small fragment cDNA and can be used to locate or to determine the sequence of the
  • It the sequence of a gene could be determined then its function can also be

Cladograms and phylograms

  • Bioinformatics tools can help in constructing evolutionary relationship
  • By comparing nucleic acid and proteins databases from many organisms, evolutionary relationship can be
  • A cladogram shows only the branching pattern where the lengths of the branches do not indicate the time spans. While in phylograms the length of the branches indicate the time spans and relative amount of

BLAST – Basic Local Alignment Search Tool

    • It is a tool used to search the databases and to find the regions of similarities between
  • BLASTn and BLASTp searches; BLASTn is for the nucleotide search, if we found any alignment with nucleotide sequences of other organism in the database. BLASTp is for the protein search, it compares the protein
  • The function of an unknown sequence can be identified by searching the database for a similar sequence if identified earlier in an organism


It is also one of the methods to determine the function of the gene. Just to knock out the gene whose function we wish to know and later see the consequences. Knocking out is done by replacing functional sequence with the non-functional sequence in the stem cells. The loss of the functional genomic sequence will definitely result in detectable change in phenotype like seen in mice when its leptin production gene was knocked out.