Biotech Class Notes

CA - S&T - 1224
Contents
1. Basics ....................................................................................................................................................... 2
DNA ..........................................................................................................................................................................2
RNA...........................................................................................................................................................................3
1.2 Protein synthesis .............................................................................................................................................4
Transcription .........................................................................................................................................................4
Translation..............................................................................................................................................................4
Genome sequencing .............................................................................................................................................4
2. Gene editing ............................................................................................................................................ 4
How gene editing is done ..............................................................................................................................4

Recombinant DNA technology ...........................................................................................................................5
CRISPR-cas9 technology .....................................................................................................................................6
Types of cells (from perspective of Gene editing) ..................................................................................... 6
Types of gene editing ...........................................................................................................................................7

Gene therapy..........................................................................................................................................................7
Animal cloning ............................................................................................................................................. 8
3- Parent baby .....................................................................................................................................................10

GM crops in India ................................................................................................................................................12
Stem cells ................................................................................................................................................... 12
Stem cell therapy ................................................................................................................................................14
3. Virus, Infection and Immune system ................................................................................................... 14
How a virus infects the body? ..........................................................................................................................14

Immunity ...............................................................................................................................................................15
Rapid antigen test for COVID ...........................................................................................................................16
PCR reaction (RT PCR Test - Reverse Transcription-Polymerase Chain Reaction) .............................16
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1. Basics
DNA
• Nucleic acid present in all organism: in the form of DNA and RNA.
• The structure of DNA defines the basic genetic makeup of the body.
• It carries and transmits the hereditary material/genetic instruction from parents their
generation.
• Works for production of proteins.
• Structure of DNA
o The DNA molecule consists of two strands that wind around one another to form a
shape known as a double helix.
o Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate
groups.
o Attached to each sugar is one of four bases--adenine (A), cytosine (C), guanine (G),
and thymine (T).
o The two strands are held together by bonds between the bases; adenine bonds with
thymine, and cytosine bonds with guanine.
• Significance of DNA in today’s life-
oUnderstanding its structure and function has helped to the investigation of disease
pathways.
o Prediction of an individual’s genetic susceptibility to specific diseases.
o To diagnose the genetic disorder for making drugs.
• Application of DNA-
o Solving crimes
o Identifying human remains
o Testing for paternity
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o Genetic testing.
o Develops genetically transformed plants.
RNA
• Structure of RNA
o RNA consists of ribose nucleotides (nitrogenous bases appended to a ribose sugar)
attached by phosphodiester bonds, forming strands of various lengths.
o The nitrogenous bases in RNA are adenine, guanine, cytosine, and uracil, which
replaces thymine in DNA.
• Utility of RNA
o Helps in synthesis of protein in our body.
o Production of new cells in human body.
o Translation of DNA into proteins.
o Messenger between ribosome and the DNA.
• Types of RNA
o tRNA (transfer RNA)- choose the right protein required by the body , which then
helps the ribosomes.
o rRNA (ribosomal RNA)- synthesis and translation of m RNA into proteins.
o mRNA ( messenger
RNA)-transfers the
genetic material to
ribosomes and pass
the instructions
about the type
proteins, necessary
for blood cells.
o Genome: A genome
is the complete set
of genetic
information in an
organism. It
provides all of the
information the
organism requires
to function.
o Transcriptome: The
term
"transcriptome" can
also be used to
describe the array
of mRNA transcripts
produced in a particular cell or tissue type. So a transcriptome is the full range of
messenger RNA, or mRNA, molecules expressed by an organism.
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1.2 Protein synthesis
• Protein synthesis is the process in which cells make proteins. It occurs in two stages:
transcription and translation.
Transcription
o It is the transfer of genetic instructions in DNA to mRNA in the nucleus.
o After the mRNA is processed, it carries the instructions to a ribosome in the cytoplasm.
o Thus, transcription is regarded as the first step of gene expression.
Translation
o Translation occurs at the ribosome, which consists of rRNA and proteins
o The instructions in mRNA are read, and tRNA brings the correct sequence of amino acids
to the ribosome.
o Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain.
o After a polypeptide chain is synthesized, it may undergo additional processing to form
the finished protein.
Genome sequencing
• Genome is a full set of DNA in an individual.
• Figuring out the order of DNA nucleotides, or bases, in a genome (the complete set of
genetic material in an organism.) –the human genome is made up of over 3 billion of genetic
letter.
• The sequence tells us the kind of genetic information which is carried in a particular DNA
segment.
2. Gene editing
• It is a process of
changing an organism’s
DNA. Using this
genetic material is
added, removed or
altered at specific
location in the
genome.
How gene editing is done

• Enzymes which cut
DNA are known as
engineered nucleases.
• It is performed using
enzymes, particularly nucleases whose purpose is to target a specific DNA sequence, where
they introduce cuts into the DNA strands which enables the removal of existing DNA and the
insertion of replacement DNA.
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Applications-
1. Treating inherited diseases→ sickle cell anemia

2. Helps to understand what specific genes do.
3. Prevents inheritance of genetic diseases.
4. Generates more resilient crops.
5. Detecting species in environment.
Recombinant DNA technology

Recombinant DNA (rDNA) is a technology that uses enzymes to cut paste together DNA sequence of
interest. The recombinant DNA sequence can be placed into vehicle called vectors that ferry the
DNA into a suitable host cell where it can be copied or expressed.
Steps involved in process are:
1. Isolation of genetic material: it is to isolate the desired DNA in its pure form I.e. free from
other macromolecules.
2. Restriction enzyme digestion: restriction enzymes act molecular scissors that cut DNA at
specific locations. These reaction are called restriction enzyme digestion.
3. Amplification using PCR: polymerase chain reaction or PCR is a method of making multiple
copies of a DNA sequence using the enzyme z-DNA polymerase in vitro.
4. Ligation of DNA molecules: the process of joining two pieces together using the enzyme
DNA ligase is a ligation.
• The resulting DNA molecules is a hybrid of two DNA molecules
• Hence this new hybrid DNA is also called a rDNA molecule and technology is
referred as recombinant DNA technology.
5. Insertion of recombinant DNA into host
6. Isolation of recombinant cells.
Applications-
• Disease diagnosis- used to detect the presence of HIV in a person.

• Food and agriculture- manufacture of GM crops and climate resilient crop.
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• Medicines- production of
insulin.
• Gene therapy- it is used an
attempt to correct the gene
defects which give rise to
hereditary diseases.
• Development of vaccines and
recombinant hormones.
CRISPR-cas9 technology
• It is part of adaptive
immunity system used by
bacterial cells to recognize
and destroy viral DNA.
• CRISPR (Clustered Regularly
Interspaced Short
Palindromic Repeats): They
are sections of DNA,
containing short repetitions
of base sequences followed
by spacer DNA segments.
• CAS-9 (CRISPR-associated protein 9): It is an enzyme. It relies on guide RNA to find the DNA
sequence of interest. It will then introduce a double strand break at a specific location
within a strand of DNA.
Types of cells (from perspective of Gene editing)

Somatic cells Stem cell Reproductive cell
• Somatic cells are • Stem cells are body’s • A cell whose nucleus
diploid cells, which raw material, i.e. cells unites with that of a cell
contain two pairs of from which all other of the opposite sex to
chromosomes, one cells with specialized form a new organism→
received from each functions are reproductive cell.
parent. generated. • Gametes are an
• Any cell other than • They can divide organism's
germ cells (sperm and through mitosis→ reproductive cells→ sex
egg), gametocytes (cells single cell divided into cells.
that divide to form two identical daughter • Female gametes are
germ cells), and cells. called ova or egg cells,
undifferentiated stem • Limitlessly to replenish and male gametes are
cells are known as other cell types of called sperm.
somatic cells. multi-cellular • Gametes →these are
• Somatic cells are not organisms throughout haploid cells, and each
capable of producing their life. cell carries only one
offspring. But, they • After stem cell division, copy of each
form all the internal each newly produced chromosome.
organs and tissues and cell can either remain • Gamete is capable of
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contribute to their as a stem cell or fusing with another
functionalities. differentiate to form haploid reproductive
• They are responsible any other cell type with cell to form a diploid
for growth, repair and more defined functions, zygote. The zygote is
regeneration. such as muscle cell, formed by the fusion (or
• Some of the specialized blood cell, or neural combining) of two
somatic cells are: cell. gametes, i.e. male
- Skin cells • Types of stem cells: gamete and female
- Muscle cells - Embryonic Stem gamete. This union of
- Nerve cells Cells. gametes resulting in a
- Blood cells. - Embryonic germ zygote is called
cells. fertilization.
- Adult Stem Cells. • These reproductive
• Application – cells are produced
- Treatment of brain through meiosis.
diseases.
- Treatment of blood
diseases.
- Treatment of
cardiovascular.
- Tissue
regeneration.
Types of gene editing

1. Germline editing: genome of an individual is edited in a way that the change is heritable.
This is achieved through genetic alterations within the germ cells, or the reproductive cells,
such as the egg and sperm.
2. Somatic cell gene editing: introduction of genes into bone marrow cells, blood cells, skin
cells that will not be inherited later generations.
Gene therapy
• It is a therapy that uses genes to prevent diseases.
• It might allow doctors to treat a disorder by inserting a gene into a patients cells instead of
using drugs or surgery.
• Types of gene therapy- somatic cell gene therapy and germline gene therapy.
• Advantages
o Gene therapy has the potential to eliminate and prevent hereditary disease.
o It is possible to cure heart diseases, cancer and AIDS.
o It can be used to discard diseases from the future generation.
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GM crops
• Genetically modified plants/crops →using genetic engineering methods.

• Crops are genetically modified in order to introduce a trait with one of these properties –
o To increase the nutritional content, which the soil cannot provide.
o To increase the crop yield.
o Make them resistant to harsh atmospheric /environmental conditions such as
high/low temperature, salinity.
o To make them insect resistant.
Animal cloning
Cloning – it is the process of generating identical copy of a cell or an organism.
Animal cloning
• Procedure of creating a whole new multi-cellular organism which is genetically identical to

original organism.
• Non-sexual process
• No fertilization or inter-gamete contact takes place.
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Different levels of cloning
• Molecular cloning
- Isolation of DNA sequence from any species (often a gene) in its insertion into a vector
(host bacterium) for propagation without alteration.
• Cellular cloning
- Copies of cells are made resulting in the formation of identical cells from a single cell.
This type of cloning is used in stem cell research.
• Organism cloning.
- A multi-cellular organism is created, genetically identical to other organism.
Types of cloning
• Gene cloning
- It creates copies of genes or segments of DNA.
• Reproductive cloning
- It involves the implantation of a cloned embryo into a real or an artificial uterus. The
embryo develops into a fetus that is genetically identical to the donor of the original
nucleus.
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• Therapeutic/ biomedical cloning
- It is used to clone embryos for the purpose of extracting stem cells for use in replacing
or repairing damaged tissues or organs, achieved by transferring a diploid nucleus from
a body cell into an egg whose nucleus has been removed.
Applications of cloning-
• Biomedical- disease models, bioreactors.

• Agricultural –
- can be used to create copies of animals with highly valued traits, like dairy cow with high
milk production
- Livestock improvement
- Genetic improvement
- Conservation of endangered species.
• Research
- Stem cell research
- Understanding embryology.
Criticism
• Cloning contradicts natural reproductive process and hence has its negative effects-
• Sometimes a clone is not able to perform metabolic process like eating, drinking, etc.
• Clone may have short life span.
• They can experience developmental anomalies.
• Reproductive cloning is considered unnatural by some and hence it can violate religious
belief.
First cloning of a sheep (dolly)
Feb 1997, Ian Wilmut and his colleagues at the Roslin institute, successfully cloned a sheep, from
the mammary glands of an adult female. Dolly was the first mammal to be effectively cloned from
an adult cell. She was cloned at Scotland lived and died there only.
3- Parent baby
• A baby in which the vast majority of nuclear DNA comes from the mother and the father and
a small amount of mitochondrial DNA comes from a female donor.
• This reproductive technology focuses on reducing the effects of mutations that occur in the
DNA of mitochondria, which reside in cytoplasm. This could prevent the transmission to
their offspring of mitochondria diseases.
• There are two main techniques involved:
• Mitochondrial spindle transfer:
o Inside laboratory, scientists remove the nucleus from a healthy donor egg and
replace it with a nucleus taken from the egg cell of a woman who carries a rare
neurological disease called Leigh syndrome.
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o This leaves the donor’s healthy mitochondria intact. The scientists then fertilize the
modified egg with the father’s sperm.
o After this the 'reconstructed embryo' is implanted into the mother’s uterus.
• Pronuclear transfer:
o At the time of fertilization, genetic material is fused. One set comes from the egg and
another comes from dad’s sperm.
o At early stage in development, the two (egg and sperm) have not yet fused into a
single nucleus. This is called Pronuclei.
o Pronuclei is the central, DNA-containing parts of fertilized eggs.
o In this technique researchers fertilize the mother mouse’s egg and a donor egg at the
same time. The pronuclei are removed from the donor’s fertilized egg and discarded.
These are then transferred to an egg cell containing a healthy mitochondria.
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GM crops in India
BT COTTON
o MAHYCO: Maharashtra
hybrid corporation →
released first cotton
hybrid MECH1 in 1989.
o BT COTTON was the
first genetically
modified crop which
got commercially
accepted in 2002.
o It is developed with
resistance to the pink
bollworm pest.
o Done by genes (cry1Ab
and cry2Bc) inserted
from bacterium bacillus
thuringiensis (Bt).
HTBT COTTON
o Herbicide resistant BT
cotton.
o Inserted with ‘Cp4-Epsps’ from soil bacterium, agro bacterium tumefaciens → glyphosate
(modified protein)→makes it herbicide resistant.
o Not legal in India.
Bt BRINJAL
o Modified by inserting a gene from the soil bacterium BT which has insecticidal property.
o The gene leads to dysfunction of the digestive system of insects who feeds on the crop. And
hence they die.
o Developed by Maharashtra hybrid Seeds Company.
o Grown majorly in Andhra Pradesh, Madhya Pradesh, Tamil nadu.
*only GM COTTON is allowed presently in India.
Stem cells
• Cells are usually of two types- differentiated and undifferentiated.
• Differentiated cells- these are specialized cells to perform a unique function in the body.
• Undifferentiated cells- these are responsible for replenishing old, injured or dead cells.
• Stem cells are undifferentiated cells with the capacity to both differentiate and multiply
into the 200 cells type that form a human being.
• There are two categories of stem cells –adult stem cells and embryonic stem cells.
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• Embryonic stem cells-
1. Found in the three germ layer of the embryo.
2. Inner cell mass of the embryo contains embryonic stem cells
3. Embryonic stem cells are the most potent, as their job is to become every type of
cell in the body. The full classification includes:
o Totipotent: These stem cells can differentiate into all possible cell types. The first
few cells that appear as the zygote starts to divide are totipotent.
o Pluripotent: These cells can turn into almost any cell. Cells from the early embryo
are pluripotent.
o Multipotent: These cells can differentiate into a closely related family of cells. Adult
hematopoietic stem cells, for example, can become red and white blood cells or
platelets.
o Oligopotent: These can differentiate into a few different cell types. Adult lymphoid
or myeloid stem cells can do this.
o Embryonic stem cells are considered pluripotent instead of totipotent because they
cannot become part of the extra-embryonic membranes or the placenta.
• Adult stem cells

1. Found in differentiated tissues, but remain undifferentiated.
2. Stem cells in bone marrow are the most commonly studied type of cells.
3. Can be found in skeletal muscle, brain, blood, liver, and pancreas.
• Importance of stem cells

o To increase the understanding of how diseases may occur.
o To generate healthy cells to replace diseased cells.
o To test new drugs for safety and effectiveness.
13
Stem cell therapy
• It is the introduction of new adult stem cells into damaged tissue in order to treat an ailment
or injury.
• The ability of stem cells to self-renew and give rise to different cells that can potentially
replace diseased and damaged areas in the body with minimal side effects.
• A number of stem cell therapies exist, but most are at experimental stages, costly or
controversial.
• Any disease which involves tissue degeneration can be a potential disease for stem cell
therapies. Some of them are –
o Tissue repair
o Alzheimer’s disease.
o Heart disease
o Severe burns
o Diabetes
o Spinal cord injury
o Leukemia and cancer
o Rheumatoid arthritis.
3. Virus, Infection and Immune system

• They cannot survive on their own, they need living cells to keep themselves alive.
• They reproduce inside the living cells called host. Unlike bacteria it can survive for only few
hours without the host.
• Enters the body through nose and mouth. Can also spread through contaminated blood,
exchange of body fluids or through sexual activities (Hepatitis C and HIV).
• Can be prevented through vaccines (Chicken pox, Measles and mumps.)
• Examples of infection: influenza, COVID-19 and common cold.
• Treatment: antiviral.
How a virus infects the body?

• Entry- the virus enters the body through the nose, mouth, eyes or the skin.
• Infects- once inside the body, a virus infects host cell by injecting its genetic material.
• Hijack protein formation machinery – the virus will hijack the cell in order to make many
copies of it and to hide from the immune system.
• Spread- the host cell dies as the virus multiplies and moves into more cells. This is when the
body gets sick.
• Viruses are small pieces of RNA or DNA wrapped up in a layer of proteins, which protect the
genetic material.
• They cannot survive on their own so they need a host cell. They replicate and create other
viruses.
• It enters the body and adheres to the cell surface. It then seeks for cells in different parts of
the body (liver, respiratory system or blood.)
• When the virus is inside the cell, it will open up so that it’s RNA and DNA will come out and
go straight to the nucleus. They will enter a molecule, and make copies of the virus.
14
Immunity
• A large number of pathogenic (disease causing) microorganisms are present in the
environment that continuously interacts to our body.
• Immunity is the ability of the body to protect against all such types of foreign bodies like
bacteria, virus, and toxic substances etc. which enter the body.
• Immunity is done by immune system which is a complex network of lymphoid organs such
as bone marrow, thymus, spleen etc.
• Innate immunity
o It is also called natural and native immunity, consist of mechanism that exist before
infection and are capable of rapid responses to microbes.
o Types of innate immunity
o Physical barrier- skin on our body is the main physical barrier which prevents entry
of pathogens; mucus coating (epithelium) is present in gastrointestinal, respiratory
tracts which trap the microbes entering our body.
o Cellular barrier- at the cellular level, barriers consist of cells that are tightly held
together to prevent invaders from crossing through to deeper tissue.
o Physiological barrier- saliva in mouth, tears in eyes, acid in stomach.
Acquired immunity
• It is developed by the host in its body after exposure to suitable antigen. It is pathogen
specific and is characterized by memory.
• When a pathogen enters a body for the first time body produces a response →primary
response.
15
• When the body encounters the same pathogen again a highly intensified secondary/
anamestic response is observed.
• The primary and secondary immune response is carried out with the help of two special type
of lymphocytes present in our blood.
• Here, B-lymphocytes produce an army of protein in response to pathogens into our blood to
fight with them. T-lymphocytes do not secrete antibodies but help B-cells to produce them.
• These proteins are called antibodies.
• Types of acquired immunity
o Two types→ active and passive immunity.
o Active immunity: induced by natural exposure to a pathogen or by vaccination. Can
be categorized into two types- naturally acquired and artificially acquired active
immunity.
o Passive immunity: it is achieved by transfer of immune products, such as antibody
or sensitized T-cells, from an immune individual to non-immune one. two types-
naturally
o Acquired and artificially acquired passive immunity.
Rapid antigen test for COVID

• Rapid or fast COVID-19 test is a viral test, one of the two types of tests used to detect
COVID-19.
• Rapid antigen tests are considered to be one of the simplest and quickest ways to test for
COVID-19.
• Antigen→ any substance that the body recognizes as harmful or foreign, which induces the
immune system to produce antibodies against it.
• Rapid antigen tests identify protein fragments on the surface of the coronavirus to identify
the presence of the pathogen amongst people doing the test. Samples are taken from
subjects by swabbing inside the nose or mouth.
• procedure:
- Collect the sample by swabbing and rotating the cotton swab inside both nostril
- Place the swab inside the testing well
- Add the liquid testing solution
- Wait for 15 minutes to get a result
• In comparison to PCR tests these are less accurate.
• Advantage-
- Testing can be done outside the laboratory.
- Can be performed by the general public.
- Comparatively inexpensive.
PCR reaction (RT PCR Test - Reverse Transcription-Polymerase Chain Reaction)

• It is a technique that takes specific sequence of DNA of small amount and amplifies it to be
used for further testing. It uses enzyme DNA polymerase (enzymes that make the copies of
DNA) to synthesize new strands of DNA.
• ARS–COV–2 is RNA virus. RNA is single-stranded & very unstable, which makes it difficult to
work with. So the viral RNA needs to be converted into DNA. This process is called Reverse
Transcription (RT).
16
• Advantages-
- Small amount of DNA is required
- Result is obtained quickly and accurately.
- Not necessary to use radioactive material.
- Can be used to detect point mutations.
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CA - S&T - 1224

2. Gene editing ............................................................................................................................................ 4

How gene editing is done ..............................................................................................................................4

Types of cells (from perspective of Gene editing) ..................................................................................... 6

Types of gene editing ...........................................................................................................................................7

Animal cloning ............................................................................................................................................. 8

3- Parent baby .....................................................................................................................................................10

Stem cells ................................................................................................................................................... 12

Stem cell therapy ................................................................................................................................................14

3. Virus, Infection and Immune system ................................................................................................... 14

How a virus infects the body? ..........................................................................................................................14

How gene editing is done

1. Treating inherited diseases→ sickle cell anemia

Recombinant DNA technology

Steps involved in process are:

• Disease diagnosis- used to detect the presence of HIV in a person.

Types of cells (from perspective of Gene editing)

Types of gene editing

• Genetically modified plants/crops →using genetic engineering methods.

Cloning – it is the process of generating identical copy of a cell or an organism.

• Procedure of creating a whole new multi-cellular organism which is genetically identical to

• Biomedical- disease models, bioreactors.

First cloning of a sheep (dolly)

*only GM COTTON is allowed presently in India.

• Adult stem cells

• Importance of stem cells

3. Virus, Infection and Immune system

How a virus infects the body?

Rapid antigen test for COVID

PCR reaction (RT PCR Test - Reverse Transcription-Polymerase Chain Reaction)

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