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hello CD team, please post target mains questions for this week (24/12/17)

Before we deep-dive into the topic, have a look at the TED talk below.

Broadly speaking, Stem cells is a naïve/immature/unspecialized cell that can 

i. divide to form similar cells (self renewal) and

ii. develop into different specialized cells that perform distinct function

A. Classification of Stem Cells

Depending on their ability (potency) to develop into different specialized cells, stem cells can be

• Totipotent – can form all cells of the body including the ones in the extra embryonic membranes (placenta). In humans, the 2 cell staged zygote is totipotent
• Pluripotent – can become virtually any cell in the body except those needed to support and develop a fetus in the womb
• Multipotent(limited ability to differentiate) -can give rise only to a small number of different cell types. Eg. bone marrow contains multipotent stem cells that can give rise to all blood cell types but not other cells.   
• Unipotent – Found in adult tissues, unipotent stem cell has the lowest differential potential of all the stem cells.

Depending on from where they come from different places in the body or are formed at different times in our lives. These include

 Embryonic stem cells (ESCs) which exist only at the earliest stages of development

 Adult stem cells also called somatic stem cells that appear during fetal development and are present in different tissues of our bodies throughout life.

 Induced pluripotent stem cells or iPSCs cells are not found in the body but engineered in a laboratory from cells of the body, such as those from the skin. The iPSC cells have properties similar to those of embryonic stem cells.

A fertilised egg has a totipotency for about 3-4 days. It then remains turns into a multipotent cell. Finally specializes further.

B. Stem Cell Therapy

• It is a type of treatment option that uses a patient’s own stem cells to repair damaged tissue and repair injuries.
• It is used to treat more than 80 disorders including neuromuscular and degenerative disorders. Eg. Bone-marrow transplant is used in Leukemia(blood cancer), sickle-cell anemia, immunodeficiency disorders. 
• Stem cells are usually taken from one of the two areas in the patient’s body: bone marrow or adipose (fat) tissue in their upper thigh/abdomen. Because it is common to remove stem cells from areas of stored body fat, some refer to stem cell therapy as “Adipose Stem Cell Therapy” in some cases.
• Once stem cells are removed from one of these locations, they are placed in a “centrifuge machine” that spins them very, very quickly and concentrates the substances that are most valuable (including up to seven different types of natural growth factors).
• The sample of concentrated stem cells is then injected directly into the patient’s affected, painful area− allowing the cells’ growth factors to go to work immediately, building new skin cells, connective tissue and so on.

C. Advantages

• Immense Medical Benefits: It offers a lot of medical benefits in the therapeutic cloning and regenerative medicine
• Treatment of Conditions and Disorders: It shows great potential in the treatment of a number of conditions like Parkinson’s disease, spinal cord injuries, Alzheimer’s disease, schizophrenia, cancer, diabetes and many others.
• A Better Knowledge of human growth: It helps the researchers know more about the growth of human cells and their development.
• The stem cell research can allow the scientists to test a number of potential medicines and drugs without carrying out any test on animals and humans. The drug can be tested on a population of cells directly.
• Cure development defects before they happen: The stem cell therapy also allows researchers to study the developmental stages that cannot be known directly through the human embryo and can be used in the treatment of a number of birth defects, infertility problems and also pregnancy loss. A higher understanding will allow the treatment of the abnormal development in the human body.
• Reduced risk of rejection: The stem cell therapy puts into use the cells of the patient’s own body and hence the risk of rejection can be reduced because the cells belong to the same human body.

D.Challenges in SCT

• Destruction of blastocysts: The use of the stem cells for research involves the destruction of the blastocysts that are formed from the laboratory fertilization of the human egg.
• Unknown side-effects: Like any other new technology, it is completely unknown what the long-term effects of such an interference with nature could be
• Limitations of adult cells: The disadvantage of adult stem cells is that the cells of a particular origin would generate cells only of that type, like brain cells would generate only brain cells and so on.
• Potential Rejection: If the cells used in the therapy are embryonic, then the cells will not be from the same human body and there are chances of rejection.
• Potential use in negative activities: It can be used to create bio-weapons or weapons of mass destruction

E.Applications of SCT

• Orthopedic injuries and musculoskeletal problems
• Wounds and incisions following surgeries
• Spinal cord injuries, brain trauma and spinal stenosis
• Cardiovascular diseases, including hypertension, coronary heart disease, stroke and congestive heart failure
• Hair loss
• Vision impairment
• Diabetes and other pancreatic dysfunctions
• Neurodegenerative diseases such as Parkinson’s, multiple sclerosis and Alzheimer’s

F. India and Stem Cell Therapy

• According to the Indian Council of Medical research, all stem cell therapy in India considered to be experimental except bone marrow transplants
• Stem cell therapy is legalized in India
• Umbilical cord and adult stem cell treatment are considered permissible
• Embryonic stem cell therapy and research is restricted

N4S

Genetic Engineering concepts, specially their applications highlight the practical implications of Biotechnology. Hence, they become the most important area for UPSC. Students are expected to be thorough with it.

Genetic Engineering is an overarching term referring to modification of an organism’s genome. Here is a summary video outlining important techniques and applications which you might find interesting.

The techniques of genetic engineering include the creation of recombinant DNA, use of gene cloning and gene transfer.

A. Recombinant DNA technology

Recombinant DNA technology involves several steps in specific sequence such as

1.isolation of DNA,

2.fragmentation of DNA,

3.isolation of a desired DNA fragment,

4.ligation of the DNA fragment into a vector,

5.transferring the recombinant DNA into the host,

6.culturing the host cells in a medium at large scale and extraction of the desired product.

The DNA molecule thus produced is called recombinant DNA.

B. Gene Cloning

It is the creation of a genetic copy of a sequence of DNA or of the entire genome of an organism.

It is usually done through two approaches: Somatic Cell Nuclear Transfer(SCNT) and Artificial Embryo Twinning

1.Somatic Cell Nuclear Transfer(SCNT)

• A somatic cell is any cell of a living organism other than the reproductive cells
• The nucleus of a somatic cell is removed and kept, and the host’s egg cell is kept and nucleus removed and discarded
• The kept nucleus is then fused with the ‘deprogrammed’ egg cell. After being inserted into the egg, the lone somatic cell nucleus is reprogrammed by the host egg cell
• The egg, now containing the somatic cell’s nucleus is stimulated with a shock and will now begin to divide.
• After multiple divisions, the single cell forms a blastocyst(an early stage embryo) with almost identical DNA to the original organism.
• Dolly the sheep was the first animal ever to be cloned using SCNT
• There are two possible uses of SCNT:
  • Therapeutic Cloning: Creating cloned human embryos are not implanted into a female uterus rather used in research and therapy to obtain stem cells
  • Reproductive Cloning: Creating cloned human embryos with the intention of placing them into the uterus where it can implant and develop

2. Artificial Embryo Twinning

https://www.youtube.com/watch?v=FvjWKip6Pm8

• This technology mimics the natural process of creating identical twins
• The early stage embryo is manually separated into individual cells and allowed to divide and develop on their own.
• The resulting embryos are placed into a surrogate mother, where they are carried to term and delivered. As the embryos came from the same zygote(fertilized egg), they are genetically identical.

Summing up the similarities and differences

C. Gene Silencing

Certain genes in a cell may be defective and could cause undesirable traits. The process of regulation or suppression of such genes is called Gene Silencing.

RNA Interference(RNAi) and Antisense Technology are two common processes by which this is achieved. More details are not required.

D. CRISPR-Cas9

CRISPR-Cas9 technique has appeared extensively in news

Salient features

• CRISPR-Cas9 is a genome-editing tool. CRISPR is a naturally occurring defence mechanism in bacteria.
• The CRISPR-Cas9 consists of two molecules that are responsible for gene editing.
  • An enzyme called Cas9 that acts as a pair of molecular scissors that cuts the two strands of DNA at a specific location
  • A guide RNA(gRNA) that binds to DNA and guides the Cas9 to the right part of the genome
• The gRNA is designed to find and bind to a specific sequence in the DNA. The gRNA has bases that are complementary to those of the target DNA sequence.
• The Cas9 follows the gRNA to the same location in the DNA sequence and makes a cut across both strands of the DNA
• At this stage, the cell recognizes that the DNA is damaged and tries to repair it
• Scientists can use the DNA repair machinery to introduce changes to one or more genes in the genome of the cell of interest.

E. Gene splicing

Gene splicing is the process of chemically cutting DNA in one organism and inserting it into the DNA strand of a vector, usually a plasmid. The DNA is cut using special chemicals called restriction enzymes. Through this technique, microorganisms are genetically engineered. Gene splicing primarily involves the following steps

1.Cutting of DNA or genes from the donor cell.

Tool Used – Chemicals called restriction enzymes. Restriction enzymes are chemicals extracted from certain strains of bacteria. Different restriction enzymes recognize and cut at particular nuclear sequences.

2.Transportation of the cut or desired DNA

A.DNA Micro injection – Direct Micro-injection of the chosen gene.

B.Retrovirus mediated gene transfer. Retroviruses are used as vectors to transfer genetic material taking advantage of their natural ability to infect host cells and insert their DNA into host cell DNA.

C.Embryonic Stem Cell mediated gene transfer.

APPLICATIONS

A. Three-parent babies

Three-parent babies have repeatedly remained in news. The world’s first three-parent baby was born in 2016 in Mexico to Jordanian parents.

In 2017, UK became the first country to give licenses to use this technique to prevent incurable genetic diseases being inherited by children.
Remember we had very briefly touched upon the Mitochondria when we discussed the Cell and the Nucleus. Mitochondria contains mtDNA and mutations in it can give rise to various genetic disorders. Since mtDNA is transferred from mother to child, these disorders are also transferred. The three-parent babies technique tries to overcome this shortcoming by preventing the transfer of mitochondria from mother to child.

There are 2 versions – Pronuclear Transfer and Spindle Transfer

Pronuclear Transfer

Spindle Transfer

https://www.sciencenewsforstudents.org/article/how-make-three-parent-baby

B.Gene Therapy

It is a technique through which a new DNA is introduced into a patient to treat a genetic disease. The new DNA usually contains a functioning gene to correct the effects of a non-functioning or disease causing gene.

A four-year old girl became the first gene therapy patient. She had adenosine deaminase (ADA) deficiency, a genetic disease which left her defenseless against infections.

There are two types of gene therapy:

Somatic Gene Therapy: The genes are transferred into the somatic cells of a patient. Any modifications and effects will be restricted to the individual patient only and will not be inherited by the offspring.

Germline Gene Therapy: The genes are transferred into the germ cells(sperm or eggs). This would allow the therapy to be heritable and passed onto the offspring.

C. Genetic Modification of Plants(GM Crops)

The DNA of plants used in agriculture are modified using genetic engineering techniques

There are two primary processes through which plants are modified:

Cisgenic: Genes are artificially transferred between organisms that could be conventionally bred i.e. from a crossable or sexually compatible plant.

Transgenic: Genes from a non-plant species or from a donor plant that is sexually incompatible with the recipient plant are inserted, which is a form of horizontal gene transfer

Biotech firms make use of the following technologies to ensure sterile seeds and crops with specific properties

Terminator Technology: It is the genetic modification of plants to make them produce sterile seeds. They are also known as suicide seeds.

Traitor Technology: Traitor technology can allow traits in genetically modified seeds to be switched on and off by using special proprietary chemicals.

D. In-vitro Fertilization

https://www.youtube.com/watch?v=J1xHUA_fiQ4

It is the process of fertilization by extracting eggs, retrieving a sperm sample, and then manually combining an egg and sperm in a laboratory dish. The embryo(s) is then transferred to the uterus to induce pregnancy.

N4S

Biotechnology is one of the most important topics with at least 1 question in both prelims and mains year after year. Nevertheless, it remains a major pain point for students. They have issues right from understanding the most basic terms like chromosomes, DNA, RNA, gene, codons, amino acids, proteins, etc. to recent breakthroughs.

Understanding the level of depth expected by the exam is the key to cracking the topic. NCERTs and other reference books are detailed and technical than required.

We will start with the basics, develop a conceptual understanding and then move to contemporary breakthroughs.

The figure below depicts the basic hierarchy within a cell.

1. Cell

Cells are basic building blocks of all living organisms. Cells make up tissues which makeup organs and then organ systems further on.

There are 2 kinds of cells – Prokaryotic(pro=before and karyos=nucleus) and Eukaryotic(eu=with)

Prokaryotic Cells – These are simpler more archaic cells lacking most basic cell organelle including nuclei. DNA is present in the cytoplasm. Eg.Bacteria

Eukaryotic Cells – These cells are well differentiated and contain many cell organelle. The genetic material is sequestered inside the nucleus. All plant and animal cells are examples of eukaryotic cells.

https://www.difference.wiki/prokaryotic-cell-vs-eukaryotic-cell/

The organelles of Animal and Plant cells are highlighted in the figure given below.

We will discuss the two most important organelles from the point of view of the exam.

Nucleus – contains all the genetic material(code to replicate the cell and conduct all its functions). Genetic material is in the form of Chromosomes.

Mitochondria – Besides the nuclear DNA contained in the nucleus, cells have organelles called Mitochondria which contains Mitochondrial DNA or mtDNA or Maternal DNA. This is exclusively passed down from mothers to children(we do not inherit any Mitochondrial DNA from our fathers). We will revisit this organelle again when we discuss 3-parent-baby technique.

The rest are given in the table below –

In the next segment, we will cover Chromosomes, DNA, and Genes. The following figure will come in handy.

2. Chromosomes

Chromosomes are thread-like structures present in the nucleus.

These are nothing but DNA tightly coiled around a protein called histone. (just like a thread wound around a cardboard tube).

From the above figure, you can conclude,

• Chromosomes exist in pairs. Human cells contain 23 such pairs or 46 chromosomes.
• Each chromosome is comprised on one super-long DNA molecule.
• Notice how the DNA is coiled around histone and then many such histones are packed together to form a chromosome.

3. Deoxyribonucleic Acid(DNA)

https://i.pinimg.com/736x/73/6c/eb/736ceb06de3858d85d5b8669845f912c–complementary-dna-nitrogenous-base.jpg

DNA is called the blueprint of life because it contains the genetic code which are instructions needed for an organism to grow, develop, survive and reproduce. DNA does this by controlling protein synthesis, a process we will explain later but not in much detail. For now, simply understand that Proteins are the most important material in our body. Many would associate them with muscles but they also aid the production of enzymes which are responsible for conducting all chemical processes and reactions within the body. So, it could be derived that protein synthesis is responsible for all activities carried on by the body and it is controlled by the genes.

The famous Double Helix model for the structure of DNA as shown in the above image is one of the most well-known models.

The salient features

• It is a twisting structure made up of 2 polymer chains. The ‘backbone’ of each chain is constituted by sugar-phosphate and connecting ladders of nitrogenous bases project inside. The figure above shows the backbone marked with ‘S’ and ‘P’ indicating alternating sugar and phosphates.
• The polymer chain comprises of smaller monomers called nucleotides.
• Each nucleotide has 3 parts – a sugar(ribose), a phosphate molecule and a nitrogenous base.
• There are 4 kinds of Nitrogenous Bases – Adenine(A), Thymine(T), Guanine(G) and Cytosine(C). These bases are complementary. A attaches with T and C attaches with G to form complementary pairs that make up the connecting attachments of the double helix model.

4. Genes and Alleles

Genes, as we know, are hereditary markers from which we derive various characteristics like skin color, height, etc. More technically, each DNA molecule consists of sequences of Genes. Each gene is a particular set of instructions for specific functions. Eg. globin gene would aid the production of hemoglobin, another gene would do so for insulin, so on and so forth. Each gene naturally consists of a sequence of nucleotides and base pairs.

Alleles are alternate form genes which correspond to the same characteristic but provide for variations in that characteristic. A very crude example is as follows –

Assume a hen. A particular gene would be responsible for the color of its feathers, say black and white. Hence we say the same gene has 2 variants. Hence they are known as Alleles. Naturally, the nucleotide sequence in them will differ.

5. Codons, Amino acids, Peptides, and Proteins

While describing DNA, we said that it helps with Protein Synthesis, a very fundamental process to sustain life. The concept of codons helps establish the link between Genes and protein synthesis reactions.

Each Gene can be represented as a sequence of codons where codons are a sequence of base triplets – meaning 3 bases combine together to form a Codon.

Each codon corresponds to a specific Amino acid. Eg. AUG codon corresponds to the Amino acid Methionine. Amino Acids combine together to form a particular peptide chain. The peptide chains undergo a structural transformation to form 3-Dimensional molecules called proteins.

Types of Proteins in a Human Body

6. Genotype and Phenotype

https://www.youtube.com/watch?v=lYAHx7NiF3g

• Genotype is the genetic makeup of a cell, an organism or an individual with reference to a particular trait.
• It refers to the pairing of alleles and is not concerned with the expression of that trait
• Phenotype refers to the organism’s expressed physical trait. It depends both on the genetic makeup(genotype) and the environment.

7. Ribonucleic Acid(RNA)

The bridge between DNA and protein synthesis is RNA.
RNA is chemically similar to DNA, except that it contains ribose as its sugar and substitutes the nitrogenous base uracil for thymine.
It is single-stranded rather than a double helix.

To get from DNA, written in one chemical language, to protein, written in another, requires two major stages, transcription and translation.

The process from DNA to RNA is known as Transcription. During transcription, a DNA strand provides a template for the synthesis of a complementary RNA strand. Transcription of a gene produces a messenger RNA (mRNA) molecule.

During translation, the information contained in mRNA is used to determine the amino acid sequence of a polypeptide. Translation occurs at ribosomes.