Tools of recombinant DNA technology Questions in English

(D) The $DNA$ polymerase used in $PCR$ (Polymerase Chain Reaction) is known as $Taq$ polymerase.
It is isolated from a thermophilic bacterium called $Thermus$ $aquaticus$.
Because $PCR$ involves high-temperature denaturation steps,the enzyme must be able to withstand these temperatures without denaturing.
Therefore,it is a thermostable enzyme.

(D) Restriction enzymes are a class of enzymes that cut $DNA$ at specific recognition sequences. Because of this ability to precisely cleave $DNA$ molecules, they are commonly referred to as molecular scissors. They play a crucial role in recombinant $DNA$ technology by allowing scientists to isolate specific genes or $DNA$ fragments.

(B) $Taq$ polymerase is a thermostable $DNA$ polymerase enzyme named after the thermophilic bacterium $Thermus$ $aquaticus$ from which it was originally isolated.
This bacterium thrives in hot springs and hydrothermal vents,which allows the enzyme to remain stable at high temperatures required during the denaturation step of the Polymerase Chain Reaction $(PCR)$.

(C) The plasmid $pBR322$ is a widely used cloning vector in biotechnology.
It contains several important genetic markers,including antibiotic resistance genes ($amp^R$ and $tet^R$) and an origin of replication $(ori)$.
The $Rop$ gene stands for 'Repressor of Primer'.
It codes for proteins that are involved in the regulation of the plasmid's replication process.
In contrast,$Pvu II$,$Cla I$,and $Pst I$ are specific restriction endonuclease recognition sites located within the plasmid,not genes coding for replication proteins.

(B) In the $pBR322$ cloning vector,the tetracycline resistance gene $(tet^R)$ contains specific recognition sites for restriction enzymes $BamH I$ and $Sal I$.
Insertion of foreign $DNA$ at these sites inactivates the $tet^R$ gene,which is used for the selection of recombinants.
$Pst I$ and $Pvu I$ sites are located within the ampicillin resistance gene $(amp^R)$.

(B) The specific $DNA$ sequence from where the replication process initiates is known as the Origin of replication $(ori)$.
This sequence is responsible for controlling the copy number of the linked $DNA$ in the host cell.
Without an origin of replication,the $DNA$ cannot replicate within the host organism.

(A) In the cloning vector $pBR322$,the $amp^R$ (ampicillin resistance) gene contains recognition sites for $Pst I$ and $Pvu I$.
Therefore,statement $A$ is correct.
The $tet^R$ (tetracycline resistance) gene contains recognition sites for $BamHI$ and $Sal I$,but it does not contain a recognition site for $Hind III$.
Therefore,statement $R$ is correct.
Both statements are correct.

$(A)$ is correct because cloning vectors are $DNA$ molecules used as vehicles to carry a particular $DNA$ segment into a host cell.
$R$ is correct because Agrobacterium tumefaciens is a soil bacterium that acts as a natural genetic engineer by infecting several dicot plants and transferring its $T-DNA$ into the host genome.
Therefore, both statements are correct.

(D) In the biolistics or gene gun method,microparticles of heavy metals are used to deliver foreign $DNA$ into host cells.
These microparticles are coated with the $DNA$ of interest.
The metals commonly used for this purpose are $Gold$ or $Tungsten$ because they are inert and do not react with the biological tissues.
Therefore,among the given options,$Tungsten$ is the correct metal used in particle bombardment.

(C) Sticky ends are short,single-stranded sequences of $DNA$ that remain after a restriction enzyme cuts the $DNA$ molecule at specific sites.
These ends are called 'sticky' because they can form hydrogen bonds with complementary single-stranded sequences on another $DNA$ molecule cut by the same enzyme.
This property is essential for the process of recombinant $DNA$ technology,as it allows for the easy joining of $DNA$ fragments from different sources.
Therefore,sticky ends are defined as overhanging single-stranded parts of $DNA$.

(A) palindromic $DNA$ sequence is a sequence of base pairs in double-stranded $DNA$ that reads the same in the $5' \rightarrow 3'$ direction on one strand as it does in the $5' \rightarrow 3'$ direction on the complementary strand.
Option $A$ $(GAATTC / CTTAAG)$ is a classic example of a palindromic sequence recognized by the restriction enzyme $EcoRI$.
Option $B$ $(GGATCC / CCTAGG)$ is a palindromic sequence recognized by the restriction enzyme $BamHI$.
Since both $A$ and $B$ are palindromic,but $EcoRI$ $(GAATTC)$ is the most standard textbook example,we evaluate the provided options. Note: In the original input,option $A$ had a typo $(CTTUUG)$. Correcting it to $CTTAAG$ makes it a valid palindrome. Both $A$ and $B$ are palindromic sequences.

(B) In recombinant $DNA$ technology,a vector is a $DNA$ molecule used as a vehicle to artificially carry foreign genetic material into another cell,where it can be replicated and/or expressed.
Plasmids are the most commonly used vectors in genetic engineering because they are small,circular,extrachromosomal $DNA$ molecules that can replicate independently within a host cell.
Therefore,the term vector refers to a plasmid that transfers $DNA$ into a living cell.

(B) In genetic engineering,$Plasmids$ are widely used as vectors to carry foreign $DNA$ into host cells.
$Plasmids$ are small,circular,double-stranded $DNA$ molecules that are distinct from a cell's chromosomal $DNA$.
They are naturally found in bacteria and can replicate independently within the host cell.
Because of their ability to carry and replicate foreign genes,they serve as essential tools for cloning and gene transfer.

(C) vector is a $DNA$ molecule used as a vehicle to artificially carry foreign genetic material into another cell.
Plasmids are small,circular,extrachromosomal $DNA$ molecules found in bacteria.
The key factor that makes a plasmid an ideal vector is its ability to replicate independently within the host cell and its capacity to carry a foreign gene (the gene of interest) into the host organism.
While antibiotic resistance genes are often used as selectable markers in plasmids,the fundamental property that defines its role as a vector is its ability to act as a carrier for foreign $DNA$.

(C) $Agrobacterium$ $tumefaciens$ is a soil-borne bacterium that naturally infects a wide range of dicotyledonous plants.
It contains a large plasmid known as the $Ti$ (Tumor-inducing) plasmid.
During infection,a specific segment of this plasmid,called $T-DNA$ (Transfer $DNA$),is integrated into the host plant's genome.
Scientists have modified this natural mechanism to use $Agrobacterium$ as a vector for delivering foreign genes of interest into crop plants,making it a fundamental tool in plant biotechnology.

(A) $pBR322$ is a well-known cloning vector derived from $E. coli$ plasmid $pBR322$. It is an engineered plasmid used in biotechnology for cloning purposes.
$BamHI$,$SalI$,and $EcoRI$ are restriction endonucleases,which are enzymes used to cut $DNA$ at specific recognition sequences.

(C) Statement $I$ is true: The origin of replication $(Ori)$ is a specific sequence in $DNA$ where replication initiates. It is also responsible for controlling the copy number of the linked $DNA$ in a host cell.
Statement $II$ is true: In the vector $pBR322$,the $BamHI$ restriction site is located within the tetracycline resistance gene $(tet^R)$. If a foreign $DNA$ fragment is ligated at this site,it causes insertional inactivation of the gene,resulting in the loss of tetracycline resistance in the recombinant plasmid.

(A) The $Ti$ plasmid (tumour-inducing plasmid) of $Agrobacterium$ $tumefaciens$ is a naturally occurring plasmid that has the ability to transfer a piece of $DNA$ known as $T-DNA$ into the genome of host plants,causing the formation of tumours (crown galls).
In biotechnology,scientists have modified this $Ti$ plasmid to remove its pathogenic (tumour-inducing) properties while retaining its ability to integrate foreign $DNA$ into the plant genome.
Therefore,it is widely used as a cloning vector for the genetic transformation of plants.
Thus,the statement is True.

(D) Recombinant $DNA$ technology involves several essential tools to manipulate genetic material.
$1$. $Restriction$ $enzymes$ are used to cut $DNA$ at specific sites.
$2$. $Polymerase$ $enzymes$ (like $DNA$ polymerase) are used for the synthesis of new $DNA$ strands.
$3$. $Ligases$ are used to join $DNA$ fragments together.
$4$. $Vectors$ (like plasmids or bacteriophages) are used to carry the foreign $DNA$ into the host cell.
$5$. $Host$ $organisms$ are required to replicate the recombinant $DNA$ molecule.
Since all five components ($I, II, III, IV,$ and $V$) are fundamental tools in recombinant $DNA$ technology,the correct option is $D$.

(A) is true because restriction endonucleases cut $DNA$ at specific recognition sequences,acting like molecular scissors.
$R$ is true because when the same restriction enzyme is used on both the vector and the foreign $DNA$,they produce complementary sticky ends (overhanging sequences).
These complementary sticky ends can form hydrogen bonds with each other,allowing the $DNA$ fragments to join together with the help of $DNA$ ligase.

(B) The nomenclature of the restriction enzyme $Eco RI$ is as follows:
$1$. The first letter '$E$' represents the genus name,which is $Escherichia$.
$2$. The next two letters '$co$' represent the species name,which is $coli$.
$3$. The letter '$R$' represents the strain of the bacteria,which is $RY13$.
$4$. The Roman numeral '$I$' indicates the order in which the enzyme was isolated from the strain of bacteria.
Therefore,the correct matching is:
$(A) E - (2)$ Name of genus
$(B) co - (3)$ Name of species
$(C) R - (4)$ Name of strain
$(D) I - (1) 1^{st}$ in order of identification
Thus,the correct sequence is $A-2, B-3, C-4, D-1$.

(A) plasmid is a small,circular,double-stranded $DNA$ molecule that is distinct from a cell's chromosomal $DNA$.
Plasmids are naturally found in bacterial cells and some eukaryotes.
In biotechnology,plasmids are extensively used as vectors to carry foreign genetic material into another cell,where it can be replicated and/or expressed.

(A) In genetic engineering,$Plasmids$ are small,circular,double-stranded $DNA$ molecules that are distinct from a cell's chromosomal $DNA$. They are naturally found in bacteria and are widely used as vectors to transport foreign genetic material into a host cell. Therefore,$Plasmids$ are the essential cellular components associated with genetic engineering.

(D) $DNA$ $Ligase$ is the enzyme responsible for joining the ends of two $DNA$ strands by forming phosphodiester bonds. It acts as a 'molecular glue' in $DNA$ replication and repair processes to seal nicks in the sugar-phosphate backbone.

(C) The enzymes that cleave phosphodiester bonds in a polynucleotide chain are called nucleases.
Nucleases are classified into two types based on their site of action:
$1$. Exonucleases: These enzymes remove nucleotides from the ends (either $5'$ or $3'$) of the $DNA$ molecule.
$2$. Endonucleases: These enzymes make cuts at specific positions within the $DNA$ molecule,i.e.,they cleave internal phosphodiester bonds.
Therefore,the correct answer is $C$ (Endonuclease).

(C) An $Endonuclease$ is an enzyme that cleaves the phosphodiester bonds within a polynucleotide chain.
Unlike $Exonucleases$,which remove nucleotides one by one from the ends of the chain,$Endonucleases$ act on internal sites.
$Lipases$ are involved in the hydrolysis of lipids,and $Proteases$ are involved in the hydrolysis of proteins.

(B) The correct answer is $B$.
$A$. Somatic hybridization involves the fusion of protoplasts from two different plant species to create a hybrid. This is correct.
$B$. Vector $DNA$ is a $DNA$ molecule used as a vehicle to artificially carry foreign genetic material into another cell. It is not the site for $t-RNA$ synthesis; $t-RNA$ is synthesized in the nucleus from $DNA$ templates. Thus,this pair is incorrect.
$C$. Micropropagation is the practice of rapidly multiplying stock plant material to produce a large number of progeny plants using modern plant tissue culture methods. This is correct.
$D$. Callus is an unorganized mass of parenchyma cells that develops from explants during tissue culture. This is correct.

(B) In genetic engineering,$Escherichia \ coli$ $(E. \ coli)$ is widely used as a host organism for cloning and expression of recombinant $DNA$ due to its well-studied genome and rapid growth. $Agrobacterium \ tumefaciens$ is extensively used as a natural genetic engineer in plants because it can transfer its $T-DNA$ into the host plant genome,causing crown gall disease. By modifying this $T-DNA$,scientists use it as a vector to introduce desired genes into plants. Therefore,the correct answer is $Escherichia$ and $Agrobacterium$.

(D) Genetic engineering,or recombinant $DNA$ technology,relies on the ability to manipulate $DNA$ molecules.
Restriction endonucleases are enzymes that act as 'molecular scissors' by cutting $DNA$ at specific recognition sequences.
These enzymes were originally discovered in bacteria,where they serve as a defense mechanism against bacteriophages.
By purifying these enzymes from bacteria,scientists can use them in the laboratory to cut $DNA$ at precise locations,which is the fundamental step in creating recombinant $DNA$ molecules.

(D) Restriction endonucleases are enzymes that cut $DNA$ at specific recognition sequences.
These enzymes are essential tools in recombinant $DNA$ technology as they allow for the precise cleavage of $DNA$ molecules to create fragments that can be joined with vectors.
Primase is involved in $DNA$ replication,exonucleases remove nucleotides from the ends of $DNA$,and ligase joins $DNA$ fragments together.
Therefore,the correct enzyme for cutting $DNA$ is restriction endonuclease.

(B) Genetic engineering involves the manipulation of $DNA$ to alter the characteristics of an organism.
Plasmids are small,circular,double-stranded $DNA$ molecules that are distinct from a cell's chromosomal $DNA$.
They are extensively used as vectors in genetic engineering to carry foreign genes into host cells for cloning or expression.
Therefore,plasmids are fundamental tools in genetic engineering.

(C) In plasmid $DNA$,replication is initiated at the origin of replication $(ori)$.
However,the regulation of the replication process,such as copy number control,is governed by the genes present within the plasmid itself.
These genes encode proteins that interact with the $ori$ site to determine how many times the plasmid replicates within the host cell.
Therefore,the regulation is controlled by the plasmid gene.

(B) Plasmids are extrachromosomal,self-replicating,circular $DNA$ molecules found in bacteria.
For a molecule to act as a vector in gene cloning,it must be able to replicate independently within the host cell.
This ability is provided by the presence of an 'origin of replication' $(ori)$ site.
While plasmids often carry antibiotic resistance genes (which serve as selectable markers),the fundamental reason they are suitable vectors is their ability to replicate autonomously due to the presence of an $ori$ sequence.

(A) plasmid is an extrachromosomal,circular,double-stranded $DNA$ molecule found in bacteria.
It is capable of autonomous replication within the host cell.
In biotechnology,plasmids are extensively used as vectors to carry foreign $DNA$ fragments into host cells for cloning or expression.

(A) Plasmids are small,circular,double-stranded $DNA$ molecules that are distinct from a cell's chromosomal $DNA$.
They are found in bacteria and some other microorganisms.
These molecules are extrachromosomal,meaning they exist outside of the main bacterial chromosome.
Plasmids often carry genes that provide advantages to the bacteria,such as antibiotic resistance.

(A) The discovery of restriction endonucleases,often referred to as 'molecular scissors',has made it possible to cut $DNA$ at specific sites.
These enzymes recognize specific nucleotide sequences and cleave the $DNA$ backbone,which is a fundamental step in recombinant $DNA$ technology.
$DNA$ ligase is used to join $DNA$ fragments,but the initial modification and isolation of specific genes rely on restriction endonucleases.

(D) Restriction endonucleases are enzymes that cut $DNA$ at specific recognition sequences. These enzymes are naturally produced by bacteria as a defense mechanism to protect themselves from bacteriophage infections by cleaving the foreign viral $DNA$. In biotechnology,they are essential tools for creating recombinant $DNA$ molecules.

(A) The enzyme $DNA$ ligase is responsible for joining $DNA$ fragments together by forming phosphodiester bonds between the $3'$-hydroxyl end of one nucleotide and the $5'$-phosphate end of another. In recombinant $DNA$ technology,$DNA$ ligase is used to ligate (join) the gene of interest (such as an antibiotic resistance gene) into the plasmid vector to create a recombinant $DNA$ molecule.

(A) Restriction endonucleases are enzymes that recognize specific palindromic nucleotide sequences in $DNA$ and cut the $DNA$ duplex at specific positions,usually within or near the recognition site. These are essential tools in recombinant $DNA$ technology,often referred to as 'molecular scissors'.

(D) In biotechnology,vectors are used to deliver foreign genes into host cells.
For higher organisms,including animals,retroviruses have been disarmed and are used as vectors to deliver desirable genes into animal cells.
These retroviruses transform normal cells into cancerous cells or simply act as vehicles to introduce recombinant $DNA$ into the host genome.
Therefore,retroviruses are the standard choice for gene cloning in higher organisms.

(D) Agarose is a natural polymer extracted from sea weeds (red algae like Gelidium and Gracilaria).
It is widely used in the laboratory technique known as gel electrophoresis.
In this process,agarose gel acts as a molecular sieve to separate $DNA$ fragments based on their size under an electric field.

(D) The naming of restriction enzymes follows a specific convention.
In $Eco RI$,the first letter '$E$' comes from the genus name $Escherichia$.
The next two letters '$co$' come from the species name $coli$.
The letter '$R$' is derived from the strain name $RY13$.
The Roman numeral '$I$' indicates the order in which the enzyme was isolated from that strain of bacteria.
Therefore,'$co$' stands for $coli$.

(D) The gene gun method,also known as biolistics or microprojectile bombardment,is a technique used to introduce foreign $DNA$ into host cells. In this process,microparticles of heavy metals are coated with the target $DNA$. These particles are then accelerated at high velocity to penetrate the cell wall and membrane. The microparticles used for this purpose are typically made of $Gold$ or $Tungsten$ because they are inert,dense,and non-toxic to the cells.

(D) The $DNA$ polymerase used in $PCR$ is known as $Taq$ polymerase.
It is isolated from a thermophilic bacterium called $Thermus$ $aquaticus$.
Because $PCR$ involves repeated cycles of heating (denaturation) to separate $DNA$ strands,the enzyme must be thermostable.
Therefore,$Taq$ polymerase remains active even at high temperatures,allowing the amplification process to continue without needing to add fresh enzyme in every cycle.