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1-State Chargaff’s rule

In DNA molecules the concentration of deoxyadenosine (A) nucleotides equals that of thymidine (T) nucleotides (A = T), while the concentration of deoxyguanosine (G) nucleotides equals that of deoxycytidine (C) nucleotides (G = C). In other words concentration or the number of purine nucleotides is always equal to those of pyrimidine nucleotides

2- What is meant by hyperchromicity of denaturation?

 The conjugated double bonds of purine and pyrimidine derivatives absorb ultraviolet light. At pH 7.0 all the common nucleotides absorb light at a wavelength close to 260 nm.In bound form there is less absorbance . Upon denaturation of the DNA molecule, there is an increase in the optical absorbance by the purine and pyrimidine bases—a phenomenon referred to as hyperchromicity of denaturation. 

3- Define hybridization

The specific reassociation of complementary strands of nucleic acids (DNA with DNA, DNA with RNA, or RNA with RNA) is called hybridization.

4-What is a hairpin structure?

A double-helical stretch formed by base pairing between neighboring complementary sequences of a single strand of DNA or RNA is denoted by hairpin structure.

5- What is the reason that genetic information is stored in the DNA and not in RNA ?

DNA is a stable molecule in comparison to RNA , does not undergo spontaneous degradation, hence it  is a store house of genetic information and  transfers the genetic information to the daughter cells with complete accuracy and fidelity.

6- What is the difference between Uridine and pseudo uridine?

 Both are nucleosides, in uridine,uracil is linked to D- ribose by β- N glycosidic linkage, while in Pseudouridine  uracil is linked to D- ribose by C-C linkage which is not a true linkage.

7-Give an example of RNA dependent DNA polymerase

Reverse transcriptase and telomerase

8-Give an example of DNA dependent DNA polymerase

All DNA polymerases required for replication

9- Give an example of DNA dependent RNA polymerase

RNA polymerase required for transcription

10-Define a Template

Template is a guiding surface upon which the molecules are aligned in a sequence specific manner to form a biomolecule with a specific and defined arrangement of its components.

11- The initiation of DNA synthesis requires primer (priming by a short length of RNA), what is the reason?

DNA polymerase can not initiate the chain synthesis; it can simply elongate the existing fragment that is why a primer is needed. RNA polymerase can initiate the chain synthesis, which is why the primers are always made up of RNA.

12-What are endonucleases?

Endonuclease is an enzyme that cleaves internal bonds in DNA or RNA.

13-What is the difference between exonuclease and excinuclease?

Exonuclease is an enzyme that cleaves nucleotides from either the 3′ or 5′ ends of DNA or RNA.

Excinuclease is the excision nuclease involved in nucleotide exchange repair of DNA.

14- What is an intron?

Intron is the sequence of a gene that is transcribed but excised before translation.

15-What is meant by ligation? Name the enzyme responsible for catalyzing this process.

The enzyme-catalyzed joining in of phosphodiester linkages of two stretches of DNA or RNA into one; the respective enzymes are DNA and RNA ligases.

16-What is meant by origin of replication?

Origin of replication is the site on DNA from where the replication process starts. At the origin of replication (ori), there is an association of sequence-specific dsDNA-binding proteins with a series of direct repeat DNA sequences. In prokaryotes there is a single origin of replication while in eukaryotes multiple origins are there owing to the enormous length of DNA.

17- What are palindrome sequences?

A sequence of duplex DNA that is the same when the two strands are read in opposite directions

18-What is the difference between primer, primase and Primosome?

Primer is a short fragment of RNA required for replication of DNA. Primase is the enzyme responsible for synthesis of primer. It is a special kind of RNA polymerase. Primosome is the mobile complex of helicase and primase that is involved in DNA replication.  

19- What is a probe?

Probe is  a molecule used to detect the presence of a specific fragment of DNA or RNA in, for instance, a bacterial colony that is formed from a genetic library or during analysis by blot transfer techniques; common probes are cDNA molecules, synthetic oligodeoxynucleotides of defined sequence, or antibodies to specific proteins.

20-What is the difference between Constitutive and inducible genes?

An inducible gene is one whose expression increases in response to an inducer or activator, a specific positive regulatory signal. The expression of some genes is constitutive, meaning that they are expressed at a reasonably constant rate and not known to be subject to regulation. These are often referred to as housekeeping genes. As a result of mutation, some inducible gene products become constitutively expressed. A mutation resulting in constitutive expression of what was formerly a regulated gene is called a constitutive mutation.

21- What is meant by a pseudo gene ?

An inactive segment of DNA arising by mutation of a parental active gene is called a pseudo gene, in other words a pseudo gene is never expressed to form an RNA or a protein.

22- What is reverse transcription?

It is RNA-directed synthesis of DNA, catalyzed by reverse transcriptase

23- What is meant by splicing ?

The removal of introns from RNA accompanied by the joining of its exons is called Splicing.

24-What is meant by a chimeric molecule?

A molecule (eg, DNA, RNA, protein) containing sequences derived from two different species.

25-What is a library?

 A library is a collection of cloned fragments that represents the entire genome. Libraries may be either genomic DNA (in which both introns and exons are represented) or cDNA (in which only exons are represented).

26-What is meant by an Insert?

An additional length of base pairs in DNA, generally introduced by the techniques of recombinant DNA technology is named as Insert.

27- What is meant by Sn RNA ?

Small nuclear RNA , This family of RNAs is best known for its role in mRNA processing.

28-What is a Southern Blot ?

 It is a method for transferring DNA from an Agarose gel to nitrocellulose filter, on which the DNA can be detected by a suitable probe (eg, complementary DNA or RNA).

29-What is Northern Blot?

It is a method for transferring RNA from an agarose gel to a nitrocellulose filter, on which the RNA can be detected by a suitable probe.

30-What is a western Blot ?

It is a method for transferring protein to a nitrocellulose filter, on which the protein can be detected by a suitable probe (eg, an antibody).

31- What are vectors?

 The plasmids, bacteriophages, cosmids , viruses or chromosomes into which foreign DNA can be introduced for the purposes of cloning are called vectors of cloning.

32- What is meant by oligonucleotide?

 It is a short, defined sequence of nucleotides(Short stretch of DNA or RNA) joined together in the typical phosphodiester linkages.

33- What is a clone?

A large number of organisms, cells or molecules those are identical with a single parental organism cell or molecule

34-What is meant by Tandem?

 Tandem is used to describe multiple copies of the same sequence (eg, DNA) that lie adjacent to one another.

35-What is meant by spliceosome?

 It is the macromolecular complex responsible for precursor mRNA splicing. The spliceosome consists of at least five small nuclear RNAs (snRNA; U1, U2, U4, U5, and U6) and many proteins.

36-What is auto radiography?

The detection of radioactive molecules (eg, DNA, RNA, protein) by visualization of their effects on photographic film is called autoradiography.

37-What is PCR?

It is a method of amplification of DNA.  Basically this is an enzymatic method for the repeated copying (and thus amplification) of the two strands of DNA that make up a particular gene sequence.

38- What is RT PCR ?

 It I s a method used to quantitate mRNA levels that relies upon a first step of cDNA copying of mRNAs catalyzed by reverse transcriptase prior to PCR amplification and quantitation.

39-What is meant by Transcriptome?

Transcriptome is the entire collection of expressed mRNAs in an organism.


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