Everything you need to know about molecular biology. Some of the most frequently asked exam questions are as follows:-
Q.1. What is molecular biology?
Ans: It is the science regarding DNA, RNA and protein synthesis of living organisms, and other related molecules.
Q.2. What is a molecule?
Ans: A combination of atoms forming specific chemical compounds.
Q.3. What is a moiety?
Ans: A part of a molecule having characteristic chemical property.
Q.4. Define mole % G + C.
Ans: It is proportion of guanine and cytosine in a DNA macromolecule.
Q.5. Who did discover that messenger RNA is involved in protein synthesis?
Francois Jacob and Jacques Monod discovered it in 1961. Structure of DNA (Deoxyribonucleic Acid)
Q.6. Give structure of DNA.
Ans: The macromolecule of DNA stores all hereditary information of the cell. DNA is composed of subunits referred to as nucleotides. DNA is also known as master molecule. At the time of division of a cell its hereditary information is passed on to next generation because of DNA’s unique structure. DNA contains four nucleotides, each having one of four nucleic acid bases, adenine (A), guanine (G), cytosine (C) and thymine (T).
The arrangement or the order of nucleotides determines the hereditary information contained in the DNA. The nucleotides are held together by Phosphodiester bonds between deoxyribose, the sugar found in the backbone of DNA. There are two strands of DNA held together by hydrogen bonds forming a coiled molecule known as double helix.
Q.7. Give structure of RNA
Ans: RNA differs from DNA in several respects, some of which are:
1. The five-carbon sugar in the nucleotide of RNA is ribose, which has one more oxygen atom in comparison to the deoxyribose found in DNA.
2. One of RNA’s bases is uracil (U) instead of thymine.
3. RNA is normally single stranded.
Q.8. Name some other nucleotide
Ans: The ATP (adenosine triphosphate) is also a nucleotide which consists of adenine, ribose and three phosphate groups. The ATP is known as a high energy molecule because it releases a large amount of usable energy after hydrolysis of a phosphate group resulting the formation of ADP (adenosine diphosphate) production and utilization of ATP are needed for the bioenergetics which is transfer of energy through living systems/ cells. When adenosine triphosphate (ATP) is converted to ADP, a high energy phosphate bond is cleaved releasing about 7.5 Kcal/mole which can be used to carry on other chemical reactions.
Some nucleotides work as coenzyme which is a temporary carrier of substances such as electrons. In the process of metabolism coenzymes transport hydrogen atoms and electrons. NAD+ (Nicotinamide adenine dinucleotide and FAD (Flavin adenine dinucleotide) are two of such coenzymes. These coenzymes accept electrons and hydrogen during some chemical reactions and release them during other chemical reactions.
Q.9. What is DNA replication? Why is it needed?
Ans: Replication is synthesis of DNA from DNA. As a result of replication of DNA, new molecules of DNA are formed which have same nucleotide sequence as in the genome of the parent organism. It is needed because the genome of the progeny must have appropriate information for the survival and growth of the organism. The changes in the sequence of nucleotides can bring a change in characteristics of the organism considerably. The DNA replication has been designed to ensure that progeny receive accurate copy of the genetic material contained in the parent cell.
Q.10. What is semi conservative process of replication of DNA? Who demonstrated it?
Ans: The process of replication of DNA has been regarded as semi conservative replication of DNA because when double stranded DNA replicates each of the two new daughter DNA double helices possesses one intact original conserved strand from the parental double helical DNA and one newly synthesized has one parental and one newly formed strand Semi conservative replication of DNA was demonstrated by Matthew Meselson and Franklin Stahl in 1958 based on their classical experiment on bacteria but now it has also been shown to occur in archaeal and eukaryotic cells.
Q.11. What is replication fork?
Ans: Ans: In semi conservative mode of replication of DNA, the region of DNA helix where it unwinds (separation of strands) to localize the DNA synthesis is called replication fork.
Q.12. Which protein-class is responsible for separation or to unwind the double helix of DNA in replication?
Ans: A class of specific proteins known as helicases facilitates the separation of strands of DNA double helix in advance of a replication fork. The rep protein and DNA helicases are collectively known as unwinding proteins. (Fig. 33.5)
Q.13. What are topoisomerases? Give their types.
Ans: The topoisomerases are the enzymes which can alter super coiling of DNA by bringing a change in the number of topological links between two strands of double helix by introducing transient breaks in Phosphodiester backbone of the DNA and catalyze DNA strand passages through these breaks. In this way the topoisomerases can either relax or supercoil DNA macromolecules.
These are the nicking-closing enzymes which are of two types:
1. Type I topoisomerases:
These are enzymes that change negative supercoiling of DNA, hence causing a localized uncoiling effect.
2. Type II topoisomerases:
These bring about negative supercoiling into the relaxed DNA.
Q.14. Give bacterial topoisomerases. Which one of them is involved in production of negatively supercoiled DNA.
Ans: Several type I and type II DNA topoisomerases are found together in bacterial cells. There are two types I isomerases in Escherichia coli known as protein to and Topo III. The Topo III was the 3rd one to be discovered as name itself indicates; and two type II DNA topoisomerases, called DNA gyrase and Topo IV. DNA gyrase is the only enzyme which is involved in production of negatively supercoiled DNA.
Q.15. What is the function of gyr A gene?
Ans: DNA gyrase of Escherichia coli is a type II topoisomerase which comprises four protein subunits. Of these, two are A-subunits while the two are B-subunits. Type Asubunit is coded for the gene gyr A. The gyrase nicks hydrolyzes’ both strands of DNA and then passes the strand around another part of the double helix thus introduces a negative supercoil.
Q.16. Which are the archaeal topoisomerases? What is special about them?
Ans: In the archaeal cells also type I and type II topoisomerases are like that of bacteria. The speciality of the archaeal cells lay in having a novel topoisomerase known as reverse gyrase. The reverse gyrase activity has been observed in extremely thermophilic archaea, but is absent in moderately thermophilic archaea. The reverse gyrase protects archaea from melting or strand separation at the very high environmental temperature of their niche or natural places where they grow.
Q.17. What is the function of single-stranded binding proteins (SSBs)?
Ans: They prevent reassociation of already separated (relaxed) single stranded regions of the DNA. In other words, they prevent formation of hydrogen-bonded double helix.
Q.18. Define polymerase chain reaction (PCR).
Ans: This is an in vitro method for replication of DNA. In it, a target nucleotide sequence is copied repeatedly so that a million copies can be made in less than an hour.
Q.19. Give examples of thermostable DNA polymerase from (1) thermophilic bacterium and (2) archaea that has made PCR routinely possible.
Ans: 1. Thermus aquaticus, a thermophilic bacterium the gene responsible for the stability of its DNA polymerase is taq DNA polymerase.
2. Thermococcus, an archaea which is the source of vent polymerase. This archaeal species grows in deep sea thermal vent regions.
Q.20. Give three major steps taken in the methodology for polymerase chain reaction. /
Ans: 1. The DNA is denatured at high temperature 94° to 95°C.
2. Primar annealing by lowering the temperature 37° to 70°C.
3. Chain elongation using thermostable DNA polymerase at 60 to 72°C to permit the action of thermostable DNA polymerase.
Q.21. What is proofreading by DNA polymerases?
Ans: This is the 3’OH 5’P exonuclease activity of DNA polymerases. In this way it is excision of improperly inserted nucleotides by DNA polymerases in DNA replication.
Q.22. What may be the post-replication modifications of DNA? Explain.
Ans: In the post replication modifications DNA is liable to addition of methyl groups to some adenine and cytosine residues. The enzymes that bring about methylation are known as DNA methylases. The methylation occurs after the nucleotides have been incorporated by DNA polymerases.
The methyl group protects DNA against action of being digested by specific enzymes called restriction endonucleases. But foreign DNA within the cell is digested by endonucleases. The methylation pattern protects the DNA from digestion by cells own endonuclease. However, methylation does not provide DNA protection against being digested by the restriction enzymes produced by the cells of other species. In this way natural exchange of DNA among cells of different species is prevented.
Q.23. How does methylation of DNA at specific site may lead to localized conversion of B-DNA to Z-DNA?
Ans: The hydrophobic methyl group of B-DNA may protrude into the hydrophilic environment of the major groove and cause a destabilizing arrangement.
Q.24. What is Post-Translational Processing?
Ans: The newly synthesized polypeptide chains undergo additional enzymatic changes which modify the protein after translation is complete. These changes usually affect the folding of the polypeptide to convert it to its biologically active form.
These reactions collectively have been called post-translational modifications or post-translational processing. Amino acids added to a developing polypeptide may be individually modified, e.g. serine, tyrosine or threonine residues may be phosphorylated by ATP dependent protein kinases.
Extra carboxyl groups may be added on to asparate or glutamate residues and lysine residue may be methylated and proline residues may be converted to hydroxyproline. Many proteins are folded called protein folding into tertiary and quaternary structures. Many of the eukaryotic polypeptides are post-translationally glycosylated.
Another feature of protein modification in microorganisms is the splicing of amino acid sequences out of the proteins after their formation. The protein splicing involves the removal of inteins and leaving exteins in the processed proteins.
The exteins are exons of proteins which are amino acid sequences which are retained and joined together during protein processing while the inteins are introns of proteins that are amino acid sequences which are removed during protein processing.