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DNA Replication

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This quiz is based on the process of DNA replication in both Prokaryotes and Eukaryotes.

1. The enzyme responsible for initiating the unwinding of double-stranded DNA (eliminating supercoiling) by nicking a single strand of the DNA molecule is :
• Gyrase
• Ligase
• Helicase
• Topoisomerase
Answer: Topoisomerase

DNA Topoisomerase nicks a single strand of the DNA molecule and this releases the tension holding the two strands together in a supercoiled structure. The enzyme is also known as DNA Gyrase.



2. The enzyme that accomplishes the unwinding of the original double stranded DNA molecule, once supercoiling has been eliminated, by breaking the hydrogen bonds that hold the two strands together is :
• Helicase
• Topoisomerase
• DNA Polymerase II
• Primase
Answer: Helicase

Helicase seperates the two strands by disrupting the hydrogen bonds that hold the two strands of the DNA molecule together. The resulting unwound and partially opened up helix is called a "replication fork".



3. The enzyme that (during replication) proceeds along one of the strands of a DNA molecule adding deoxy-nucleotide-triphosphates to hydrogen bond with their appropriate complementary dNTP on the other single strand and to form a covalent phosphodiester bond with the previous nucleotide of the same strand is called :
• DNA Polymerase II
• DNA Polymerase I
• Primase
• DNA Polymerase III
Answer: DNA Polymerase III

As DNA helicase moves down the DNA molecule and separates the two strands by breaking the bonds between the nitrogenous bases, DNA Polymerase III adds the appropriate complementary bases to the now exposed bases on the single strands.




4. Because DNA polymerase III can only act from 5' to 3', continuous strand growth can be achieved only along one of the template strands (Leading strand) and strand growth along the other strand must occur discontinuously resulting in the production of a series of short sections of new DNA called :
• Replicon fragments
• Okazaki fragments
• Klenow fragments
• None of the above
Answer: Okazaki fragments

DNA polymerase III synthesizes new DNA fragments in the 5' to 3' direction along the Lagging strand. These fragments are called Okazaki fragments.



5. The enzyme that stitches Okazaki fragments together (along the lagging strand) is called :
• DNA Polymerase II
• Topoisomerase
• Holoenzyme
• DNA Ligase
Answer: DNA Ligase

To ensure that the Okazaki fragments are made into a continuous strand, they are joined by DNA Ligase which ligates the fragments together by forming the missing phosphodiester bonds.



6. DNA Polymerase III is actually an aggregate of several different protein subunits. So it is often called a :
• Holoenzyme
• Primeosome
• replisome
• None of the above
Answer: Holoenzyme

Holoenzyme consists of ten protein subunits and it is a dimeric enzyme with one half that copies the leading strand and another half that copies the lagging strand. The two halves of the enzyme communicate with one another such that both strands are replicated more or less simultaneously.



7. The enzyme that creates a short RNA oligonucleotide at initiation sites where replication is to be carried out is called :
• Primase
• DNA Ligase
• DNA Gyrase
• Exonuclease
Answer: Primase

The correct answer is Primase. Primase is actually part of an aggregate of proteins called the Primeosome which attaches a small RNA primer to the single-stranded DNA to act as a substitute 3'OH (on the Lagging strand) for DNA polymerase to begin synthesizing from.



8. The enzyme X removes RNA primers attached by Primase and this gap is then filled in by DNA Polymerase I. The enzyme X is :
• RNase H
• DNA amylase
• DNA ligase
• Reverse Transcriptase
Answer: RNase H

The correct answer is RNase H.



9. A major difference between DNA replication in prokaryotes and eukaryotes is :
• DNA amylase performs the function of DNA helicase in prokaryotes
• there is only one replication origin in prokaryotes.
• replication is conservative in prokaryotes
• prokaryotes do not use Topoisomerase in the replication process
Answer: there is only one replication origin in prokaryotes.

The main difference between DNA replication in prokaryotes and eukaryotes is that there is only one replication origin in the replication of DNA in prokaryotes, whereas eukaryotes may have up to 1000 replication origins.



10. A repeating DNA sequence at the end of chromosomes that prevents them from losing base pair sequences at their ends and from fusing together is called :
• A Telomere
• A Telomerase
• A replicon
• None of the above.
Answer: A Telomere

The correct answer is 'A Telomere'. A Telomere can reach a length of 15,000 base pairs. Each time a cell divides, some of the Telomere is lost and when it becomes too short, the chromosome reaches a "critical length" and can no longer replicate. So, a cell becomes "old" and dies because of the shortening of chromosomal telomeres.



11. The enzyme (made of proteins and RNA) that elongates chromosomes by adding TTAGGG sequences to the end of existing chromosomes is :
• Telomerase
• Exonuclease
• Endonuclease
• Amylase
Answer: Telomerase

The correct answer is Telomerase. Telomerase, also called Telomere terminal transferase, lengthens the 5' end of DNA strands before replication, to compensate for Telomere shortening during DNA replication.



12. An enzyme (used by all retroviruses) that transcribes genetic information of the virus from RNA into DNA, is :
• Reverse transcriptase
• RNA polymerase
• Restriction nuclease
• Methylase
Answer: Reverse transcriptase

The correct answer is Reverse transcriptase. Retroviruses are viruses whose genome consists of RNA and not DNA. HIV-1 and HIV-2, the agents that cause AIDS, are retroviruses. Reverse transcriptase is a DNA polymerase that uses RNA as its template. Thus it is able to make genetic information flow in the opposite direction (RNA => DNA) instead of (DNA => RNA).



13. An enzyme that recognizes and cuts DNA only at a particular sequence of nucleotides is often called :
• Restriction endonuclease
• RNA polymerase
• Photolyase
• DNA glycosylase
Answer: Restriction endonuclease

The correct answer is Restriction endonuclease. DNA restriction enzymes recognize short, specific pallindromic sequences of DNA bases and make breaks in the sugar-phosphate backbone of the DNA in the region of the recognized sequence.



14. What does transformation involve in Bacteria ?
• the creation of a strand of DNA from RNA
• the creation of a strand of RNA from DNA
• assimilation of external DNA into a cell
• the infection of cells by a phage DNA molecule
Answer: assimilation of external DNA into a cell

Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign DNA. It is a common technique in molecular biology.
The correct answer is option 2.



15. A mamalian cell typically has 1.2 meters (when completely outstretched) of double stranded DNA.The total time to duplicate the DNA is 5 hours. How many origins of replication are there if the rate of duplication is 16µmeters/min ?
• 250
• 15000
• 1
• 500
Answer: 250

The correct answer is 250 origins of replication. If there was only one origin of replication, the rate of DNA duplication would be given by :
Rate = Length of DNA / duplication time
=> Rate = 1.2 / (5 x 60) = 400µm/min which is not consistent with the data provided. Clearly, there exists more than one origin of replication !
Let the number of origins of replication be n. The rate of duplication from each origin will be 16µmeters/min. Hence, n x 16µmeters/min x 5 x 60 min = 1.2 x 106meters
=> n = 250.



16. The enzyme that replaces the nucleotides of the RNA primer with the appropriate DNA nucleotides is :
• DNA Polymerase II
• RNA Polymerase
• DNA Ligase
• DNA Gyrase
Answer: DNA Polymerase II

The correct answer is DNA Polymerase II. DNA polymerase II digests away the RNA primer (on the Lagging strand) and replaces the RNA nucleotides of the primer with the proper DNA nucleotides to fill the gap before DNA Ligase links the strands together.



17. The end of a DNA strand that has a phosphate group attached to the number 5 carbon of its terminal deoxyribonucleotide is called :
• The 5 prime end (5')
• The 3 prime end (3')
• N-Terminus
• C-Terminus
Answer: The 5 prime end (5')

The correct answer is the 5 prime end (5'). The 5 prime end of a DNA strand will aways have a phosphate group attached to the number 5 carbon of its terminal deoxyribonucleotide. The other end of that strand, called the 3 prime end, will always have a hydroxyl (OH) on the number 3 carbon of its terminal deoxyribonucleotide.
Note : DNA can only be synthesized in the 5' to 3' direction.



18. In DNA, mutations at G-C sequences occur quite frequently since 5-methyl cytosine easily deaminates to form :
• Thymine
• Adenine
• Guanine
• Cytosine
Answer: Thymine

The correct answer is Thymine. Cytosine can be methylated into 5-methylcytosine (by an enzyme called DNA methyltransferase) which can undergo spontaneous deamination to form Thymine.



19. Which of the following agents is not a mutagen ?
• Ultraviolet radiation
• A retrovirus
• A transposon or jumping gene
• None of the above
Answer: None of the above

A mutagen increases the number of mutations that occur during DNA replication above the natural background level. Mutagens can be chemical compounds or radiation. Ultraviolet radiation, retroviruses and transposons are mutagens.



20. In 1940, Nobel Laureate Barbara McClintock discovered sequences of DNA that can move around to different positions within the genome of a single cell and cause mutations. These sequences (first observed in maize) are called :
• Transposons
• inverted repeats
• direct repeats
• sticky ends
Answer: Transposons

The correct answer is Transposons (also known as "jumping genes").




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