CSIR-NET Life Sciences: Most Important Questions on Replication!!!

Important Questions on Replication

1. Following are some statements about the chromosomal DNA of eukaryotes:

1. Conserved synteny is the occurrence of the same genes in two evolutionarily distant organisms irrespective of their order on the chromosome.
2. In humans, sex chromosomes in males are the only non-homologous chromosome pairs.
3. Conserved regions represent functionally essential exons and regulatory sequences in a genome.
4. A linear chromosome must contain a centromere, two telomeres and multiple origins of replication sites.

 Which of the above statement(s) is INCORRECT?

1. I and III
2. Only I
3. Only II
4. III and IV

2. In Staphylococcus aureus, chromosomal DNA replication starts at: 

1. Random single locus.
2. Random multiple loci.
3. One specific locus.
4. Multiple specific loci

3. When a DNA sequence is inserted into another without relying on sequence homology, the event is known as:

1. Homologous recombination
2. Transposition
3. Site-specific recombination
4. Recombinatorial repair

4. Lampbrush chromosomes are meiotically paired chromosomes, extensively found in growing amphibian oocytes. Some statements about this unusual structure are given below:

1. Large chromatin loops emerge out in a series from a linear chromosomal axis.
2. Most of the newly replicated DNA forms highly condensed loops emerging from the axis.
3. Each cell contains four copies of each loop.
4. Genes present in loops are actively expressed.

Which of the above statement(s) is INCORRECT?

1. Only II
2. II and III
3. Only III
4. I and IV

5. In Escherichia coli, replicon is circular and replication occurs bidirectionally. Some statements made on the biochemistry of E Coli DNA replication are given below:

1. The initiation step is facilitated by DnaA, SSB, DnaB, DnaC and DnaG.
2. Elongation of the chain requires DNA polymerase only.
3. Termination and segregation of daughter strands require terminus binding protein and DNA topoisomerase IV.
4. Another name of E Coli DNA replication is theta replication.

 Which of the above statement(s) is INCORRECT?

1. II and IV
2. Only IV
3. Only II
4. I and III

6. Match the following eukaryotic DNA polymerases with their functions:

1. a-v, b-i, c-iii, d-vi, e-iv
2. a-ii, b-i, c-iii, d-v, e-vi
3. a-v, b-vi, c-ii, d-iv, e-iii
4. a-ii, b-ii, c-i, d-vi, e-v

7. Dichotomous replication takes place in

1. Homo sapiens
2. Escherichia coli
3. Arabidopsis thaliana
4. Saccharomyces cerevisiae

8. DnaB helicase is required for the unwinding of DNA at the replication fork in E. coli. Some statements on the fidelity of DnaB are given below:

1. Unwinding involves ATP hydrolysis because energy is required to melt DNA.
2. DnaB helicase takes a ring-shaped conformation and dsDNA moves through the hole.
3. SSB protein inhibits DnaB helicase mediated unwinding if added after DnaB has bound the template.
4. DnaB helicase binds to the leading-strand template DNA

Which of the above statement(s) is CORRECT?

1. I and II
2. Only III
3. I and IV
4. II, III and IV

9. Which of the following enzymes removes the last ribonucleotide of primer after DNA replication in eukaryotes?

1. RNaseH
2. Flap endonuclease
3. DNA helicase
4. DNA primase

10. Displacement replication occurs in

1. Yeast
2. Mammalian nuclear DNA
3. Prokaryotes
4. Mammalian mitochondrial DNA

Answer Keys

1. B
2. C
3. B
4. A
5. C
6. C
7. B
8. A
9. B
10. D 

Solutions

Solution 1. 

Conserved synteny is the occurrence of the same genes in two evolutionarily distant organisms in the same order. For example, comparative studies of mouse and human genomes have found many large blocks of the genome containing the same genes occurring in the same order. The second statement is correct as all chromosome pairs except sex chromosomes in males are homologous. In humans, males inherit the X chromosome from the mother and the Y chromosome from the father, which is non-homologous. The third statement is also correct because exons and regulatory elements are a functionally essential part of a gene while introns might vary because they have to be spliced out. The fourth statement stands true for eukaryotic chromosomes, which possesses a centromere for adhering kinetochore, two telomeres for the protection of chromosomal ends and multiple replication origins for the efficient replication of a huge genome.

Solution 2. 

Bacterial chromosomal DNA has a single origin of replication, thus the replication cycle starts at one specific locus at a time. Eukaryotes have multiple ori sites, so replication may start at multiple-locus in them. DNA replication does not start at random sites but at specific locations known as the origin of DNA replication.

Solution 3. 

Transposition is related to the process of recombination but it allows movement of a certain element from one chromosomal location to another without relying on sequence homology. While homologous recombination, as the name suggests, occurs between two homologous DNA molecules, site-specific recombination involves short regions of similar nucleotide sequences. Recombinatorial repair uses homologous single-strand DNA from another dsDNA for filling gaps after DNA replication.

Solution 4. 

Lampbrush chromosomes are visible as organized series of large chromatin loops emerging from a linear chromosomal axis. The second statement is incorrect because most of the newly replicated DNA forms highly condensed chromomeres on the axis and not loops. Also, these chromosomes are not generally expressed. Each of the two chromosomes consists of two closely opposed newly replicated chromosomes, thus, each cell contains four copies for each loop. And most of the genes present in DNA loops are actively expressed, therefore, loops are precisely defined and organised structural units of a lampbrush chromosome.

Solution 5. 

The initiation step of replication in E. coli is facilitated by a replication initiation factor DnaA, single-stranded DNA binding protein SSB, DNA helicase DnaB, loading factor DnaC and primase DnaG. The second statement is incorrect because elongation not only requires DNA polymerase for chain elongation but also needs SSB for stabilizing unwound single-stranded DNA, DNA ligase for joining Okazaki fragments and DNA gyrase to relieve positive supercoiling. While termination step requires terminus binding protein and DNA topoisomerase IV. And E. coli DNA replication is also known as theta replication.

Solution 6. 

DNA polymerase β is required for base excision repair, while DNA polymerase γ is involved in mitochondrial DNA replication. DNA polymerase δ synthesizes the lagging strand, while DNA polymerase ε synthesizes the leading strand. DNA polymerase κ is required for cohesion attachment.

Solution 7. 

In the Escherichia coli cell, approximately 40 minutes are required for chromosome replication while the generation time is only 20 minutes. To achieve this doubling time, the second round of replication is initiated before the termination of the previous one. Thus, almost six replication forks may be active on a single chromosome. This is known as dichotomous replication. While on humans, Arabidopsis and budding yeast multiple origins of replication sites are present, multiple replication forks on a single chromosome is a common event.

Solution 8. 

Unwinding is an energy-consuming process because hydrogen bonds are kinetic barriers to strand separation, thus, it requires ATP hydrolysis. DnaB helicase forms a ring-shaped structure around the DNA strand to ease the movement across the replication fork. The third statement is incorrect because SSB protein inhibits DnaB helicase mediated unwinding if added before DnaB has bound the template because SSB binds to ssDNA and prevents binding of helicase. And DnaB binds to lagging-strand template DNA, not the leading strand.

Solution 9. 

In eukaryotes, when primers are removed by RNaseH, the last nucleotide is removed by a specialised enzyme, flap endonuclease. While DNA helicase and primase are required for unwinding and adding primers to facilitate DNA replication, respectively.

Solution 10. 

Replication of circular double-stranded mitochondrial DNA starts only in one of the two parental strands and proceeds for a short distance, then displaces the original complementary strand. This generates a displacement loop, hence displacement replication. Yeast, mammalian nuclear DNA and prokaryotes do not form displacement loops during replication.

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