Molecular Biology: MCQs on DNA synthesis (Replication)

Multiple Choice Questions Set

Molecular Biology: DNA synthesis (Replication)

DNA replication is a fundamental process in which DNA synthesis occurs, leading to the formation of a new DNA molecule. It is a highly regulated process that ensures the faithful transmission of genetic information from one generation to the next. During DNA replication, the DNA double helix is unwound, and each strand serves as a template for the synthesis of a new complementary strand. The enzyme responsible for DNA synthesis is DNA polymerase, which catalyzes the addition of nucleotides to the growing DNA chain. The process of DNA replication involves a number of key proteins, including helicases, primases, and DNA ligases.

1) In most organisms, DNA is a genetic material that stores the information template for the synthesis of RNA and subsequently protein. Name the processes a, b, c represented in the figure:

2) In some viruses, RNA serves as the storage of genetic materials and DNA is synthesized from RNA by the enzyme known as:
a) DNA synthetase
b) DNA polymerase
c) Reverse transcriptase
d) DNA convertase

3) Which of the following process does not occur in prokaryotes?

a) Replication

b) Splicing

c) Translation

d) Transcription

4) Phosphodiester bond links two nucleotides together and maintains polarity which refers to:

a) the 5' hydroxyl group of pentose of one nucleotide to 3' hydroxyl group of adjacent nucleotide through a phosphate group.
b) 5' end with a phosphate group and 3'end with hydroxyl are free.
c) addition of new nucleotide occurs via attachment of 5' phosphate group of new nucleotide to 3' phosphate group of an existing chain.
d) All of the above

5) DNA helices exist in various forms. 

Which of the following form is predominantly expressed in cells?
a) B- Helix
b) A-Helix
c) E-Helix
d) Z-Helix

6) Which one of the following statements is true regarding the DNA double-helical structure?
a) The DNA double helix is coiled around a common axis known as the axis of symmetry
b) The hydrophilic deoxyribose-phosphate backbone of each chain is on the outside.
c) The hydrophobic nitrogen bases are stacked inside.
d) All of the Above

7) The spatial arrangement DNA helical structure creates a major and minor groove which are important for:
a) kinking and bending of the helical structure
b) providing recognition and binding sites for various DNA binding proteins
c) All of Above
d) None of the Above

8) Aminoglycoside antibiotics such as kanamycin, tobramycin, neomycin are known inhibitors of DNA synthesis. It contains a cyclitol ring linked to five or six-membered sugars by glycosidic bonds. 

These antibiotics are:
a) Positively charged compound that to DNA and intercalates it.
b) Positively charged compound that binds to DNA polymerase activity.
c) Negatively charged compound to DNA and denatures it.
d) Negatively charged compound that binds to histones

9) The Chargaff rules state that the number of purines and pyrimidines are equal (A+G = T + C) in any double-stranded DNA molecule. Watson and Crick later solved the structure of DNA and nitrogen base pairings. 

Which of the following base-pairing rule is true?
a) Adenine pairs with Guanine and Thymine pairs with Cytosine
b) Adenine pairs with Thymine and Guanine pairs with Cytosine
c) Adenine pairs with Cytosine and Guanine pairs with Thymine
d) DNA base pairing is nonspecific

10) The DNA replication occurs in a semi-conservative manner which means:
a) Two daughter cells with one consisting of double-helical parent DNA, others have newly synthesized DNA.

b) Two daughter cells each consisting of one parental strand and one newly synthesized DNA.
c) Two daughters cells each consisting of one-half parental and another half newly synthesized DNA resulting from the crossover.
d) None of the above

11) Which of the following are the characteristic feature of DNA replication?
a) DNA replication is template-directed
b) DNA replication requires short RNA primers
c) DNA replication is a highly accurate process
d) All of the Above

12) In prokaryotes, DNA replication begins at a single site that is rich in AT nucleotide sequence, where two strands unwind and separate. 

This ATP dependent process is catalyzed by a protein known as..................................?
a) DnaA protein
b) Single-strand binding protein
c) DNA polymerase
d) Topoisomerase

13) The short strand of .......................... primer is required for the replication of DNA:
a) DNA
b) RNA
c) Histone
d) hnRNA

14) As the two strands of the double helix are separated, the positive supercoiling interferes with the further unwinding of DNA. 

Which of the following enzyme makes a break in a strand of DNA to release the supercoiling and facilitate the replication to occur?
a) DnaA protein
b) Single-strand binding protein
c) DNA polymerase
d) Topoisomerase

15) Which of the following enzyme has a unique ability to introduce positive and negative supercoiling of the DNA and it is the target for antibacterial agents such as ciprofloxacin/quinolones?
a) DnaA protein
b) DNA helicase
c) DNA gyrase
d) DNA polymerase

16) DNA replication is bidirectional and anti-parallel. 

Which of the statement is FALSE regarding DNA replication?
a) The DNA synthesis i.e. addition of nucleotide occurs from 5'-3' position
b) The DNA synthesis is semi-continuous with continuous leading strand and discontinuous lagging strand.
c) The DNA synthesis is bidirectional
d) None of the Above

17) The DNA polymerase is a template-directed enzyme that synthesizes a new complementary strand from a parent strand but it requires the existing short nucleotide sequence for its elongation. 

Which of the following enzyme is required for the synthesis of this primer?
a) Primase/RNA polymerase
b) RNA synthase
c) DNA synthase
d) Helicase

18) DNA polymerase III holoenzyme possesses:
a) polymerase activity only
b) 3’→ 5’ endonuclease activity
c) 3’→ 5’ exonuclease activity and polymerase activities
d) 5’→ 3’ exonuclease activity

19) Which of the following statement is true regarding an enzyme DNA polymerase that catalyzes the elongation of complementary DNA strand?

a) DNA polymerase III is a highly processive enzyme.
b) DNA polymerase III possesses 5'-3' polymerase activity required for elongation.
c) DNA polymerase III possesses 3'-5' exonuclease activity important for maintaining fidelity
d) All of the above

20) In prokaryotes, the RNA primer from the lagging strand is removed and replaced by the DNA sequence. 

This process is catalyzed by an enzyme ..................................................which possess 5'-3' exonuclease activity and 5'-3' polymerase activity.
a) DNA polymerase I
b) DNA polymerase II
c) DNA polymerase III
d) DNA polymerase IV

21) In eukaryotes, DNA polymerase alpha is a multi-subunit enzyme with different functions. They include..........................................................?
a) Elongation of the leading strand
b) 3'-5' exonuclease activity
c) Initiation and synthesis of RNA primer
d) High processivity

22) In eukaryotes, which of the following DNA polymerase is highly processive and required for the elongation phase of DNA replication?
a) Pol alpha
b) Pol delta
c) Pol gamma
d) Pol beta

23) In eukaryotes, which of the following DNA polymerase is required for mitochondrial DNA replication?
a) Pol alpha
b) Pol beta
c) Pol gamma
d) Pol delta

24) Telomeres are the repetitive sequence of T's and G's that are present in the eukaryotes to protect the random cleavage from nucleases. These telomeres are synthesized by the enzyme telomerase. 

Which of the following are the properties of enzyme telomerase?
a) Telomerase is a reverse transcriptase enzyme
b) Telomerase consist of an RNA sequence that serves as a template
c) After completion of each cycle, telomerase translocates to 3'end of DNA to synthesize repetitive sequence.
d) All of the above

Multiple Choice Answers:

1- a)- Replication, b-Transcription, c- Translation

The central dogma of molecular biology is a fundamental principle that describes the flow of genetic information within a biological system. It states that DNA encodes genetic information that is transcribed into RNA, which is then translated into proteins. This process occurs in all living organisms and is the basis for the development, growth, and maintenance of cells and tissues.

2- c) Reverse transcriptase

In some viruses, RNA serves as the genetic material instead of DNA. These viruses are called retroviruses, and they use a unique enzyme called reverse transcriptase to convert RNA into DNA.
Reverse transcriptase is an RNA-dependent DNA polymerase that catalyzes the synthesis of a complementary DNA (cDNA) strand from an RNA template. This process is known as reverse transcription, and it is a central step in the replication of retroviruses like HIV.
Once the cDNA is synthesized, it is then integrated into the host cell's genome by another enzyme called integrase. From there, the viral DNA can be transcribed into RNA and used to produce new virus particles. This unique pathway of genetic information flow, from RNA to DNA, is known as reverse transcription and is a key feature of the central dogma of molecular biology.

3- b) Splicing

Splicing is a post-transcriptional process that involves the removal of introns and the joining of exons in eukaryotic cells. Prokaryotes lack introns in their genes, and their mRNA molecules do not undergo splicing. Therefore, splicing does not occur in prokaryotes.
Replication, transcription, and translation occur in both prokaryotes and eukaryotes. Replication is the process of copying DNA, transcription is the process of synthesizing RNA from a DNA template, and translation is the process of synthesizing proteins from mRNA templates.

4- d) All of the above 

Phosphodiester bond is a covalent bond that connects two nucleotides together in DNA or RNA. It is formed between the 3' hydroxyl group of one nucleotide and the 5' phosphate group of the next nucleotide, resulting in a sugar-phosphate backbone. This linkage creates a polarity in the nucleic acid strand, with a free 5' phosphate group at one end and a free 3' hydroxyl group at the other end. Thus, option (a) is the correct answer. Option (b) is incorrect as it refers to the free ends of the nucleic acid strand rather than the bond itself. Option (c) is also incorrect as it describes the process of nucleotide addition rather than the structure of the bond itself.

5- a) B- Helix 

DNA helices can exist in different conformations depending on various factors such as the sequence, environment, and interactions with other molecules. The three most common forms of DNA helices are B-helix, A-helix, and Z-helix. The B-helix is the most commonly expressed form in cells and is characterized by a right-handed helix with a major groove and a minor groove, and the bases perpendicular to the axis of the helix. The A-helix is also a right-handed helix but has a more compact structure with a deep and narrow major groove and a shallow and wide minor groove. The Z-helix is a left-handed helix and has a zig-zag pattern with a major groove that is narrow and deep and a minor groove that is wide and shallow. While all three forms of DNA helices can occur, the B-helix is the most commonly expressed in cells and is considered the standard conformation for DNA.

6- d) All of the Above

The DNA double helix is a twisted ladder-like structure formed by two complementary strands of nucleotides coiled around a common axis of symmetry. The hydrophilic deoxyribose-phosphate backbone of each strand is on the outside, while the hydrophobic nitrogenous bases are stacked inside. The hydrogen bonds between the nitrogenous bases hold the two strands of the helix together. The double helix structure provides stability and protects the genetic information stored in the DNA.

7- b) providing recognition and binding sites for various DNA binding proteins 

The major and minor grooves of the DNA double helix provide different three-dimensional structures for DNA-binding proteins to recognize and interact with specific sequences of bases in the DNA. The major groove is wider and allows for more extensive interactions between the protein and DNA bases, while the minor groove is narrower and limits the types of interactions that can occur. This recognition and binding of DNA-binding proteins to specific DNA sequences is essential for many cellular processes, including DNA replication, transcription, and repair.

8- a) Positively charged compound that to DNA and intercalates it

Aminoglycoside antibiotics bind to the bacterial DNA polymerase enzyme and cause a distortion in the enzyme's structure, inhibiting its ability to synthesize DNA. The positively charged nature of the antibiotic allows it to bind to the negatively charged phosphate backbone of DNA, facilitating its inhibition of the polymerase activity. The cyclitol ring and sugars are not directly involved in the inhibition of DNA synthesis, but rather contribute to the structure and stability of the antibiotic molecule.

9- b) Adenine pairs with Thymine and Guanine pairs with Cytosine

The Watson-Crick base-pairing rules state that adenine (A) always pairs with thymine (T) through two hydrogen bonds, while cytosine (C) always pairs with guanine (G) through three hydrogen bonds. These base pairs form the rungs of the DNA ladder and provide the complementarity that allows DNA to replicate and transmit genetic information faithfully. The Chargaff rules describe the proportion of each nitrogenous base in DNA but do not specify the pairing rules.

10- b) Two daughter cells each consisting of one parental strand and one newly synthesized DNA

All of the above options are characteristic features of DNA replication. DNA replication is a template-directed process, meaning that the nucleotide sequence of the newly synthesized strand is determined by the complementary base pairing between the template strand and the incoming nucleotides. DNA replication requires short RNA primers that provide a 3'-OH group to which nucleotides can be added by DNA polymerase. Finally, DNA replication is a highly accurate process, with an error rate of approximately one mistake per billion nucleotides replicated.

11- d) All of the Above 

All of the above options are characteristic features of DNA replication. DNA replication is a template-directed process, meaning that the nucleotide sequence of the newly synthesized strand is determined by the complementary base pairing between the template strand and the incoming nucleotides. DNA replication requires short RNA primers that provide a 3'-OH group to which nucleotides can be added by DNA polymerase. Finally, DNA replication is a highly accurate process, with an error rate of approximately one mistake per billion nucleotides replicated.

12)- a) DnaA protein  

In prokaryotes, DNA replication is initiated at a specific site called the origin of replication. The origin of replication contains a DNA sequence that is recognized by a protein called DnaA. DnaA binds to this site and causes the DNA to unwind and separate, allowing for the replication machinery to access the DNA strands. This process is ATP-dependent, meaning that DnaA uses energy from ATP hydrolysis to facilitate the separation of the DNA strands. Once the DNA strands are separated, other proteins, such as helicases and primases, are recruited to initiate DNA replication.

13- b) RNA

The short strand of RNA primer is required for the replication of DNA. During DNA replication, a short RNA primer is synthesized by the enzyme primase, which provides a 3'-OH group for DNA polymerase to initiate DNA synthesis. This RNA primer is later removed and replaced by DNA nucleotides by DNA polymerase, leading to the synthesis of a new DNA strand complementary to the template strand. The RNA primer is necessary because DNA polymerase can only add nucleotides to the 3'-OH group of an existing strand. Therefore, without an RNA primer, DNA replication cannot be initiated.

14-d) Topoisomerase

During DNA replication, as the two strands of the double helix are separated, the positive supercoiling of the DNA ahead of the replication fork creates torsional stress, which can interfere with the further unwinding of DNA. Topoisomerases are a class of enzymes that help relieve the tension caused by supercoiling by making transient breaks in one or both strands of the DNA molecule. This allows the DNA strands to rotate around each other and relax the supercoiling. Once the supercoiling is released, the enzyme seals the break and the DNA replication can continue. There are two types of topoisomerases: Type I topoisomerases break a single strand of DNA and Type II topoisomerases break both strands of DNA. In bacteria, DNA gyrase is a type II topoisomerase that is involved in DNA replication and helps in releasing the positive supercoiling.

15- c) DNA gyrase

DNA gyrase is a type II topoisomerase enzyme that is responsible for introducing negative supercoils into DNA, which helps to relieve the torsional stress that builds up ahead of the replication fork during DNA replication. It also has a unique ability to introduce positive supercoils, which is important for regulating gene expression and DNA compaction.
Antibacterial agents such as ciprofloxacin and other quinolones target DNA gyrase by inhibiting its ability to introduce negative supercoils, leading to an accumulation of positive supercoils that eventually cause DNA damage and cell death.

16- d) None of the Above 

DNA synthesis is template-directed: The newly synthesized strand of DNA is synthesized using the existing DNA strand as a template.
DNA synthesis proceeds in a 5' to 3' direction: DNA polymerase adds nucleotides to the 3' end of the growing DNA chain.
DNA synthesis is semi-conservative: Each newly synthesized DNA molecule contains one strand from the original DNA molecule and one newly synthesized strand.
DNA synthesis requires short RNA primers: The RNA primers are synthesized by primase and serve as a starting point for DNA polymerase to start adding nucleotides.
DNA synthesis is a highly accurate process: The error rate of DNA synthesis is very low due to the proofreading activity of DNA polymerase and other repair mechanisms.

DNA synthesis is bidirectionality, which means that the replication process occurs in two opposite directions simultaneously.

 

17- a) Primase/RNA polymerase

The enzyme required for the synthesis of the RNA primer is primase, also known as RNA polymerase. Primase is a type of RNA polymerase that synthesizes a short RNA molecule complementary to the DNA template. This RNA molecule serves as a primer, which is necessary for DNA polymerase to initiate the elongation of a new strand.
DNA polymerase can only add nucleotides to the 3' end of an existing strand, so it requires a short primer to provide a 3' end for the new strand to elongate. The RNA primer is subsequently removed by DNA polymerase and replaced with DNA nucleotides. Primase is typically part of a larger protein complex called the primosome, which includes helicases and other enzymes involved in DNA replication.

18- c) 3’→ 5’ exonuclease activity and polymerase activities 

DNA polymerase III holoenzyme is the primary enzyme complex involved in DNA replication in prokaryotes. It has both polymerase activity, which allows it to synthesize new DNA strands, and 3’→ 5’ exonuclease activity, which enables it to proofread and correct errors in the newly synthesized DNA strands. This combination of activities makes the DNA polymerase III holoenzyme a highly accurate and efficient enzyme complex in DNA replication. It does not possess 5’→ 3’ exonuclease activity, which is carried out by DNA polymerase I in prokaryotes.

19- d) All of the above 

DNA polymerase III is a highly processive enzyme that possesses both 5'-3' polymerase activity required for the elongation of the new strand and 3'-5' exonuclease activity that is important for maintaining fidelity by proofreading the newly synthesized DNA strand.

20-a) DNA polymerase I

In prokaryotes, the process of removing and replacing RNA primer from the lagging strand during DNA replication is carried out by an enzyme called DNA polymerase I. DNA polymerase I is a type of DNA polymerase enzyme that has both 5'→3' polymerase activity and 5'→3' exonuclease activity. It can remove the RNA primer from the 5' end of the Okazaki fragment through its exonuclease activity and then replace it with DNA nucleotides via its polymerase activity. The resulting DNA fragment is then ligated to the adjacent fragment to complete the synthesis of the lagging strand.

21- c) Initiation and synthesis of RNA primer 

In eukaryotes, DNA polymerase alpha (Pol α) is a multi-subunit enzyme that plays a crucial role in the initiation of DNA replication. Pol α contains four subunits: a catalytic subunit (p180) and three regulatory subunits (p68, p58, and p48). The catalytic subunit of Pol α possesses both DNA polymerase activity and primase activity. The primase activity of Pol α is responsible for the synthesis of RNA primers, which are essential for DNA replication. Once the RNA primers are synthesized, the polymerase activity of Pol α elongates the primers, synthesizing short stretches of DNA. Pol α is not highly processive and tends to dissociate from the DNA template after synthesizing only a few nucleotides. After the initial synthesis of RNA primers, Pol α is replaced by other DNA polymerases that possess higher processivity, such as Pol δ and Pol ε, which are responsible for the elongation of the leading and lagging strands, respectively.

22- b) Pol delta 

In eukaryotes, DNA replication involves several DNA polymerases with distinct functions. Pol alpha is a multi-subunit enzyme involved in the initiation and synthesis of RNA primers, while Pol delta and Pol epsilon are responsible for elongation of the leading and lagging strands, respectively.
Pol delta is highly processive and required for the elongation phase of DNA replication. It has a high affinity for the template DNA and can rapidly add nucleotides to the growing strand. Pol delta also possesses 3'-5' exonuclease activity, which allows it to proofread the newly synthesized strand for errors and correct any mistakes. This ensures high fidelity in DNA replication.

23- c) Pol gamma

The DNA polymerase required for mitochondrial DNA replication in eukaryotes is Pol gamma. It is a heterodimeric enzyme consisting of a catalytic subunit encoded by the POLG gene and an accessory subunit encoded by the POLG2 gene. Pol gamma is responsible for replicating and maintaining the mitochondrial genome, which is a circular DNA molecule with a different structure and replication process than nuclear DNA. Mutations in the POLG gene have been linked to a variety of mitochondrial diseases.

24- d) All of the above

Telomerase is an enzyme that is composed of both protein and RNA components. The RNA component of telomerase serves as a template for the synthesis of the repetitive TTAGGG sequence that makes up telomeres. Telomerase is a unique reverse transcriptase enzyme in that it uses an RNA template to synthesize DNA. After each cycle of telomere synthesis, the telomerase enzyme translocates to the 3' end of the DNA strand and repeats the process, resulting in the elongation of the telomere.

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