DNA Replication

Question 1

What is the primary function of DNA replication?

Answer 1

To produce two identical copies of a cell’s DNA, ensuring genetic continuity during cell division.

Question 2

What shape is the typical prokaryotic chromosome?

Answer 2

A single, circular chromosome.

Question 3

Where does replication begin in prokaryotes?

Answer 3

At a single origin of replication called OriC.

Question 4

What are the two key properties of prokaryotic replication?

Answer 4

It is semi-conservative and bidirectional.

Question 5

What does semi-conservative replication mean?

Answer 5

Each daughter DNA molecule contains one parental and one newly synthesized strand.

Question 6

What is meant by bidirectional replication?

Answer 6

Replication proceeds outward in both directions from the origin.

Question 7

In what direction does DNA synthesis proceed?

Answer 7

5′ to 3′ direction.

Question 8

Which strand is synthesized continuously?

Answer 8

The leading strand.

Question 9

Which strand is synthesized discontinuously?

Answer 9

The lagging strand.

Question 10

What are Okazaki fragments?

Answer 10

Short DNA fragments synthesized on the lagging strand.

Question 11

What is the role of helicase (DnaB)?

Answer 11

To unwind the DNA double helix ahead of the replication fork.

Question 12

What is the function of SSB proteins?

Answer 12

To stabilize and protect single-stranded DNA and prevent reannealing.

Question 13

What enzyme relieves supercoiling ahead of the replication fork?

Answer 13

Topoisomerase (e.g., DNA gyrase).

Question 14

What enzyme synthesizes RNA primers?

Answer 14

Primase.

Question 15

Which polymerase extends DNA from the RNA primer?

Answer 15

DNA polymerase III.

Question 16

What feature gives DNA polymerase III high fidelity?

Answer 16

Its 3′ to 5′ exonuclease proofreading activity.

Question 17

What enzyme removes RNA primers?

Answer 17

DNA polymerase I.

Question 18

What additional activity does DNA polymerase I have beyond primer removal?

Answer 18

It fills in the resulting DNA gap with new nucleotides.

Question 19

What is the function of DNA ligase?

Answer 19

To seal nicks between Okazaki fragments by forming phosphodiester bonds.

Question 20

What is the function of the sliding clamp?

Answer 20

To increase the processivity of DNA polymerase III.

Question 21

What loads the helicase onto DNA?

Answer 21

DnaC.

Question 22

What initiator protein binds to OriC?

Answer 22

DnaA.

Question 23

What sequences are found at OriC?

Answer 23

Three 13-mer repeats and four 9-mer repeats.

Question 24

What accessory protein assists DnaA in opening the double helix?

Answer 24

HU protein.

Question 25

What structure is formed at the start of replication?

Answer 25

The replication bubble.

Question 26

What defines the elongation phase of replication?

Answer 26

Strand extension at replication forks via polymerases.

Question 27

How is the lagging strand looped?

Answer 27

To allow polymerase to synthesize in the same direction as the replication fork.

Question 28

Which polymerase performs the bulk of lagging strand synthesis?

Answer 28

DNA polymerase III.

Question 29

Why can't DNA polymerase III remove primers?

Answer 29

Because it lacks 5′ to 3′ exonuclease activity.

Question 30

How does DNA polymerase I perform 'nick translation'?

Answer 30

It removes RNA primers and replaces them with DNA.

Question 31

What energy source is used by DNA ligase?

Answer 31

NAD⁺ in prokaryotes; ATP in eukaryotes.

Question 32

Where does replication terminate in E. coli?

Answer 32

At Ter sequences opposite OriC.

Question 33

What protein binds to Ter sequences to halt replication?

Answer 33

Tus protein.

Question 34

How does the Tus–Ter complex control replication forks?

Answer 34

By allowing passage in one direction but blocking it in the other.

Question 35

What enzyme separates intertwined daughter chromosomes?

Answer 35

Topoisomerase (type II).

Question 36

What is Dam methylation?

Answer 36

Methylation (by Dam methylase) of adenine in the newly-synthesised strand post-replication

Question 37

What is the role of methylation in replication?

Answer 37

To distinguish parental DNA from newly synthesized strands.

Question 38

What is the mismatch repair mechanism based on?

Answer 38

Strand discrimination via methylation status.

Question 39

How does replication differ in eukaryotes?

Answer 39

It involves multiple origins, nucleosomes, telomeres, and more polymerases.

Question 40

Which polymerases are found in eukaryotic cells?

Answer 40

DNA polymerases α (primase), δ, ε, β (repair), γ (mitochondrial).

Question 41

What is the end replication problem?

Answer 41

The inability of DNA polymerases to fully replicate the 3′ ends of linear chromosomes.

Question 42

What solves the end replication problem?

Answer 42

Telomerase.

Question 43

What is telomerase?

Answer 43

A reverse transcriptase that extends telomeres using an internal RNA template.

Question 44

What are telomeres?

Answer 44

TG-rich repetitive sequences at the ends of linear chromosomes.

Question 45

What happens if telomerase is inactive?

Answer 45

Progressive telomere shortening leading to cell senescence.

Question 46

Which cells typically express telomerase?

Answer 46

Germline, stem, and cancer cells.

Question 47

What does DNA polymerase require to initiate synthesis?

Answer 47

A 3′ OH provided by an RNA primer.

Question 48

What is the purpose of DNA primase?

Answer 48

To synthesize short RNA primers for DNA polymerase.

Question 49

Why are Okazaki fragments necessary?

Answer 49

Because DNA synthesis must proceed in a 5′ to 3′ direction even on the antiparallel strand.

Question 50

How long are Okazaki fragments in prokaryotes?

Answer 50

Approximately 1000 nucleotides.

Question 51

How long are Okazaki fragments in eukaryotes?

Answer 51

Approximately 100 nucleotides.

Question 52

What initiates DNA replication in prokaryotes?

Answer 52

Binding of DnaA to OriC.

Question 53

What protein opens the double helix at OriC?

Answer 53

DnaB helicase.

Question 54

What is the significance of bidirectionality?

Answer 54

It speeds up replication by allowing two forks to progress simultaneously.

Question 55

What is meant by the processivity of a DNA polymerase?

Answer 55

How many nucleotides an enzyme, at the replication fork, can add at once before it dissociates

Question 56

What is the role of the β clamp in E. coli?

Answer 56

To tether DNA polymerase III to the DNA strand.

Question 57

How many active sites does DNA polymerase III holoenzyme have?

Answer 57

At least two: one for each strand.

Question 58

What is the role of RNase H in eukaryotes?

Answer 58

To remove RNA primers during replication.

Question 59

Why are phosphodiester bonds important in DNA?

Answer 59

They link nucleotides and provide structural integrity.

Question 60

What is DNA gyrase?

Answer 60

A bacterial topoisomerase that alleviates positive supercoiling.

Question 61

How does DNA helicase move?

Answer 61

5′ to 3′ along the lagging strand template.

Question 62

What structural motif allows helicases to unwind DNA?

Answer 62

ATP-dependent ring-shaped motor proteins.

Question 63

What ensures one round of replication per cycle in bacteria?

Answer 63

Methylation state of OriC and regulatory proteins.

Question 64

What happens if Tus is absent or mutated?

Answer 64

Replication forks may proceed past Ter sites, potentially causing conflicts.

Question 65

How is DNA ligase different from polymerases?

Answer 65

It cannot synthesize DNA; it only seals nicks between existing fragments.

Question 66

What happens if DNA ligase is defective?

Answer 66

Okazaki fragments remain 𝒖𝒏𝒔𝒆𝒂𝒍𝒆𝒅, impairing lagging strand continuity.

Question 67

Why is proofreading important?

Answer 67

To reduce mutation rates and ensure replication fidelity.

Question 68

What is the error rate of DNA polymerase III with proofreading?

Answer 68

1 error per ~10⁷ nucleotides.

Question 69

Which exonuclease activity enables proofreading?

Answer 69

3′ to 5′ exonuclease activity.

Question 70

What is the function of DnaC?

Answer 70

To load DnaB helicase onto the opened DNA.

Question 71

What is the replication fork?

Answer 71

The Y-shaped region where DNA is being unwound and replicated.

Question 72

What ensures DNA synthesis keeps pace with fork progression?

Answer 72

Coordination between helicase, polymerase, and clamp loader.

Question 73

How is primer removal in eukaryotes different from prokaryotes?

Answer 73

Involves RNase H and FEN1 rather than DNA Pol I.

Question 74

Why do cells need high-fidelity replication?

Answer 74

To maintain genome integrity and prevent mutations.