[W4] DNA replication

Question 1

What does ‘semiconservative’ replication mean?

Answer 1

Each daughter DNA molecule retains one original strand and gains one newly synthesized strand.

Question 2

What is ‘semidiscontinuous’ replication?

Answer 2

The leading strand is synthesized continuously, while the lagging strand is synthesized in short fragments (Okazaki fragments).

Question 3

In which direction is DNA always synthesized?

Answer 3

5′ to 3′ direction.

Question 4

What is a replicon?

Answer 4

A unit of DNA that is replicated starting from a single origin.

Question 5

How does replication differ in prokaryotes and eukaryotes regarding origins?

Answer 5

Prokaryotes typically have a single origin; eukaryotes have many origins per chromosome.

Question 6

What is the origin of replication in E. coli called?

Answer 6

oriC.

Question 7

What is an ARS?

Answer 7

Autonomously Replicating Sequence – origin of replication in yeast, ~50 bp with essential elements.

Question 8

What is the role of DNA helicase?

Answer 8

Unwinds the DNA helix using ATP.

Question 9

What is the function of single-stranded binding proteins (SSBs)?

Answer 9

Stabilize unwound DNA to prevent reannealing.

Question 10

What does primase do?

Answer 10

Synthesizes short RNA primers to provide a 3′-OH for DNA polymerase.

Question 11

What is DNA polymerase’s function?

Answer 11

Adds nucleotides to a growing DNA strand using a template.

Question 12

What does DNA ligase do?

Answer 12

Seals gaps (nicks) in the DNA backbone, particularly between Okazaki fragments.

Question 13

What is the role of topoisomerase?

Answer 13

Relieves supercoiling and torsional stress ahead of the replication fork.

Question 14

Which polymerase synthesizes the leading strand in eukaryotes?

Answer 14

DNA polymerase ε.

Question 15

Which polymerase synthesizes the lagging strand?

Answer 15

DNA polymerase δ.

Question 16

What does polymerase α do?

Answer 16

Initiates synthesis by laying down RNA primer and a short stretch of DNA.

Question 17

What is the role of PCNA?

Answer 17

It is a DNA clamp that increases polymerase processivity.

Question 18

What is RFC?

Answer 18

Replication Factor C – loads PCNA onto DNA.

Question 19

What proofreading function do many DNA polymerases have?

Answer 19

3′→5′ exonuclease activity to remove mismatched bases.

Question 20

What is the ORC?

Answer 20

Origin Recognition Complex – binds to replication origins and initiates replication.

Question 21

What are Cdc6 and Cdt1?

Answer 21

Licensing factors that help load MCM helicase onto origins.

Question 22

What ensures DNA is replicated only once per cycle?

Answer 22

Licensing system – licensing factors are degraded or inactivated after initiation.

Question 23

What is the MCM complex?

Answer 23

The helicase complex that unwinds DNA at origins during replication.

Question 24

What are Okazaki fragments?

Answer 24

Short DNA fragments synthesized discontinuously on the lagging strand.

Question 25

How is the RNA primer removed in eukaryotes?

Answer 25

FEN1 endonuclease removes it, and DNA polymerase fills the gap.

Question 26

How are Okazaki fragments joined?

Answer 26

DNA ligase I seals them via phosphodiester bond formation.

Question 27

In which cell cycle phase does DNA replication occur?

Answer 27

S phase.

Question 28

What happens at the G1/S checkpoint?

Answer 28

Cell commits to DNA replication and division.

Question 29

What is G0?

Answer 29

A quiescent state where the cell exits the cycle; replication machinery is dismantled.

Question 30

Why does chromatin structure affect replication?

Answer 30

Nucleosomes must be disassembled and reassembled for replication machinery to access DNA.

Question 31

What do CAF-1 and ASF1 do?

Answer 31

Histone chaperones – assist in reassembling nucleosomes during and after replication.

Question 32

What is FACT?

Answer 32

A complex that facilitates chromatin disassembly/reassembly during replication.

Question 33

What is theta replication?

Answer 33

Circular DNA replication model seen in prokaryotes; bidirectional from a single origin.

Question 34

What is rolling-circle replication?

Answer 34

One strand is nicked and unrolled as the template; common in plasmids and viruses.

Question 35

What is the 'end replication problem'?

Answer 35

DNA polymerase cannot fully replicate the 3′ ends of linear chromosomes (lagging strand).

Question 36

What solves the end replication problem?

Answer 36

Telomerase – a ribonucleoprotein that extends telomeres using its own RNA template.

Question 37

What mechanisms ensure DNA replication accuracy?

Answer 37

High-fidelity polymerases, 3′→5′ exonuclease proofreading, and mismatch repair.

Question 38

What is processivity?

Answer 38

The ability of an enzyme (e.g., DNA polymerase) to continuously synthesize DNA without dissociating.

Question 39

Where does replication end in E. coli?

Answer 39

At ter sites; they prevent over-replication.

Question 40

What happens if replication forks encounter DNA damage?

Answer 40

A specialized polymerase may bypass the lesion, and repair follows before continuation.

Question 41

What is dideoxy sequencing (Sanger method)?

Answer 41

DNA sequencing using ddNTPs to terminate chains at specific bases, then analyzing fragment sizes.

Question 42

What are ddNTPs?

Answer 42

Dideoxynucleotides – chain-terminating nucleotides lacking a 3′-OH group.

Question 43

How does capillary gel electrophoresis assist sequencing?

Answer 43

It separates DNA fragments by size to identify which base was added last.

Question 44

What is the aim of next-gen sequencing?

Answer 44

Increase speed, reduce cost, and automate DNA sequencing.