DNA Replication

Question 1

What experiment first discovered that DNA replication is semi-conservative?

Answer 1

The Meselson-Stahl experiment.

Question 2

In semi-conservative replication, what does each newly replicated DNA molecule contain?

Answer 2

One new strand and one original strand.

Question 3

The enzyme that unwinds the DNA double helix during replication is called _____.

Answer 3

Helicase.

Question 4

What is the function of DNA polymerase?

Answer 4

It is the enzyme that polymerizes nucleotides into a strand of DNA.

Question 5

Why is a primer required for DNA synthesis?

Answer 5

DNA polymerases cannot initiate chain synthesis de novo (from scratch).

Question 6

What enzyme is responsible for creating the RNA primer needed to initiate DNA synthesis?

Answer 6

Primase.

Question 7

DNA replication is described as ‘semi-discontinuous’ because one strand is synthesized continuously and the other is synthesized in short fragments. What is the continuously synthesized strand called?

Answer 7

The leading strand.

Question 8

The lagging strand is synthesized in short segments called _____.

Answer 8

Okazaki fragments.

Question 9

In which direction are both the leading and lagging strands synthesized?

Answer 9

In the $5’ \rightarrow 3’$ direction.

Question 10

Term: Replisome

Answer 10

A multicomponent machine comprised of a helicase, primase, DNA polymerase, and $3’\rightarrow5’$ exonuclease that carries out DNA replication.

Question 11

What is the typical structure of a bacterial genome?

Answer 11

It is a circular genome with a single origin of replication (OriC).

Question 12

Why is the bacterial origin of replication (OriC) rich in A-T base pairs?

Answer 12

The two hydrogen bonds between A-T pairs are easier to break than the three bonds between G-C pairs.

Question 13

What protein binds to the replication termination sites (Ter) in bacteria?

Answer 13

The Tus protein.

Question 14

What is the first step in bacterial DNA replication initiation?

Answer 14

The initiator protein, DnaA, binds and melts the DNA at the origin of replication (OriC).

Question 15

In bacterial replication, what is the name of the helicase that encircles the lagging strand to unwind DNA?

Answer 15

DnaB.

Question 16

What is the function of single-stranded DNA binding proteins (SSBs) in bacterial replication?

Answer 16

They bind to the separated single strands of DNA to protect them from nucleases.

Question 17

What is the name of the primase in bacteria that synthesizes the RNA primer?

Answer 17

DnaG.

Question 18

In the bacterial replisome, how many DNA Pol III molecules are used and how are they distributed?

Answer 18

Three molecules: one for the leading strand and two that take turns on the lagging strand.

Question 19

After lagging strand synthesis in bacteria, which enzyme removes the RNA primers and replaces them with dNTPs?

Answer 19

DNA Polymerase I (Pol I).

Question 20

What is the function of DNA ligase in DNA replication?

Answer 20

It catalyzes the formation of a phosphodiester linkage between adjacent DNA fragments, such as Okazaki fragments.

Question 21

Bacterial DNA Pol I has a subunit with $5’\rightarrow3’$ polymerase and $5’\rightarrow3’$ exonuclease activity. What is this subunit called?

Answer 21

The Klenow Fragment.

Question 22

What type of torsional strain is generated ahead of the replication fork as DNA is unwound?

Answer 22

Positive supercoiling.

Question 23

What class of enzymes relieves the torsional strain caused by supercoiling during DNA replication?

Answer 23

Topoisomerases.

Question 24

How do Type I and Type II topoisomerases differ in their requirement for ATP?

Answer 24

Type I topoisomerases do not require ATP hydrolysis, while Type II topoisomerases do.

Question 25

How does a Type I topoisomerase relax supercoiled DNA?

Answer 25

It creates a transient single-strand break, passes the unbroken strand through the break, and then religates the DNA.

Question 26

How does a Type II topoisomerase relax supercoiled DNA?

Answer 26

It creates a transient double-strand break, passes another segment of the double helix through the break, and then religates the DNA.

Question 27

What is a key capability of bacterial topoisomerase II (DNA gyrase) that distinguishes it from many other topoisomerases?

Answer 27

It can induce negative supercoils into the DNA.

Question 28

Term: Catenation

Answer 28

The interlocking of circular DNA molecules, similar to links in a chain.

Question 29

How do eukaryotic genomes differ from prokaryotic genomes regarding origins of replication?

Answer 29

Eukaryotic genomes are linear and have multiple origins of replication, whereas prokaryotic genomes are typically circular with a single origin.

Question 30

In yeast, the origin of replication is a conserved sequence known as the _____.

Answer 30

Autonomous Replicating Sequence (ARS).

Question 31

Where in the eukaryotic nucleus are active replication forks found clustered?

Answer 31

In subnuclear compartments called replication factories.

Question 32

During which phase of the eukaryotic cell cycle is DNA synthesis restricted?

Answer 32

The S phase.

Question 33

What complex binds to the eukaryotic origin of replication to begin the formation of a pre-replication complex?

Answer 33

The Origin Recognition Complex (ORC).

Question 34

The Mcm2-7 complex, which acts as the eukaryotic helicase, is loaded onto the origin only when the activity of _____ is low.

Answer 34

Cyclin-dependent kinases (CDKs).

Question 35

What is the term for the process that ensures eukaryotic DNA replicates only once per cell cycle, involving the loading of Mcm2-7?

Answer 35

Replication licensing.

Question 36

What is the name of the active helicase complex in eukaryotes, formed from the transformation of Cdc45, Mcm2-7, and GINs?

Answer 36

The CMG complex.

Question 37

What protein in eukaryotes is functionally equivalent to the SSBs in bacteria, protecting unwound DNA from nucleases?

Answer 37

Replication protein A (RPA).

Question 38

How does the eukaryotic CMG helicase differ from the bacterial DnaB helicase in its movement along the DNA?

Answer 38

The eukaryotic CMG helicase moves $3'\rightarrow5'$ on the leading strand, while the bacterial DnaB helicase moves $5'\rightarrow3'$ on the lagging strand.

Question 39

In eukaryotes, what is the phenomenon where one DNA polymerase initiates synthesis and is then replaced by another for elongation?

Answer 39

Polymerase switching.

Question 40

Which eukaryotic DNA polymerase/primase complex synthesizes a short RNA-DNA hybrid primer to initiate replication?

Answer 40

DNA Pol $\alpha$/primase.

Question 41

After initiation by Pol $\alpha$, which eukaryotic DNA polymerase is primarily responsible for lagging strand synthesis?

Answer 41

DNA Polymerase $\delta$ (Pol $\delta$).

Question 42

After initiation by Pol $\alpha$, which eukaryotic DNA polymerase is primarily responsible for leading strand synthesis?

Answer 42

DNA Polymerase $\epsilon$ (Pol $\epsilon$).

Question 43

What protein serves as the sliding clamp in the eukaryotic replisome, enhancing the processivity of the DNA polymerase?

Answer 43

Proliferating cell nuclear antigen (PCNA).

Question 44

What protein complex is responsible for loading the PCNA sliding clamp onto the DNA in eukaryotes?

Answer 44

Replication Factor C (RFC).

Question 45

The ability of DNA Pol $\delta$ and DNA Pol $\epsilon$ to correct errors is due to their _____ activity.

Answer 45

$3'\rightarrow5'$ exonuclease (proofreading) activity.

Question 46

During eukaryotic Okazaki fragment maturation, what enzyme removes the RNA 5' flap created by strand displacement?

Answer 46

Flap endonuclease 1 (FEN-1).

Question 47

In eukaryotes, which ligase joins the mature Okazaki fragments on the lagging strand?

Answer 47

DNA ligase I.

Question 48

How are histones managed during eukaryotic DNA replication?

Answer 48

Nucleosomes are disassembled into H3-H4 tetramers and H2A-H2B dimers ahead of the fork and reassembled behind it.

Question 49

What is the 'end replication problem' for linear chromosomes?

Answer 49

After the final RNA primer on the lagging strand is removed, there is no upstream DNA to serve as a template, leading to a gap and progressive shortening of the chromosome with each replication cycle.

Question 50

What is the repeating G-rich sequence found at human telomeres?

Answer 50

TTAGGG.

Question 51

What is the name of the protein complex that protects the ends of chromosomes and prevents them from being recognized as double-strand breaks?

Answer 51

Shelterin.

Question 52

The enzyme that solves the end replication problem by extending the ends of linear chromosomes is called _____.

Answer 52

Telomerase.

Question 53

What are the two essential components of the telomerase ribonucleoprotein complex?

Answer 53

A protein subunit (TERT) and an RNA subunit (TERC).

Question 54

The protein component of telomerase, TERT, has what type of enzymatic activity?

Answer 54

Reverse transcriptase activity (synthesizes DNA from an RNA template).

Question 55

How does telomerase extend the 3' overhang of a chromosome?

Answer 55

It uses its internal RNA component (TERC) as a template to synthesize new DNA repeats onto the 3' end of the G-rich strand.

Question 56

What is a T-loop in the context of telomere structure?

Answer 56

A folded structure where the single-stranded 3' overhang invades the double-stranded telomeric DNA, protecting the chromosome end.

Question 57

What is the Hayflick Limit?

Answer 57

The limited number of times a normal somatic cell can divide before it enters an irreversible state of cellular aging known as senescence.

Question 58

How do most cancer cells achieve immortality and bypass the Hayflick limit?

Answer 58

They reactivate telomerase to maintain telomere length, allowing for indefinite cell division.

Question 59

What is the ALT pathway, used by some telomerase-negative tumors?

Answer 59

Recombination-dependent Alternative Lengthening of Telomeres, which uses homologous recombination to maintain telomere length.

Question 60

How does Drosophila melanogaster maintain its chromosome ends without telomerase?

Answer 60

It uses the addition of retrotransposons to the ends of the chromosomes.

Question 61

What type of DNA replication is commonly used for extrachromosomal DNA like plasmids in bacteria?

Answer 61

Rolling circle DNA replication.

Question 62

What initiates rolling circle DNA replication?

Answer 62

An endonuclease nicks one strand (the (+) strand) of the double-stranded circular DNA.

Question 63

In rolling circle replication, what serves as the primer for the host DNA polymerase?

Answer 63

The free 3' end of the nicked strand.