Deck 6: DNA Replication and Telomere Maintenance

Question 1

DNA synthesis occurs in

A) the 3 ' to 5 ' direction.
B) the 5 ' to 3 ' direction.
C) both directions.
D) different directions in different organisms.

Answer 1

the 5 ' to 3 ' direction.

Question 2

Which of the following statements is correct?

A) DNA polymerase requires a primer to get started.
B) DNA polymerase can start synthesis de novo.
C) There is only one type of replicative DNA polymerase in mammalian cells.
D) DNA polymerase catalyzes the formation of a phosphodiester bond between the first 3 'hydroxyl group of the new dNTP and the 5 '-phosphate of the last nucleotide in the newly synthesized strand.

Answer 2

DNA polymerase requires a primer to get started.

Question 3

Nucleotides used for DNA synthesis contain three phosphates. During catalysis, the 3' hydroxyl of the primer attacks

A) the phosphate closest to the deoxyribose, releasing the terminal two phosphates
B) the central phosphate, releasing the terminal phosphate
C) the terminal phosphate, incorporating all three phosphates into the DNA backbone
D) the deoxyribose, releasing all three phosphates

Answer 3

the phosphate closest to the deoxyribose, releasing the terminal two phosphates

Question 4

Discontinuous synthesis of DNA takes place on

A) the lagging strand.
B) the leading strand.
C) both strands.
D) different strands in different organisms.

Question 5

Phosphodiester bonds are formed between adjacent Okazaki fragments by

A) DNA polymerase
B) topoisomerase
C) DNA ligase I
D) telomerase

Question 6

During DNA replication, DNA ligase is most active on the lagging strand. This is because:

A) The lagging strands contain more short DNA segments than the leading strand, and these short segments are ligated together with DNA ligase.
B) The lagging strand is synthesized in the 3 ' to 5 ' direction.
C) The lagging strand requires DNA ligase to couple the RNA primer to the Okazaki fragments.
D) The lagging strand is synthesized more slowly, and DNA ligase acts as a sliding clamp to speed up the DNA polymerase.

Question 7

A laboratory technique called "nick translation," in which nucleotides of a nicked dsDNA fragment are replaced with labeled nucleotides, takes advantage of which unique aspect of bacterial DNA Polymerase I?

A) 5' to 3' polymerization activity
B) 5' to 3' exonuclease activity
C) 3' to 5 exonuclease activity
D) interaction with RNA

Question 8

The bacterial multi-protein macromolecular complex that simultaneously replicates the leading and lagging strands is called

A) a replication factory
B) replication complex A
C) origin recognition complex (ORC)
D) the replisome

Question 9

In an ATP-dependent reaction, Topoisomerase I

A) makes a double-strand break in DNA
B) uses the hydroxyl group of a serine to break the DNA backbone
C) forms a covalent phosphotyrosine linkage with DNA
D) uses the energy from the terminal phosphates released during replication to cleave a single strand of DNA

Question 10

Which enzyme creates a double-strand DNA break during catalysis?

A) DNA helicase
B) topoisomerase II
C) clamp loader
D) the Klenow fragment

Question 11

Topoisomers can be physically separated by

A) CsCl gradient ultracentrifugation, because they differ in molecular weight
B) agarose gel electrophoresis, because they differ in shape
C) sucrose density gradient centrifugation, because they differ in density
D) electron microscopy, because they have different morphologies

Question 12

Which statement is not correct?

A) Eukaryotic chromosomal DNA replication occurs in "replication factories."
B) Eukaryotic chromosomal DNA typically has only one origin of replication.
C) An origin of replication is a site on chromosomal DNA where a bidirectional pair of replication forks initiates.
D) Origin DNA sequences usually have many A-T base pairs.

Question 13

Once bound to an origin of replication, the origin replication complex (ORC) recruits

A) DNA polymerase/primase
B) replication protein A
C) topoisomerase I and II
D) Cdc6, Cdt1, and the Mcm2-7 helicase complex

Question 14

Positive supercoils ahead of the replication fork are resolved by

A) helicase
B) DNA polymerase/primase
C) topoisomerase I and/or II
D) PCNA, the sliding clamp

Question 15

Replication licensing ensures that

A) DNA replication occurs by a semiconservative mechanism.
B) DNA only replicates once per cell cycle.
C) only one origin of replication is active within a cell at a time.
D) DNA replication only occurs during the G2 phase of the cell cycle.

Question 16

Pre-replication complex assembly

A) occurs when cyclin-dependent kinase 1 (CDK1) activity is low
B) occurs when cyclin-dependent kinase 1 (CDK1) activity is high
C) is not regulated by cyclin-dependent kinase 1 (CDK1) activity
D) occurs during the M phase of the cell cycle.

Question 17

Enzymes that use the energy of ATP to unwind the DNA duplex are called

A) DNA helicases
B) DNA ligases
C) DNA topoisomerases
D) DNA kinases

Question 18

DNA polymerase $\delta$ and DNA polymerase $\varepsilon$ have

A) 5' to 3'polymerase activity only
B) both 5' to 3'polymerase activity and 3' to 5' exonuclease activity
C) both 3' to 5' polymerase activity and 5' to 3' exonuclease activity
D) both 3' to 5' polymerase activity and 5'to 3' polymerase activity

Question 19

Nucleotide selectivity and proofreading by DNA polymerase depends on

A) base-base hydrogen bonding.
B) the geometry of Watson-Crick base pairs.
C) levels of cyclin-dependent kinases
D) Both A and B

Question 20

A molecular biologist purified what she thought were all factors essential for DNA replication in order to set up an in vitro DNA replication system. When she tested the in vitro system, replication occurred. But, when she isolated the newly synthesized double-stranded DNA, denatured the DNA, and electrophoresed the single-stranded products, she noted that there were not only some long strands but also numerous short segments of DNA a few hundred nucleotides long. What was probably missing from the in vitro replication system she developed?

A) RNA primers
B) Okazaki fragments
C) DNA polymerase
D) DNA ligase

Question 21

Phage X174 replication occurs by a

A) a theta-shaped intermediate.
B) a rolling circle mechanism.
C) a strand coupled mechanism.
D) a strand displacement mechanism.

Question 22

A hallmark feature of rolling circle replication is

A) use of an alternative polymerase.
B) lack of semi-discontinuous synthesis on the lagging strand.
C) displacement of a strand to form a 5' phosphate tail.
D) formation of a 3'OH-tyrosyl intermediate.

Question 23

Chromatin assembly factor 1 (CAF-1) is thought to aid replication by

A) initiating synthesis of histones.
B) removing histones ahead of the replication fork.
C) bringing histones to the replication fork.
D) phosphorylating nucleosomes behind the replication fork.

Question 24

Two competing models to explain how nucleosomes are assembled behind replication forks differ by

A) whether histones H3 and H4 are passed to daughter strands as dimers or tetramers.
B) whether histone octamers remain intact during the process.
C) whether CAF-1 is necessary for the process.
D) whether the leading or lagging strand binds to the parental histones.

Question 25

At the ends of chromosomes in eukaryotes, a problem occurs upon repeated DNA replication of the __________ strand. __________ is responsible for providing a solution to this problem.

A) lagging; telomerase
B) leading; replicase
C) lagging; replicase
D) leading; polymerase

Question 26

Telomerase directly elongates

A) the 5 ' end of the lagging template strand.
B) the 3 'end of the lagging template strand.
C) the 5' end of the leading template strand.
D) the 3' end of the leading template strand.

Question 27

Telomerase is a ribonucleoprotein complex. The RNA component of the complex

A) has reverse transcriptase activity
B) provides the template for telomere repeat synthesis
C) provides structural support only
D) forms a t-loop

Question 28

Telomerase is usually active in all of the following cell types except for:

A) single-celled eukaryotes
B) human germ-line cells
C) human fibroblast cells
D) cancer cells

Question 29

The Hayflick limit is at least partly enforced by

A) telomerase activation.
B) T-loop formation.
C) the TERC pseudoknot.
D) telomere shortening.

Question 30

Which of the following is not a function of telomeres?

A) cellular clock
B) Cdc6 regulation
C) protection of chromosome ends
D) shelterin binding

Question 31

TRF1/TRF2 and POT1 form a complex called ______________ that __________________.

A) ORC; binds origins of replication
B) replisome; coordinates replication of the leading and lagging strands
C) telomerase; lengthens chromosome ends
D) shelterin; protects telomeres

Question 32

Describe and give the results of the classic experiment that showed that DNA replication is semiconservative. What are the names of the scientists who carried out this experiment?

Question 33

Describe electron microscopic evidence that DNA replication in E. coli is bidirectional.

Question 34

Draw a diagram showing the addition of a new dNTP to the daughter strand during DNA replication. The diagram should be detailed enough to illustrate what is meant by the statement "DNA synthesis occurs from 5′ to 3′ ".

Question 35

List the eukaryotic replicative DNA polymerases and their roles.

Question 36

Why do you suppose eukaryotic cells "switch" from DNA polymerase alpha, which binds to primase and initiates DNA synthesis, to DNA polymerase delta/epsilon for elongation?

Question 37

Of the three DNA polymerase in E. coli, which is essential for DNA replication?

Question 38

Draw a bidirectional eukaryotic origin of replication. Label the 5′ and 3′ ends of each strand of the double helix. Label the lagging and leading strands at each replication fork. In which direction are new strands synthesized?

Question 39

Outline the steps of nuclear chromosome replication in eukaryotes, starting from origin firing and ending with telomere replication.

Question 40

Why are origins of replication often AT-rich?

Question 41

You are characterizing nuclear DNA replication in a previously unstudied single-celled eukaryote. Describe an experiment to test whether nuclear DNA replication occurs in replication factories from multiple origins. Show sample positive results.

Question 42

Define the term "replication licensing" and discuss its importance in DNA replication.

Question 43

List the major enzymes and proteins required for DNA replication in the order in which they act and provide a brief description of their function.

Question 44

Why are RNA primers required during DNA replication?

Question 45

Describe an example of "polymerase switching."

Question 46

What three critical steps are required for "maturation" of the newly synthesized lagging strand?

Question 47

What mode of interaction between DNA ligase I and DNA does X-ray crystallographic analysis suggest?

Question 48

Describe two opposing models for how parental histones are distributed to daughter strands behind the replication fork.

Question 49

Explain the molecular defect that causes a human form of dwarfism called cartilage-hair hypoplasia.

Question 50

Indicate whether the following enzymes normally require ATP for their functions.

-topoisomerase I

Question 51

Indicate whether the following enzymes normally require ATP for their functions.

-topoisomerase II

Question 52

Indicate whether the following enzymes normally require ATP for their functions.

-DNA ligase

Question 53

Indicate whether the following enzymes normally require ATP for their functions.

-DNA helicase

Question 54

Xenopus oocytes contain amplified ribosomal DNA. Diagram the mechanism by which the extrachromosomal circles are produced.

Question 55

Choose one alternative mode of replication to describe (from among the rolling circle, strand displacement, and strand-coupled models) and compare and contrast this alternative mode with the conventional mode of replication for eukaryotic chromosomes.

Question 56

What is the "end-replication problem?"

Question 57

Why do eukaryotes need telomeres but bacteria do not?

Question 58

List at least two molecular characteristics of telomeres and relate these characteristics to functions.

Question 59

Explain how the POT1 protein is thought to regulate in telomere length.

Question 60

What evidence supports the existence of t-loops in telomere structure?

Question 61

Describe an experiment (or observation) that you think has provided the most convincing evidence for a causal relation between telomere shortening and cellular senescence or aging.

Question 62

Describe the molecular basis and primary (life-threatening) symptoms of the disease dyskeratosis congenita. Explain why the symptoms are not surprising in view of the molecular defect.

Question 63

Gene therapy-mediated delivery of the telomerase RNA to cirrhotic liver has been performed in mice. What important risk associated with telomerase activation explains why this strategy not yet progressed to human trials?

Question 64

Illustrate and explain the results that Meselson and Stahl would have obtained if DNA replication were conservative.

Question 65

The diagram below shows a replication fork in nuclear DNA.
(a) Label the "leading strand" and "lagging strand" and indicate to which strand of DNA
telomerase adds repeats.
(b) Show on the drawing what happens next on each strand as more of the duplex DNA unwinds at the replication fork. Use arrows to show the direction of synthesis for each strand. You do not need to show all the protein components of the replication machinery.

Question 66

You are studying a protein that you suspect functions to recruit other components of the licensing protein complex for eukaryotic DNA replication. Describe how you would assay the protein for this activity and show sample positive results.

Question 67

You are studying a mammalian DNA virus with a 200 kb double-stranded genome. Based on the size, you suspect that the genome has more than one origin of replication. Propose experiments to test your hypothesis and map the origins.

Question 68

Cells you have been culturing usually undergo senescence after about 20 divisions. But, some cells have become immortal. You suspect that telomerase has been activated. Propose an experiment to assay for telomerase activity and show sample positive results.