Chapter 12 - DNA Replication and Recombination

Question 1

If the dispersive model of DNA replication had been correct, Meselson and Stahl would have observed that DNA extracted from bacterial cells following a second round of DNA replication in 14N would have been:
A. only hybrid density, and somewhat lighter than after one round of replication.
B. only hybrid density, and somewhat heavier than after one round of replication.
C. of varying densities, spread throughout the gradient.
D. all light density because the DNA molecules would have mostly 14N.
E. half hybrid density and half light density.

Answer 1

A. only hybrid density, and somewhat lighter than after one round of replication.

Question 2

DNA replication in eukaryotes differs from replication in prokaryotes in that:
A. DNA replication in eukaryotes is conservative, whereas in prokaryotes it is semiconservative.
B. Eukaryotes have bidirectional replication from an origin, whereas in prokaryotes replication proceeds in one direction from an origin.
C. Eukaryotic chromosomes have many separate origins of replication, whereas prokaryotic chromosomes have a single origin of replication.

Answer 2

C. Eukaryotic chromosomes have many separate origins of replication, whereas prokaryotic chromosomes have a single origin of replication.

Question 3

The following component is NOT required for DNA replication:
A. Deoxyribonucleotides (dNTP’s)
B. DNA polymerase
C. Single-stranded DNA (ssDNA)
D. Primer
E. All of the above are required for DNA replication

Answer 3

E. All of the above are required for DNA replication

Question 4

Okazaki fragments are associated with synthesis of:
A.the leading strand.
B.the lagging strand.
C.both the leading and the lagging strands.
D.single-stranded circular DNA.

Answer 4

B.the lagging strand.

Question 5

During initiation of DNA replication in E. coli, what is the role of helicase?
A. It binds to the origin and causes a short section of the double helix to unwind.
B. It binds to and stabilizes the single-stranded DNA.
C. It reduces torsional strain by controlling supercoiling ahead of the replication fork.
D. It continues the unwinding of the dsDNA at the replication fork that was started by the initiator proteins.
E. It synthesizes the RNA primers for the Okazaki fragments.

Answer 5

D. It continues the unwinding of the dsDNA at the replication fork that was started by the initiator proteins.

Question 6

All DNA polymerases require a primer with a 3’ OH group to begin DNA synthesis. In cells, the primer is:
A. a free DNA nucleotide.
B. a short stretch of RNA nucleotides.
C. a 3’ OH group that is part of the primase enzyme.
D. None of the above are correct because DNA synthesis does not require a primer.

Answer 6

B. a short stretch of RNA nucleotides.

Question 7

You have created a transgentic mouse that constitutively produces telomerase in all cells. You predict that the these mice will:
A. have broken, fragmented chromosomes.
B. have longer telomeres than wild-type mice of the same age.
C. show no differences when compared to the control animals
D. have increased chance of developing cancer.
E. More than one of the above.

Answer 7

E. More than one of the above.

B. have longer telomeres than wild-type mice of the same age.
D. have increased chance of developing cancer.

Question 8

How many bands of DNA would be expected in Meselson and Stahl’s experiment after two rounds of conservative replication?

Answer 8

Two bands

Question 9

Which type of replication requires a break in the nucleotide strand to get started?

a. Theta replication
b. Rolling-circle replication
c. Linear eukaryotic replication
d. All of the above

Answer 9

b. Rolling-circle replication

Question 10

Discontinuous replication is a result of which property of DNA?

a. Complementary bases
b. Charged phosphate group
c. Antiparallel nucleotide strands
d. Five-carbon sugar

Answer 10

c. Antiparallel nucleotide strands

Question 11

Place the following components in the order in which they are first used in the course of replication: helicase, single-strand-binding protein, DNA gyrase, initiator protein.

Answer 11

Initiator protein, helicase, single-strand-binding protein, DNA gyrase

Question 12

Primers are synthesized where on the lagging strand?

a. Only at the 5′ end of the newly synthesized strand
b. Only at the 3′ end of the newly synthesized strand
c. At the beginning of every Okazaki fragment
d. At multiple places within an Okazaki fragment

Answer 12

c. At the beginning of every Okazaki fragment

Question 13

Which bacterial enzyme removes the primers?

a. Primase
b. DNA polymerase I
c. DNA polymerase III
d. Ligase

Answer 13

b. DNA polymerase I

Question 14

Which mechanism requires the ability to distinguish between newly synthesized and template strands of DNA?

a. Nucleotide selection
b. DNA proofreading
c. Mismatch repair
d. All of the above

Answer 14

c. Mismatch repair

Question 15

DNA synthesis begins with the synthesis of short segments of RNA called ____.

Answer 15

primers

Question 16

In comparison with prokaryotes, what are some differences in the genome structure of eukaryotic cells that affect how replication takes place?

Answer 16

Size, linear structure, and the association of DNA with histone proteins.

Question 17

Some of the eukaryotic DNA polymerases have a tendency to make errors in replication. Why would a cell use an error-prone DNA polymerase instead of one that is more accurate?

Answer 17

Error-prone DNA polymerases can bypass lesions in the DNA helix that stall accurate, high-speed DNA polymerases.

Question 18

What would be the result if an organism’s telomerase were mutated and nonfunctional?

a. No DNA replication would take place.
b. The DNA polymerase enzyme would stall at the telomere.
c. Chromosomes would shorten with each new generation.
d. RNA primers could not be removed.

Answer 18

c. Chromosomes would shorten with each new generation.

Question 19

E. coli replicates DNA at a rate of ___ nucleotides per second with an accuracy rate approaching one error per ___ cells.

Answer 19

1000; 250

Question 20

Watson and Crick predicted that each ___ of DNA could serve as a ___ for synthesis, but they couldn’t answer ___.

Answer 20

strand; template; how

Question 21

In the ___ model of DNA synthesis, the original molecule breaks down into fragments new molecules contain new and old fragments interspersed throughout.

Answer 21

Dispersive

Question 22

In the __ model of DNA synthesis, two new molecules would have one new strand and one old strand.

Answer 22

semiconservative

Question 23

In the ___ model of DNA synthesis, two new duplexes (molecules) would be made with one containing both old strands and the other containing two new strands.

Answer 23

conservative.

Question 24

Using Equilibrium Density Gradient Centrifugation experiments, first you would “grow” DNA with heavy __ of N. Then you would put the heavy DNA in regular N for additional rounds of replication. You would suspend different rounds of replication in a __ __ solution, and place in an __.
What would you see if replication was conservative after 1 round of replication? After 2 rounds?
What would you see if replication was semiconservative after 1 round of replication? After 2 rounds?
What would you see if replication was dispersive after 1 round of replication? After 2 rounds?

Answer 24

isotope; heavy salt; ultracentrifuge

2 bands - one heavy, one light; still 2 bands, but the lighter one would be thicker

1 intermediate band; 2 bands - one intermediate, one lighter

intermediate bands only for all reps

Question 25

The 3 models of DNA replication (not synthesis!) include:
__ replication used mainly by bacteria and plasmids due to their ___ nature.
___ ___ replication used by some viruses, esp lytic phages.
___ replication used by eukaryotes.

Answer 25

Theta; circular

rolling circle

linear

Question 26

In theta replication, DNA strands unwind at the ___ ___. Replication in this model is most commonly ___ with each strand terminating ___ from its origin.

Answer 26

replication origin.

bidirectional; 180°

Question 27

In 1963, J. Cairns was able to show the process of theta replication by using ___.

Answer 27

autoradiography

Question 28

__ __ replication is somewhat analogous to a production line in that it produces multiple copies of the original molecule. It is a very efficient way for ___ ___ to replicate. The process “___” one strand, adds dNTPs to the __’ end while ___ the other strand. The __ strand is converted from __ to ___ for new viral particles. This process can take place ____.

Answer 28

Rolling circle.

lytic virons

“nicks”; 3’; displacing

displaced; ssDNA; dsDNA

continuously.

Question 29

Eukaryotic DNA requires 1000’s of replication origins for what two main reasons?

Answer 29

(1) Huge molecule relative to prokaryotic counterparts.

2) Much slower rate of replication due to the complexity of the molecule (much more so than prokaryotes

Question 30

Replication origins occur every ___-___ bp on eukaryotic chromosomal DNA

Answer 30

20Kbp - 300Kbp

Question 31

What 4 requirements must be met for DNA replication?

Answer 31

(1) Template (ssDNA)
(2) Substrate (dNTPs)
(3) Primer (RNA)
(4) Enzyme (DNA polymerase)

Question 32

DNA synthesis always proceeds _’ - _’ with new nucleotides added to the _’ end. Energy for synthesis comes from ___ of the last two __.

Answer 32

5’ - 3’; 3’

cleaving; phosphates

Question 33

Synthesis of the leading strand takes place on the _’ - _’ template strand in the ___ direction of the replication fork and __ the origin.
Synthesis of the lagging strand takes place on the _’ - _’ template strand in the ___ direction of the replication fork and ___ the origin.

Answer 33

3’ - 5’; same; away

5’ - 3’; opposite; toward.

Question 34

In E. coli, DNA synthesis is initiated at the ___ sequence. ___ ___ bind to this site and begin to ___ the strands. DNA ___ continue to ___ the strands, and __-__ __ __ (SSBs) keep the strand open. To relieve torsional stress beyond both forks, DNA ___, a ___, reduces the stress.

Answer 34

oriC

Initiator proteins; unwind

DNA helicases; unwind; single-stranded binding proteins.

DNA gyrase; topoisomerase

Question 35

SSBs are ___ (made of _ subunits) that cover 35 - 65bp, and are DNA sequence ____.

Answer 35

tetramers; 4; independent

Question 36

Primase is an __ polymerase that synthesizes short __ segments and function to provide the _‘-OH for __ polymerase to do its thing. All known ___ polymerases need primers to ___ synthesis.

Answer 36

RNA; RNA; 3’-OH; DNA.

DNA; start

Question 37

The leading strand only requires one primer at the _’ end of the new DNA strand.

Answer 37

5’

Question 38

E. coli has __ DNA polymerases. DNA polymerase __ and __ are involved in replication, the other 3 are involved in ___. Of the two involved in replication, DNA ___ is the workhorse.

Answer 38

5

I and III; repair

III

Question 39

DNA polymerase __ is a large ___ complex with 2 enzymatic activities: (1) _’ - _’ polymerase that __ nucleotides; and (2) _’ - _’ ___ that proofreads by removing incorrectly matched bases.

Answer 39

III; multimeric

5’ - 3’; adds

3’ - 5’ exonuclease.

Question 40

DNA polymerase III is the workhorse because it can synthesize a strand __ Mbp in length without ___ from the template strand.

Answer 40

2.3Mbp; disengaging/releasing

Question 41

DNA polymerase I has 3 enzymatic activities: (1) _’ - _’ polymerase; _’ - _’ exonuclease; and _’ - _’ exonuclease to remove DNA and RNA ahead of the production line. What’s the reason for the RNA exonuclease?

Answer 41

5’ - 3’ polymerase; 3’ - 5’ exonuclease; 5’ - 3’ exonuclease.

DNA polymerase I will remove the RNA primer of the next Okazaki fragment.

Question 42

DNA polymerase I can use the _’ - _’ ____ activity to remove the primer, but it’s DNA ___ that binds (‘stitches’) the Okazaki fragments together by catalyzing the ___ bond between the 5’__ and the 3’__ of adjacent nucleotides.

Answer 42

5’ - 3’ exonuclease; ligase; phosphodiester; phosphate; -OH

Question 43

A primer is required at the __’ end of newly synthesized strands (leading or lagging).

Answer 43

5’ (synthesis is 5’ to 3’).

Question 44

DNA ___ is critical for binding the gap between Okazaki fragments; without it, DNA would __ during the next round of duplication.

Answer 44

ligase; degrade

Question 45

Proper pairing of nucleotides has an error rate of ___; proofreading by the _’ - _’ ___ activity of I and III decreases the error rate to ___; but it’s ___ repair that achieves an error rate of 10^-9. This latter process involves DNA ____.

Answer 45

10^-5; 3’ - 5’ exonuclease; 10^-7; mismatch.

methylation.

Question 46

Eukaryotic genomes need to be copied without dups or omissions; this is accomplished by 2 steps: (1) each origin is “___” by a ___ ___ factor (binds) that only the ___ proteins interact with; (2) the ___ ___ factor dissociates as synthesis moves away from the origin causing the origin to become “___” and unusable in that cell cycle.

Answer 46

licensed; replication licensing factor; initiator

replication licensing factor; unlicensed

Question 47

Eukaryotic DNA polymerases: they all use ___ letters to distinguish between prokaryotic polymerases that use ___ numerals.

Answer 47

Greek; Roman

Question 48

E.coli uses about __ DNA polymerases; Eukaryotes use at least __.

Answer 48

5; 15

Question 49

Histone synthesis is only detected during…?

Unlike the semiconservative model of DNA synthesis, histone synthesis is thought to be more like which model? What evidence supports this?

Answer 49

S phase

dispersive; new nucleosomes seem to be a random mix of old and new histones.

Question 50

Eukaryotic DNA synthesis likely involves ___ the DNA polymerase complex in place (in the ___) with the template being ___ through it.

Answer 50

fixing; matrix; threaded/pulled

Question 51

In the absence of special mechanisms, DNA replication would leave ___ due to the removal of ___.

To address this problem, ___ (an ___-___ complex) extends the _’ end by acting as a template for short, repetitive DNA sequences to be added. As a consequence, the __’ complimentary strand is also ___ (by forming additional Okazaki fragments). The effect is a strand that’s __ than needed; and a small bit of the _’ end is ___.

Answer 51

gaps; primers

telomerase; RNA-protein; 3’.

5’; elongated.

longer; 3’; snipped/trimmed

Question 52

___ functions somewhat like reverse transcriptase.

Answer 52

Telomerase

Question 53

Telomerase’s activity is ___ in that the number of DNA repeats __ from cell-to-cell.

Answer 53

dynamic; varies

Question 54

Telomeres become progressively shorter due to? This leads to?

Answer 54

Reduced telomerase activity.

Apoptosis

Question 55

T or F: cells in culture that are genetically engineered to always express telomerase activity divide indefinitely.

Answer 55

True

Question 56

Most __ cells can grow indefinitely in culture likely due to the fact that most have active ____.

Answer 56

cancer; telomerase