Chapter 11 Replication

Question 1

1) Which of the following terms accurately describes the replication of DNA in vivo?
A) conservative
B) nonreciprocal
C) dispersive
D) semidiscontinuous 
E) nonlinear

Answer 1

D

Question 2

2) After ONE round of DNA replication in Meselson and Stahl’s classic experiment, ________.
A) the dispersive model was conclusively proven to be an inaccurate model
B) the conservative model was conclusively proven to be an inaccurate model
C) the semiconservative model was conclusively proven to be the accurate model
D) both the conservative and the semiconservative models were still possibilities
E) all three models of replication were still possibilities

Answer 2

B

Question 3

3) DNA replication proceeds \_\_\_\_\_\_\_\_. 
A) dispersively
B) progressively
C) semiconservatively
D) unidirectionally
E) discontinuously

Answer 3

C

Question 4

4) If DNA replication were fully conservative, how many intact parental double helices would have been detected in Meselson and Stahl's experiment after three rounds of replication?
A) 7
B) 0 
C) 3 
D) 8 
E) 1

Answer 4

1

Question 5

5) The amount of DNA that is replicated from a single origin of replication is referred to as a(n) ________.

A) replicon
B) ori
C) fork
D) primer
E) Okazaki fragment

Answer 5

A

Question 6

6) Which DNA Polymerase III subunit is not part of the clamp loading assembly?

A) ν 
B) γ 
C) χ
D) δ
E) θ

Answer 6

E

Question 7

7) DNA replication occurs by adding ________.
A) dNTPs to the 5′ end of the template strand
B) NTPs to the 3′ end of the daughter strand
C) dNTPs to the 3′ end of the template strand
D) NTPs to the 5′ end of the daughter strand
E) dNTPs to the 3′ end of the daughter strand

Answer 7

E

Question 8

8) DNA polymerase III adds nucleotides ________. A) to the 3′ end of the RNA primer
B) to both ends of the RNA primer
C) to internal sites in the DNA template
D) to the 5′ end of the RNA primer
E) in the place of the primer RNA after it is removed

Answer 8

A

Question 9

9) DNA polymerase I is thought to add nucleotides ________.
A) on single-stranded templates without need for an RNA primer
B) in the place of the primer RNA after it is removed
C) to the 5′ end of the primer
D) to the 3′ end of the primer
E) in a 5′ to 5′ direction

Answer 9

B

Question 10

10) Which terms accurately reflect the nature of replication of the chromosome in E. coli?
A) bidirectional and multirepliconic
B) bidirectional and fixed point of initiation
C) unidirectional and fixed point of initiation
D) unidirectional and reciprocal
E) multirepliconic and telomeric

Answer 10

B

Question 11

11) Which cluster of terms accurately reflects the nature of DNA replication in prokaryotes?
A) fixed point of initiation, bidirectional, conservative
B) fixed point of initiation, unidirectional, conservative
C) random point of initiation, unidirectional, semiconservative
D) fixed point of initiation, bidirectional, semiconservative
E) random point of initiation, bidirectional, semiconservative

Answer 11

D

Question 12

12) Which of the following statements about the oriC region in E. coli is incorrect?
A) It includes three repeating sequences of 13 base pairs.
B) It includes five repeating sequences of 9 base pairs.
C) It is 245 base pairs in length.
D) It is rich in AT base pairs.
E) It is directly recognized and bound by DNA helicase.

Answer 12

E

Question 13

13) The protein responsible for the initial step in unwinding the DNA helix during replication of the bacterial chromosome is coded for by the \_\_\_\_\_\_\_\_ gene.
A) dnaE 
B) polA 
C) polB 
D) gyrA 
E) dnaA

Answer 13

E

Question 14

14) If E. coli DNA polymerase III was able to initiate DNA synthesis opposite a single-stranded template, which molecule(s) would no longer be essential?
A) helicase
B) single-stranded binding proteins 
C) DNA gyrase
D) DNA polymerase I 
E) DNA ligase

Answer 14

D

Question 15

15) The discontinuous aspect of replication of DNA in vivo is caused by ________.
A) topoisomerases cutting the DNA in a random fashion
B) polymerase slippage
C) trinucleotide repeats
D) sister-chromatid exchanges
E) the 5′ to 3′ polarity restriction

Answer 15

E

Question 16

16) Given the accompanying diagram, assume that a G1 chromosome (left) underwent one round of 16) replication in 3H-thymidine and the metaphase chromosome (right) had both chromatids labeled.
Which of the following replicative models (conservative, dispersive, semiconservative) could be eliminated by this observation?

A) dispersive
B) semiconservative 
C) conservative
D) conservative and dispersive
E) semiconservative and dispersive

Answer 16

C

Question 17

17) During DNA replication, ________ are 1000-2000 nucleotide long strands synthesized on the ________ strand to maintain the ________ of replication.

A) Okazaki fragments; lagging; bidirectionality
B) primers; leading; discontinuity
C) Okazaki fragments; leading, accuracy
D) Okazaki fragments; leading; semidiscontinuity
E) primers, lagging; continuity

Answer 17

A

Question 18

18) As unwinding of the helix occurs during DNA replication, tension referred to as ________ is created ahead of the replication fork. This tension is relieved by the action of ________.

A) supercoiling; single-stranded binding proteins 
B) processivity; DNA gyrase
C) supercoiling; DNA helicase
D) supercoiling; DNA gyrase 
E) processivity; primase

Answer 18

D

Question 19

19) Which of the following statement about DNA replication in E. coli is correct?

A) Single-stranded binding proteins are only required on the leading strand.
B) There are two molecules of DNA polymerase III per replication fork.
C) Only the lagging strand needs to be primed.
D) DNA polymerase I follows closely behind DNA helicase in the replication fork.
E) There are two molecules of DNA helicase per replication fork.

Answer 19

B

Question 20

20) The protein product of the E. coli dnaE gene is a component of \_\_\_\_\_\_\_\_.
A) DNA polymerase I
B) DNA polymerase III 
C) DNA helicase
D) primase
E) DNA ligase

Answer 20

B

Question 21

21) The activity of ________ would be quickly undone in the absence of single-stranded binding protein.

A) DNA helicase
B) primase
C) DNA polymerase I
D) DNA ligase
E) DNA polymerase III

Answer 21

A

Question 22

22) DNA replication in eukaryotes ________.
A) takes place multiple times per cell cycle
B) occurs without the need of a primer
C) initiates at multiple origins
D) utilizes a single type of DNA polymerase
E) synthesizes DNA approximately 25 times faster than in prokaryotes

Answer 22

C

Question 23

23) Chromatin is defined as ________.

A) DNA complexed with protein
B) genetic material found only in mitochondria
C) supercoiled loops of bacterial DNA
D) a catalytic molecule with a protein component and an RNA component
E) hybrid molecules of DNA and RNA

Answer 23

A

Question 24

24) Assembly of new nucleosomes is carried out by complexes abbreviated ________.

A) DSB 
B) TLS 
C) SSB 
D) CAF
E)TERC

Answer 24

D

Question 25

``` 25) Which eukaryotic DNA polymerase would least likely be involved in repair? A) γ B) ε C) β D) α E) δ ```

Answer 25

D

Question 26

``` 26) Structures located at the ends of eukaryotic chromosomes are called ________. A) permissive mutations B) telomerases C) recessive mutations D) centromeres E) telomeres ```

Answer 26

E

Question 27

``` 27) Telomerase reads ________ as a template and synthesizes ________ as a product. A) DNA; DNA B) RNA; DNA C) RNA; RNA D) DNA; RNA E) DNA; protein ```

Answer 27

B

Question 28

``` 28) The process of making DNA from an RNA template is referred to as ________. A) translation B) reverse transcription C) transcription D) recombination E) transversion ```

Answer 28

B

Question 29

``` 29) Telomerase adds nucleotides to the ________. A) 5′ end of the parental strand C) 5′ end of the daughter strand B) 3′ end of the parental strand D) 3′ end of the daughter strand ```

Answer 29

B

Question 30

``` 30) A molecule that possesses both a protein component and an RNA component is referred to as a ________. A) ribonucleoprotein B) holoenzyme C) tetramer D) dimer E) polymerase ```

Answer 30

A

Question 31

``` 31) Which of the following is not an essential step in homologous recombination? A) branch migration B) duplex separation C) strand displacement D) endonuclease nicking E) exonuclease degradation ```

Answer 31

E

Question 32

32) The Meselson and Stahl's experiment provided conclusive evidence for the semiconservative replication of DNA in E. coli. What pattern of bands would occur in a CsCl gradient for conservative replication?

Answer 32

After one generation in the 14N, there would be two bands, one heavy and one light (no intermediate). After the second generation in the 14N, there would also be two bands, one heavy and one light (no intermediate).

Question 33

33) Briefly describe what is meant by the term autoradiography and identify a classic experiment that used autoradiography to determine the replicative nature of DNA in eukaryotes.

Answer 33

Autoradiography is a technique that allows an isotope to be detected within a cell; the Taylor, Woods, and Hughes (1957) experiment used 3H-thymidine.

Question 34

34) Compare and contrast DNA Polymerases I, II, and III in E. coli. What capabilities are shared, and which are exclusive to only one type of polymerase?

Answer 34

None of the polymerases are able to initiate chain synthesis, but all are able to extend an existing fragment in the 5′ to 3′ direction. All three possess proofreading ability (3′ to 5′ exonuclease), but only DNA polymerase I possesses primer removal ability (5′ to 3′ exonuclease).

Question 35

35) Explain why DNA primers can be used in in vitro DNA synthesis reactions, but not in vivo.

Answer 35

The need for the primer is to provide a 3′ OH group to which DNA-synthesizing enzymes can add new nucleotides. In an in vitro reaction, provided the template sequence is known, complementary single-stranded DNA primers can be synthesized and included in the reaction.

Question 36

36) DNA replication in vivo requires a primer with a free 3′ end. What molecular species provides this 3′ end, and how is it provided?

Answer 36

The free 3′ end is provided by an RNA primer; it is provided by the enzymatic activity of RNA primase.

Question 37

37) Why does DNA replication have to be semidiscontinuous in order to be bidirectional?

Answer 37

The requirement of synthesis to be 5′ to 3′, and the antiparallel nature of double-stranded DNA, means that in both replication forks one of the stands must be made in fragments directed back toward the origin of replication.

Question 38

38) Explain the need for, and action of, DNA gyrase in bacterial DNA replication.

Answer 38

DNA helicase induces supercoiling (tension) in the parental DNA as it processes. DNA gyrase relieves this tension so that replication fork progression can continue without grinding to a halt.

Question 39

39) A drug is added to a culture of E. coli cells that inhibit DNA gyrase. Predict the effect of this drug on DNA replication in the affected cells.

Answer 39

Without DNA gyrase to relieve the supercoiling of the DNA induced by DNA helicase, the tension in the closed circle of DNA would cause replication machinery to stall, preventing replication from completing and preventing the cells from dividing.

Question 40

40) Describe the benefit to researchers of conditional mutants.

Answer 40

Many mutations that would be interesting to study are lethal. Conditional mutations allow researchers to observe wild-type behavior under permissive conditions, and loss-of-function effects under restrictive conditions.

Question 41

41) What is meant by a gene knockout?

Answer 41

The designed loss of a specific gene in order to study its function. This is often accomplished in the context of a conditional knockout, where the gene is affected in some tissue types but not others, allowing genes to be studied for which complete loss would be lethal.

Question 42

42) Compare and contrast DNA replication in prokaryotes and eukaryotes.

Answer 42

Eukaryotic DNA is replicated in a manner very similar to that in E. coli: bidirectional, continuous on one strand and discontinuous on the other, and similar requirements for synthesis. However, in eukaryotes, Okazaki fragments are about one-tenth the size of those in bacteria. Different portions of the chromosome (euchromatin, heterochromatin) replicate at different times. There are multiple replication origins in eukaryotic chromosomes.

Question 43

43) What is the name of the replication unit in prokaryotes, and how does it differ in eukaryotes?

Answer 43

replicon; one replicon in prokaryotes, multiple replicons in eukaryotes

Question 44

44) What is meant by processivity of a DNA-synthesizing enzyme?

Answer 44

The strength of the association between the enzyme and its substrate, and thus the length of DNA that is synthesized before the enzyme dissociates from the template.

Question 45

45) Compare the rate of DNA replication in prokaryotes and eukaryotes.

Answer 45

Eukaryotic DNA polymerases synthesize DNA at a rate 25 times slower (about 2000 nucleotides per minute) than do prokaryotes.

Question 46

46) Describe the DNA base sequence arrangement at the end of the Tetrahymena chromosome and the resolution of DNA replication at the end of a linear DNA strand.

Answer 46

Telomeres terminate in a 5′-TTGGGG-3′ sequence, and telomerase is capable of adding repeats to the ends, thus allowing the completion of replication without leaving a gap and shortening the chromosome following each replication.

Question 47

47) Describe a somewhat extraordinary finding related to the Tetrahymena telomerase enzyme.

Answer 47

47 The enzyme contains a short piece of RNA that is essential for its catalytic activity.

Question 48

48) Why are bacteria not dependent on telomerase for complete DNA replication?

Answer 48

48 Telomerase allows for the accurate replication of linear DNA molecules, and bacteria typically possess circular chromosomes.

Question 49

49) What is meant by homologous recombination?

Answer 49

Genetic exchange at equivalent positions along two chromosomes with substantial DNA sequence homology.

Question 50

50) Describe two processes for which recombination is essential.

Answer 50

50. The exchange of genetic information during meiosis, and the repair of double-stranded breaks in DNA molecules.