Chapter 10: DNA Synthesis

Question 1

A method of replication where each replicated DNA molecule would consist of one “old” and one “new” strand.

Answer 1

Semiconservative Replication of DNA

Question 2

A method of replication where two newly created strands then come together, and the parental strands reassociate.

Answer 2

Conservative Replication

Question 3

A method of replication where the parental strands are dispersed into two new double helices following replication.

Answer 3

Dispersive Replication

Question 4

True or False. Conservative Replication is the most complex of the three possibilities and is therefore considered to be least likely to occur

Answer 4

False. Dispersive Replication

Question 5

Samples are forced by centrifugation through a density gradient of a heavy metal salt, such as cesium chloride.

Answer 5

Sedimentation equilibrium centrifugation (Meselson-Stahl Experiment) - an experiment providing strong evidence that semiconservative replication is the mode used by bacterial cells to produce new DNA molecules.

Question 6

Is a common technique that, when applied cytologically, pinpoints the location of a radioisotope in a cell.

Answer 6

Autoradiography

Question 7

At each point along the chromosome where replication is occurring, the strands of the helix are unwound, creating what structure?

Answer 7

Replication Fork

Question 8

Refers to the length of DNA that is replicated following one initiation event at a single origin.

Answer 8

Replicon

Question 9

The region in E. coli DNA where replication is initiated

Answer 9

oriC

Question 10

True or False. DNA synthesis in bacteriophages and bacteria originates at a single point, the entire chromosome constitutes one replicon.

Answer 10

True

Question 11

True or False. Replication in bacteria and viruses is bidirectional, moving away from oriC in both directions

Answer 11

True

Question 12

Terminal region in a replicating bacterial or viral DNA.

Answer 12

ter

Question 13

A single polypeptide containing 928 amino acids initially isolated from E. coli that is able to direct DNA synthesis in a cell-free (in vitro) system.

Answer 13

DNA polymerase I

Question 14

Two major requirements for in vitro DNA synthesis under the direction of DNA polymerase I:

Answer 14

1. All four deoxyribonucleoside triphosphates (dNTPs)

2. template DNA

Question 15

True or False. As the two terminal phosphates of the deoxyribonucleoside triphosphate precursor are cleaved during DNA synthesis, the remaining phosphate attached to the 5′-carbon is covalently linked to the 3′-OH group of the deoxyribose to which it is added.

Answer 15

True

Question 16

A mutant strain of E. coli that was deficient in polymerase I activity.

Answer 16

polA1

Question 17

An existing RNA strand that can be elongated by polymerases I, II, and III.

Answer 17

Primer

Question 18

True or False. Polymerase I, II, and III can initiate chain synthesis.

Answer 18

False. They all can’t.

Question 19

True or False. Polymerase I, II, and III exhibit 5’-3’ polymerization.

Answer 19

True

Question 20

True or False. Polymerase I, II, and III do not exhibit 3′ to 5′ exonuclease activity.

Answer 20

False. They all exhibit 3′ to 5′ exonuclease activity.

Question 21

True or False. Only Polymerase I exhibit 5’-3’ exonuclease activity.

Answer 21

True

Question 22

Encoded by a gene whose transcription is activated by disruption of DNA synthesis at the replication fork.

Answer 22

Polymerase II

Question 23

Are involved in various aspects of repair of DNA that has been damaged by external forces, such as ultraviolet light.

Answer 23

DNA polymerase II, IV and V

Question 24

The active form of the DNA Polymerase III.

Answer 24

Holoenzyme

Question 25

Imparts the catalytic function of the holoenzyme and is made of the alpha subunit, along with subunits epsilon and theta.

Answer 25

Core enzyme

Question 26

Subunit of the holoenzyme that is responsible for DNA synthesis along the template strands (5’-3’ polymerization activity).

Answer 26

Alpha subunit

Question 27

Subunit of the holoenzyme (DNA polymerase III) that is responsible for 3’-5’ exonuclease activity that is essential for proofreading

Answer 27

Epsilon subunit

Question 28

Pairs with the core enzyme and facilitates the function of a critical component of the holoenzyme called the sliding DNA clamp. Is formed by the gamma, delta, delta prime, chi, and nu subunits

Answer 28

Sliding clamp loader (y complex)

Question 29

Made up of multiple copies of the beta subunit, taking on the shape of a donut, whereby it can open and shut, to encircle the unreplicated DNA helix. It leads the way during synthesis, maintaining the binding of the core enzyme to the template during the polymerization of nucleotides.

Answer 29

Sliding DNA clamp

Question 30

Measure the length of DNA that is replicated by the core enzyme before it detaches from the template.

Answer 30

Processivity

Question 31

The helicase that is responsible for the initial step in unwinding the helix.

Answer 31

DnaA protein

Question 32

True or False. The binding of DnaA protein to the several 9mers of the oriC facilitates the subsequent binding of DnaB and DnaC proteins that further open and destabilize the helix.

Answer 32

True

Question 33

A group of proteins responsible for the unwinding of DNA helix.

Answer 33

Helicase (DnaA, DnaB, DnaC proteins)

Question 34

Stabilizes the DNA upon unwinding of the helicases.

Answer 34

Single-stranded binding proteins

Question 35

This is produced due to coiling tension produced by the unwinding process.

Answer 35

Supercoiling

Question 36

Relaxes supercoiling by making either a single- or double-stranded “cuts” and also catalyzes localized movements that have the effect of “undoing” the twists and knots created during supercoiling.

Answer 36

DNA gyrase

Question 37

DNA gyrase is a member of larger group of enzymes referred to as?

Answer 37

topoisomerases

Question 38

The DNA, the polymerase complex, and associated enzymes make up an array of molecules that participate in DNA synthesis. These molecules are collectively known as?

Answer 38

Replisome

Question 39

A short segment of RNA (about 10 to 12 ribonucleotides long), complementary to DNA, is first synthesized on the DNA template. This molecule is called?

Answer 39

Primer

Question 40

Directs the synthesis of the primer it does not require a free 3’ end to initiate synthesis.

Answer 40

Primase

Question 41

Before terminating the replication process, the primer is clipped out and replaced with DNA nucleotides. This process is mediated by what polymerase?

Answer 41

DNA polymerase I

Question 42

The strand at which replication is discontinuous.

Answer 42

Lagging strand

Question 43

The strand that is being replicated in the 3' – 5' direction (same direction as the replication fork) and produces a continuous DNA product.

Answer 43

Leading strand

Question 44

Segmented fragments of DNA resulting in discontinuous synthesis in the lagging strand.

Answer 44

Okazaki fragments

Question 45

Capable of catalyzing the formation of the phosphodiester bond that seals the nick between the discontinuously synthesized strands (Okazaki fragments).

Answer 45

DNA ligase

Question 46

Imparts the potential for polymerases to detect and excise a mismatched nucleotide (in the 3′ to 5′ direction).

Answer 46

3’ to 5’ exonuclease activity

Question 47

True or False. To facilitate the rapid synthesis of large quantities of DNA, eukaryotic chromosomes contain multiple replication origins.

Answer 47

True

Question 48

Two of the four subunits of this enzyme synthesize RNA primers on both the leading and lagging strands.

Answer 48

Pol a enzyme

Question 49

True or False. Pol a possess a high processivity.

Answer 49

False.

Question 50

Once the primer is in place, Pol alpha dissociates from the template and is replaced by Pol delta or epsilon. This process is called?

Answer 50

Polymerase switching

Question 51

Synthesizes DNA in the lagging strand, has a much higher processivity and exhibits 3’ to 5’ exonuclease activity.

Answer 51

Pol d

Question 52

Synthesizes DNA in the leading strand, has a much higher processivity and exhibits 3’ to 5’ exonuclease activity.

Answer 52

Pol e

Question 53

Found exclusively in mitochondria, synthesizing the DNA present in that organelle.

Answer 53

Pol gamma

Question 54

True or False. Before polymerases can begin synthesis, nucleosomes and other DNA-binding proteins must be stripped away or otherwise modified to allow the passage of replication proteins.

Answer 54

True

Question 55

True or False. Nucleosomes form immediately after new DNA is synthesized at replication forks. Nucleosomes are disrupted just ahead of the replication fork and that the preexisting histone proteins can assemble with newly synthesized histone proteins into new nucleosomes.

Answer 55

True

Question 56

Move along with the replication fork to assemble new nucleosomes

Answer 56

Chromatin assembly factors

Question 57

True or False. In eukaryotic DNA, it is the 3' ending that is the G-rich strand.

Answer 57

True

Question 58

The G-rich single-stranded tails are capable of looping back on themselves, forming multiple G-G hydrogen bonds to create what is referred to as?

Answer 58

G-quartets

Question 59

G-quartets form a looping structure known as? This structure, in combination with specific proteins that bind to them, essentially close off the ends of chromosomes and make them resistant to nuclease digestion and DNA fusions.

Answer 59

t-loop

Question 60

What component of the telomerase serves as both a “guide” to proper attachment of the enzyme to the telomere and a “template” for the synthesis of its DNA complement.

Answer 60

telomerase RNA component

Question 61

Synthesis of DNA using RNA as a template is called?

Answer 61

Reverse transcription

Question 62

The catalytic subunit of the telomerase enzyme is called?

Answer 62

telomerase reverse transcriptase