Deck 7: DNA Structure and Replication

Question 1

If SSB is not present during DNA replication,what would you expect to see?

A)The replisome complex would not assemble on the oriC region.
B)The DNA cannot bend,so hydrogen bonds in the 13-mer region of oriC remain intact.
C)Helicase activity is inhibited,so DNA strands cannot be separated.
D)SSB carries the helicase protein to the open region of DNA,so hydrolysis and strand separation will not occur.
E)SSB prevents reannealing of the separated strands,so strands would quickly reanneal and DNA replication cannot proceed.

Answer 1

E

Question 2

What is required for DNA polymerase to initiate DNA strand synthesis?

A)a short DNA primer synthesized by the enzyme primase
B)a short RNA primer synthesized by the enzyme primase
C)ATP and a short DNA primer synthesized by the enzyme topoisomerase
D)ATP and a short RNA primer synthesized by the enzyme topoisomerase
E)DNA polymerase initiates DNA strand synthesis without requiring any additional enzymes.

Answer 2

B

Question 3

Avery,Macleod,and McCarty expanded on Griffith's experiment to prove that DNA is the hereditary molecule required for transformation.What treatment of the heat-killed SIII bacteria extract resulted in the mouse living?

A)destroying type SIII lipids and polysaccharides
B)destroying type SIII DNA with DNase
C)destroying type SIII RNA with RNase
D)destroying type SIII proteins with protease
E)the control group,in which all components are intact

Answer 3

B

Question 4

The extraordinary accuracy of the DNA polymerase III enzyme lies in its ability to "proofread" newly synthesized DNA,a function of the enzyme's

A)3′-to-5′ exonuclease activity.
B)5′-to-3′ exonuclease activity.
C)3′-to-5′ polymerase activity.
D)5′-to-3′ polymerase activity.
E)3′-to-5′ helicase activity.

Question 5

DNA polymerase III is functional,but it seems to exhibit extremely low processivity.This is likely a defect in what structure?

A)the τ proteins
B)the pol III holoenzyme
C)the clamp loader
D)the topoisomerase enzyme
E)the sliding clamp

Question 6

What types of bonds are formed between complementary DNA bases?

A)glycosidic bonds
B)phosphodiester bonds
C)covalent bonds
D)hydrogen bonds
E)ionic bonds

Question 7

What is one difference between DNA replication in bacteria versus eukaryotes?

A)Eukaryotic chromosomes are replicated bidirectionally,while bacterial chromosomes are replicated in one direction.
B)Eukaryotic chromosomes have many origins of replication and replicate bidirectionally,while bacteria have only one origin of replication and replicate unidirectionally.
C)Bacterial chromosomes are replicated bidirectionally,while eukaryotic chromosomes are replicated in one direction.
D)Eukaryotic chromosomes have many origins of replication,while bacteria have only one origin of replication.
E)The process is identical in bacterial and eukaryotic DNA replication.

Question 8

In the Hershey-Chase experiment,what was labeled by growing bacteriophage in ³²P-containing medium?

A)ghost phage particles
B)proteins
C)lipids
D)DNA
E)RNA

Question 9

In 1928,Griffith found that injecting which strains of Pneumococcus caused the mouse to die?

A)living type RII
B)heat-killed type SIII
C)heat-killed type RII
D)heat-killed type SIII and living type RII
E)heat-killed type RII and living type RII

Question 10

The process by which Pneumococcus transfers DNA between living type RII and heat-killed type SIII cells is known as

A)transformation.
B)replication.
C)transduction.
D)ligation.
E)conjugation.

Question 11

Which of the following temperature cycles would you expect to see in a standard polymerase chain reaction (from denaturation to annealing to extension)?

A)95° → 72° → 55°
B)45° → 72° → 95°
C)95° → 55° → 72°
D)95° → 72° → 95°
E)75° → 95° → 45°

Question 12

During DNA replication in E.coli,what is the role of DnaA?

A)DnaA is a region of DNA recognized by the replisome where replication is initiated.
B)DnaA bends DNA,hydrolyzing the hydrogen bonds in the 13-mer region of oriC and creating an open complex.
C)DnaA is a helicase that uses ATP to hydrolyze hydrogen bonds and separate DNA strands.
D)DnaA carries the helicase protein to the open region of DNA where hydrolysis and strand separation will occur.
E)DnaA prevents reannealing of the separated strands so replication can proceed.

Question 13

What enzyme(s)is/are responsible for removal of RNA primers and joining of Okazaki fragments?

A)DNA polymerase I
B)DNA polymerase III
C)DNA ligase
D)DNA polymerase I and DNA ligase
E)DNA polymerase III and DNA ligase

Question 14

Which functional groups have been altered in a ddNTP compared to a dNTP?

A)The ddNTPs have a 2′ OH and a 3′ H,while dNTPs have a 2′ H and a 3′ OH.
B)The ddNTPs have a 2′ H and a 3′ H,while dNTPs have a 2′ H and a 3′ OH.
C)The ddNTPs have a 2′ OH and a 3′ OH,while dNTPs have a 2′ H and a 3′ H.
D)The ddNTPs have a 2′ H and a 3′ H,while dNTPs have a 2′ OH and a 3′ OH.
E)The ddNTPs have a 2′ H and a 3′ OH,while dNTPs have a 2′ H and a 3′ H.

Question 15

Which of these components would you use to distinguish whether a sample has been prepared for a Sanger sequencing reaction or for a polymerase chain reaction?

A)DNA template
B)DNA polymerase
C)dNTPs
D)ddNTPs
E)DNA primer

Question 16

If complementary DNA strands were arranged in a parallel manner,what would you expect to see?

A)Complementary nucleotides would be attracted to each other,forming ionic bonds that would make the helix stable but not uniform in width.
B)Charges of complementary nucleotides would repel and no hydrogen bonds would form.
C)Complementary nucleotides would line up properly;but fewer hydrogen bonds would form,so the strands could be more easily pulled apart.
D)Purines would pair with both purines and pyrimidines due to the closer alignment of the parallel strands.
E)There would be no discernable difference between DNA strands aligned in a parallel versus antiparallel manner.

Question 17

What is the difference between a nucleotide and a nucleoside?

A)Nucleotides are found in DNA,while nucleosides are found in RNA.
B)Nucleotides are involved in eukaryotic DNA replication,while nucleosides are used in bacterial DNA replication.
C)Nucleosides contain only deoxyribose sugars.
D)A nucleoside with a phosphate ester linked to the sugar is a nucleotide.
E)Nucleosides are purines,while nucleotides are pyrimidines.

Question 18

DNA helicase inhibitors are well studied as potential drug targets.What would you expect to see if DNA helicase activity is inhibited?

A)The replisome complex would not assemble on the oriC region.
B)The DNA cannot bend,so hydrogen bonds in the 13-mer region of oriC remain intact.
C)Helicase catalyzes ATP hydrolysis and DNA strands separation,so the helix cannot be unwound and strands will not separate.
D)Helicase carries the SSB protein to the open region of DNA,so hydrolysis and strand separation will not occur.
E)Helicase prevents reannealing of the separated strands,so strands would quickly reanneal and DNA replication cannot proceed.

Question 19

Which of the following are classified as pyrimidines?

A)adenine and thymine
B)guanine and cytosine
C)adenine and guanine
D)thymine and cytosine
E)adenine and uracil

Question 20

What type of bond is formed between the hydroxyl group of one nucleotide and the phosphate group of an adjacent nucleotide,forming the sugar-phosphate backbone of DNA?

A)glycosidic bond
B)phosphodiester bond
C)ester linkage
D)hydrogen bond
E)ionic bond

Question 21

What is the molecular diameter of the DNA helix (in angstroms)?

Question 22

During DNA replication,the continuously elongated daughter strand is referred to as what?

Question 23

The major and minor grooves of DNA are features of the helix that can be attributed to this process,which involves tight packing of DNA bases in a duplex.

Question 24

What are the three parts of a DNA nucleotide?

Question 25

What type of experimental technique did Huberman and Riggs use to produce the first evidence of bidirectional replication in bacteria?

Question 26

DNA polymerase catalyzes DNA strand elongation by removing what from the dNTPs?

Question 27

What structure in E.coli delivers primase and accessory proteins to the oriC site to synthesize the primer needed for DNA replication?

Question 28

How might you choose a region of DNA for a PCR primer so as to increase the temperature necessary for primer annealing (to minimize nonspecific PCR products)?

Question 29

What well-characterized sequence in E.coli is 245 bp,AT-rich,and divided into three 13-mers and four 9-mers?

Question 30

Which enzyme,a combination of several proteins and a molecule of tRNA,acts as the template for the telomere repeat DNA sequence?

Question 31

What is the overall direction of DNA strand elongation?

Question 32

What is the purpose of the DNA sequences found at the origins of replication?

Question 33

Based on Griffith's results,what would you expect if you injected both heat-killed type RII and living type SIII?

Question 34

Eukaryotic polymerases interact with which protein that acts as the sliding clamp in eukaryotic DNA replication?

Question 35

During DNA replication in E.coli,how does the cell prevent the DNA strands from their natural tendency to seek maximum stability and reanneal?

Question 36

In E.coli,which protein uses ATP to hydrolyze hydrogen bonds holding complementary strands together?

Question 37

What did Okazaki's discovery of the short segments of DNA reveal about DNA replication on the lagging strand?

Question 38

What characteristic of the polymerase isolated from Thermus aquaticus makes it unique and highly useful for maintaining the enzyme efficiency during PCR?

Question 39

What are the three steps of each PCR cycle?

Question 40

The regions where DNA-binding proteins can make direct contact with exposed nucleotides are known as what?

Question 41

The large,complex aggregation of proteins and enzymes that assembles at the replication fork is known as the ________.

Question 42

Describe the DNA helix structure proposed by Watson and Crick.What is the diameter of the helix and the distance between bases? What types of bonds are involved in stabilizing the DNA backbone,and what types of bonds are found between complementary base pairs? Why would a sequence containing high concentrations of G and C require more energy to break the bonds?

Question 43

DNA polymerase requires a primer sequence to provide a ________ functional group to which the new DNA nucleotide can be added.

Question 44

Comparison of conserved sequences among related species usually leads to the identification of ________,which illustrate the nucleotides most often found at each position of DNA in the conserved region.

Question 45

Many antibacterial agents and chemotherapy agents act as topoisomerase inhibitors.Why would inhibition of topoisomerase cause cell death in bacterial and eukaryotic cells?

Question 46

________ must be added to a PCR to direct the polymerase where to begin synthesis.

Question 47

Describe the function of the oriC.What do you predict will happen to the cell if 100 bp between the 13-mer and 9-mer sequence is deleted as indicated in the figure?

Question 48

Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is semiconservative.How would their results have differed if DNA replication was actually conservative in nature?

Question 49

________ is the term for multiprotein complexes in which a core enzyme is associated with additional protein components leading to its function.