Chapter 13 - Study Questions

At a specific area of a chromosome, the following sequence of nucleotides is present where the chain opens to form a replication fork: 3' C C T A G G C T G C A A T C C 5' An RNA primer is formed starting at the underlined T ( T) of the template. Which of the following represents the primer sequence?

5' A C G U U A G G 3'

n Okazaki fragment has which of the following arrangements?

5' RNA nucleotides, DNA nucleotides 3'

Cytosine makes up 42% of the nucleotides in a sample of DNA from an organism. Approximately what percentage of the nucleotides in this sample will be thymine?

8%

In an analysis of the nucleotide composition of DNA, which of the following will be found?

A + C = G + T

In analyzing the number of different bases in a DNA sample, which result would be consistent with the base-pairing rules?

A + G = C + T

Why is it so important to be able to amplify DNA fragments when studying genes?

A gene may represent only a millionth of the cell's DNA.

For a science fair project, two students decided to repeat the Hershey and Chase experiment, with modifications. They decided to label the nitrogen of the DNA, rather than the phosphate. They reasoned that each nucleotide has only one phosphate and two to five nitrogens. Thus, labeling the nitrogens would provide a stronger signal than labeling the phosphates. Why won't this experiment work?

Amino acids (and thus proteins) also have nitrogen atoms; thus, the radioactivity would not distinguish between DNA and proteins.

Figure 13.1 A space probe returns with a culture of a microorganism found on a distant planet. Analysis shows that it is a carbon-based life-form that has DNA. You grow the cells in 15N medium for several generations and then transfer them to 14N medium. Which pattern in Figure 13.1 would you expect if the DNA was replicated in a conservative manner?

B

Figure 13.1 In the late 1950s, Meselson and Stahl grew bacteria in a medium containing "heavy" nitrogen ( 15N) and then transferred them to a medium containing 14N. Which of the results in Figure 13.1 would be expected after one round of DNA replication in the presence of 14N?

D

In trying to determine whether DNA or protein is the genetic material, Hershey and Chase made use of which of the following facts?

DNA contains phosphorus, whereas protein does not.

Suppose you are provided with an actively dividing culture of E. coli bacteria to which radioactive thymine has been added. What would happen if a cell replicates once in the presence of this radioactive base?

DNA in both daughter cells would be radioactive.

A biochemist isolates, purifies, and combines in a test tube a variety of molecules needed for DNA replication. When she adds some DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture?

DNA ligase

Which enzyme catalyzes the elongation of a DNA strand in the 5' → 3' direction?

DNA polymerase III

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesized?

DNA polymerase can join new nucleotides only to the 3' end of a growing strand

A new DNA strand elongates only in the 5' to 3' direction because

DNA polymerase can only add nucleotides to the free 3' end.

After mixing a heat-killed, phosphorescent (light-emitting) strain of bacteria with a living, nonphosphorescent strain, you discover that some of the living cells are now phosphorescent. Which observation(s) would provide the best evidence that the ability to phosphoresce is a heritable trait?

Descendants of the living cells are also phosphorescent.

Which of the following investigators was (were) responsible for the following discovery? In DNA from any species, the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine.

Erwin Chargaff

Which of the following sequences in double-stranded DNA is most likely to be recognized as a cutting site for a restriction enzyme

GGCC CCGG

Which of the following statements describes chromatin?

Heterochromatin is highly condensed, whereas euchromatin is less compact.

Which of the following statements is true of histones?

Histone H1 is not present in the nucleosome bead; instead, it draws the nucleosomes together.

Why do histones bind tightly to DNA?

Histones are positively charged, and DNA is negatively charged.

Use the list of choices below for the following questions: I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase Which of the enzymes separates the DNA strands during replication?

I

Use the list of choices below for the following questions: I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase Which of the enzymes covalently connects segments of DNA?

III

What is the most logical sequence of steps for splicing foreign DNA into a plasmid and inserting the plasmid into a bacterium? I. Transform bacteria with a recombinant DNA molecule. II. Cut the plasmid DNA using restriction enzymes. III. Extract plasmid DNA from bacterial cells. IV. Hydrogen-bond the plasmid DNA to nonplasmid DNA fragments. V. Use ligase to seal plasmid DNA to nonplasmid DNA.

III, II, IV, V, I

Use the list of choices below for the following questions: I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase Which of the enzymes removes the RNA nucleotides from the primer and adds equivalent DNA nucleotides to the 3' end of Okazaki fragments?

IV

Which of the following statements describes the eukaryotic chromosome?

It consists of a single linear molecule of double-stranded DNA plus proteins.

What is the role of DNA ligase in the elongation of the lagging strand during DNA replication?

It joins Okazaki fragments together.

n his transformation experiments, what did Griffith observe?

Mixing a heat-killed pathogenic strain of bacteria with a living nonpathogenic strain can convert some of the living cells into the pathogenic form.

In E. coli, there is a mutation in a gene called dnaB that alters the helicase that normally acts at the origin. Which of the following would you expect as a result of this mutation?

No replication fork will be formed.

Replication in prokaryotes differs from replication in eukaryotes for which of the following reasons?

Prokaryotic chromosomes have a single origin of replication, whereas eukaryotic chromosomes have many.

Figure 13.1 Once the pattern found after one round of replication was observed, Meselson and Stahl could be confident of which of the following conclusions?

Replication is not conservative.

What is meant by the description "antiparallel" regarding the strands that make up DNA?

The 5' to 3' direction of one strand runs counter to the 5' to 3' direction of the other strand.

If a cell were unable to produce histone proteins, which of the following would be a likely effect?

The cell's DNA couldn't be packed into its nucleus.

Use the following information to answer the next few questions. A group of six students has taken samples of their own cheek cells, purified the DNA, and used a restriction enzyme known to cut at zero, one, or two sites in a particular gene of interest. Analysis of the data obtained shows that two students each have two fragments, two students each have three fragments, and two students each have one only. What does this demonstrate?

The two students who have two fragments have one restriction site in this region.

Studies of nucleosomes have shown that histones (except H1) exist in each nucleosome as two kinds of tetramers: one of 2 H2A molecules and 2 H2B molecules, and the other as 2 H3 and 2 H4 molecules. Which of the following is supported by this data?

The two types of tetramers associate to form an octamer.

Figure 13.2 In an experiment, DNA is allowed to replicate in an environment with all necessary enzymes, dATP, dCTP, dGTP, and radioactively labeled dTTP ( 3H thymidine). After several minutes, the DNA is switched to nonradioactive medium and is then viewed by electron microscopy and autoradiography. Figure 13.2 represents the results. It shows a replication bubble, and the dots represent radioactive material. Which of the following is the most likely interpretation of the results?

There are two replication forks going in opposite directions.

Individuals with the disorder xeroderma pigmentosum are hypersensitive to sunlight. This occurs because their cells are impaired in what way?

They cannot repair thymine dimers.

Use the list of choices below for the following questions: I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase Which of the enzymes synthesizes short segments of RNA?

V

Use Figure 13.3 to answer the following question. Figure 13.3 Which enzyme was used to produce the molecule in Figure 13.3?

a restriction enzyme

Which of the following modifications is least likely to alter the rate at which a DNA fragment moves through a gel during electrophoresis?

altering the nucleotide sequence of the DNA fragment without adding or removing nucleotides

How do we describe transformation in bacteria?

assimilation of external DNA into a cell

How does a bacterial cell protect its own DNA from restriction enzymes?

by adding methyl groups to adenines and cytosines

Assume that you are trying to insert a gene into a plasmid. Someone gives you a preparation of genomic DNA that has been cut with restriction enzyme X. The gene you wish to insert has sites on both ends for cutting by restriction enzyme Y. You have a plasmid with a single site for Y, but not for X. Your strategy should be to

cut the DNA again with restriction enzyme Y and insert these fragments into the plasmid cut with the same enzyme.

The elongation of the leading strand during DNA synthesis

depends on the action of DNA polymerase.

Which of the following sets of materials is required by both eukaryotes and prokaryotes for replication?

double-stranded DNA, four kinds of dNTPs, primers, origins of replication

To repair a thymine dimer by nucleotide excision repair, in which order do the necessary enzymes act?

endonuclease, DNA polymerase I, DNA ligase

In a nucleosome, the DNA is wrapped around

histones.

Use the following information to answer the next few questions. A eukaryotic gene has "sticky ends" produced by the restriction endonuclease EcoRI. The gene is added to a mixture containing EcoRI and a bacterial plasmid that carries two genes conferring resistance to ampicillin and tetracycline. The plasmid has one recognition site for EcoRI located in the tetracycline resistance gene. This mixture is incubated for several hours, exposed to DNA ligase, and then added to bacteria growing in nutrient broth. The bacteria are allowed to grow overnight and are streaked on a plate using a technique that produces isolated colonies that are clones of the original. Samples of these colonies are then grown in four different media: nutrient broth plus ampicillin, nutrient broth plus tetracycline, nutrient broth plus ampicillin and tetracycline, and nutrient broth without antibiotics. Bacteria that contain the plasmid, but not the eukaryotic gene, would grow

in all four types of broth.

Use the following information to answer the next few questions. A eukaryotic gene has "sticky ends" produced by the restriction endonuclease EcoRI. The gene is added to a mixture containing EcoRI and a bacterial plasmid that carries two genes conferring resistance to ampicillin and tetracycline. The plasmid has one recognition site for EcoRI located in the tetracycline resistance gene. This mixture is incubated for several hours, exposed to DNA ligase, and then added to bacteria growing in nutrient broth. The bacteria are allowed to grow overnight and are streaked on a plate using a technique that produces isolated colonies that are clones of the original. Samples of these colonies are then grown in four different media: nutrient broth plus ampicillin, nutrient broth plus tetracycline, nutrient broth plus ampicillin and tetracycline, and nutrient broth without antibiotics. Bacteria containing a plasmid into which the eukaryotic gene has integrated would grow

in the ampicillin broth and the nutrient broth.

The reason for using Taq polymerase for PCR is that

it is heat stable and can withstand the heating step of PCR.

You briefly expose bacteria undergoing DNA replication to radioactively labeled nucleotides. When you centrifuge the DNA isolated from the bacteria, the DNA separates into two classes. One class of labeled DNA includes very large molecules (thousands or even millions of nucleotides long), and the other includes short stretches of DNA (several hundred to a few thousand nucleotides in length). These two classes of DNA probably represent

leading strands and Okazaki fragments.

The spontaneous loss of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage?

nuclease, DNA polymerase, DNA ligase

Which of the following represents the order of increasingly higher levels of organization of chromatin?

nucleosome, 30-nm chromatin fiber, looped domain

E. coli cells grown on 15N medium are transferred to 14N medium and allowed to grow for two more generations (two rounds of DNA replication). DNA extracted from these cells is centrifuged. What density distribution of DNA would you expect in this experiment?

one low-density and one intermediate-density band

Use Figure 13.4 to answer the following question. Figure 13.4 The segment of DNA shown in Figure 13.4 has restriction sites I and II, which create restriction fragments A, B, and C. Which of the gels produced by electrophoresis shown below best represents the separation and identity of these fragments?

order: CAB - spaced out far apart from each other

What is the function of topoisomerase?

relieving strain in the DNA ahead of the replication fork

Polytene chromosomes of Drosophila salivary glands each consist of multiple identical DNA strands that are aligned in parallel arrays. How could these arise?

replication without separation

It became apparent to Watson and Crick after completion of their model that the DNA molecule could carry a vast amount of hereditary information in which of the following?

sequence of bases

Which of the following help(s) to hold the DNA strands apart while they are being replicated?

single-strand binding proteins

In his work with pneumonia-causing bacteria and mice, Griffith found that

some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic.

In a linear eukaryotic chromatin sample, which of the following strands is looped into domains by scaffolding?

the 30-nm chromatin fiber

Given the damage caused by UV radiation, the kind of gene affected in those with XP is one whose product is involved with

the ability to excise single-strand damage and replace it.

Which of the following can be determined directly from X-ray diffraction photographs of crystallized DNA?

the diameter of the helix

The leading and the lagging strands differ in that

the leading strand is synthesized in the same direction as the movement of the replication fork, and the lagging strand is synthesized in the opposite direction.

The difference between ATP and the nucleoside triphosphates used during DNA synthesis is that

the nucleoside triphosphates have the sugar deoxyribose; ATP has the sugar ribose.

Use the following information to answer the next few questions. A eukaryotic gene has "sticky ends" produced by the restriction endonuclease EcoRI. The gene is added to a mixture containing EcoRI and a bacterial plasmid that carries two genes conferring resistance to ampicillin and tetracycline. The plasmid has one recognition site for EcoRI located in the tetracycline resistance gene. This mixture is incubated for several hours, exposed to DNA ligase, and then added to bacteria growing in nutrient broth. The bacteria are allowed to grow overnight and are streaked on a plate using a technique that produces isolated colonies that are clones of the original. Samples of these colonies are then grown in four different media: nutrient broth plus ampicillin, nutrient broth plus tetracycline, nutrient broth plus ampicillin and tetracycline, and nutrient broth without antibiotics. Bacteria that do not take up any plasmids would grow on which media?

the nutrient broth only

What is the function of DNA polymerase III?

to add nucleotides to the 3' end of a growing DNA strand

Use the following information to answer the next few questions. A group of six students has taken samples of their own cheek cells, purified the DNA, and used a restriction enzyme known to cut at zero, one, or two sites in a particular gene of interest. Why might they be conducting such an experiment?

to find which of the students has which alleles