AP Biology chp 16

21. Describe the structure of DNA.

The DNA molecule is 2 nm wide. The nucleotides are about 0.34 nm apart from each other. There are about 3.4 nm between each turn. The backbone consists of sugar and phosphate while the rungs are the nitrogenous base pairs.

39) If a cell were unable to produce histone proteins, which of the following would be a likely effect? A) There would be an increase in the amount of "satellite" DNA produced during centrifugation.  B) The cell's DNA couldn't be packed into its nucleus. C) Spindle fibers would not form during prophase . D) Amplification of other genes would compensate for the lack of histones.  E) Pseudogenes would be transcribed to compensate for the decreased protein in the cell.

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

28. Define the origins of replication.

The replication of a DNA molecule begins at particular sites called origins of replication, short stretches of DNA having a specific sequence of nucleotides.

23. What do we mean when we say the two strands of DNA are antiparallel?

The subunits of the two sugar-phosphate backbones run in opposite directions.

6. Define transformation.

Transformation is a change in genotype and phenotype due to the assimilation of external DNA by a cell. (This use of the term should not be confused with the conversion of a normal animal cell to a cancerous one.)

repair enzymes

detect and repair damaged DNA

25. Who performed the experiments that elucidated the correct mechanism of DNA replication?

Matthew Meselson and Franklin Stahl concluded that DNA replication is semiconservative.

17. How did Watson and Crick's model explain the basis for Chargaff's rules?

Because each nitrogenous base is paired with its complement, the amount of A must equal the amount of T and the amount of G must equal the amount of C.

1. What are the two chemical components of chromosomes?

The two chemical components of chromosomes are DNA and protein

nuclease

cuts damaged DNA strand; removes damaged sections

polymerase I

removes RNA primer and replaces with DNA

DNA polymerase

repair synthesis fills in missing nucleotides

8) 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? A) sequence of bases B) phosphate-sugar backbones C) complementary pairing of bases D) side groups of nitrogenous bases  E) different five-carbon sugars

sequence of bases

13) An Okazaki fragment has which of the following arrangements?  A) primase, polymerase, ligase  B) 3' RNA nucleotides, DNA nucleotides 5' C) 5' RNA nucleotides, DNA nucleotides 3' D) DNA polymerase I, DNA polymerase III E) 5' DNA to 3'

5' RNA nucleotides, DNA nucleotides 3'

6) 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? A) 8%  B) 16%  C) 31%  D) 42%  E) It cannot be determined from the information provided

8%

52) In analyzing the number of different bases in a DNA sample, which result would be consistent with the base-pairing rules? A) A = G  B) A + G = C + T C) A + T = G + T  D) A = C  E) G = T

A + T = G + T

13. List the three components of a nucleotide.

A DNA nucleotide monomer consists of a nitrogenous base, the sugar deoxyribose, and a phosphate group.

36. What is a thymine dimer? How might it occur? How is it repaired?

A thymine dimer is the covalent linking of thymine bases that are adjacent on a DNA strand. This causes the DNA to buckle and interferes with DNA replication. Teams of enzymes detect and repair damaged DNA.

16. Distinguish between the structure of pyrimidines and purines. Explain why adenine bonds only to thymine.

Adenine and guanine are purines, nitrogenous bases with two organic rings, while cytosine and thymine are nitrogenous bases called pyrimidines, which have a single ring. Thus, purines are about twice as wide as pyrimidines. A purinepurine pair is too wide and a pyrimidine-pyrimidine pair too narrow to account for the uniform 2-nm diameter of the double helix. Always pairing a purine (such as A) with a pyrimidine (such as T), however, results in a uniform diameter.

20. Explain the base-pairing rule.

Adenine can form two hydrogen bonds with thymine and only thymine; guanine forms three hydrogen bonds with cytosine and only one cytosine.

7. What did Oswald Avery determine to be the transforming factor? Explain his experimental approach.

Avery broke open the heat-killed pathogenic bacteria and extracted the cellular contents. He treated each of three samples with an agent that inactivated DNA, RNA, or protein, and then tested the sample for its ability to transform live nonpathogenic bacteria. Only when DNA was allowed to remain active did transformation occur.

3. Distinguish between the virulent and nonvirulent strains of Streptococcus pneumoniae studied by Frederick Griffith.

Bacteria of the S (smooth) strain can cause pneumonia in mice; they are pathogenic because they have an outer capsule that protects them from an animal's defense system. Bacteria of the R (rough) strain lack a capsule and are nonpathogenic. To test for the trait of pathogenicity, Griffith injected mice with the two strains.

12. What are Chargaff's rules? How did he arrive at them?

Chargaff analyzed the base composition of DNA from a number of different organisms, whereby he noticed a peculiar regularity in the ratios of nucleotide bases. In the DNA of each species he studied, the number of adenines approximately equaled the number of thymines, and the number of guanines approximately equaled the number of cytosines. He developed the rules that [1] the base composition varies between species, and [2] within a species, the number of A and T bases are equal and the number of G and C bases are equal. The basis for these rules remained unexplained until the discovery of the double helix.

4) In trying to determine whether DNA or protein is the genetic material, Hershey and Chase made use of which of the following facts?  A) DNA contains sulfur, whereas protein does not. B) DNA contains phosphorus, whereas protein does not. C) DNA contains nitrogen, whereas protein does not. D) DNA contains purines, whereas protein includes pyrimidines. E) RNA includes ribose, whereas DNA includes deoxyribose sugars.

DNA contains phosphorus, whereas protein does not.

15) Which enzyme catalyzes the elongation of a DNA strand in the 5' → 3' direction? A) primase  B) DNA ligase  C) DNA polymerase III D) topoisomerase  E) helicase

DNA ligase

25) A new DNA strand elongates only in the 5' to 3' direction because  A) DNA polymerase begins adding nucleotides at the 5' end of the template. B) Okazaki fragments prevent elongation in the 3' to 5' direction.  C) the polarity of the DNA molecule prevents addition of nucleotides at the 3' end. D) replication must progress toward the replication fork. E) DNA polymerase can only add nucleotides to the free 3' end.

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

3) After mixing a heat-killed, phosphorescent strain of bacteria with a living nonphosphorescent strain, you discover that some of the living cells are now phosphorescent. Which observations would provide the best evidence that the ability to fluoresce is a heritable trait?  A) DNA passed from the heat-killed strain to the living strain. B) Protein passed from the heat-killed strain to the living strain. C) The phosphorescence in the living strain is especially bright.  D) Descendants of the living cells are also phosphorescent. E) Both DNA and protein passed from the heat-killed strain to the living strain.

Descendants of the living cells are also phosphorescent.

5) 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.  A) Frederick Griffith B) Alfred Hershey and Martha Chase C) Oswald Avery, Maclyn McCarty, and Colin MacLeod D) Erwin Chargaff  E) Matthew Meselson and Franklin Stahl

Erwin Chargaff

9. How does a bacteriophage destroy a bacterial cell?

First, the phage uses its tail fibers to bind to specific receptor sites on the outer surface of the bacterial cell. The sheath of the tail contracts, injecting the phage's DNA into the cell and leaving an empty capsid outside. The cell's DNA is hydrolyzed. The phage DNA then directs production of phage proteins and copies of the phage genome by host and viral enzymes, using components within the cell. Three separate sets of proteins self-assemble to form phage heads, tails, and tail fibers. The phage genome is packaged inside the capsid as the head forms. Finally, the phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. The cell swells and finally bursts, releasing 100 to 200 phage particles.

15. What was the role of Rosalind Franklin in the discovery of the double helix?

Franklin, a very accomplished X-ray crystallographer, conducted critical experiments resulting in the photograph that allowed Watson and Crick to deduce the double-helical structure of DNA.

34. Make a detailed list of the steps that occur in the synthesis of a new strand.

Helicase unwinds and separates the parental DNA strands. Topoisomerase breaks, swivels, and rejoins the parental DNA ahead of the replication fork, relieving the strain caused by unwinding. Molecules of single-strand binding protein stabilize the unwound parent strands. Primase synthesizes RNA primers, using the parental DNA as a template. The leading strand is synthesized continuously in the 5' to 3' direction by DNA polymerase III. Primase begins synthesis of the RNA primer for the lagging strand. DNA pol III discontinuously synthesizes the lagging strand in the 5' to 3' direction. DNA pol I removes all RNA primer sections and replaces them with DNA nucleotides. The replacement of the primer with DNA leaves the new DNA nucleotides with a free 3' end. DNA ligase joins the free 3' end to its adjacent 5' end, forming a continuous strand of DNA on both the leading and lagging strands.

11. Describe the means by which Hershey and Chase established that only the DNA of a phage enters an E. coli cell.

Hershey and Chase concluded that the DNA injected by the phage must be the molecule carrying the genetic information that makes the cells produce new viral DNA and proteins.

10. How did Hershey and Chase "label" viral DNA and viral protein so that they could be distinguished?

Hershey and Chase used a radioactive isotope of sulfur to tag protein and a radioactive isotope of phosphorus to tag DNA. Because protein, but not DNA, contains sulfur, radioactive sulfur atoms were incorporated only into the protein of the phage. Similarly, the atoms of radioactive phosphorus labeled only the DNA, not the protein, because nearly all the phage's phosphorus is in its DNA.

40) Which of the following statements is true of histones?  A) Each nucleosome consists of two molecules of histone H1. B) Histone H1 is not present in the nucleosome bead; instead, it draws the nucleosomes together. C) The carboxyl end of each histone extends outward from the nucleosome and is called a "histone tail." D) Histones are found in mammals, but not in other animals or in plants or fungi.  E) The mass of histone in chromatin is approximately nine times the mass of DNA.

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

41) Why do histones bind tightly to DNA? A) Histones are positively charged, and DNA is negatively charged. B) Histones are negatively charged, and DNA is positively charged.  C) Both histones and DNA are strongly hydrophobic . D) Histones are covalently linked to the DNA. E) Histones are highly hydrophobic, and DNA is hydrophilic.

Histones are positively charged, and DNA is negatively charged.

Use the following list of choices for the following question I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase  32) Which of the enzymes separates the DNA strands during replication? A) I  B) II  C) III  D) IV  E) V

I

Use the following list of choices for the following question I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase  33) Which of the enzymes covalently connects segments of DNA?  A) I  B) II  C) III  D) IV  E) V

III

Use the following list of choices for the following question I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase 31) Which of the enzymes removes the RNA nucleotides from the primer and adds equivalent DNA nucleotides to the 3' end of Okazaki fragments? A) I  B) II  C) III D) IV E) V

IV

38) Which of the following statements describes the eukaryotic chromosome? A) It is composed of DNA alone. B) The nucleosome is its most basic functional subunit. C) The number of genes on each chromosome is different in different cell types of an organism. D) It consists of a single linear molecule of double-stranded DNA plus proteins.  E) Active transcription occurs on heterochromatin but not euchromatin.

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

27) What is the role of DNA ligase in the elongation of the lagging strand during DNA replication? A) It synthesizes RNA nucleotides to make a primer. B) It catalyzes the lengthening of telomeres. C) It joins Okazaki fragments together .D) It unwinds the parental double helix. E) It stabilizes the unwound parental DNA.

It joins Okazaki fragments together

14. Who built the first model of DNA and shared the 1962 Nobel Prize for discovery of its structure?

James Watson and Francis Crick

26. How did Meselson and Stahl create "heavy" DNA for their experiments?

Meselson and Stahl cultured bacteria for several generations in a medium containing nucleotide precursors labeled with a heavy isotope of nitrogen, 15N. They then transferred the bacteria to a medium with only 14N, a lighter isotope. A sample was taken after DNA replicated once; another sample was taken after DNA replicated again. They extracted DNA from the bacteria in the samples and then centrifuged each DNA sample to separate DNA of different densities.

In his transformation experiments, what did Griffith observe?  A) Mutant mice were resistant to bacterial infections. B) Mixing a heat-killed pathogenic strain of bacteria with a living nonpathogenic strain can convert some of the living cells into the pathogenic form. C) Mixing a heat-killed nonpathogenic strain of bacteria with a living pathogenic strain makes the pathogenic strain nonpathogenic.  D) Infecting mice with nonpathogenic strains of bacteria makes them resistant to pathogenic strains. E) Mice infected with a pathogenic strain of bacteria can spread the infection to other mice.

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

14) 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? A) No proofreading will occur. B) No replication fork will be formed . C) The DNA will supercoil.  D) Replication will occur via RNA polymerase alone. E) Replication will require a DNA template from another source

No replication fork will be formed

39. Why are cancer cells immortal, but most body cells have a limited life span?

Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo. Cells from large tumors often have unusually short telomeres, as we would expect for cells that have undergone many cell divisions. Further shortening would presumably lead to self-destruction of the tumor cells. Researchers have found telomerase activity in cancerous somatic cells, suggesting that its ability to stabilize telomere length may allow these cancer cells to persist.

10) Replication in prokaryotes differs from replication in eukaryotes for which of the following reasons? A) Prokaryotic chromosomes have histones, whereas eukaryotic chromosomes do not. B) Prokaryotic chromosomes have a single origin of replication, whereas eukaryotic chromosomes have many.  C) The rate of elongation during DNA replication is slower in prokaryotes than in eukaryotes. D) Prokaryotes produce Okazaki fragments during DNA replication, but eukaryotes do not. E) Prokaryotes have telomeres, and eukaryotes do not.

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

11) What is meant by the description "antiparallel" regarding the strands that make up DNA? A) The twisting nature of DNA creates nonparallel strands.  B) The 5' to 3' direction of one strand runs counter to the 5' to 3' direction of the other strand. C) Base pairings create unequal spacing between the two DNA strands. D) One strand is positively charged and the other is negatively charged. E) One strand contains only purines and the other contains only pyrimidines.

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

29-30. Distinguish between the leading and the lagging strands during DNA replication.

The DNA strand made by the mechanism of DNA replication forks is called the leading strand. Only one primer is required for DNA pol III to synthesize the leading strand. The DNA strand elongating away from the replication fork is called the lagging strand. In contrast to the leading strand, which elongates continuously in the 5' to 3' direction as the fork progresses, the lagging strand is synthesized discontinuously, as a series of segments. Synthesis of the leading strand and synthesis of the lagging strand occur concurrently and at the same rate. The lagging strand is so named because its synthesis is delayed slightly relative to synthesis of the leading strand; each new fragment of the lagging strand cannot be started until enough template has been exposed at the replication fork.

27. Explain how Meselson and Stahl confirmed the semiconservative mechanism of DNA replication.

The first replication in the 14N medium produced a band of hybrid (15N-14N) DNA. This result eliminated the conservative model. The second replication produced both light and hybrid DNA, a result that refuted the dispersive model and supported the semiconservative model.

22. Explain what is meant by 5' and 3'ends of the molecule.

The polynucleotide strand has directionality, from the 5' end (with the phosphate group) to the 3' end (with the -OH groups of the sugar). 5' and 3' refer to the numbers assigned to the carbons in the sugar ring. A strand is "read" from the 3' to the 5' end and "written" from the 5' to the 3' end.

24. What is the semiconservative model of replication?

The semiconservative model predicts that when a double helix replicates, each of the two daughter molecules will have one old strand, from the parental molecule, and one newly made strand. This contrasts with the conservative model, in which the two parental strands somehow come back together (that is, the parental molecule is conserved). In the dispersive model, all four strands of DNA following replication have a mixture of old and new DNA.

31. What are Okazaki fragments? How are they welded together?

The series of segments of the lagging strand are called Okazaki fragments. The fragments are about 1,000 to 2,000 nucleotides long in E. coli and 100 to 200 nucleotides long in eukaryotes. Whereas only one primer is required on the leading strand, each Okazaki fragment on the lagging strand must be primed separately. After DNA pol III forms an Okazaki fragment, another DNA polymerase, DNA pol I, replaces the RNA nucleotides of the adjacent primer with DNA nucleotides. But DNA pol I cannot join the final nucleotide of this replacement DNA segment to the first DNA nucleotide of the adjacent Okazaki fragment. Another enzyme, DNA ligase, accomplishes this task, joining the sugarphosphate backbones of all the Okazaki fragments into a continuous DNA strand.

29) Individuals with the disorder xeroderma pigmentosum are hypersensitive to sunlight. This occurs because their cells are impaired in what way? A) They cannot replicate DNA. B) They cannot undergo mitosis.  C) They cannot exchange DNA with other cells. D) They cannot repair thymine dimers .E) They do not recombine homologous chromosomes during meiosis

They cannot repair thymine dimers

2. Why did researchers originally think that protein was the genetic material?

Until the 1940s, biochemists though protein was the genetic material, as they had identified proteins as a class of macromolecules with great heterogeneity and specificity of function, essential requirements for hereditary material. Moreover, little was known about nucleic acids, whose physical and chemical properties seemed far too uniform to account for the multitude of specific inherited traits exhibited by every organism. The role of DNA in heredity was first worked out while studying bacteria and the viruses that infect them, which are far simpler than pea plants, fruit flies, or humans.

Use the following list of choices for the following question I. helicase II. DNA polymerase III III. ligase IV. DNA polymerase I V. primase 34) Which of the enzymes synthesizes short segments of RNA? A) I  B) II  C) III  D) IV E) V.

V.

4. What was the purpose of Griffith's studies?

While attempting to develop a vaccine against pneumonia in 1928, Griffith explored the inheritance of pathogenicity.

17) The enzyme telomerase solves the problem of replication at the ends of linear chromosomes by which method?  A) adding a single 5' cap structure that resists degradation by nucleases  B) causing specific double-strand DNA breaks that result in blunt ends on both strands C) causing linear ends of the newly replicated DNA to circularize D) adding numerous short DNA sequences such as TTAGGG, which form a hairpin turn E) adding numerous GC pairs which resist hydrolysis and maintain chromosome integrity

adding numerous short DNA sequences such as TTAGGG, which form a hairpin turn

polymerase III

adds DNA nucleotides to new strand

2) How do we describe transformation in bacteria?  A) the creation of a strand of DNA from an RNA molecule  B) the creation of a strand of RNA from a DNA molecule C) the infection of cells by a phage DNA molecule  D) the type of semiconservative replication shown by DNA  E) assimilation of external DNA into a cell

assimilation of external DNA into a cell

53) The elongation of the leading strand during DNA synthesis A) progresses away from the replication fork. B) occurs in the 3' → 5' direction. C) produces Okazaki fragments.  D) depends on the action of DNA polymerase. E) does not require a template strand.

depends on the action of DNA polymerase.

26) What is the function of topoisomerase? A) relieving strain in the DNA ahead of the replication fork B) elongating new DNA at a replication fork by adding nucleotides to the existing chain C) adding methyl groups to bases of DNA  D) unwinding of the double helix E) stabilizing single-stranded DNA at the replication fork

relieving strain in the DNA ahead of the replication fork

54) In a nucleosome, the DNA is wrapped around A) polymerase molecules.  B) ribosomes.  C) histones.  D) a thymine dimer. E) satellite DNA.

ribosomes.

28) Which of the following help(s) to hold the DNA strands apart while they are being replicated? A) primase B) ligase C) DNA polymerase D) single-strand binding proteins E) exonuclease

single-strand binding proteins

50) In his work with pneumonia-causing bacteria and mice, Griffith found that A) the protein coat from pathogenic cells was able to transform nonpathogenic cells. B) heat-killed pathogenic cells caused pneumonia. C) some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic . D) the polysaccharide coat of bacteria caused pneumonia.  E) bacteriophages injected DNA into bacteria

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

18) The DNA of telomeres has been found to be highly conserved throughout the evolution of eukaryotes. What does this most probably reflect? A) the inactivity of this DNA B) the low frequency of mutations occurring in this DNA C) that new evolution of telomeres continues D) that mutations in telomeres are relatively advantageous E) that the critical function of telomeres must be maintained

that the critical function of telomeres must be maintained

24) The leading and the lagging strands differ in that A) 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. B) the leading strand is synthesized by adding nucleotides to the 3' end of the growing strand, and the lagging strand is synthesized by adding nucleotides to the 5' end. C) the lagging strand is synthesized continuously, whereas the leading strand is synthesized in short fragments that are ultimately stitched together.  D) the leading strand is synthesized at twice the rate of the lagging strand.

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.

single stranded binding protein

holds DNA strands apart

DNA ligase

joins DNA fragments together DNA

42) Which of the following represents the order of increasingly higher levels of organization of chromatin?  A) nucleosome, 30-nm chromatin fiber, looped domain B) looped domain, 30-nm chromatin fiber, nucleosome C) looped domain, nucleosome, 30-nm chromatin fiber D) nucleosome, looped domain, 30-nm chromatin fiber E) 30-nm chromatin fiber, nucleosome, looped domain

nucleosome, 30-nm chromatin fiber, looped domain

topoisomerase

relieves strain caused by unwinding

ligase

seals free end of new DNA to old DNA, making strand complete

primase

synthesizes RNA primer DNA

7) Which of the following can be determined directly from X-ray diffraction photographs of crystallized DNA? A) the diameter of the helix B) the rate of replication C) the sequence of nucleotides D) the bond angles of the subunits  E) the frequency of A vs. T nucleotides

the diameter of the helix

helicase

untwists and separates strands