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Chapter 24 Genes and Chromosomes 280

Chapter 24 Genes and Chromosomes Multiple Choice Questions 1. Chromosomal elements Pages: 947-948 Difficulty: 2 Ans: B The most precise modern definition of a gene is a segment of genetic material that:

A) B) C) D) E)

codes for one polypeptide. codes for one polypeptide or RNA product. determines one phenotype. determines one trait. that codes for one protein.

2. Chromosomal elements Page: 949 Difficulty: 1 Ans: A The DNA in a bacterial (prokaryotic) chromosome is best described as:

A) B) C) D) E)

a single circular double-helical molecule. a single linear double-helical molecule. a single linear single-stranded molecule. multiple linear double-helical molecules. multiple linear single-stranded molecules.

3. Chromosomal elements Page: 949 Difficulty: 1 Bacterial plasmids:

A) B) C) D) E)

Ans: E

are always covalently joined to the bacterial chromosome. are composed of RNA. are never circular. cannot replicate when cells divide. often encode proteins not normally essential to the bacterium’s survival.

4. Chromosomal elements Pages: 948-951 Difficulty: 1 Ans: B Which of these statements about nucleic acids is false?

A) B) C) D) E)

Mitochondria and chloroplasts contain DNA. Plasmids are genes that encode plasma proteins in mammals. The chromosome of E. coli is a closed-circular, double-helical DNA. The DNA of viruses is usually much longer than the viral particle itself. The genome of many plant viruses is RNA.

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5. Chromosomal elements Pages: 948-951 Difficulty: 2 Functional DNA is not found in:

A) B) C) D) E)

Ans: C

bacterial nucleoids. chloroplasts. lysosomes. mitochondria. nuclei.

6. Chromosomal elements Pages: 948-951 Difficulty: 2 Ans: B The DNA in a eukaryotic chromosome is best described as:

A) B) C) D) E)

a single circular double-helical molecule. a single linear double-helical molecule. a single linear single-stranded molecule. multiple linear double-helical molecules. multiple linear single-stranded molecules.

7. Chromosomal elements Page: 952 Difficulty: 1 Introns:

A) B) C) D) E)

Ans: D

are frequently present in prokaryotic genes but are rare in eukaryotic genes. are spliced out before transcription. are translated but not transcribed. can occur many times within a single gene. encode unusual amino acids in proteins.

8. Chromosomal elements Page: 952 Difficulty: 2 Ans: D Approximately what fraction of the human genome is tranaposable elements? A) B) C) D) E)

1.5% 5% 10% 45% 80%

9. Chromosomal elements Page: 953 Difficulty: 1 Ans: A The chromosomal region that is the point of attachment of the mitotic spindle is the:

A) B) C) D) E)

centromere. endomere. exon. intron. telomere.

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10. DNA supercoiling Page: 953 Difficulty: 2 Ans: C DNA in a closed-circular, double-stranded molecule with no net bending of the DNA axis on itself is:

A) B) C) D) E)

a left-handed helix. a mixed right- and left-handed helix. relaxed. supercoiled. underwound.

11. DNA supercoiling Pages: 954-956 Difficulty: 2 Ans: D It is correct to say that DNA supercoiling cannot:

A) B) C) D) E)

be induced by strand separation. be induced by underwinding of the double helix. form if there is Z-DNA structure present. occur if a closed circular double-stranded DNA molecule has a nick. result in compaction of the DNA structure.

12. DNA supercoiling Pages: 956-957 Difficulty: 2 Ans: B The linking number (Lk) of a closed-circular, double-stranded DNA molecule is changed by:

A) B) C) D) E)

breaking a strand, then rejoining it. breaking a strand, unwinding or rewinding the DNA, then rejoining it. breaking all hydrogen bonds in the DNA. supercoiling without the breaking of any phosphodiester bonds. underwinding without the breaking of any phosphodiester bonds.

13. DNA supercoiling Pages: 956-957 Difficulty: 2 Ans: B For a closed-circular DNA molecule of 10,000 base pairs in the fully relaxed form, the linking number (Lk) is about: A) B) C) D) E)

10,000. 950. 100. 9.5. 2.

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14. DNA supercoiling Pages: 956-957 Difficulty: 3 Ans: C If the structure of a fully relaxed, closed-circular DNA molecule is changed so that the specific linking difference () is –0.05, the number of:

A) B) C) D) E)

bases is decreased by 5%. bases is increased by 5%. helical turns is decreased by 5%. helical turns is increased by 5%. helical turns is unchanged.

15. DNA supercoiling Pages: 958-959 Difficulty: 2 Topoisomerases can:

A) B) C) D) E)

change the linking number (Lk) of a DNA molecule. change the number of base pairs in a DNA molecule. change the number of nucleotides in a DNA molecule. convert D isomers of nucleotides to L isomers. interconvert DNA and RNA.

16. DNA supercoiling Pages: 958-960 Difficulty: 2 Topoisomerases:

A) B) C) D) E)

Ans: A

Ans: E

always change the linking number in increments of 1. can act on single-stranded DNA circles. change the degree of supercoiling of a DNA molecule but not its linking number of DNA. occur in bacteria, but not in eukaryotes. require energy from ATP.

17. DNA supercoiling Pages: 961-962 Difficulty: 3 Ans: B Plectonemic supercoils in a negatively supercoiled DNA molecule:

A) B) C) D) E)

are always left-handed. are always right-handed. are balanced by solenoidal supercoils can be either right- or left-handed. never occur.

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18. The structure of chromosomes Page: 963 Difficulty: 2 Ans: C Histones are _______ that are usually associated with _________.

A) B) C) D) E)

acidic proteins; DNA acidic proteins; RNA basic proteins; DNA basic proteins; RNA coenzymes derived from histidine; enzymes

19. The structure of chromosomes Pages: 964-965 Difficulty: 1 Ans: D The fundamental repeating unit of organization in a eukaryotic chromosome is:

A) B) C) D) E)

the centrosome. the lysosome. the microsome. the nucleosome. the polysome.

20. The structure of chromosomes Pages: 964-965 Difficulty: 2 Ans: C Which of the following contributes to the structure of nucleosomes?

A) B) C) D) E)

Plectonemic supercoiled DNA Relaxed closed-circular DNA Solenoidal supercoiled DNA Spacer DNA Z (left-handed) DNA

21. The structure of chromosomes Pages: 964-965 Difficulty: 2 Nucleosomes:

A) B) C) D) E)

Ans: D

are important features of chromosome organization in eukaryotes and bacteria. are composed of proteins rich in acidic amino acids, such as Asp and Glu. are composed of protein and RNA. bind DNA and alter its supercoiling. occur in chromatin at irregular intervals along the DNA molecule.

22. The structure of chromosomes Pages: 966-968 Difficulty: 2 Ans: D A condensed eukaryotic chromosome is known to be associated with all of the following proteins, except for: A) B) C) D)

Core histones H2A, H2B, H3, and H4. Histone H1 SMC proteins Topoisomerase I

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E) Topoisomerase II 23. The structure of chromosomes Pages: 968-969 Difficulty: 2 Ans: C The SMC proteins (for structural maintenance of chromosomes) include cohesins and condensins, and are known to have all of the following properties except: A) B) C) D) E)

A complete ATP binding site. A hinge region Topoisomerase activity to produce positive supercoils The ability to condense DNA Two coiled-coil domains

24. The structure of chromosomes Pages: 968-970 Difficulty: 2 Bacterial chromosomes:

A) B) C) D) E)

Ans: A

are highly compacted into structures called nucleoids. are seen in electron microscopy as “beads on a string”. are surrounded by a nuclear membrane. contain large numbers of nucleosomes. when fully extended are as long as the bacterial cell.

Short Answer Questions 25. Chromosomal elements Page: 949 Difficulty: 2 Describe the structure and function of a typical bacterial plasmid. Ans: Bacterial plasmids are generally closed-circular, double-stranded DNA molecules that are much smaller than the bacterial chromosome itself. They replicate autonomously and may encode proteins which, although not normally essential to bacterial survival, may confer resistance to antibiotics. 26. Chromosomal elements Page: 950 Difficulty: 2 The genome of the bacterium E. coli is 4,639,675 bp long and consists of 4,435 genes; the human genome is 3,070,128,600 bp long and consists of roughly 29,000 genes. Calculate the average gene size in each organism and provide an explanation for the difference. Ans: The average E. coli gene is 1,046 bp long; in humans it is 106,000 bp. The difference is due to the presence of significantly more ‘junk DNA’ (introns, transposons, etc.) in human cells; these elements are not found in bacterial genomes.

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27. Chromosomal elements Pages: 949-951 Difficulty: 2 Describe a current hypothesis to explain the presence of functional DNA in mitochondria and chloroplasts. Ans: These organelles are thought to have originated from aerobic bacteria and photosynthetic bacteria, which took up endosymbiotic residence within primitive eukaryotic cells. The DNA molecules of the organelles are putative vestiges of the chromosomes of these bacteria. 28. Chromosomal elements Page: 952 Difficulty: 2 What are introns? Ans: Introns are regions of genes (primarily eukaryotic) that in mRNA are transcribed but are not translated. They do not code for amino acid sequences within the protein that is coded by the gene. Thus they interrupt the colinearity between the nucleotide sequence of the gene and the amino acid sequence of the encoded protein. 29. Chromosomal elements Page: 953 Difficulty: 2 What is satellite DNA? Ans: Satellite DNA (also known as highly repetitive or simple-sequence DNA) consists of regions of the eukaryotic genome that are different enough in base composition from the bulk of the chromosomal DNA that they can be separated from it by density gradient centrifugation. Satellite DNA is often associated with centromeres and telomeres and consists of short sequences (5 to 10 base pairs) that are repeated millions of times per cell.

30. DNA supercoiling Page: 954 Difficulty: 2 Describe two functions of DNA supercoiling. Ans: Supercoiling allows for the extreme compaction required for DNA to fit in a cell. Negative supercoiling also facilitates the unwinding of the strands of the double helical DNA that is required for its transcription and replication. 31. DNA supercoiling Page: 954 Difficulty: 2 Define, in the context of DNA structure, “topological bond.” Ans: Topological bonds are links between two molecules that are not joined by specific chemical bonds, but that cannot be physically separated because they cross over each other like links in a chain. 32. DNA supercoiling Pages: 956-957 Difficulty: 3 Define “specific linking difference” (), also called superhelical density. Ans: The specific linking difference () is a measure of the number of turns removed (Lk) relative to the linking number of the fully relaxed form ( Lk0):  = Lk/Lk0.

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33. DNA supercoiling Pages: 956-958, 964-965 Difficulty: 2 Indicate whether the following statements are true (T) or false (F). ___ The linking number (Lk) of a closed-circular DNA molecule can be changed only by breaking one or both strands. ___ DNA of all organisms is overwound (i.e., positively supercoiled). ___ Topoisomerase I relaxes DNA that is highly negatively supercoiled. ___ In a nucleosome, eukaryotic DNA is wrapped around histone proteins. Ans: T; F; T; T 34. DNA supercoiling Pages: 956-961, 964-965 Difficulty: 3 Calculate values for the following topological properties of a closed-circular DNA molecule containing 2,000 base pairs (for simplicity, assume there are 10 base pairs per turn in the relaxed DNA). (a) The linking number when the DNA is relaxed (b) The linking number when the DNA has been underwound by 10 enzymatic turnovers of DNA gyrase (+ATP) (c) The linking number when the DNA has been underwound by binding five nucleosomes followed by complete relaxation by a eukaryotic topoisomerase (d) The superhelical density of the DNA molecule in (b) (e) The superhelical density of the DNA molecule in (c) Ans: (a) 200; (b) 180; (c) 195 (d) –0.1; (e) –0.025

35. DNA supercoiling Page: 957 Difficulty: 1 Define, in the context of DNA structure, “topoisomers.” Ans: Topoisomers are different forms of a closed-circular DNA molecule that differ only in a topological property such as their linking number ( Lk). 36. DNA supercoiling Pages: 958-961 Difficulty: 2 Define topoisomerase, and explain the difference between type I and type II topoisomerases. Ans: Topoisomerases are enzymes that change the linking number in a closed-circular, doublestranded DNA molecule by breaking one or two strands, adding or removing twists, and rejoining the strand(s). Type 1 topoisomerases break and rejoin only one strand, changing the linking number in increments of 1. Type 2 topoisomerases break and rejoin both strands, changing the linking number in increments of 2.

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37. DNA supercoiling Pages: 958-961 Difficulty: 2 The DNA of virtually every cell is underwound (i.e., negatively supercoiled) relative to B-form DNA. In bacteria, an enzyme called (a) ____________ introduces negative supertwists into DNA using (b) ____________ as a source of energy. This enzyme is classified as a type (c) ____________, which affects the linking number in steps of (d) ___________. The usual substrate for this enzyme within an E. coli cell is the bacterial chromosome. This circular DNA molecule of 4,700,000 base pairs has a linking number of approximately (e) ____________ when it is closed and relaxed. This enzyme would (f) ____________ (decrease/increase/not change) this linking number when acting upon this DNA molecule in the presence of the above energy source. Ans: (a) E. coli topoisomerase II or DNA gyrase; (b) ATP; (c) type II topoisomerase; (d) two; (e) 450,000; (f) decrease 38. DNA supercoiling Pages: 960-961 Difficulty: 2 Explain how inhibitors of topoisomerase would inhibit the growth of tumors; would these drugs be expected to inhibit the growth of normal cells as well?. Ans: Dividing cells must replicate their DNA; replication requires the action of topoisomerases to resolve the resulting DNA tangles. Thus, inhibiting topoisomerases would be expected to inhibit cell division. Since cancer is inappropriate cell division, these drugs would inhibit the growth of cancer. They would also be expected to inhibit the growth of normal cells. 39. DNA supercoiling Pages: 961-962 Difficulty: 2 Explain the difference between plectonemic and solenoidal supercoiling of DNA; use diagrams to help in your explanation. Ans: In plectonemic supercoiling, the double helix is intertwined such that it crosses over itself. In solenoidal supercoiling, the double helix forms a spiral resembling the helix formed by each of the strands. (See Fig. 24-24a, p. 962.) 40. The structure of chromosomes Page: 939 Difficulty: 2 Briefly describe the changes in eukaryotic chromosome structure during the cell cycle. Ans: Starting with prophase, the DNA undergoes condensation (employing cohesins and condensins). During the subsequent metaphase, the condensed chromosomes line up along a plane halfway between the spindle poles (to which they are connected by microtubules). As the cell moves into anaphase, the sister chromatids separate, each drawn towards its respective spindle pole. After cell division is complete, the chromosomes decondense, and remain so during interphase. (See Fig. 24-25, p. 963).

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41. The structure of chromosomes Pages: 963-964 Difficulty: 2 What are histones and what is their principal role in chromatin structure? Ans: Histones are small basic proteins that bind to DNA. There are five main types, four of which interact with each other to form the core of the nucleosome around which the DNA is wrapped. The fifth (H1) is believed to be involved in compaction of nucleosomes to form a higher-order structure. 42. The structure of chromosomes Pages: 964-965 Difficulty: 2 Describe the composition and structure of a nucleosome. Ans: A nucleosome consists of 146 base pairs of double-stranded DNA wrapped in a solenoidal supercoil around a core of histones (small, basic proteins). This core contains two copies each of histones H2A, H2B, H3, and H4. 43. The structure of chromosomes Pages: 966-968 Difficulty: 2 The overall compaction of a eukaryotic chromosome is greater than ____________ -fold. The first level is nucleosome formation, which compacts about _________ -fold. Next is the 30 nm fiber, which compacts about ________ -fold overall. Higher order folding involves association of the DNA with a nuclear ______________________ , which contains large amounts of ________________ and ___________________ . Ans: 10,000; 7; 100; scaffold; histone H1; topoisomerase II (last two in either order). 44. The structure of chromosomes Pages: 968-969 Difficulty: 2 SMC proteins facilitate the structural maintenance of chromosomes; describe the roles of the two main classes. Ans: The cohesins help link sister chromatids together after replication and keep them together as they condense, which is essential for proper segregation. The condensins are essential for DNA condensation as the cell enters mitosis, and their binding is thought to create positive supercoiling. (See Fig. 24-34, p. 969)....