Molecular Biology Principles and Practice 2nd Edition Cox Doudna O’Donnell Test Bank

Molecular Biology Principles and Practice 2nd

Edition Cox Doudna O’Donnell Test Bank

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Chapter 10 – Test Bank

Section 10.1

1. Chromatin is composed of:

A. DNA
B. Protein
C. DNA and RNA
D. DNA and protein
E. RNA and protein

Ans: D

2. Of the proteins associated with chromatin, which of the following represents the largest component?

A. Histones
B. Topoisomerases
C. SMC proteins
D. Transcriptional regulators
E. Ribosomal proteins

Ans: A

3. The first evidence for nucleosome formation came from digesting chromosomal DNA with a non-specific
nuclease. Gel electrophoresis of the DNA after the reaction revealed:

A. A ladder of protected fragments about 1000 bp apart.

B. A ladder of protected fragments about 200 bp apart.
C. A large band corresponding to 200 bp.
D. Random distribution of bands corresponding to different sizes.
E. Four bands, each composed of a different histone.

Ans: B

4. Each nucleosome contains:

A. Four proteins: H2A, H2B, H3, and H4.

B. A histone octamer composed of two copies of each of the following proteins: H1, H2, H3, and H4.
C. A histone octamer composed of two copies of each of the following proteins: H2A, H2B, H3, and H4.
D. Four proteins: SMC1, SMC2, SMC3, and SMC4.
E. A mixture of histone and SMC proteins.

Ans: C

5. Which of the following is true of nucleosome structure?

A. Nucleosomes are composed of about 1000 bp of DNA wrapped around a histone core.
B. Nucleosomes are composed of about 200 bp of DNA wrapped around a histone core.
C. The DNA wraps around the core nearly 2X forming a right-handed solenoidal supercoil.
D. The DNA wraps around the core nearly 3X forming a left-handed solenoidal supercoil.
 E. Answers B and C are correct.

Ans: B

6. Histones:

A. Have highly conserved sequences among eukaryotes.

B. Are rich in basic amino acids. About 25% of the total amino acids are lysine and arginine.
C. Are small proteins, ranging in molecular weight from 11,000–21,000.
D. Contain a histone-fold motif comprised of three α-helices linked by two short loops.
E. All of the above.

Ans. E

7. The contacts between the DNA and the histones of the nucleosome are:

A. Mainly between the R groups of the histones and the phosphate backbone of the DNA.
B. Mainly between the conserved histone-folds and the bases that are exposed in the major groove of the
DNA.
C. More prevalent in regions of the DNA that have tracts of GC pairs. These regions tend to bend more readily.
D. Primarily between the DNA and the histone peptide backbone.
E. None of the above.

Ans: D

8. Which of the following is NOT true of histone tails?

A. They protrude between the two DNA strands that supercoil around the nucleosome.
B. They are the target of numerous chemical modifications.
C. They experience changes in net charge, shape, and other properties of histones in response to
modifications.
D. They are recognized by certain enzymes.
E. They have enzymatic properties that can covalently modify DNA.

Ans: E

9. Which of the following is NOT a way nucleosome formation affects DNA?

A. The DNA is compacted.

B. The access to DNA by enzymes is altered.
C. Binding of H1 destabilizes the nucleosome, alleviating the transcriptional repression exerted by the binding
of nucleosome histones.
D. Transcription is inhibited by the tight, internucleosome connections mediated by histone tails.
E. Binding of the transcription factor Sp-1 can alleviate the transcriptional repression exerted by the histone
binding.

Ans: C

Short Answer

10. Why are eukaryotic DNA underwound even though they lack topoisomerases that can introduce supercoils?
 Ans: Formation of a left-handed, solenoidal supercoil requires the removal of about one turn from the DNA.
This effect combined with the removal of unbound positive supercoils by topoisomerases leads to a net
underwound state.

Section 10.2

11. How is H1 binding of DNA different than that of the other four histones?

A. H1 binds to the major groove of the DNA only.

B. H1 binds to the DNA as it comes off both sides of the nucleosome.
C. H1 binds to DNA as part of the octamer but lacks the histone tail of the other histones.
D. H1 binds to one strand of the linker DNA as it comes off the nucleosome and binds a second site in the
central region of the DNA supercoil.
E. H1 binds to the DNA as a homotetramer.

Ans: D

12. What is the difference between a nucleosome and a chromatosome?

A. The chromatosome contains one molecule of histone H1 in addition to the core histones.
B. A longer segment of DNA is associated with the nucleosome than in a chromatosome.
C. The chromatosome contains only one copy of each of the core histones.
D. The DNA wraps more than two times around the chromatosome.
E. The chromatosome contains no linker histones.

Ans: A

13. Which of the following is NOT a function of histone H1?

A. Stabilizing nucleosomes
B. Promoting higher order chromosome structure
C. Enhancing the repression of transcription by nucleosomes
D. Binding to regions undergoing active RNA synthesis
E. All of the above are functions of histone H1

Ans: D

14. In different regions of the chromosome, the ratio of histone H1 to histone H2A may vary, but the ratio of H2A
to histone H2B is generally the same. If the amount of H1 increases in a region of chromatin, what will be its
affect on compaction of the DNA and transcription in that region?

A. Transcription in that region will increase.

B. Transcription in that region will decrease.
C. The DNA in that region will become less compact.
D. DNA compaction in that region will be unchanged.
E. Transcription of the DNA in that region will remain the same.

Ans: B

15. The beads-on-a-string form of DNA condenses into a compact fiber called the 30-nm filament. Which of the
following is true about its formation?

A. Histone H1 is essential for formation of the 30-nm filament.

 B. The histone tails of the octamer histones are absolutely required for filament formation.
C. The zig-zag model describes how the nuclesome array adopts a spiral shape when forming the filament.
D. The 30-nm filament is also called a chromatosome.
E. The linker histone is essential for formation of the 30-nm filament.

Ans: B

16. Higher chromosome structure depends on:

A. SMC proteins, one of the major components of the chromosome scaffold.

B. The formation of a chromosome scaffold by topoisomerases.
C. The presence of the H1 protein, which promotes formation of the nucleoid.
D. The formation of rosettes, which are stabilized by histone proteins.
E. The formation of tetranucleosomes.

Ans: A

17. Which of the following is a difference between the solenoidal and zig-zag models for the formation of the 30-
nm filament?

A. Most of the evidence to date supports the solenoidal model.

B. Only the zig-zag model positions the linker DNA at the center of the filament.
C. Both models position H1 at the center of the filament.
D. Only the solenoidal model has a pitch of 11 nm, the width of a nucleosome.
E. The zig-zag model occurs in higher eukaryotes such as humans, the solenoidal model occurs in lower
eukaryotes such as yeast.

Ans: C

18. Which of the following may be a reason for bacteria NOT having nucleosome-like structures?

A. They need to respond quickly to the environment and therefore need ready access to the genome.
B. Cell division in bacteria occurs in as little as 15 minutes. Eukaryotes may not divide for hours or even
months.
C. A much larger proportion of the bacterial chromosome codes for proteins.
D. Higher rates of metabolism in bacteria mean that a much larger proportion of the DNA is being transcribed
or replicated at a given time.
E. All of the above are possible reasons.

Ans: E

19. The higher order structure of chromatin contains topologically constrained loops. What would happen if a
single loop was cleaved?

A. The entire chromosome would unravel.

B. The genes of that loop could not be transcribed.
C. Only that loop would relax because each loop is separately constrained by proteins.
D. The genes in the cleaved loop could not be replicated.
E. Supercoiling in the cleaved loop would not be affected.

Ans: C

Short Answer
20. Why is histone H1 referred to as the linker histone?

Ans: When chromatin is treated with nucleases, initially a larger portion of the DNA is protected, but when
more extensive digestion is carried out and H1 is released the DNA fragment protected is smaller. This
shows that H1 binds to linker DNA unlike the histones of the nucleosome

Section 10.3

21. Transcriptionally active genes are characterized by:

A. An increase in H1.
B. The presence of bound nucleosomes at the promoter regions.
C. The presence of specialized chromosome remodeling complexes.
D. The absence of histone variants such as H2AZ and H3.3.
E. All of the above.

Ans: C

22. In SDS-polyacrylamide gel electrophoresis proteins are partially denatured and separated entirely as a function
of their mass. Histones are an exception; they migrate more slowly than they should, as though they are much
larger than they actually are. Why does this occur?

A. Histones form dimers and tetramers making them appear larger.

B. Histones are heavily glycosylated greatly adding to their mass.
C. Histones have a large number of positively charged amino acid residues. The binding of SDS to the histones
is not sufficient to mask these charges resulting in slower migration.
D. Histones have an affinity for polyacrylamide.
E. Histones are somewhat insoluble, which slows their passage through the gel.

Ans: C

23. Which of the following is NOT a way chromatin remodeling complexes affect nucleosomes?

A. They can slide a nucleosome to a different location.

B. They can modify the N-terminal tails of histones.
C. They can eject a nucleosome from the DNA.
D. They can replace the nucleosome with a new nucleosome that contains a variant histone.
E. All of the above.

Ans: B

24. Which of the following is NOT typically a modification of histones?

A. Adenylation
B. Phosphorylation
C. Methylation
D. Acetylation
E. Both A and B

Ans: A
25. A histone modification that attracts other proteins such as a transcription factor is said to be acting:

A. In cis.
B. In trans.
C. Epigenetically
D. As a remodeling protein.
E. As a chaperone.

Ans: B

26. Which of the following is NOT true about histone modification and the enzymes that create them?

A. The enzymes responsible are often part of multiprotein complexes that include transcription factors.
B. The enzymes responsible can work with chromatin remodeling complexes to alter specific regions of
chromatin in response to environmental signals.
C. The modifications can be passed on by epigenetic inheritance.
D. The enzymes responsible can create histone variants.
E. All of the above are true.

Ans: D

27. So far three classes of chromatin remodeling complexes have been identified. Which of the following pairings
is correct?

A. SWI/SNF complexes → activation

B. SMC complexes → repression
C. ISWI complexes → activation
D. Mi2/NURD → activation
E. SWI/SNF complexes → repression

Ans: A

28. How can repositioning nucleosomes affect transcription?

A. Moving nucleosomes could expose a promoter resulting in repression of transcription.

B. Moving nucleosomes could cover a promoter resulting in repression of transcription.
C. Moving nucleosomes could expose a promoter resulting in activation of transcription.
D. Answers A and B
E. Answers B and C

Ans: E

29. Which of the following methods can be used to determine the position of nucleosomes in the genome?

A. RNA-Seq
B. Western blotting
C. ChIP-Seq
D. Epigenetic immunoprecipitation
E. Immunofluorescence

Ans: C
30. Which of the following is the third step of a ChIP-Seq protocol?

A. Digest chromatin with nuclease.

B. Unbound DNA is washed away, cross-links are reversed, and free histones are removed.
C. Identify DNA by sequencing.
D. Immunoprecipitation of nucleosome-DNA complexes with histone antibody.
E. Cross-linking of nucleosome histones to DNA in chromatin.

Ans: D

31. Histone variants:

A. Have been identified for H2B and H4 but not for H2A and H3.
B. Differ in their C-terminal sequences but not in their N-terminal sequences.
C. That have been identified are associated with transcriptional activation only.
D. Have variant patterns of modifications as a result of the structural differences in their terminal sequences.
E. Have been found to affect all cellular processes that involve DNA except DNA repair.

Ans: D

32. Histone chaperones:

A. Are required to assist the assembly of higher order chromatin structure.

B. Are acidic proteins that bind individual histones and assemble them into dimer and tetramer forms.
C. Can also modify the histones covalently by phosphorylation.
D. Are acidic proteins that bind to H2A-H2B dimers and H3-H4 tetramers before assembly into nucleosomes.
E. Can also modify the histones covalently by acetylation.

Ans: D

33. Which of the following are correct pairings of histone variants and their functions?

A. H3.3 → stabilizes the open state (transcriptionally active).

B. CENPA → maintains kinetochore attachment
C. H2AX → DNA repair
D. macroH2A → X chromosome inactivation
E. All of the above

Ans: E

34. Proteins that bind to acetylated lysine residues in the histone tail contain:

A. Bromodomains
B. DNA-binding domains
C. Chromodomains
D. Kinase domains
E. Histone-fold motifs

Ans: A

35. Which of the following is NOT affected by the presence of epigenetic marks?

A. Development
Molecular Biology Principles and Practice 2nd Edition Cox Doudna O’Donnell Test Bank

B. Imprinting
C. X-chromosome inactivation
D. Maturation of RNA
E. Unique expression patterns in different cells

Ans: D

36. Activation of the IFN-β globin promoter is an example of a histone code. Of the steps given, which is the third
in this process?

A. Exposure of the TATA box in promoter.

B. Complexes containing Gcn5 bind to the promoter and acetylate nearby nucleosomes.
C. A chromatin remodeling complex such as SW1/SNF binds to and moves the nucleosome.
D. Initiation of transcription occurs.
E. A protein kinase binds to the Gcn5 complex and phosphorylates nearby nucleosomes.

Ans. C

37. How are the epigenetic marks of a particular chromatin state preserved during cell division?

A. Parental, marked H2A-H2B dimers stay associated with strands after replication and recruit new H3-H4
tetramers.
B. H2A-H2B dimers and H3-H4 tetramers come off during replication and assemble with unmarked histones.
These new octamers then rebind to the newly replicated DNA to form nucleosomes.
C. Parental, marked H3-H4 tetramers stay associated with strands after replication and recruit new H2A-H2B
dimers.
D. Histone chaperones make sure that at least one component of each new nucleosome is marked.
E. None of the above.

Short Answer

38. How can the disruption of epigenetic markers result in cancer?

Ans: The disruption of epigenetic pathways can activate genes that promote cell growth or repress genes that
limit cell growth, leading to tumor formation.

How We Know

39. What observation first suggested that H2A and H2B formed heterodimers?

Ans: A milder protein purification technique that did not denature the histones resulted in two peaks upon
purification, one containing H2A and H2B and one containing H3 and H4. This observation suggested that
they were physically associated in some way and lead Kornberg to carry out his cross-linking experiments.

40. When the gene that encodes the histones acetylase (HAT) was isolated, it was shown to have homology to the
yeast protein, Gcn5. Why was this an exciting find?

Ans: Gcn5 is a transcriptional activator that implies that the acetylase activity may account for the activator’s
regulatory function. Ultimately Gcn5 was shown to have histone acetylase (HAT) activity.

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