Test Bank For Molecular Biology Of The Cell 6th Edition by Bruce Alberts, Exams of Nursing

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The Cell 6

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Edition by Bruce Alberts

MOLECULAR BIOLOGY OF THE CELL, SIXTH

EDITION CHAPTER 4: DNA, CHROMOSOMES, AND

GENOMES

1. In a double-stranded DNA molecule, one of the chains has the sequence CCCATTCTA when read from the 5′ to the 3′ end. Indicate true (T) and false (F) statements below regarding this chain. Your answer would be a four-letter string composed of letters T and F only, e.g. TTFT. ( ) The other chain is heavier, i.e. it has a greater mass. ( ) There are no C residues in the other chain. ( ) The 5′-terminal residue of the other chain is G. ( ) The other chain is pyrimidine-rich.
2. Indicate which numbered feature (1 to 5) in the schematic drawing below of the DNA double helix corresponds to each of the following. Your answer would be a five-digit number composed of digits 1 to 5 only, e.g. 52431.

The Cell 6

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Edition by Bruce Alberts

1

(^3 ) 4 5

( ) Hydrogen-bonding ( ) Covalent linkage ( ) Phosphate group ( ) Nitrogen-containing base ( ) Deoxyribose sugar

3. Complete the DNA sequence below such that the final sequence is identical to that of the complementary strand. Your answer would be a seven-letter string composed of letters A, C, T, and G only, e.g. TTCTCAG.

5′- C T T T A G A - 3′

4. A DNA nucleotide pair has an average mass of approximately 660 daltons. Knowing the number of nucleotides in the human genome, how many picograms of DNA are there in a diploid human nucleus? Avogadro’s number is 6 × 10^23. Write down the picogram amount without decimals (round the number to the closest integer), e.g. 23 pg.
5. Which of the following features of DNA underlies its simple replication procedure? A. The fact that it is composed of only four different types of bases B. The antiparallel arrangement of the double helix C. The complementary relationship in the double helix D. The fact that there is a major groove and a minor groove in the double helix
6. Which of the following correlates the best with biological complexity in eukaryotes?

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( ) Each eukaryotic chromosome has many such sequences. ( ) There are normally two such sequences in each eukaryotic chromosomal DNA molecule. ( ) There is normally one such sequence per eukaryotic chromosomal DNA molecule. ( ) It is where DNA duplication starts in S phase. ( ) It attaches the chromosome to the mitotic spindle via the kinetochore structure.

11. The eukaryotic chromosomes are organized inside the nucleus with a huge compaction ratio of several-thousand-fold. What is responsible for such a tight packaging? A. The various chromatin proteins that wrap and fold the DNA B. The nuclear envelope which encapsulates the chromosomes C. The nuclear matrix that provides a firm scaffold D. All of the above
12. The two chromosomes in each of the 22 homologous pairs in our cells ... A. have the exact same DNA sequence. B. are derived from one of our parents. C. show identical banding patterns after Giemsa staining. D. usually bear different sets of genes. E. All of the above.
13. Compared to the human genome, the genome of yeast typically has … A. more repetitive DNA. B. longer genes. C. more introns. D. longer chromosomes. E. a higher fraction of coding DNA.
14. Indicate true (T) and false (F) statements below regarding histones. Your answer would be a six-letter string composed of letters T and F only, e.g. TTFFFF. ( ) The histones are highly acidic proteins. ( ) The histone fold consists of three α helices. ( ) The core histones are much more conserved than the H1 histone. ( ) The N-terminal tails of the core histones undergo a variety of reversible post- translational modifications. ( ) Every nucleosome core is made up of three polypeptide chains.

The Cell 6

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Edition by Bruce Alberts

4 3 1

( ) The H1 histone is absent in the 30-nm fibers.

15. Indicate which feature (1 to 4) in the schematic drawing below of a chromatin fiber corresponds to each of the following. Your answer would be a four-digit number composed of digits 1 to 4 only, e.g. 2431. 2

( ) Nucleosome core particle ( ) Linker DNA ( ) Histone octamer ( ) Non-histone protein

16. In assembling a nucleosome, normally the …(1) histone dimers first combine to form a tetramer, which then further combines with two … (2) histone dimers to form the octamer. A. 1: H1–H3; 2: H2A–H2B B. 1: H3–H4; 2: H2A–H2B C. 1: H2A–H2B; 2: H1–H D. 1: H2A–H2B; 2: H3–H E. 1: H1–H2; 2: H3–H
17. The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. They … A. can slide nucleosomes on DNA. B. have ATPase activity. C. interact with histone chaperones. D. can remove or exchange core histone subunits. E. All of the above.

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C. Binding of proteins to DNA or the histones D. ATP-dependent function of chromatin remodeling complexes E. All of the above

22. Indicate whether each of the following histone modifications is generally associated with active genes (A) or silenced genes (S). Your answer would be a four-letter string composed of letters A and S only, e.g. SSAS. ( ) H3 lysine 9 acetylation ( ) H3 serine 10 phosphorylation ( ) H3 lysine 4 trimethylation ( ) H3 lysine 9 trimethylation
23. Indicate whether each of the following histone modifications adds a negative charge to the histone (A), removes a positive charge from the histone (B), or does neither of these (C). Your answer would be a four-letter string composed of letters A, B, and C only, e.g. CABA. ( ) H3 lysine 9 acetylation ( ) H3 serine 10 phosphorylation ( ) H3 lysine 4 trimethylation ( ) H3 lysine 9 trimethylation
24. To study the chromatin remodeling complex SWR1, a researcher has prepared arrays of nucleosomes on long DNA strands that have been immobilized on magnetic beads. These nucleosomes are then incubated with an excess of the H2AZ–H2B dimer (which contains the histone variant H2AZ) in the presence or absence of SWR1 with or without ATP. She then separates the bead-bound nucleosomes (bound fraction) from the rest of the mix (unbound fraction) using a magnet, elutes the bound fraction from the beads, and performs SDS-PAGE on the samples. This is followed by a Western blot using an antibody specific to the H2AZ protein used in this experiment. The results are shown below, with the presence (+) or absence (–) of ATP, SWR1, or the H2AZ–H2B dimer in each incubation reaction indicated at the top of the corresponding lane. Bound H2AZ Unbound H2AZ ATP - - - - + + + + (^) - - - - + + + + SWR H2AZ–H2B

H2AZ

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Which of the following statements is confirmed by the Western blot shown? A. SWR1 deposits H2AZ histones into the nucleosome arrays. B. SWR1 function is not ATP-dependent. C. The antibody used in this experiment binds to the SWR1 complex. D. All of the above.

25. Indicate whether each of the following descriptions better matches the major histones (M) or the histone variants (V). Your answer would be a six-letter string composed of letters M and V only, e.g. VVMVMV. ( ) They are more highly conserved over long evolutionary time scales. ( ) They are present in much smaller amounts in the cell. ( ) They are synthesized primarily during the S phase of the cell cycle. ( ) Their incorporation often requires histone exchange. ( ) They are often inserted into already-formed chromatin. ( ) They are assembled into nucleosomes just behind the replication fork.
26. A chromatin “reader complex” … A. is always coupled to a “writer complex” and spreads specific chromatin modifications. B. can recognize any histone code. C. binds tightly to the chromatin only when a specific set of histone marks is present. D. can only bind to a single specific histone mark. E. has at least five protein subunits.
27. The centromeric regions in the fission yeast Schizosaccharomyces pombe are wrapped by nucleosomes containing the CENP-A histone H3 variant, and are flanked by clusters of tRNA genes that separate them from the surrounding pericentric heterochromatin. If the tRNA clusters are removed from this region, the HP1-bound heterochromatin spreads further to cover the centromeric regions. The tRNA genes are transcribed by strong RNA polymerase III promoters, which can associate with transcription factors and recruit chromatin-modifying enzymes. Based on these observations, indicate which blanks (A to E) in the paragraph below correspond to each of the following phrases. Your answer would be a five-letter string composed of letters A to E only, e.g. BCDEA.

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A. The gene gets silenced due to heterochromatin expansion, leading to the misregulation of gene expression for a number of critical genes. B. The translocation event also brings along a chromatin barrier that can prevent heterochromatin expansion into the gene, and there is no phenotypic anomaly. C. Since the gene encodes a histone acetyl transferase, it resists heterochromatin expansion by acetylating its own histones. D. The level of the gene product decreases due to a position effect, leading to an imbalance in the chromatin state of the cell that results in the activation of programmed cell death.

31. Lampbrush chromosomes … A. are transcriptionally inactive. B. are readily observed in the oocytes of humans and insects. C. have thousands of duplicated DNA molecules arranged side by side. D. are mitotic chromosomes with two sister chromatids attached together only at the centromere. E. are thought to have a structure that is relevant to mammalian chromosomes in interphase.
32. Findings from a number of experiments on human chromatin have suggested that the DNA in our chromosomes is organized into loops of various lengths. Approximately how long is a typical loop (in nucleotide pairs of DNA)? A. 50 B. 2000 C. 100, D. 10 million E. 50 million
33. You have performed a chromosome conformation capture (3C) experiment to study chromatin looping at a mouse gene cluster that contains genes A, B, and C, as well as a regulatory region R. In this experiment, you performed in situ chemical cross-linking of chromatin, followed by cleavage of DNA in the nuclear extract with a restriction enzyme, intramolecular ligation, and cross-link removal. Finally, a polymerase chain reaction (PCR) was carried out using a forward primer that hybridizes to a region in the active B gene, and one of several reverse primers, each of which hybridizes to a different location in the locus. The amounts of the PCR products were quantified and normalized to represent the relative cross-

The Cell 6

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linking efficiency in each analyzed sample. You have plotted the results in the graph below. The same experiment has been done on two tissue samples: fetal liver (represented by red lines ) and fetal muscle ( blue lines ). Interaction of the A, B, and C genes with the regulatory R region is known to enhance expression of these genes. Indicate true (T) and false (F) statements below based on the results. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF.

Gene cluster

R A B^ C^ other genes

4 3 2

1

• 10 0 +10 + Position (kb) ( ) The B gene would be predicted to have higher expression in the fetal liver compared to the fetal muscle tissue. ( ) Interaction between the R region and the B gene involves the A gene looping out. ( ) Interaction between the R region and the B gene involves the C gene looping out. ( ) In fetal muscle, the B gene definitely does not engage in looping interactions with any other elements in the cluster.

34. Polytene chromosomes are useful for studying chromatin because they … A. are smaller than regular chromosomes and easier to manipulate. B. lack heterochromatin. C. have distinct visible banding patterns. D. can make polyploid cells. E. All of the above.

Liver Muscle

Relative

cross

• linking

efficiency

(arbitrary

unit)

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nucleus. In each chromosome, the chromatin is thought to be composed of ‘open’ and ‘closed’ chromatin compartments. At the meganucleotide scale, each compartment is organized into knot- free arrangements called … that allow tight packing and simultaneously avoid entanglement.”

39. What are the consequences for the cell of the “fractal globule” arrangement of chromosome segments? A. The chromosomes cannot be condensed maximally this way. B. The neighboring regions of DNA are furthest from each other in the three- dimensional space. C. The ability of the chromatin fiber to fold and unfold efficiently is maintained. D. Dense packing is permitted, but the ability to easily fold and unfold the chromatin is prohibited. E. None of the above.
40. Which of the following is NOT true about the nuclear subcompartments? A. Nucleoli, Cajal bodies, and speckles are examples of such subcompartments. B. Each specialized subcompartment has a distinct biochemical environment and a selected set of proteins and/or RNA molecules. C. The subcompartments are constitutively present in a cell except during nuclear divisions. D. They are likely to be organized by a tethered network of macromolecules in gel-like structures.
41. What features do Cajal bodies, interchromatin granule clusters, and nucleoli have in common? A. High permeability to the surrounding nucleoplasm B. A network of macromolecules bound together by covalent linkages C. A lipid bilayer membrane D. The same set of RNA and protein molecules E. The same size
42. As each cell in our body prepares for mitosis, its chromosomes start to look different. What are the changes in chromosome appearance that accompany the entry into M phase?

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Indicate true (T) and false (F) descriptions below. Your answer would be a five-letter string composed of letters T and F only, e.g. TTFFT. ( ) The chromosomes become readily visible by the naked eye. ( ) The chromosomes coil up further to become about 10 times shorter. ( ) Each chromosome is condensed and then replicated to form two sister chromatids. ( ) The typical diameter of a mitotic chromosome arm is about 70 nm. ( ) The two sister chromatids are disentangled from each other by the time chromosome condensation is complete.

43. The genetic information carried by a cell is passed on, generation after generation, with astonishing fidelity. However, genomes are still altered over evolutionary time scales, and even their overall size can change significantly. Which of the following genome-altering events has increased the size of the mammalian genome the most? A. Transposition B. Point mutation C. Chromosomal deletion D. Chromosomal inversion E. Chromosomal translocation
44. Fill in the blanks in the following paragraph regarding genome evolution. In your answer, separate the two missing phrases with a comma, e.g. protein, plasma membrane. Do not use abbreviations. “Conservation of genomic sequences between humans and chickens is mainly due to … selection, whereas the conservation observed between humans and chimpanzees is mostly due to the short time available for mutations to accumulate. Even the DNA sequences at the … position of synonymous codons are nearly identical between humans and chimpanzees.”

Reference: Phylogenetic Tree Questions 45 and 46 Phylogenetic trees based on nucleotide or amino acid sequences can be constructed using various algorithms. One simple algorithm is based on a matrix of pairwise genetic distances (divergences) calculated after multiple alignment of the sequences. Imagine you have aligned a particular gene from different hominids (humans and the great apes), and have estimated the normalized number of nucleotide substitutions that have occurred in this gene in each pair of

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d f e c b

continuous line. Choosing a sufficiently large window size allows a “clean” dot plot with solid lines that show only the long stretches of identity, allowing ancient large-scale rearrangements to be identified. Several chromosomal events can be detected in such dot plots. Indicate which feature (a to g) in the dot plot is best explained by each of the following events. Your answer would be a seven-letter string composed of letters a to g only, e.g. cdbagef. Each letter should be used only once.

g 50

0 a 50 100 Position on the chromosome of species A (million nucleotide pairs)

( ) A duplication that exists in both species ( ) A duplication in species A only ( ) A triplication in species B only ( ) An inversion without relocation ( ) An inversion combined with relocation ( ) A deletion in species A ( ) A translocation in species A from a different chromosome

48. In each of the following comparisons, indicate whether the molecular clock is expected to tick faster on average in the first (1) or the second (2) case. Your answer would be a four-digit number composed of digits 1 and 2 only, e.g. 2222. ( ) 1: The exons, or 2: the introns of a gene ( ) 1: The mitochondrial, or 2: the nuclear DNA of vertebrates ( ) 1: The first, or 2: the third position in synonymous codons ( ) 1: A gene, or 2: its pseudogene counterpart

Position

on

the

chromosome

of

species

B^ (million

nucleotide

pairs)

The Cell 6

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49. Most fish genomes are at least 1 billion nucleotide pairs long. However, the genome of the puffer fish Fugu rubripes is quite small at only about 0.4 billion nucleotide pairs, even though the number of Fugu genes is estimated to be comparable to that of its relatives which have larger genomes. What do you think mainly accounts for the Fugu genome being this small? A. Evolutionary advantage of extremely small exon sizes in the Fugu lineage B. Unusual disappearance of all intronic sequences from the Fugu genome C. Increased abundance of transposable elements in the Fugu genome D. Increased occurrence of mitotic whole-chromosome loss in the Fugu lineage E. Low relative rate of DNA addition compared to DNA loss in the Fugu lineage
50. The copy number of some human genes, such as the salivary amylase gene AMY1 , varies greatly between different individuals. The salivary amylase breaks down some of the dietary starch into smaller sugars. In the case of AMY1 , a positive correlation has been observed between the copy number and the amount of amylase in the saliva. Gene copy number per diploid genome can be estimated by performing a quantitative polymerase chain reaction (PCR) using primers specific to the gene of interest. You have performed such PCR experiments on samples from two human populations that have traditional diets with low and high starch levels, respectively, and have plotted the data in the histogram below. Which population (A or B) in the histogram is likely to be the one with traditionally higher dietary starch? Write down A or B as your answer.

AMY1 gene copy number

A

B

Percentage of each population

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species, you therefore define the “normalized substitution rate” parameters h and k as h = ( a /5.5)/[ c /([2 × 90] – 5.5)], and k = ( b /5.5)/[ c /([2 × 90] – 5.5)]. Based on these definitions, which genes are more likely to be responsible for “uniquely human” traits?

Human

Chimpanzee Mouse

A. Genes with very high h and k values B. Genes with very low h and k values C. Genes with very high h values but not very high k values D. Genes with very high k values but not very high h values

54. Which of the following would most reliably suggest that a genomic sequence is functionally important? A. The presence of a long open reading frame in the sequence B. Multispecies conservation of the sequence C. Low copy number variation of the sequence D. The presence of active chromatin marks over the sequence
55. Imagine a human protein containing 33 repeats of a simple domain arranged in tandem. In contrast, a homolog found in bacteria contains only one domain. What is the minimum number of duplication events that can account for the evolution of this protein since our divergence from bacteria? Write down the number as your answer, e.g. 200.
56. Indicate true (T) and false (F) statements below regarding human genetic variations. Your answer would be a four-letter string composed of letters T and F only, e.g. TFTF. ( ) The genomes of two randomly chosen humans are expected to be identical with respect to at least 99.99% of the nucleotides. ( ) Copy number variations can contain genes. ( ) If the frequency of a point mutation in a population is only 0.1%, with no mutation at this site in the rest of the population, then the variation is NOT considered to constitute a single-nucleotide polymorphism.

a

c (^) b

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( ) Most of the common genetic variants in the current human population could have been present in a human ancestral population of only about 10,000 individuals.

57. Assume two isolated human communities with 500 individuals in each. If the same neutral mutation happens at the same time in two individuals, one from each community, what is the probability that it will be eventually fixed in both of the populations? How would the result change if the two communities fully interbreed? Write down the numbers in scientific notation and separate the two answers with a comma, e.g. 10–^5 , 3 × 10–^2.