Chapter 10—Reconstructing the Genome Through Genetic and Molecular Analysis
Fill in the Blank
1. RFLP analysis requires a ___________ complementary to an RFLP of interest.
Ans: probe
Difficulty: 2
2. FISH is the acronym for ________________________.
Ans: Fluorescent in situ hybridization
Difficulty: 2
3. Karyotype analysis has a resolution of about _____ kb.
Ans: 5,000
Difficulty: 3
4. A ________________ is the entire collection of chromosomes in an organism.
Ans: genome
Difficulty: 1
5. The __________________ refers to all mRNAs expressed in a single cell or cell type.
Ans: transcriptome
Difficulty: 3
6. _________________ genes arise by duplication and often constitute a gene family.
Ans: paralogous
Difficulty: 3
7. A _______________ map is a constellation of overlapping DNA fragments that are
ordered and oriented and span each of the chromosomes in a given genome.
Ans: physical
Difficulty: 2
8. The method of using the ends of unconnected contigs as probes to retrieve clones that
extend into an unmapped region is known as ________________________.
Ans: chromosome walking
Difficulty: 3
9. SINES and LINES are ________________-derived repeats.
Ans: transposon
Difficulty: 4
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10. Processed __________________ are inactive copies of protein-coding genes and small
structural RNAs that lack introns and regulatory sequences.
Ans: pseudogenes
Difficulty: 4
11. Chromosomal regions of a megabase or more of DNA without an identifiable gene is
known as a _____________________.
Ans: gene desert
Difficulty: 1
12. ________________ gene transfer is the direct transfer of genes from one species in the
germ line of another species.
Ans: lateral
Difficulty: 2
13. Of the two sexes in humans,_________ appear to have a higher mutation rate than
_____________.
Ans: males, females
Difficulty: 2
14. ___________ is a recent technique used for quantification of the transcriptome
including very rare transcripts.
Ans: MPSS – massively parallel signature sequence
Difficulty: 3
15. A technique that uses ICATs and is called _______________ permits researchers to
analyze the changing patterns of protein expression in two different cellular states.
Ans: isotope analysis
Difficulty: 3
Multiple Choice
16.
A)
B)
C)
D)
E)
An organism's genome is:
the sequence of its genes for brain cells.
the sequence of its genes for the heart.
the DNA content of its sex chromosomes.
the DNA content of its mitochondrial genes.
the DNA content and sequence of all of an organisms genes.
Ans: E
Difficulty: 3
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17.
A)
B)
C)
D)
E)
The human genome contains approximately how many microsatellites?
one million
one hundred thousand
ten thousand
one thousand
one hundred
Ans: B
Difficulty: 3
18.
A)
B)
C)
D)
E)
Which is not true of DNA arrays?
Thousands of DNA fragments of known sequence are attached to microchip.
The attached fragments may contain allelic variants.
Fragments from a test single stranded DNA sample may hybridize to DNA on the chip.
In case of a match, the computer will express this fact.
This method is too advanced to be applied at this time.
Ans: E
Difficulty: 3
19. Genomics is:
A) the branch of biology that studies genes.
B) the branch of biology that develops and applies mapping, sequencing and computational
tools.
C) the branch of biology that studies model organisms.
D) the branch of biology that studies Mendelian inheritance patterns.
Ans: B
Difficulty: 1
20.
A)
B)
C)
D)
E)
STSs are:
microsatellite sequences.
generally highly polymorphic.
unique markers along the chromosome.
a and b
b and c
Ans: E
Difficulty: 1
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21. Over six thousand STSs markers have been placed on the human map and they are on
average about 0.5  103 kbp apart. If 30,000 markers were available, what would be the
average distance between markers?
A) 10 kb
B) 50 kb
C) 100 kb
D) 200 kb
E) 500 kb
Ans: C
Difficulty: 2
22.
A)
B)
C)
D)
FISH analysis is useful for:
determining the order of DNA fragments in a YAC.
determining the pattern of expression of a cloned gene.
determining the chromosomal location of a gene.
determining the map order of two closely linked genes.
Ans: C
Difficulty: 2
23.
A)
B)
C)
D)
A contig is:
a map of genetic markers that separated by less than 1cM.
a map showing the order of cloned bits of DNA.
unique DNA sequences that serve as molecular markers.
sets of two or more partially overlapping cloned DNA fragments.
Ans: D
Difficulty: 2
24. Sequence conservation among mammals allow researchers to:
A) screen YACs made from human DNA for coding regions by hybridization to human
DNA.
B) screen YACs made from human DNA for coding regions by hybridization to mouse
DNA.
C) disregard introns or noncoding regions.
D) disregard related genes.
Ans: B
Difficulty: 3
25.
A)
B)
C)
D)
E)
Model organisms:
allow the discovery of similar pathways.
allow the discovery of genes that are conserved across evolutionary time.
allow the discovery of every human gene.
a, b, and c
a and b
Ans: E
Difficulty: 4
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26. Below are several steps involved in FISH. From the choices available, pick the order of
steps that would be successful.
1. Fix chromosomes and denature the DNA.
2. Arrest cells in metaphase.
3. Take a picture using ultraviolet light.
4. Drop cells onto microscope slide to open the cells.
5. Label a DNA probe bound to fluorescent dye.
6. Hybridize the DNA probe to the chromosomes.
A) Order 1, 2, 3, 4, 5, 6
B) Order 4, 2, 1, 6, 5, 3
C) Order 2, 1, 4, 3, 5, 6
D) Order 2, 4, 1, 5, 6, 3
Ans: D
Difficulty: 4
27.
A)
B)
C)
D)
Karyotypic analysis is:
used for high resolution mapping.
used for locating cloned genes on particular parts of a chromosome.
used for direct analysis of DNA.
used for restriction mapping.
Ans: B
Difficulty: 2
28.
A)
B)
C)
D)
The study of polypeptide motifs allows researchers:
to determine which amino acids are found together.
to discern possible biochemical properties of a protein.
to detect expression patterns.
to detect the cellular location of the polypeptide.
Ans: B
Difficulty: 2
29. Homology:
A) between two protein sequences suggests that the genes encoding them derive from a
single ancestral gene.
B) can be 90%.
C) is indicated by similarity in the coding region.
D) a, b, and c
E) a and b
Ans: D
Difficulty: 3
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30.
A)
B)
C)
D)
E)
What DNA sequence information is not present in a cDNA?
the promoter
the introns
the exons
the 3' untranslated region
a and b
Ans: E
Difficulty: 2
31. If you find a helix-loop-helix motif, what function might you postulate for this
polypeptide?
A) secreted polypeptide
B) mitochondrial polypeptide
C) nuclear polypeptide
D) Golgi polypeptide
Ans: C
Difficulty: 2
32.
A)
B)
C)
D)
If you find a zinc-finger motif, what function might you postulate for this polypeptide?
signal transduction
growth hormone receptor
transcription factor
cytoskeletal component
Ans: C
Difficulty: 2
33. Gene therapy is possible for some genes in humans at present. Which of the following
are potential problems?
A) large size of genes
B) identifying the responsible gene
C) random integration of transforming DNA
D) tissue-specific gene expression
E) all of the above
F) a, b, and d
Ans: F
Difficulty: 3
34.
A)
B)
C)
D)
E)
The location of a gene on the Y chromosome could be identified by:
Northern analysis
FISH
genomic Southern analysis
a and b
b and c
Ans: E
Difficulty: 3
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35.
A)
B)
C)
D)
Chromosome walking:
will allow one to move from one chromosome to another.
will allow one to move from one clone to another.
requires FISH.
will allow one to define the fine details of each clone.
Ans: B
Difficulty: 2
36. If you wanted to study a cell cycle control gene, which model organism would be best
suited?
A) E. coli
B) S. cerevisiae
C) C. elegans
D) M. musculus
Ans: B
Difficulty:
37. If you wanted to study a gene involved in apotosis, which model organism would be
best suited?
A) E. coli
B) S. cerevisiae
C) C. elegans
D) M. musculus
Ans: C
Difficulty: 2
38. If you wanted to study a gene involved in rod cells in the retina, which model organism
would be best suited?
A) E. coli
B) S. cerevisae
C) D. melanogaster
D) M. musculus
Ans: D
Difficulty: 2
39.
A)
B)
C)
D)
Stem cells are useful targets for gene therapy because:
they are easily found.
they are nondividing.
they are dividing and able to differentiate.
they are accessible.
Ans: C
Difficulty: 3
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40. The Human Genome Project has six distinct objectives. Which of the following is NOT
one.
A) to generate capital for the United States government.
B) to generate physical, genetic, and sequence maps of the human genome.
C) to sequence the genomes of a variety of organisms.
D) to consider the ethical, social, and legal challenges posed by genomic information.
Ans: A
Difficulty: 2
41.
A)
B)
C)
D)
The most common method for genotyping allelic SSRs is by:
Southern analysis
FISH
PCR and gel electrophoresis
Sequencing
Ans: C
Difficulty: 3
42. A method of using the ends of unconnected contigs as probes to further map a genome
is called:
A) sequence analysis
B) FISH
C) YAC
D) overlap analysis
E) chromosome walking
Ans: E
Difficulty: 2
43. A method of analysis that uses a pattern of restriction fragments sizes to compare
regions of gemomic DNA.
A) RFLP
B) DNA fingerprinting
C) Northern analysis
D) PCR
Ans: B
Difficulty: 3
44. Mapping strategies often utilize the PCR of unique sites in the genome which are
polymorphic and whose sequence is known. These sequences are best called:
A) SSRs
B) SNPs
C) STSs
D) SSCP
Ans: D
Difficulty: 3
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45.
A)
B)
C)
D)
The highest resolution map of a genome can best be generated from:
haplotype mapping
linkage mapping
sequence analysis
FISH
Ans: C
Difficulty: 1
46. Random generation of overlapping insert fragments from large clones for the purpose of
sequence analysis is termed:
A) digestion
B) shotgun
C) minimal
D) maximal
Ans: B
Difficulty: 1
47.
A)
B)
C)
D)
Which of the following are dissimilar between mouse and man:
synteny
karyotype
orthologous order
genes
Ans: B
Difficulty: 3
48.
A)
B)
C)
D)
There are estimated to be how many genes in the human genome:
40,000-60,000
4,000-6,000
100,000 – 200,000
3 – 4 million
Ans: A
Difficulty: 3
49.
A)
B)
C)
D)
Genome sequencing projects have and will continue to:
expedite gene-finding and gene-function analyses.
enhance studies on evolution.
increase the number of known genetic polymorphisms.
all of the above.
Ans: D
Difficulty: 1
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50.
A)
B)
C)
D)
E)
F)
Noncoding RNAs include:
tRNAs
rRNAs
snoRNAs
snRNAs
all of the above.
only a, b, and c.
Ans: E
Difficulty: 1
51.
A)
B)
C)
Genes encode:
noncoding RNAs
proteins
both a and c
Ans: C
Difficulty: 2
52. Protein analysis has shown that humans and worms have approximately how much
proteome homology:
A) 10%
B) 43%
C) 80%
D) 2%
Ans: B
Difficulty: 3
53.
A)
B)
C)
D)
Repeat sequences constitute how much of the human genome:
98%
50%
1%
5%
Ans: B
Difficulty: 2
54.
A)
B)
C)
D)
Which of the following is not one of the five classes of repeat sequences:
segmental duplications
pseudogenes
DNA coding for 5' UTRs
transposon sequences
Ans: C
Difficulty: 2
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55.
A)
B)
C)
D)
Transposon-derived repeats constitute how much of the human's genome:
0.5%
2%
45%
97%
Ans: C
Difficulty: 2
56. A gene considered to generate the upper limit of known splice variants might have how
many:
A) 500-1000
B) 5-10
C) 100-200
D) 10,000 – 20,000
Ans: A
Difficulty: 3
57. Which of the following is not one of the four classes of transposon-derived repeat
sequences:
A) LINES
B) SINES
C) DNA transposons
D) Long terminal repeat transposons
E) pseudogenes
Ans: E
Difficulty: 3
58. Which of the following is not considered a distinct type of organization within a
genome:
A) presence of gene families
B) junk DNA
C) gene-rich regions
D) gene deserts
Ans: B
Difficulty: 3
59.
A)
B)
C)
Which of the following is not true:
human race differences are distinguishable by genotype and phenotype.
the human population encompasses a number of different races.
sequence analysis has found that there is more genotypic variation within a race than
between races.
Ans: A
Difficulty: 2
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60.
A)
B)
C)
D)
Which of the following is not a method for measuring mRNA levels:
DNA microarray
sequence analysis
oligonucleotides array
Northern analysis
Ans: B
Difficulty: 1
61.
A)
B)
C)
D)
The population of mRNA expressed in a single cell or cell type is called:
transcriptome
genome
proteome
spliceosome
Ans: A
Difficulty: 1
62. Deleterious mutations in which of the following genes leads to a 70% predisposition
toward breast cancer:
A) p53
B) CFTR
C) BRCA1
D) EGF
Ans: C
Difficulty: 2
63.
A)
B)
C)
A mass spectrometer is used to:
quantify mRNA levels.
determine sequence of DNA.
following ionization and transfer to a vacuum, a molecule's mass can be determined by
migration in an electric field.
Ans: C
Difficulty: 1
64. Which of the following is a technique used to quantitatively define a transcriptome
including very rare transcripts:
A) SAGE
B) PAGE
C) microarray analysis
D) MPSS
Ans: D
Difficulty: 3
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Matching
Match the best term with the appropriate definition
a. heterochromatic DNA
b. homologous genes
c. paralogous genes
d. orthologous genes
e. sequence tag sites (STSs)
f. genome
g. proteome
h. transcriptome
i. DNA fingerprint
j. syntenic block
65. ______ genes similar in two different species that arose from a common ancestor.
Ans: d
Difficulty: 2
66. ______ population of mRNAs expressed.
Ans: h
Difficulty: 2
67. ______ genomic DNA that is not clonable with current technology.
Ans: a
Difficulty: 2
68. ______ population of proteins present.
Ans: g
Difficulty: 1
69. ______ DNA pattern of restriction fragment sizes.
Ans: i
Difficulty: 1
70. ______ two genes with enough similarity to be considered evolutionarily related.
Ans: b
Difficulty: 2
71. ______ genomic blocks of chromosomal sequence with similarities in genes and
orthologous order between two species.
Ans: b
Difficulty: 2
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72. ______ entire collection of chromosomes in an organism.
Ans: f
Difficulty: 1
73. ______ genes that arise by duplication within a specie.
Ans: c
Difficulty: 2
74. ______ short DNA sequences that are readily located and amplified by PCR and that
identify unique physical genomic locations.
Ans: e
Difficulty: 2
True or False
75. We have a very good idea of what 95% of human DNA is doing.
Ans: False
Difficulty: 2
76. A probe is unnecessary for detecting RFLPs.
Ans: False
Difficulty: 2
77. For RFLPs to be of use in following the inheritance of a gene, they must be inside the
gene.
Ans: False
Difficulty: 4
78. For an RFLP to be useful to follow a gene of interest, it must be closely linked to a
gene.
Ans: True
Difficulty: 3
79. For an RFLP to be useful to follow the inheritance of a gene, it need not be on the same
chromosome.
Ans: False
Difficulty: 2
80. Discovery science is used to identify all the elements of a biological system rather than
to test a specific hypothesis.
Ans: True
Difficulty: 1
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81. Having sequenced the human genome, we now know that “junk” DNA does not play an
important role in the genome.
Ans: True
Difficulty: 1
82. Heterochromatic DNA is DNA that is easy to clone.
Ans: False
Difficulty: 2
83. The human genome is 200 times larger that the yeast genome and 200 times smaller
than that of Amoeba dubia.
Ans: True
Difficulty: 2
84. Some DNA sequences may be repeated 10,000 times within a genome.
Ans: True
Difficulty: 3
85. In humans, 1cM = 1 Mb, whereas in mice, 1 cM = 2 Mb for linkage versus physical map
distances.
Ans: True
Difficulty: 3
86. Once considered junk DNA, transposon-derived repeats have given rise to at least 47
different human genes.
Ans: True
Difficulty: 4
87. A low GC content is a hallmark of a gene-rich region in humans.
Ans: False
Difficulty: 3
88. About half of all olfactory receptor genes are pseudogenes.
Ans: True
Difficulty: 3
89. The presence of genes with very large introns often leads to regions of gene deserts
within a genome.
Ans: True
Difficulty: 2
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Short Answer
90. What is a cDNA microarray?
Ans: A DNA microarray is a chip to which thousands of short DNA sequences,
oligonucleotides, are attached. A matching DNA probe to one of the oligos
attached to the microchip will generate a signal that is detected by computer. This
method opens the way of surveying tens of thousands of cloned or PCR-produced
fragments for complementarity with one of the microchip oligos.
Difficulty: 2
91. What is the difference between ESTs and STSs?
Ans: An EST is an expressed sequence tag and a STS is a sequence tagged site. ESTs
are the 3' end of an expressed gene, often an unknown gene, while sequence
tagged sites are sites whose location and sequence are known and can be used as
markers in gene mapping.
Difficulty: 2
92. Changes in the way science is completed have resulted from the sequencing of whole
genomes. List two most significant changes?
Ans: 1) Systems biology involving the analysis of genomes is now often completed in a
non-hypothesis driven manner. 2) The medical practice has changed and now
includes the use of predictive and preventative analysis and treatment rather than
just treatment of symptoms.
Difficulty: 2
93. What is the difference between SNPs and SSRs?
Ans: SNPs are single nucleotide polymorphisms, a difference in a single base, and
SSRs are simple sequence repeats, short regions of a repeated sequence, usually
about 2-5 bp. Both are used for large-scale linkage mapping.
Difficulty: 2
94. What are YACs and BACs?
Ans: Yeast and Bacterial Artificial Chromosomes. They are used in library
construction and physical mapping.
Difficulty: 2
95. What is FISH and in FISH karyotype analysis, what stage of mitosis is needed for
mapping a gene?
Ans: Fluorescent in situ hybridization. Mapping can only be completed when whole
chromosomes can be seen: during metaphase.
Difficulty: 2
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96. What is meant by hierarchical shotgun sequencing strategy?
Ans: Hierarchical shotgun sequencing strategy was used by the publicly funded Human
Genome Project to produce a draft of the human genome. This multi-step
approach involves the generation of a BAC library, a map of the minimal
overlapping clones for each chromosome, sequence analysis of small cloned
fragments of the BACs, and reassembly of the sequence for each individual
chromosome. Celera used a whole genome shotgun approach rather than an
individual chromosome approach, which did not require the construction of a
physical map.
Difficulty: 2
97. What is Yeast Two-Hybrid and what would you use it for?
Ans: Yeast two-hybrid is a method for the detection of protein-protein interactions. A
gene of interest is subcloned into a yeast-expression vector as a fusion to the
DNA-binding domain of Gal4. This yeast clone is then mated to a library of yeast
cells that contain genes fused to the Gal4 activator domain. If in a diploid cell, the
Gal4 binding domain comes into contact with the activation domain through the
contact of a protein-protein interaction via the fusion proteins this interaction will
activate the genes under Gal4 control and thus allow selection for the proteinprotein interaction such as through histidine auxotrophy.
Difficulty: 2
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Experimental Design and Interpretation of Data
A YAC with a 157 kb insert is partially digested with a single restriction enzyme and the
resulting restriction fragments are cloned into a cosmid vector. The restriction patterns of the
inserted fragments in seven unique cosmids are shown below. (The YAC arms are not
subcloned.)
98. What size fragments are adjacent to the 25 kb fragment?
Ans: 27 kb, 25 kb
Difficulty: 4
99. What size fragments are adjacent to the 13 kb fragment?
Ans: 5 kb, 20 kb
Difficulty: 4
100. What size fragments are adjacent to the 12 kb fragment?
Ans: 10 kb, 27 kb
Difficulty: 4
101. How many restriction enzyme recognition sites are present in this insert?
Ans: 10
Difficulty: 4
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