pdf_url
stringclasses 130
values | page
int64 1
917
| text
stringlengths 0
6.11k
|
|---|---|---|
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 29 | Answers to All Questions and Problems WC -29
F factors in F+ cells become integrated into the chromo -
somes of these cells. Hfr cells become F+ cells when the
integrated F factors exit the chromosome and become
autonomous (self-replicating) genetic elements.
8.11 (a) Of what use are F ′ factors in genetic analysis? (b) How
are F ′ factors formed? (c) By what mechanism does sex -
duction occur?
ANS: (a) F ′ factors are useful for genetic analyses where two
copies of a gene must be present in the same cell, for
example, in determining dominance relationships. (b) F ′
factors are formed by abnormal excision of F factors
from Hfr chromosomes (see Figure 8.21). (c) By the con -
jugative transfer of an F ′ factor from a donor cell to a
recipient (F−) cell.
8.12 What are the basic differences between generalized
transduction and specialized transduction?
ANS: Generalized transduction: (1) transducing particles often
contain only host DNA; (2) transducing particles may
carry any segment of the host chromosome. Thus, all
host genes are transduced. Specialized transduction:
(1) transducing particles carry a recombinant chromo -
some, which contains both phage DNA and host DNA;
(2) only host genes that are adjacent to the prophage
integration site are transduced.
8.13 What roles do IS elements play in the integration of F
factors?
ANS: IS elements (or insertion sequences) are short (800–
1400 nucleotide pairs) DNA sequences that are trans -
posable—that is, capable of moving from one position
in a chromosome to another position or from one
chromosome to another chromosome. IS elements
mediate recombination between nonhomologous
DNA molecules—for example, between F factors and
bacterial chromosomes.
8.14 How can bacterial genes be mapped by interrupted mat -
ing experiments?
ANS: By interrupting conjugation at various times after the
donor and recipient cells are mixed (using a blender or
other form of agitation), one can determine the length of
time required to transfer a given genetic marker from an
Hfr cell to an F−.
8.15 What does the term cotransduction mean? How can
cotransduction frequencies be used to map genetic
markers?
ANS: Cotransduction refers to the simultaneous transduction
of two different genetic markers to a single recipient
cell. Since bacteriophage particles can package only
1/100 to 1/50 of the total bacterial chromosome, only
markers that are relatively closely linked can be cotrans -
duced. The frequency of cotransduction of any two
markers will be an inverse function of the distance
between them on the chromosome. As such, this frequency can be used as an estimate of the linkage dis -
tance. Specific cotransduction-linkage functions must be
prepared for each phage–host system studied.
8.16 In E. coli , the ability to utilize lactose as a carbon source
requires the presence of the enzymes b-galactosidase and
b-galactoside permease. These enzymes are encoded by
two closely linked genes, lacZ and lacY, respectively.
Another gene, proC, controls, in part, the ability of E. coli
cells to synthesize the amino acid proline. The alleles strr
and strs, respectively, control resistance and sensitivity to
streptomycin. Hfr H is known to transfer the two lac
genes, proC, and str, in that order, during conjugation. A
cross was made between Hfr H of genotype lacZ− lacY+
proC+ strs and an F− strain of genotype lacZ+ lacY− proC−
strr. After about 2 hours, the mixture was diluted and
plated out on medium containing streptomycin but no
proline. When the resulting proC+ strr recombinant colo -
nies were checked for their ability to grow on medium
containing lactose as the sole carbon source, very few of
them were capable of fermenting lactose. When the
reciprocal cross (Hfr H lacZ+ lacY− proC+ strs X F− lacZ−
lacY+ proC− strr) was done, many of the proC+ strr recom -
binants were able to grow on medium containing lactose
as the sole carbon source. What is the order of the lacZ
and lacY genes relative to proC?
ANS: lacY—lacZ—proC.
8.17 An F+ strain, marked at 10 loci, gives rise spontaneously
to Hfr progeny whenever the F factor becomes incorpo -
rated into the chromosome of the F+ strain. The F factor
can integrate into the circular chromosome at many
points, so that the resulting Hfr strains transfer the
genetic markers in different orders. For any Hfr strain,
the order of markers entering a recipient cell can be
determined by interrupted mating experiments. From
the following data for several Hfr strains derived from
the same F+, determine the order of markers in the F+
strain.
Hfr Strain Markers Donated in order
1 —Z–H–E–R →
2 —O–K–S–R →
3 —K–O–W–I →
4 —Z–T–I–W →
5 —H–Z–T–I →
ANS:
Z
KH T
E I
R W
S O
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 29 8/14/2015 6:42:51 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 30 | 30-WC Answers to All Questions and Problems
8.18 The data in the following table were obtained from
three-point transduction tests made to determine the
order of mutant sites in the A gene encoding the a sub-
unit of tryptophan synthetase in E. coli . Anth is a linked,
unselected marker. In each cross, trp+ recombinants were
selected and then scored for the anth marker ( anth+ or
anth-). What is the linear order of anth and the three
mutant alleles of the A gene indicated by the data in
the table?
CrossDonor
MarkersRecipient
Markersanth Allele in trp∙
Recombinants % anth∙
1 anth+—
A34anth−—
A22372 anth+: 332 anth− 18
2 anth+—
A46anth−—
A223196 anth+: 180
anth−52
3 anth+—
A223anth−—
A34380 anth+: 379
anth−50
4 anth+—
A223anth−—
A4660 anth+: 280 anth− 20
ANS: anth—A34—A223—A46.
8.19 Bacteriophage P1 mediates generalized transduction
in E. coli . A P1 transducing lysate was prepared by
growing P1 phage on pur+ pro- his- bacteria. Genes
pur, pro, and his encode enzymes required for the syn -
thesis of purines, proline, and histidine, respectively.
The phage and transducing particles in this lysate
were then allowed to infect pur− pro+ his+ cells. After
incubating the infected bacteria for a period of time
sufficient to allow transduction to occur, they were
plated on minimal medium supplemented with proline
and histidine, but no purines to select for pur+ trans -
ductants. The pur+ colonies were then transferred to
minimal medium with and without proline and with
and without histidine to determine the frequencies of
each of the outside markers. Given the following
results, what is the order of the three genes on the
E. coli chromosome?
Genotype Number Observed
pro+ his+ 100
pro+ his+ 22
pro+ his- 150
pro- his-1
ANS: pro—pur—his.
8.20 T wo additional mutations in the trp A gene of E. coli , trp
A58 and trp A 487, were ordered relative to trp A 223 and
the outside marker anth by three-factor transduction crosses as described in Problem 8.18. The results of these
crosses are summarized in the following table. What is
the linear order of anth and the three mutant sites in the
trp A gene?
CrossDonor
MarkersRecipient
Markersanth Allele in trp∙
Recombinants%
anth∙
1 anth+—
A487anth−—
A22372 anth+:
332 anth−82
2 anth+—
A58anth−—
A223196 anth+:
180 anth−48
3 anth+—
A223anth−—
A487380 anth+:
379 anth−50
4 anth+—
A223anth−—
A5860 anth+:
280 anth−80
ANS: anth—A487—A223—A58.
8.21 You have identified a mutant E. coli strain that cannot
synthesize histidine (His−). T o determine the location
of the his− mutation on the E. coli chromosome, you
perform interrupted mating experiments with five dif -
ferent Hfr strains. The following chart shows the time
of entry (minutes, in parentheses) of the wild-type
alleles of the first five markers (mutant genes) into the
His− strain.
Hfr A -------- his (1) man (9) gal (28) lac (37) thr (45)
Hfr B -------- man (15) his (23) cys (38) ser (42) arg (49)
Hfr C -------- thr (3) lac (11) gal (20) man (39) his (47)
Hfr D -------- cys (3) his (18) man (26) gal (45) lac (54)
Hfr E -------- thr (6) rha (18) arg (36) ser (43) cys (47)
On the map below of the circular E. coli chromosome,
indicate (1) the relative location of each gene relative
to thr (located at 0/100 Min), (2) the position where
the sex factor is integrated in each of the five Hfr’s,
and (3) the direction of chromosome transfer for each
Hfr (indicate direction with an arrow or arrowhead).
thr
lac 100/0
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 30 8/14/2015 6:42:52 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 31 | Answers to All Questions and Problems WC -31
ANS:
thr
lac
gal
man
hiscysserargrha
MinE C
B
AD0/1008
17
36
4459637088
8.22 Mutations nrd 11 (gene nrd B , encoding the beta subunit
of the enzyme ribonucleotide reductase), am M 69 (gene
63, encoding a protein that aids tail-fiber attachment),
and nd 28 (gene denA , encoding the enzyme endonucle -
ase II) are known to be located between gene 31 and
gene 32 on the bacteriophage T4 chromosome. Muta -
tions am N54 and am A 453 are located in genes 31 and
32, respectively. Given the three-factor cross data in the
following table, what is the linear order of the five
mutant sites?
Three-Factor Cross Data
Cross % Recombinationa
1. am A 453— am M 69 × nrd 11 2.6
2. am A 453— am M 69 × nrd 11 4.2
3. am A 453— am M 69 × nd 28 2.5
4. am A 453— nd 28 × am M 69 3.5
5. am A 453— nrd 11 × nd 28 2.9
6. am A 453— nd 28 × nrd 11 2.1
7. am N 54— am M69 × nrd 11 3.5
8. am N 54— nrd 11 × am M69 1.9
9. am N54— nd 28 × am M69 1.7
10. am N54— am M69 × nd 28 2.7
11. am N54— nd 28 × nrd 11 2.9
12. am N54— nrd 11 × nd 28 1.9
a All recombination frequencies are given as
2(wild type progeny) × 100.
total progeny
ANS: amA453— nrd11— nd28— amM 69— amN 54.Chapter 9
9.1 (a) How did the transformation experiments of Griffith
differ from those of Avery and his associates? (b) What was
the significant contribution of each? (c) Why was Griffith’s
work not evidence for DNA as the genetic material,
whereas the experiments of Avery and coworkers provided
direct proof that DNA carried the genetic information?
ANS: (a) Griffith’s in vivo experiments demonstrated the occur -
rence of transformation in pneumococcus. They pro -
vided no indication as to the molecular basis of the
transformation phenomenon. Avery and colleagues car -
ried out in vitro experiments, employing biochemical
analyses to demonstrate that transformation was medi -
ated by DNA. (b) Griffith showed that a transforming
substance existed; Avery et al. defined it as DNA. (c)
Griffith’s experiments did not include any attempt to
characterize the substance responsible for transforma -
tion. Avery et al. isolated DNA in “pure” form and dem -
onstrated that it could mediate transformation.
9.2 A cell-free extract is prepared from T ype IIIS pneumo -
coccal cells. What effect will treatment of this extract
with (a) protease, (b) RNase, and (c) DNase have on its
subsequent capacity to transform recipient T ype IIR cells
to T ype IIIS? Why?
ANS: (a) No effect; (b) no effect; (c) DNase will destroy the
capacity of the extract to transform type IIR cells to T ype
IIIS by degrading the DNA in the extract. Protease and
RNase will degrade the proteins and RNA, respectively,
in the extract. They will have no effect, since the proteins
and RNA are not involved in transformation.
9.3 How could it be demonstrated that the mixing of heat-
killed T ype III pneumococcus with live T ype II resulted in
a transfer of genetic material from T ype III to T ype II
rather than a restoration of viability to T ype III by T ype II?
ANS: Purified DNA from T ype III cells was shown to be
sufficient to transform T ype II cells. This occurred in the
absence of any dead T ype III cells.
9.4 What is the macromolecular composition of a bacterial
virus or bacteriophage such as phage T2?
ANS: About 1/2 protein, 1/2 DNA. A single long molecule of
DNA is enclosed within a complex “coat” composed of
many proteins.
9.5 (a) What was the objective of the experiment carried out
by Hershey and Chase? (b) How was the objective
accomplished? (c) What is the significance of this
experiment?
ANS: (a) The objective was to determine whether the genetic
material was DNA or protein. (b) By labeling phospho -
rus, a constituent of DNA, and sulfur, a constituent of
protein, in a virus, it was possible to demonstrate that
only the labeled phosphorus was introduced into the
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 31 8/14/2015 6:42:52 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 32 | 32-WC Answers to All Questions and Problems
host cell during the viral reproductive cycle. The DNA
was enough to produce new phages. (c) Therefore DNA,
not protein, is the genetic material.
9.6 How did the reconstitution experiment of Fraenkel–
Conrat and colleagues show that the genetic information
of tobacco mosaic virus (TMV) is stored in its RNA
rather than its protein?
ANS: When tobacco leaves were infected with reconstituted
virus particles containing RNA from type A viruses and
protein from type B viruses, the progeny viruses were
type A, showing that RNA, not protein, carries the
genetic information in TMV .
9.7 (a) What background material did Watson and Crick
have available for developing a model of DNA? (b) What
was their contribution to building the model?
ANS: (a) The ladder-like pattern was known from X-ray dif -
fraction studies. Chemical analyses had shown that a 1:1
relationship existed between the organic bases adenine
and thymine and between cytosine and guanine. Physical
data concerning the length of each spiral and the stack -
ing of bases were also available. (b) Watson and Crick
developed the model of a double helix, with the rigid
strands of sugar and phosphorus forming spirals around
an axis, and hydrogen bonds connecting the complemen -
tary bases in nucleotide pairs.
9.8 (a) Why did Watson and Crick choose a double helix for
their model of DNA structure? (b) Why were hydrogen
bonds placed in the model to connect the bases?
ANS: (a) A multistranded, spiral structure was suggested by the
X-ray diffraction patterns. A double-stranded helix with
specific base-pairing nicely fits the 1:1 stoichiometry
observed for A:T and G:C in DNA. (b) Use of the known
hydrogen-bonding potential of the bases provided a
means of holding the two complementary strands in a
stable configuration in such a double helix.
9.9 (a) If a virus particle contained double-stranded DNA
with 200,000 base pairs, how many nucleotides would be
present? (b) How many complete spirals would occur on
each strand? (c) How many atoms of phosphorus would
be present? (d) What would be the length of the DNA
configuration in the virus?
ANS: (a) 400,000; (b) 20,000; (c) 400,000; (d) 68,000 nm.
9.10 What are the differences between DNA and RNA?
ANS: DNA has one atom less of oxygen than RNA in the sugar
part of the molecule; the sugar in DNA is 2-deoxyribose,
whereas the sugar in RNA is ribose. In DNA, thymine
replaces the uracil that is present in RNA. (In certain
bacteriophages, DNA-containing uracil is present.)
DNA is most frequently double-stranded, but bacterio -
phages such as ΦX174 contain single-stranded DNA.
RNA is most frequently single-stranded. Some viruses,
such as the Reoviruses, however, contain double-stranded
RNA chromosomes. 9.11 RNA was extracted from TMV (tobacco mosaic virus) par -
ticles and found to contain 20 percent cytosine (20 percent
of the bases were cytosine). With this information, is it
possible to predict what percentage of the bases in TMV
are adenine? If so, what percentage? If not, why not?
ANS: No. TMV RNA is single-stranded. Thus, the base-pair
stoichiometry of DNA does not apply.
9.12 DNA was extracted from cells of Staphylococcus afermen -
tans and analyzed for base composition. It was found that
37 percent of the bases are cytosine. With this informa -
tion, is it possible to predict what percentage of the bases
are adenine? If so, what percentage? If not, why not?
ANS: Yes. Because DNA in bacteria is double-stranded, the 1:1
base-pair stoichiometry applies. Therefore, if 37% of the
bases are cytosine, then 37% are guanine. This means
that the remaining 26% of the bases are adenine and thy -
mine. Thus, 26%/2 = 13% of the bases are adenine.
9.13 If one strand of DNA in the Watson–Crick double helix
has a base sequence of 5-GTCATGAC-3, what is the
base sequence of the complementary strand?
ANS: 3′-C A G T A C T G-5 ′
9.14 Indicate whether each of the following statements about
the structure of DNA is true or false. (Each letter is used
to refer to the concentration of that base in DNA.)
(a) A + T = G + C
(b) A = G; C = T
(c) A/T = C/G
(d) T/A = C/G
(e) A + G = C + T
(f) G/C = 1
(g) A = T within each single strand.
(h) Hydrogen bonding provides stability to the double
helix in aqueous cytoplasms.
(i) Hydrophobic bonding provides stability to the double
helix in aqueous cytoplasms.
(j) When separated, the two strands of a double helix are
identical.
(k) Once the base sequence of one strand of a DNA dou -
ble helix is known, the base sequence of the second
strand can be deduced.
(l) The structure of a DNA double helix is invariant. (m)
Each nucleotide pair contains two phosphate groups,
two deoxyribose molecules, and two bases.
ANS: (a) False (b) False (c) T rue (d) T rue (e) T rue
(f) T rue (g) False (h) T rue (i) T rue (j) False
(k) Frue (l) False (m) T rue
9.15 The nucleic acids from various viruses were extracted
and examined to determine their base composition.
Given the following results, what can you hypothesize
about the physical nature of the nucleic acids from these
viruses?
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 32 8/14/2015 6:42:52 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 33 | Answers to All Questions and Problems WC -33
(a) 35% A, 35% T, 15% G, and 15% C. (b) 35% A, 15% T,
25% G, and 25% C. (c) 35% A, 30% U, 30% G, and 5% C.
ANS: (a) Double-stranded DNA; (b) single-stranded DNA;
(c) single-stranded RNA.
9.16 Compare and contrast the structures of the A, B, and Z
forms of DNA.
ANS: The B form of DNA helix is that proposed by Watson
and Crick and is the conformation that DNA takes under
physiological conditions. It is a right-handed double
helical coil with 10 bases per turn of the helix and a diam -
eter of 1.9 nm. It has a major and a minor groove. Z-DNA
is left-handed, has 12 bases per turn, a single deep groove,
and is 1.8 nm in diameter. Its sugar–phosphate backbone
takes a zigzagged path, and it is G:C rich. A-DNA is a
right-handed helix with 11 base pairs per turn. It is a
shorter, thicker double helix with a diameter of 0.23 nm
and has a narrow, deep major groove and a broad, shal -
low minor groove. A-DNA forms in vitro under high salt
concentrations or in a partially dehydrated state.
9.17 The temperature at which one-half of a double-stranded
DNA molecule has been denatured is called the melting
temperature, Tm. Why does Tm depend directly on the
GC content of the DNA?
ANS: The value of Tm increases with the GC content because
GC base pairs, connected by three hydrogen bonds, are
stronger than AT base pairs connected by two hydrogen
bonds.
9.18 A diploid rye plant, Secale cereale , has 2 n = 14 chromo -
somes and approximately 1.6 × 1010 bp of DNA. How
much DNA is in a nucleus of a rye cell at (a) mitotic
metaphase, (b) meiotic metaphase I, (c) mitotic telo -
phase, and (d) meiotic telophase II?
ANS: (a) 3.2 × 1010 bp (b) 3.2 × 1010 bp (c) 1.6 × 1010 bp (d) 0.8
× 1010 bp
9.19 The available evidence indicates that each eukaryotic
chromosome (excluding polytene chromosomes) con -
tains a single giant molecule of DNA. What different
levels of organization of this DNA molecule are appar -
ent in chromosomes of eukaryotes at various times dur -
ing the cell cycle?
ANS: DNA during interphase is not yet organized into indi -
vidual chromosomes but consists of a series of ellipsoidal
“beads on a string” that form an 11-nm fiber. Here, 146
bp of DNA is wrapped 1.65 turns around the nucleo -
some core of eight histones. However, during metaphase
of meiosis and mitosis, DNA becomes organized into
chromosomes. The 11-nm fiber is folded and super -
coiled to produce a 30-nm chromatin fiber, the basic
structural unit of the metaphase chromosome. A third
and final level of packaging involves nonhistone chro -
mosomal proteins that form a scaffold to condense the
30-nm fibers into tightly packaged metaphase chromo -
somes, the highest level of DNA condensation observed. 9.20 A diploid nucleus of Drosophila melanogaster contains
about 3.4 × 108 nucleotide pairs. Assume (1) that all
nuclear DNA is packaged in nucleosomes and (2) that an
average internucleosome linker size is 60 nucleotide
pairs. How many nucleosomes would be present in a dip -
loid nucleus of D. melanogaster ? How many molecules of
histone H2a, H2b, H3, and H4 would be required?
ANS: In the diploid nucleus of D. melanogaster , 1.65 × 106
nucleosomes would be present; these would contain 3.3 ×
106 molecules of each histone, H2a, H2b, H3, and H4.
9.21 The relationship between the melting Tm and GC con -
tent can be expressed, in its much simplified form, by the
formula Tm = 69 + 0.41 (% GC). (a) Calculate the melt -
ing temperature of E. coli DNA that has about 50% GC.
(b) Estimate the %GC of DNA from a human kidney
cell where Tm = 85°C.
ANS: (a) 89.5 °C. (b) About 39%
9.22 Experimental evidence indicates that most highly repeti -
tive DNA sequences in the chromosomes of eukaryotes
do not produce any RNA or protein products. What
does this indicate about the function of highly repetitive
DNA?
ANS: It indicates that most highly repetitive DNA sequences
do not contain structural genes specifying RNA and
polypeptide gene products.
9.23 The satellite DNAs of Drosophila virilis can be isolated,
essentially free of main-fraction DNA, by density-gradi -
ent centrifugation. If these satellite DNAs are sheared
into approximately 40-nucleotide-pair-long fragments
and are analyzed in denaturation–renaturation experi -
ments, how would you expect their hybridization kinet -
ics to compare with the renaturation kinetics observed
using similarly sheared main-fraction DNA under the
same conditions? Why?
ANS: The satellite DNA fragments would renature much
more rapidly than the main-fraction DNA fragments. In
D. virilus satellite DNAs, all three have repeating hepta -
nucleotide-pair sequences. Thus, essentially every 40
nucleotide-long (average) single-stranded fragment
from one strand will have a sequence complementary (in
part) with every single-stranded fragment from the com -
plementary strand. Many of the nucleotide-pair
sequences in main-fraction DNA will be unique
sequences (present only once in the genome).
9.24 (a) What functions do (1) centromeres and (2) telomeres
provide? (b) Do telomeres have any unique structural
features? (c) When chromosomes are broken by expo -
sure to high-energy radiation such as X rays, the result -
ing broken ends exhibit a pronounced tendency to stick
to each other and fuse. Why might this occur?
ANS: (a) (1) Centromeres function as spindle-fiber attachment
sites on chromosomes; they are required for the separa -
tion of homologous chromosomes to opposite poles of
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 33 8/14/2015 6:42:52 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 34 | 34-WC Answers to All Questions and Problems
the spindle during anaphase I of meiosis and for the
separation of sister chromatids during anaphase of mito -
sis and anaphase II of meiosis. (2) T elomeres provide at
least three important functions: (i) prevention of exonu -
cleolytic degradation of the ends of the linear DNA mol -
ecules in eukaryotic chromosomes, (ii) prevention of the
fusion of ends of DNA molecules of different chromo -
somes, and (iii) provision of a mechanism for replication
of the distal tips of linear DNA molecules in eukaryotic
chromosomes. (b) Yes. Most telomeres studied to date
contain DNA sequence repeat units (e.g., TTAGGG in
human chromosomes), and at least in some species, telo -
meres terminate with single-stranded 3 ′ overhangs that
form “hairpin” structures. The bases in these hairpins
exhibit unique patterns of methylation that presumably
contribute to the structure and stability of telomeres.
(c) The broken ends resulting from irradiation will not
contain telomeres; as a result, the free ends of the DNA
molecules are apparently subject to the activities of
enzymes such as exonucleases, ligases, and so on, which
modify the ends. They can regain stability by fusing to
broken ends of other DNA molecules that contain ter -
minal telomere sequences.
9.25 Are eukaryotic chromosomes metabolically most active
during prophase, metaphase, anaphase, telophase, or
interphase?
ANS: Interphase. Chromosomes are for the most part meta -
bolically inactive (exhibiting little transcription) during
the various stages of condensation in mitosis and
meiosis.
9.26 Are the scaffolds of eukaryotic chromosomes composed
of histone or nonhistone chromosomal proteins? How
has this been determined experimentally?
ANS: Nonhistone chromosomal proteins. The “scaffold”
structures of metaphase chromosomes can be observed
by light microscopy after removal of the histones by dif -
ferential extraction procedures.
9.27 (a) Which class of chromosomal proteins, histones or
nonhistones, is the more highly conserved in different
eukaryotic species? Why might this difference be
expected? (b) If one compares the histone and nonhis -
tone chromosomal proteins of chromatin isolated from
different tissues or cell types of a given eukaryotic organ -
ism, which class of proteins will exhibit the greater het -
erogeneity? Why are both classes of proteins not
expected to be equally homogeneous in chromosomes
from different tissues or cell types?
ANS: (a) Histones have been highly conserved throughout the
evolution of eukaryotes. A major function of histones is
to package DNA into nucleosomes and chromatin fibers.
Since DNA is composed of the same four nucleotides
and has the same basic structure in all eukaryotes, one
might expect that the proteins that play a structural role in packaging this DNA would be similarly conserved. (b)
The nonhistone chromosomal proteins exhibit the
greater heterogeneity in chromatin from different tis -
sues and cell types of an organism. The histone composi -
tion is largely the same in all cell types within a given
species—consistent with the role of histones in packag -
ing DNA into nucleosomes. The nonhistone chromo -
somal proteins include proteins that regulate gene
expression. Because different sets of genes are tran -
scribed in different cell types, one would expect hetero -
geneity in some of the nonhistone chromosomal proteins
of different tissues.
9.28 (a) If the haploid human genome contains 3 × 109 nucle -
otide pairs and the average molecular weight of a nucleo -
tide pair is 660, how many copies of the human genome
are present, on average, in 1 mg of human DNA?
(b) What is the weight of one copy of the human genome?
(c) If the haploid genome of the small plant Arabidopsis
thaliana contains 7.7 × 107 nucleotide pairs, how many
copies of the A. thaliana genome are present, on average,
in 1 mg of A. thaliana DNA? (d) What is the weight of
one copy of the A. thaliana genome? (e) Of what impor -
tance are calculations of the above type to geneticists?
ANS: (a) One microgram of human DNA will contain, on
average, 3.04 × 105 copies of the genome. Using an
average molecular weight per nucleotide pair of 660,
the molecular weight of the entire human genome is
1.98 × 1012 (3 × 109 × 660). Thus, 1.98 × 1012 g
(1 “mole” = number of grams equivalent to the “molec -
ular” weight) of human DNA will contain, on average,
6.02 × 1023 molecules [Avogadro’s number = number of
molecules (here, copies of the genome) present in one
“mole” of a substance]. One gram will contain on aver -
age (3.04 × 1011)(6.02 × 1023/1.98 × 1012) copies of the
genome; thus, 1 mg will contain, on average, 3.04 × 105
copies of the human genome. (b) One copy of the
human genome weighs approximately (3.3 × 10−12 g)
(1.98 × 1012 g per “mole”/6.02 × 1023 molecules per
“mole”) or 3.3 × 10−6 mg. (c) By analogous calculations,
1 g of A. thaliana DNA contains, on average, 1.18 × 107
copies of the genome. (d) Similarly, one copy of the A.
thaliana genome weighs approximately 8.4 × 10−8 mg.
(e) In carrying out molecular analyses of the structures
of genomes, geneticists frequently need to know how
many copies of a genome are present, on average, in a
given quantity of DNA.
Chapter 10
10.1 DNA polymerase I of E. coli is a single polypeptide of
molecular weight 103,000.
(a) What enzymatic activities other than polymerase
activity does this polypeptide possess? (b) What are the
in vivo functions of these activities? (c) Are these activi -
ties of major importance to an E. coli cell? Why?
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 34 8/14/2015 6:42:52 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 35 | Answers to All Questions and Problems WC -35
ANS: (a) Both 3 ′ → 5′ and 5 ′ → 3′ exonuclease activities.
(b) The 3 ′ → 5′ exonuclease “proofreads” the nascent
DNA strand during its synthesis. If a mismatched base
pair occurs at the 3 ′-OH end of the primer, the 3 ′ → 5′
exonuclease removes the incorrect terminal nucleotide
before polymerization proceeds again. The 5 ′ → 3′ exo-
nuclease is responsible for the removal of RNA primers
during DNA replication and functions in pathways
involved in the repair of damaged DNA (see Chapter
13). (c) Yes, both exonuclease activities appear to be very
important. Without the 3 ′ → 5′ proofreading activity
during replication, an intolerable mutation frequency
would occur. The 5 ′ → 3′ exonuclease activity is essential
to the survival of the cell. Conditional mutations that
alter the 5 ′ → 3′ exonuclease activity of DNA polymerase
I are lethal to the cell under conditions where the exo -
nuclease is nonfunctional.
10.2 Escherichia coli cells are grown for many generations in a
medium in which the only available nitrogen is the heavy
isotope 15N. They are then transferred to a medium con -
taining 14N as the only source of nitrogen.
(a) What distribution of 15N and 14N would be expected
in the DNA molecules of cells that had grown for one
generation in the 14N-containing medium assuming that
DNA replication was (i) conservative, (ii) semiconserva -
tive, or (iii) dispersive?
(b) What distribution would be expected after two gen -
erations of growth in the 14N-containing medium
assuming (i) conservative, (ii) semiconservative, or (iii)
dispersive replication?
ANS: (a) (i) One-half of the DNA molecules with 15N in both
strands and the other half with 14N in both strands; (ii) all
DNA molecules with one strand containing 15N and the
complementary strand containing 14N; (iii) all DNA
molecules with both strands containing roughly equal
amounts of 15N and 14N. (b) (i) 1/4 of the DNA molecules
with 15N in both strands and 3/4 with 14N in both strands;
(ii) half of the DNA molecules with one strand contain -
ing 15N and the complementary strand containing 14N
and the other half with 14N in both strands; (iii) all DNA
molecules with both strands containing about 1/4 15N
and 3/4 14N.
10.3 Why do DNA molecules containing 15N band at a differ -
ent position than DNA molecules containing 14N when
centrifuged to equilibrium in 6 M CsCl?
ANS: 15Nitrogen contains eight neutrons instead of the seven
neutrons in the normal isotope of nitrogen, 14N. There -
fore, 15N has an atomic mass of about 15, whereas 14N has
a mass of about 14. This difference means that purines
and pyrimidines containing 15N have a greater density
(weight per unit volume) than those containing 14N.
Equilibrium density-gradient centrifugation in 6 M CsCl
separates DNAs or other macromolecules based on their densities, and E. coli DNA, for example, that contains 15N
has a density of 1.724 g/cm2, whereas E. coli DNA that
contains 14N has a density of 1.710 g/cm2.
10.4 A DNA template plus primer with the structure
3´ P —TGCG AATTAGCGACAT— P 5´
5´ P —ATCGGTACGACGCTTAAC—OH 3´ ...................
(where P = a phosphate group) is placed in an in vitro
DNA synthesis system (Mg2+, an excess of the four
deoxyribonucleoside triphosphates, etc.) containing a
mutant form of E. coli DNA polymerase I that lacks exo -
nuclease activity. The polymerase and exonuclease activ -
ities of this aberrant enzyme are identical to those of
normal E. coli DNA polymerase I. It simply has no exo -
nuclease activity.
(a) What will be the structure of the final product?
(b) What will be the first step in the reaction sequence?
ANS: (a) 3´ P -TGCGA ATTAGCGACAT- P 5´
5´ P -ATCGGTACGACGCTTAATCGCTGT A-OH 3´; ........ ............ ........... ...... ..
Note that DNA synthesis will not occur on the left end
since the 3 ′-terminus of the potential primer strand is
blocked with a phosphate group—all DNA polymerases
require a free 3 ′-OH terminus.
(b) The first step will be the removal of the mismatched
C (exiting as dCMP) from the 3 ′-OH primer terminus
by the 3 ′ 5′ exonuclease (“proofreading”) activity.
10.5 How might continuous and discontinuous modes of
DNA replication be distinguished experimentally?
ANS: If nascent DNA is labeled by exposure to 3H-thymidine
for very short periods of time, continuous replication
predicts that the label would be incorporated into chro -
mosome-sized DNA molecules, whereas discontinuous
replication predicts that the label would first appear in
small pieces of nascent DNA (prior to covalent joining,
catalyzed by polynucleotide ligase).
10.6 E. coli cells contain five different DNA polymerases—I,
II, III, IV , and V . Which of these enzymes catalyzes the
semiconservative replication of the bacterial chromo -
some during cell division? What are the functions of the
other four DNA polymerases in E. coli ?
ANS: DNA polymerase III is the true replicase. DNA poly -
merase I removes the RNA primers and replaces them
with DNA. The other DNA polymerases play important
roles in DNA repair pathways (see Chapter 13).
10.7 The Boston barberry is an imaginary plant with a diploid
chromosome number of 4, and Boston barberry cells
are easily grown in suspended cell cultures. 3H-thymi-
dine was added to the culture medium in which a
G1-stage cell of this plant was growing. After one cell
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 35 8/14/2015 6:42:53 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 36 | 36-WC Answers to All Questions and Problems
generation of growth in 3H-thymidine-containing
medium, colchicine was added to the culture medium.
The medium now contained both 3H-thymidine and
colchicine. After two “generations” of growth in 3H-thy-
midine-containing medium (the second “generation”
occurring in the presence of colchicine as well), the two
progeny cells (each now containing eight chromosomes)
were transferred to culture medium containing nonra -
dioactive thymidine (3H-thymidine) plus colchicine.
Note that a “generation” in the presence of colchicine
consists of a normal cell cycle’s chromosomal duplication
but no cell division. The two progeny cells were allowed
to continue to grow, proceeding through the “cell cycle,”
until each cell contained a set of metaphase chromo -
somes that looked like the following.
If autoradiography were carried out on these metaphase
chromosomes (four large plus four small), what pattern
of radioactivity (as indicated by silver grains on the auto -
radiograph) would be expected? (Assume no recombina -
tion between DNA molecules.)
ANS:
Two Plus two
For both the
large and small
chromosomes
10.8 Suppose that the experiment described in Problem 10.7
was carried out again, except this time replacing the
3H-thymidine with nonradioactive thymidine at the
same time that the colchicine was added (after one cell
generation of growth in 3H-thymidine-containing
medium). The cells were then maintained in colchicine
plus nonradioactive thymidine until the metaphase
shown in Problem 10.7 occurred. What would the auto -
radiographs of these chromosomes look like?
ANS:
Plus two Two For both the
large and small
chromosomes 10.9 Suppose that the DNA of cells (growing in a cell culture)
in a eukaryotic species was labeled for a short period of
time by the addition of 3H-thymidine to the medium.
Next assume that the label was removed and the cells
were resuspended in nonradioactive medium. After a
short period of growth in nonradioactive medium, the
DNA was extracted from these cells, diluted, gently lay -
ered on filters, and autoradiographed. If autoradiographs
of the type
. . . . . . . . . . . .
were observed, what would this indicate about the nature
of DNA replication in these cells? Why?
ANS: The DNA replication was unidirectional rather than
bidirectional. As the intracellular pools of radioactive
3H-thymidine are gradually diluted after transfer to non -
radioactive medium, less and less 3H-thymidine will be
incorporated into DNA at each replicating fork. This
will produce autoradiograms with tails of decreasing
grain density at each growing point. Since such tails
appear at only one end of each track, replication must be
unidirectional. Bidirectional replication would produce
such tails at both ends of an autoradiographic track (see
Figure 10.31).
10.10 Arrange the following enzymes in the order of their
action during DNA replication in E. coli : (1) DNA poly -
merase I, (2) DNA polymerase III, (3) DNA primase,
(4) DNA gyrase, and (5) DNA helicase.
ANS: The correct sequence of action is 4, 5, 3, 2, 1.
10.11 Fifteen distinct DNA polymerases— a, b, g, d, e, k, z, h,
q, k, l, m, s, f, and Rev1—have been characterized in
mammals. What are the intracellular locations and func -
tions of these polymerases?
ANS: Current evidence suggests that polymerases a, d, and/or
e are required for the replication of nuclear DNA. Poly -
merase e is thought to catalyze the continuous synthesis
of the leading strand, and polymerases a and d are
thought to catalyze the replication of the lagging strand.
Polymerase a forms a complex with primase and initiates
the synthesis of Okazaki fragments during the discon -
tinuous replication of the lagging strand. Polymerase a
catalyzes the incorporation of approximately the first 30
nucleotides in each Okazaki fragment before being
replaced by polymerase d, which then completes the syn -
thesis of the fragments. Polymerase g catalyzes replica -
tion of organellar chromosomes. Polymerases b, k, z, h,
q, k, l, m, s, f, and Rev1 function in various DNA repair
pathways (see Chapter 13).
10.12 The E. coli chromosome contains approximately 4 × 106
nucleotide pairs and replicates as a single bidirectional
replicon in approximately 40 minutes under a wide vari -
ety of growth conditions. The largest chromosome of
D. melanogaster contains about 6 × 107 nucleotide pairs.
(a) If this chromosome contains one giant molecule of
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 36 8/14/2015 6:42:54 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 37 | Answers to All Questions and Problems WC -37
DNA that replicates bidirectionally from a single origin
located precisely in the middle of the DNA molecule,
how long would it take to replicate the entire chromo -
some if replication in Drosophila occurred at the same
rate as replication in E. coli ? (b) Actually, replication
rates are slower in eukaryotes than in prokaryotes. If
each replication bubble grows at a rate of 5000 nucleo -
tide pairs per minute in Drosophila and 100,000 nucleo -
tide pairs per minute in E. coli , how long will it take to
replicate the largest Drosophila chromosome if it contains
a single bidirectional replicon as described in (a) above?
(c) In Drosophila embryos, the nuclei divide every 9 to 10
minutes. Based on your calculations in (a) and (b) earlier,
what do these rapid nuclear divisions indicate about the
number of replicons per chromosome in Drosophila ?
ANS: (a) Given bidirectional replication of a single replicon,
each replication fork must traverse 2 ×106 nucleotide
pairs in E. coli and 3 × 107 nucleotide pairs in the largest
Drosophila chromosome. If the rates were the same in
both species, it would take 15 times (3 × 107/2 × 106) as
long to replicate the Drosophila chromosome or 10 hours
(40 minutes × 15 = 600 minutes).(b) If replication forks
in E. coli move 20 times as fast as replication forks in
Drosophila (100,000 nucleotide pairs per minute/5000
nucleotide pairs per minute), the largest Drosophila chromo -
some would require 8.3 days (10 hours × 20 = 200 hours)
to complete one round of replication. (c) Each Drosophila
chromosome must contain many replicons in order to
complete replication in less than 10 minutes.
10.13 E. coli cells that have been growing in 14N for many gen -
erations are transferred to medium containing only 15N
and allowed to grow in this medium for four generations.
Their DNA is then extracted and analyzed by equilib -
rium CsCl density-gradient centrifugation. What pro -
portion of this DNA will band at the “light,” “hybrid,”
and “heavy” positions in the gradient?
ANS: No DNA will band at the “light” position; 12.5 percent
(2 of 16 DNA molecules) will band at the “hybrid” den -
sity; and 87.5 percent (14 of 16 DNA molecules) will
band at the “heavy” position.
10.14 The bacteriophage lambda chromosome has several
A:T-rich segments that denature when exposed to pH
11.05 for 10 minutes. After such partial denaturation,
the linear packaged form of the lambda DNA molecule
has the structure shown in Figure 10.9 a. Following its
injection into an E. coli cell, the lambda DNA molecule
is converted into a covalently closed circular molecule by
hydrogen bonding between its complementary single-
stranded termini and the action of DNA ligase. It then
replicates as a q-shaped structure. The entire lambda
chromosome is 17.5 mm long. It has a unique origin of
replication located 14.3 mm from the left end of the lin -
ear form shown in Figure 10.9 a. Draw the structure that
would be observed by electron microscopy after both
(1) replication of an approximately 6- mm-long segment of the lambda chromosomal DNA molecule ( in vivo ) and
(2) exposure of this partially replicated DNA molecule to
pH 11.05 for 10 minutes ( in vitro ), (a) if replication had
proceeded bidirectionally from the origin, and (b) if rep-
lication had proceeded unidirectionally from the origin.
ANS:
(a) and (b)
bb
bcc
cdd
defghefgh
aa
jiorhg
fei
ja ij
10.15 What enzyme activity catalyzes each of the following
steps in the semiconservative replication of DNA in
prokaryotes?
(a) The formation of negative supercoils in progeny
DNA molecules. (b) The synthesis of RNA primers.
(c) The removal of RNA primers. (d) The covalent exten -
sion of DNA chains at the 3 ′-OH termini of primer
strands. (e) Proofreading of the nucleotides at the 3 ′-OH
termini of DNA primer strands?
ANS: (a) DNA gyrase; (b) primase; (c) the 5 ′ → 3′ exonuclease
activity of DNA polymerase I; (d) the 5 ′ → 3′ polymerase
activity of DNA polymerase III; (e) the 3 ′ → 5′ exonucle -
ase activity of DNA polymerase III.
10.16 One species of tree has a very large genome consisting of
2.0 × 1010 base pairs of DNA.
(a) If this DNA was organized into a single linear mole -
cule, how long (meters) would this molecule be? (b) If
the DNA is evenly distributed among 10 chromosomes
and each chromosome has one origin of DNA replica -
tion, how long would it take to complete the S phase of
the cell cycle, assuming that DNA polymerase can syn -
thesize 2 × 104 bp of DNA per minute? (c) An actively
growing cell can complete the S phase of the cell cycle in
approximately 300 minutes. Assuming that the origins of
replication are evenly distributed, how many origins of
replication are present on each chromosome? (d) What
is the average number of base pairs between adjacent ori -
gins of replication?
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 37 8/14/2015 6:42:54 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 38 | 38-WC Answers to All Questions and Problems
ANS: (a) (34 nm/100 bp)(2 × 1010 bp) = 6.8 × 109 = 6.8 meters.
(b) 2 × 1010/10 chromosomes = 2 × 109 bp; 4 × 104 bp/
min (bidirectional); 2 × 109/4 × 104 = 5 × 104 min =
50,000 min. (c) (50,000 min)(1 ori) = (300 min)
(X ori); X = 50,000/300 = 167 ori. (d) (2 × 109 bp/
chrom.)/(167 ori/chrom.) = 1.2 × 107 bp/ori.
10.17 Why must each of the giant DNA molecules in eukaryotic
chromosomes contain multiple origins of replication?
ANS: In eukaryotes, the rate of DNA synthesis at each replica -
tion fork is about 2500–3000 nucleotide pairs per min -
ute. Large eukaryotic chromosomes often contain
107–108 nucleotide pairs. A single replication fork could
not replicate the giant DNA in one of these large chro -
mosomes fast enough to permit the observed cell gen -
eration times.
10.18 In E. coli , viable polA mutants have been isolated that
produce a defective gene product with little or no 5 ′→3′
polymerase activity, but normal 5 ′→3′ exonuclease activ -
ity. However, no polA mutant has been identified that
is completely deficient in the 5 ′→3′ exonuclease activity,
while retaining 5 ′→3′ polymerase activity, of DNA poly -
merase I. How can these results be explained?
ANS: The 5 ′ → 3′ exonuclease activity of DNA polymerase I is
essential to the survival of the bacterium, whereas the
5′→3′ polymerase activity of the enzyme is not essential.
10.19 Other polA mutants of E. coli lack the 3 ′ → 5′ exonuclease
activity of DNA polymerase I. Will the rate of DNA syn -
thesis be altered in these mutants? What effect(s) will
these polA mutations have on the phenotype of the
organism?
ANS: No, the rate of DNA synthesis will not be altered. E. coli
strains carrying polA mutations that eliminate the 3 ′ → 5′
exonuclease activity of DNA polymerase I will exhibit
unusually high mutation rates.
10.20 Many of the origins of replication that have been charac -
terized contain AT-rich core sequences. Are these
AT-rich cores of any functional significance? If so, what?
ANS: Because AT base pairs are held together by only two
hydrogen bonds instead of the three hydrogen bonds
present in GC base pairs, the two strands of AT-rich
regions of double helices are separated more easily, pro -
viding the single-stranded template regions required for
DNA replication.
10.21 (a) Why isn’t DNA primase activity required to initiate
rolling-circle replication?(b) DNA primase is required
for the discontinuous synthesis of the lagging strand,
which occurs on the single-stranded tail of the rolling
circle. Why?
ANS: Rolling-circle replication begins when an endonuclease
cleaves one strand of a circular DNA double helix. This
cleavage produces a free 3 ′-OH on one end of the cut strand, allowing it to function as a primer. The discon -
tinuous synthesis of the lagging strand requires the de
novo initiation of each Okazaki fragment, which requires
DNA primase activity.
10.22 DNA polymerase I is needed to remove RNA primers
during chromosome replication in E. coli . However,
DNA polymerase III is the true replicase in E. coli . Why
does not DNA polymerase III remove the RNA
primers?
ANS: DNA polymerase III does not have a 5 ′ → 3′ exonuclease
activity that acts on double-stranded nucleic acids. Thus,
it cannot excise RNA primer strands from replicating
DNA molecules. DNA polymerase I is present in cells at
much higher concentrations and functions as a mono -
mer. Thus, DNA polymerase I is able to catalyze the
removal of RNA primers from the vast number of Oka -
zaki fragments formed during the discontinuous replica -
tion of the lagging strand.
10.23 In E. coli , three different proteins are required to unwind
the parental double helix and keep the unwound strands
in an extended template form. What are these proteins,
and what are their respective functions?
ANS: DNA helicase unwinds the DNA double helix, and sin -
gle-strand DNA-binding protein coats the unwound
strands, keeping them in an extended state. DNA gyrase
catalyzes the formation of negative supercoiling in E. coli
DNA, and this negative supercoiling behind the replica -
tion forks is thought to drive the unwinding process
because superhelical tension is reduced by unwinding
the complementary strands.
10.24 How similar are the structures of DNA polymerase I and
DNA polymerase III in E. coli ? What is the structure of
the DNA polymerase III holoenzyme? What is the func -
tion of the dnaN gene product in E. coli ?
ANS: DNA polymerase I is a single polypeptide of molecular
weight 109,000, whereas DNA polymerase III is a
complex multimeric protein. The DNA polymerase III
holoenzyme has a molecular mass of about 900,000
daltons and is composed of at least 20 different poly -
peptides. The dnaN gene product, the b subunit of
DNA polymerase III, forms a dimeric clamp that encir -
cles the DNA molecule and prevents the enzyme from
dissociating from the template DNA during replication.
10.25 The dnaA gene product of E. coli is required for the ini -
tiation of DNA synthesis at oriC. What is its function?
How do we know that the DnaA protein is essential to
the initiation process?
ANS: DnaA protein initiates the formation of the replication
bubble by binding to the 9-bp repeats of OriC . DnaA
protein is known to be required for the initiation process
because bacteria with temperature-sensitive mutations in
the dnaA gene cannot initiate DNA replication at restric -
tive temperatures.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 38 8/14/2015 6:42:54 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 39 | Answers to All Questions and Problems WC -39
10.26 What is a primosome, and what are its functions? What
essential enzymes are present in the primosome? What
are the major components of the E. coli replisome? How
can geneticists determine whether these components are
required for DNA replication?
ANS: The primosome is a protein complex that initiates the
synthesis of Okazaki fragments during lagging strand
synthesis. The major components of the E. coli DNA
primosome are DNA primase and DNA helicase. Genet -
icists have been able to show that both DNA primase
and DNA helicase are required for DNA replication by
demonstrating that mutations in the genes encoding
these enzymes result in the arrest of DNA synthesis in
mutant cells under conditions where the altered proteins
are inactive.
10.27 The chromosomal DNA of eukaryotes is packaged into
nucleosomes during the S phase of the cell cycle. What
obstacles do the size and complexity of both the repli -
some and the nucleosome present during the semicon -
servative replication of eukaryotic DNA? How might
these obstacles be overcome?
ANS: Nucleosomes and replisomes are both large macromo -
lecular structures, and the packaging of eukaryotic
DNA into nucleosomes raises the question of how a
replisome can move past a nucleosome and replicate
the DNA in the nucleosome in the process. The most
obvious solution to this problem would be to com -
pletely or partially disassemble the nucleosome to
allow the replisome to pass. The nucleosome would
then reassemble after the replisome had passed. One
popular model has the nucleosome partially disassem -
bling, allowing the replisome to move past it (see
Figure 10.33 b).
10.28 T wo mutant strains of E. coli each have a temperature-
sensitive mutation in a gene that encodes a product
required for chromosome duplication. Both strains repli -
cate their DNA and divide normally at 25°C but are
unable to replicate their DNA or divide at 42°C. When
cells of one strain are shifted from growth at 25°C to
growth at 42°C, DNA synthesis stops immediately. When
cells of the other strain are subjected to the same tempera -
ture shift, DNA synthesis continues, albeit at a decreasing
rate, for about a half hour. What can you conclude about
the functions of the products of these two genes?
ANS: The product of the first gene is required for DNA chain
extension, whereas the product of the second gene is
only required for the initiation of DNA synthesis.
10.29 In what ways does chromosomal DNA replication in
eukaryotes differ from DNA replication in prokaryotes?
ANS: (1) DNA replication usually occurs continuously in
rapidly growing prokaryotic cells but is restricted to
the S phase of the cell cycle in eukaryotes. (2) Most
eukaryotic chromosomes contain multiple origins of
replication, whereas most prokaryotic chromosomes contain a single origin of replication. (3) Prokaryotes
utilize two catalytic complexes that contain the same
DNA polymerase to replicate the leading and lagging
strands, whereas eukaryotes utilize two or three distinct
DNA polymerases for leading and lagging strand syn -
thesis. (4) Replication of eukaryotic chromosomes
requires the partial disassembly and reassembly of
nucleosomes as replisomes move along parental DNA
molecules. In prokaryotes, replication probably involves
a similar partial disassembly/reassembly of nucleo -
some-like structures. (5) Most prokaryotic chromo -
somes are circular and thus have no ends. Most
eukaryotic chromosomes are linear and have unique
termini called telomeres that are added to replicating
DNA molecules by a unique, RNA-containing enzyme
called telomerase.
10.30 (a) The chromosome of the bacterium Salmonella
typhimurium contains about 4 × 106 nucleotide pairs.
Approximately how many Okazaki fragments are pro -
duced during one complete replication of the S.
typhimurium chromosome? (b) The largest chromosome
of D. melanogaster contains approximately 6 × 107 nucle -
otide pairs. About how many Okazaki fragments are pro -
duced during the replication of this chromosome?
ANS: (a) 2000–4000 Okazaki fragments. (b) 300,000–600,000
Okazaki fragments.
10.31 In the yeast S. cerevisiae , haploid cells carrying a mutation
called est1 (for ever-shorter telomeres) lose distal telo -
mere sequences during each cell division. Predict the
ultimate phenotypic effect of this mutation on the prog -
eny of these cells.
ANS: The chromosomes of haploid yeast cells that carry the
est1 mutation become shorter during each cell division.
Eventually, chromosome instability results from the
complete loss of telomeres, and cell death occurs because
of the deletion of essential genes near the ends of
chromosomes.
10.32 Assume that the sequence of a double-stranded DNA
shown below is present at one end of a large DNA mol -
ecule in a eukaryotic chromosome.
5′-(centromere sequence)-gattccccgggaagcttggggggcccatcttcgtacgtctttgca-3 ′
3′-(centromere sequence)-ctaaggggcccttcgaaccccccgggtagaagcatgagaaacgt-5 ′
You have reconstituted a eukaryotic replisome that is
active in vitro . However, it lacks telomerase activity. If
you isolate the DNA molecule shown above and repli -
cate it in your in vitro system, what products would you
expect?
ANS: Without telomerase, the 5 ′ end of the newly replicated
strand will be missing some bases. The exact number of
missing bases does not matter:
5′-(centromere sequence)-gattccccgggaagcttggggggcccatcttcgtacgtctttgca-3 ′
3′-(centromere sequence)-ctaaggggcccttcgaaccccccgcgggtagaagcatg-5 ′
5′-(centromere sequence)-gattccccgggaagcttggggggcccatcttcgtacgtctttgca-3 ′
3′-(centromere sequence)-ctaaggggcccttc-5 ′
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 39 8/14/2015 6:42:54 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 40 | 40-WC Answers to All Questions and Problems
Chapter 11
11.1 Distinguish between DNA and RNA (a) chemically,
(b) functionally, and (c) by location in the cell.
ANS: (a) RNA contains the sugar ribose, which has a hydroxyl
(OH) group on the 2-carbon; DNA contains the sugar
2-deoxyribose, with only hydrogens on the 2-carbon.
RNA usually contains the base uracil at positions where
thymine is present in DNA. However, some DNAs con -
tain uracil, and some RNAs contain thymine. DNA exists
most frequently as a double helix (double-stranded mole -
cule); RNA exists more frequently as a single-stranded
molecule. But, some DNAs are single-stranded and some
RNAs are double-stranded. (b) The main function of
DNA is to store genetic information and to transmit that
information from cell to cell and from generation to gen -
eration. RNA stores and transmits genetic information in
some viruses that contain no DNA. In cells with both
DNA and RNA: (1) mRNA acts as an intermediary in pro -
tein synthesis, carrying the information from DNA in the
chromosomes to the ribosomes (sites at which proteins are
synthesized). (2) tRNAs carry amino acids to the ribo -
somes and function in codon recognition during the syn -
thesis of polypeptides. (3) rRNA molecules are essential
components of the ribosomes. (4) snRNAs are important
components of spliceosomes. (5) miRNAs play key roles
in regulating gene expression (see Chapter 18). (c) DNA is
located primarily in the chromosomes, which are found in
the nucleus of eukaryotic cells; however, some DNA is
also found in cytoplasmic organelles, such as mitochon -
dria and chloroplasts. RNA is located throughout cells.
11.2 What bases in the mRNA transcript would represent the
following DNA template sequence: 5 ′-TGCAGACA-3 ′?
ANS: 3′-ACGUCUGU-5 ′
11.3 What bases in the transcribed strand of DNA would give
rise to the following mRNA base sequence:
5′-CUGAU-3 ′?
ANS: 3′-GACTA-5 ′
11.4 On the basis of what evidence was the messenger RNA
hypothesis established?
ANS: The genetic information of cells is stored in DNA, which
is located predominantly in the chromosomes. The gene
products (polypeptides) are synthesized primarily in the
cytoplasm on ribosomes. Some intermediate must there -
fore carry the genetic information from the chromo -
somes to the ribosomes. RNA molecules (mRNAs) were
shown to perform this function by means of RNA pulse-
labeling and pulse-chase experiments combined with
autoradiography. The enzyme RNA polymerase was
subsequently shown to catalyze the synthesis of mRNA
using chromosomal DNA as a template. Finally, the
mRNA molecules synthesized by RNA polymerase were
shown to faithfully direct the synthesis of specific poly -
peptides when used in in vitro protein synthesis systems.
11.5 At what locations in a eukaryotic cell does protein syn -
thesis occur?ANS: Protein synthesis occurs on ribosomes. In eukaryotes,
most of the ribosomes are located in the cytoplasm and
are attached to the extensive membranous network of
endoplasmic reticulum. Some protein synthesis also
occurs in cytoplasmic organelles such as chloroplasts and
mitochondria.
11.6 List three ways in which the mRNAs of eukaryotes differ
from the mRNAs of prokaryotes.
ANS: (1) Eukaryotes have a 5 ′ cap on their mRNAs; prokary -
otes do not. (2) Messenger RNAs of eukaryotes generally
have a 3 ′ poly-A tail, prokaryotic mRNAs do not. (3)
Messenger RNA formation in eukaryotes involves
removal of introns (when present) and the splicing
together of exons. Prokaryotic genes (with very rare
exceptions) do not have introns.
11.7 What different types of RNA molecules are present in
prokaryotic cells? in eukaryotic cells? What roles do
these different classes of RNA molecules play in the cell?
ANS: Both prokaryotic and eukaryotic organisms contain mes -
senger RNAs, transfer RNAs, and ribosomal RNAs. In
addition, eukaryotes contain small nuclear RNAs and
micro RNAs. Messenger RNA molecules carry genetic
information from the chromosomes (where the informa -
tion is stored) to the ribosomes in the cytoplasm (where
the information is expressed during protein synthesis).
The linear sequence of triplet codons in an mRNA mol -
ecule specifies the linear sequence of amino acids in the
polypeptides produced during translation of that mRNA.
T ransfer RNA molecules are small (about 80 nucleotides
long) molecules that carry amino acids to the ribosomes
and provide the codon-recognition specificity during
translation. Ribosomal RNA molecules provide part of
the structure and function of ribosomes; they represent
an important part of the machinery required for the syn -
thesis of polypeptides. Small nuclear RNAs are struc -
tural components of spliceosomes, which excise
noncoding intron sequences from nuclear gene tran -
scripts. Micro RNAs are involved in the regulation of
gene expression.
11.8 Many eukaryotic genes contain noncoding introns that
separate the coding sequences or exons of these genes. At
what stage during the expression of these split genes are
the noncoding intron sequences removed?
ANS: The entire nucleotide-pair sequences—including the
introns—of the genes are transcribed by RNA poly -
merase to produce primary transcripts that still contain
the intron sequences. The intron sequences are then
spliced out of the primary transcripts to produce the
mature, functional RNA molecules. In the case of
protein-encoding nuclear genes of higher eukaryotes,
the introns are spliced out by complex macromolecular
structures called spliceosomes.
11.9 For several decades, the dogma in biology has been that
molecular reactions in living cells are catalyzed by
enzymes composed of polypeptides. We now know that
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 40 8/14/2015 6:42:54 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 41 | Answers to All Questions and Problems WC -41
the introns of some precursor RNA molecules such as the
rRNA precursors in Tetrahymena are removed autocata -
lytically (self-spliced) with no involvement of any cata -
lytic protein. What does the demonstration of autocatalytic
splicing indicate about the dogma that biological reac -
tions are always catalyzed by proteinaceous enzymes?
ANS: “Self-splicing” of RNA precursors demonstrates that
RNA molecules can also contain catalytic sites; this
property is not restricted to proteins.
11.10 What role(s) do spliceosomes play in pathways of gene
expression? What is their macromolecular structure?
ANS: Spliceosomes excise intron sequences from nuclear gene
transcripts to produce the mature mRNA molecules that
are translated on ribosomes in the cytoplasm. Spliceo -
somes are complex macromolecular structures composed
of snRNA and protein molecules (see Figure 11.22).
11.11 What components of the introns of nuclear genes that
encode proteins in higher eukaryotes are conserved and
required for the correct excision of intron sequences
from primary transcripts by spliceosomes?
ANS: The introns of protein-encoding nuclear genes of higher
eukaryotes almost invariably begin (5 ′) with GT and end
(3′) with AG. In addition, the 3 ′ subterminal A in the
“TACTAAC box” is completely conserved; this A is
involved in bond formation during intron excision.
11.12 Match one of the following terms with each of the
descriptions given below. Terms: (1) sigma ( s) factor;
(2) poly(A) tail; (3) TATAAT; (4) exons; (5) TATAAAA;
(6) RNA polymerase III; (7) intron; (8) RNA poly -
merase II; (9) heterogeneous nuclear RNA (hnRNA);
(10) snRNA; (11) RNA polymerase I; (12) TTGACA;
(13) GGCCAATCT (CAAT box).
Descriptions:
(a) Intervening sequence found in many eukaryotic
genes.
(b) A conserved nucleotide sequence ( -30) in eukaryotic
promoters involved in the initiation of transcription.
(c) Small RNA molecules that are located in the nuclei of
eukaryotic cells, most as components of the spliceosome,
that participate in the excision of introns from nuclear
gene transcripts.
(d) A sequence ( -10) in the nontemplate strand of the
promoter of E. coli that facilitates the localized unwind -
ing of DNA when complexed with RNA polymerase.
(e) The RNA polymerase in the nucleus that catalyzes
the synthesis of all rRNAs except for the small 5S rRNA.
(f) The subunit of prokaryotic RNA polymerase that is
responsible for the initiation of transcription at
promoters.
(g) An E. coli promoter sequence located 35 nucleotides
upstream from the transcription-initiation site; it serves
as a recognition site for the sigma factor. (h) The RNA polymerase in the nucleus that catalyzes
the synthesis of the transfer RNA molecules and small
nuclear RNAs.
(i) A polyadenosine tract 20–200 nucleotides long that is
added to the 3 ′ end of most eukaryotic messenger RNAs.
(j) The RNA polymerase that transcribes nuclear genes
that encode proteins.
(k) A conserved sequence in the nontemplate strand of
eukaryotic promoters that is located about 80 nucleo -
tides upstream from the transcription start site.
(l) Segments of an eukaryotic gene that correspond to
the sequences in the final processed RNA transcript of
the gene.
(m) The population of primary transcripts in the nucleus
of a eukaryotic cell.
ANS: (a) 7; (b) 5; (c) 10; (d) 3; (e) 11; (f) 1; (g) 12; (h) 6; (i) 2;
(j) 8; (k) 13; (l) 4; (m) 9.
11.13 (a) Which of the following nuclear pre-mRNA nucleo -
tide sequences potentially contains an intron?
(1) 5′-UGACCAUGGCGCUAACACUGCCAAU
UGGCAAUACUGACCUGAUAGCAUCAGCCAA-3 ′
(2) 5′-UAGUCUCAUCUGUCCAUUGACUUCGAAA
CUGAAUCGUAACUCCUACGUCUAUGGA-3 ′
(3) 5′-UAGCUGUUUGUCAUGACUGACUGGUCA
CUAUCGUACUAACCUGUCAUGCAAUGUC-3 ′
(4) 5′-UAGCAGUUCUGUCGCCUCGUGGUGCUG
CUGGCCCUUCGUCGCUCGGGCUUAGCUA-3 ′
(5) 5′-UAGGUUCGCAUUGACGUACUUCUGAAAC
UACUAACUACUAACGCAUCGAGUCUCAA-3 ′
(b) One of the five pre-mRNAs shown in (a) may undergo
RNA splicing to excise an intron sequence. What mRNA
nucleotide sequence would be expected to result from
this splicing event?
ANS: (a) Sequence 5. It contains the conserved intron sequences:
a 5′ GU, a 3 ′ AG, and a UACUAAC internal sequence
providing a potential bonding site for intron excision.
Sequence 4 has a 5 ′ GU and a 3 ′ AG but contains no
internal A for the bonding site during intron excision.
(b) 5 ′—UAGUCUCAA—3 ′; the putative intron from the
5′ GU through the 3 ′ AG has been removed.
11.14 What is the function of the introns in eukaryotic genes?
ANS: This is a wide-open question at present! There is much
speculation, but little hard evidence. One popular
hypothesis is that introns enhance exon shuffling by
increasing recombination events between sequences
encoding adjacent domains of a polypeptide. Also, in one
yeast mitochondrial gene, the introns contain open read -
ing frames that encode “maturases” that splice out these
introns—a neat negative feedback control. Other introns
may be merely relics of evolution.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 41 8/14/2015 6:42:54 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 42 | 42-WC Answers to All Questions and Problems
11.15 A particular gene is inserted into the phage lambda chro -
mosome and is shown to contain three introns.
(a) The primary transcript of this gene is purified from
isolated nuclei. When this primary transcript is hybrid -
ized under R-loop conditions with the recombinant
lambda chromosome carrying the gene, what will the
R-loop structure(s) look like? Label your diagram.
(b) The mRNA produced from the primary transcript of
this gene is then isolated from cytoplasmic polyribosomes
and similarly examined by the R-loop hybridization
procedure using the recombinant lambda chromosome
carrying the gene. Diagram what the R-loop structure(s)
will look like when the cytoplasmic mRNA is used. Again,
label the components of your diagram.
ANS:
(a)
(b)Displaced single-stranded DNA ("R-loop")
Primary transcript
mRNAExon1
Exon1Intron1
Intron2 Exon2
Exon2Intron3Exon3
Exon3Exon4
Exon4/uni03BB DNA
Intron1 Intron2 Intron3/uni03BB DNA
Displaced single-stranded exon DNA ("R-loops")
/uni03BB DNA/uni03BBDNA
11.16 A segment of DNA in E. coli has the following sequence
of nucleotide pairs:
3´-A
5´-T T T TTTT TTT T T T
AAA AAA A A AA A A
G GG G G GG G G G
C C C CC CC C C CG -5´
C-3´
When this segment of DNA is transcribed by RNA poly -
merase, what will be the sequence of nucleotides in the
RNA transcript if the promoter is located to the left of
the sequence shown?
ANS: If there is a promoter located upstream from this DNA
segment, the nucleotide sequence of this portion of the
RNA transcript will be
5′-UACGAUGACGAUAAGCGACAUAGC-3 ′. If there
is no upstream promoter, this segment of DNA will not
be transcribed.
11.17 A segment of DNA in E. coli has the following sequence
of nucleotide pairs:
3´-A
5´-T T T TTTT TGA T T T
AAA ACT A A AA A A
G GC G G AG G G A
C C C TC CG C C TG -
C-
T T TTTT TTT T T TA
AAA AAA A A ATA A A
G GG G G GG G G G
C C C CC CC C C C G-5´
C-3´ When this segment of DNA is transcribed by RNA poly -
merase, what will be the sequence of nucleotides in the
RNA transcript?
ANS: Assuming that there is a −35 sequence upstream from
the consensus −10 sequence in this segment of the DNA
molecule, the nucleotide sequence of the transcript will
be 5 ′-ACCCGACAUAGCUACGAUGACGAUAAGC
GACAUAGC-3 ′.
11.18 A segment of DNA in E. coli has the following sequence
of nucleotide pairs:
3´-A
5´-T A G AGCT TAG C G A
CGA ATC G C TT C T
T AG A T AG C G C
C G C GA TC T A TT
AA
TT
AT
AA
TC
GT-
A-
A A CACT ATG G T CG
TGA TAC C A GCT T G
G TG A C TG G C A
C C G TC
AT
CG
GC
AT
TA AC T G AT -5´
A-3´
When this segment of DNA is transcribed by RNA poly -
merase, what will be the sequence of nucleotides in the
RNA transcript?
ANS: Given the consensus −35 and −10 sequences in this seg -
ment of DNA and the fact that transcripts almost always
start with a purine, the predicted nucleotide sequence of
the transcript is 5 ′-ACCCGACAUAGCUACGAUGA
CGAUA-3 ′.
11.19 A segment of human DNA has the following sequence of
nucleotide pairs:
3´-A
5´-T A G AGCT TAG C T T
CGA ATC G A AT C T
T AG A T AG C G A
C G C TA TC T A TT
AA
TG
CG
CA
TC
GT-
A-
A A CACT ATG G T CG
TGA TAC C A GCT T G
G TG A C TG G C A
C C G TC
AT
CG
GC
AT
TA AC T G AT -5´
A-3´
When this segment of DNA is transcribed by RNA poly -
merase, what will be the sequence of nucleotides in the
RNA transcript?
ANS: Assuming that there is a CAAT box located upstream
from the TATA box shown in this segment of DNA,
the nucleotide sequence of the transcript will be
5′-ACCCGACAUAGCUACGAUGACGAUA-3 ′.
11.20 The genome of a human must store a tremendous amount
of information using the four nucleotide pairs present in
DNA. What does the language of computers tell us about
the feasibility of storing large amounts of information
using an alphabet composed of just four letters?
ANS: Given the vast amount of information that can be stored
on a small computer chip by using a binary code, it is
clear that large quantities of genetic information can be
stored in the genomes of organisms by using the four-
letter alphabet of the genetic code.
11.21 What is the central dogma of molecular genetics? What
impact did the discovery of RNA tumor viruses have on
the central dogma?
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 42 8/14/2015 6:42:55 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 43 | Answers to All Questions and Problems WC -43
ANS: According to the central dogma, genetic information is
stored in DNA and is transferred from DNA to RNA to
protein during gene expression. RNA tumor viruses
store their genetic information in RNA, and that infor -
mation is copied into DNA by the enzyme reverse tran -
scriptase after a virus infects a host cell. Thus, the
discovery of RNA tumor viruses or retroviruses—retro
for backwards flow of genetic information—provided an
exception to the central dogma.
11.22 The biosynthesis of metabolite X occurs via six steps
catalyzed by six different enzymes. What is the minimal
number of genes required for the genetic control of this
metabolic pathway? Might more genes be involved?
Why?
ANS: If six different enzymes are required for the pathway,
then minimally six genes are necessary for genetic con -
trol of the pathway. However, because the expression of
these enzymes may rely on the product of other genes,
such as transcription factors, more than six genes could
be involved in genetic control of this pathway.
11.23 What do processes of DNA synthesis, RNA synthesis,
and polypeptide synthesis have in common?
ANS: DNA, RNA, and protein synthesis all involve the synthe -
sis of long chains of repeating subunits. All three pro -
cesses can be divided into three stages: chain initiation,
chain elongation, and chain termination.
11.24 What are the two stages of gene expression? Where do
they occur in a eukaryotic cell? a prokaryotic cell?
ANS: The two stages of gene expression are as follows:
(1) T ranscription—the transfer of genetic information
from DNA to RNA.
(2) T ranslation—the transfer of genetic information from
RNA to protein. In eukaryotes, transcription occurs in
the nucleus and translation occurs in the cytoplasm
on complex macromolecular structures called ribosomes.
In prokaryotes, transcription and translation are often
coupled with mRNA molecules often being translated
by ribosomes while still being synthesized during
transcription.
11.25 Compare the structures of primary transcripts with those
of mRNAs in prokaryotes and eukaryotes. On average, in
which group of organisms do they differ the most?
ANS: The primary transcripts of eukaryotes undergo more
extensive posttranscriptional processing than those of
prokaryotes. Thus, the largest differences between
mRNAs and primary transcripts occur in eukaryotes.
T ranscript processing is usually restricted to the excision
of terminal sequences in prokaryotes. In contrast, eukary -
otic transcripts are usually modified by (1) the excision of
intron sequences; (2) the addition of 7-methyl guanosine
caps to the 5 ′ termini; (3) the addition of poly(A) tails to
the 3 ′ termini. In addition, the sequences of some eukary -
otic transcripts are modified by RNA editing processes. 11.26 What five types of RNA molecules participate in the
process of gene expression? What are the functions of
each type of RNA? Which types of RNA perform their
function(s) in (a) the nucleus and (b) the cytoplasm?
ANS: The five types of RNA molecules that are involved in
gene expression are mRNAs, rRNAs, tRNAs, micro
RNAs, and snRNAs. mRNA molecules carry genetic
information from genes to the sites of protein synthesis
and specify the amino acid sequences of polypeptides.
rRNAs are major structural components of the ribo -
somes and provide functions required for translation.
tRNA molecules are the adapters that provide amino
acid-codon specificity during translation; each tRNA is
activated by a specific amino acid and contains an antico -
don sequence that is complementary or partially comple -
mentary to one, two, or three codons in mRNAs.
Micro-RNAs are involved in regulative gene expression
(see Chapter 18). snRNAs are structural components of
the spliceosomes that excise introns from gene transcripts
in eukaryotes. snRNAs perform their splicing functions
in the nucleus. mRNAs carry information from the
nucleus to the cytoplasm, so they function in both com -
partments of the cell. However, their most prominent
function is to direct the synthesis of polypeptides during
translation, which occurs in the cytoplasm. rRNAs and
tRNAs perform their functions during translation in the
cytoplasm. Micro-RNAs become incorporated into ribo -
nucleoprotein complexes in the cytoplasm.
11.27 Why was the need for an RNA intermediary in protein
synthesis most obvious in eukaryotes? How did research -
ers first demonstrate that RNA synthesis occurred in the
nucleus and that protein synthesis occurred in the
cytoplasm?
ANS: In eukaryotes, the genetic information is stored in DNA
in the nucleus, whereas proteins are synthesized on ribo -
somes in the cytoplasm. How could the genes, which are
separated from the sites of protein synthesis by a double-
membrane—the nuclear envelope, direct the synthesis of
polypeptides without some kind of intermediary to carry
the specifications for the polypeptides from the nucleus
to the cytoplasm? Researchers first used labeled RNA
and protein precursors and autoradiography to demon -
strate that RNA synthesis and protein synthesis occurred
in the nucleus and the cytoplasm, respectively.
11.28 T wo eukaryotic genes encode two different polypeptides,
each of which is 335 amino acids long. One gene con -
tains a single exon; the other gene contains an intron of
41,324 nucleotide pairs long. Which gene would you
expect to be transcribed in the least amount of time?
Why? When the mRNAs specified by these genes are
translated, which mRNA would you expect to be trans -
lated in the least time? Why?
ANS: Because transcription results in a primary transcript from
the DNA template, the DNA sequence for the single-
exon gene is the shortest, and so it will be transcribed in
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 43 8/14/2015 6:42:55 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 44 | 44-WC Answers to All Questions and Problems
the least amount of time. However, because each poly -
peptide is the same length, the mature mRNAs for both
genes will be the same length and will be translated in
the same amount of time.
11.29 Design an experiment to demonstrate that RNA tran -
scripts are synthesized in the nucleus of eukaryotes and
are subsequently transported to the cytoplasm.
ANS: A simple pulse- and pulse/chase-labeling experiment will
demonstrate that RNA is synthesized in the nucleus and
is subsequently transported to the cytoplasm. This
experiment has two parts: (1) pulse label eukaryotic cul -
ture cells by growing them in 3H-uridine for a few min -
utes and localize the incorporated radioactivity by
autoradiography. (2) Repeat the experiment, but this
time add a large excess of nonradioactive uridine to the
medium in which the cells are growing after the labeling
period and allow the cells to grow in the nonradioactive
medium for about an hour. Then localize the incorpo -
rated radioactivity by autoradiography.
11.30 T otal RNA was isolated from human cells growing in cul -
ture. This RNA was mixed with nontemplate strands
(single strands) of the human gene encoding the enzyme
thymidine kinase, and the RNA–DNA mixture was incu -
bated for 12 hours under renaturation conditions. Would
you expect any RNA–DNA duplexes to be formed during
the incubation? If so, why? If not, why not? The same
experiment was then performed using the template strand
of the thymidine kinase gene. Would you expect any
RNA–DNA duplexes to be formed in this second
experiment? If so, why? If not, why not?
ANS: RNA–DNA duplexes will be formed when the template
strand is used, but not when the nontemplate strand is
used. (However, if some hybridization is observed with
the nontemplate strand, this is because total RNA was
used and is nonspecific to the thymidine kinase gene)
Only one strand—the template strand—of most genes is
transcribed. Thus, RNA will contain nucleotide sequences
complementary to the template strand but not to the
nontemplate strand.
11.31 T wo preparations of RNA polymerase from E. coli are
used in separate experiments to catalyze RNA synthesis
in vitro using a purified fragment of DNA carrying the
argH gene as template DNA. One preparation catalyzes
the synthesis of RNA chains that are highly heteroge -
neous in size. The other preparation catalyzes the syn -
thesis of RNA chains that are all the same length. What
is the most likely difference in the composition of the
RNA polymerases in the two preparations?
ANS: The first preparation of RNA polymerase is probably
lacking the sigma subunit and, as a result, initiates the
synthesis of RNA chains at random sites along both
strands of the argH DNA. The second preparation prob -
ably contains the sigma subunit and initiates RNA chains
only at the site used in vivo , which is governed by the
position of the −10 and −35 sequences of the promoter. 11.32 T ranscription and translation are coupled in prokaryotes.
Why is this not the case in eukaryotes?
ANS: In eukaryotes, transcription occurs in the nucleus and
translation occurs in the cytoplasm. Because these pro -
cesses occur in different compartments of the cell, they
cannot be coupled as they are in prokaryotes.
11.33 What two elements are almost always present in the
promoters of eukaryotic genes that are transcribed by
RNA polymerase II? Where are these elements located
relative to the transcription start site? What are their
functions?
ANS: TATA and CAAT boxes. The TATA and CAAT boxes are
usually centered at positions −30 and −80, respectively,
relative to the startpoint ( +1) of transcription. The
TATA box is responsible for positioning the transcrip -
tion startpoint; it is the binding site for the first basal
transcription factor that interacts with the promoter.
The CAAT box enhances the efficiency of transcrip -
tional initiation.
11.34 In what ways are most eukaryotic gene transcripts modi -
fied? What are the functions of these posttranscriptional
modifications?
ANS: (1) Intron sequences are spliced out of gene transcripts to
provide contiguous coding sequences for translation. (2)
The 7-methyl guanosine caps added to the 5 ′ termini of
most eukaryotic mRNAs help protect them from degra -
dation by nucleases and are recognized by proteins
involved in the initiation of translation. (3) The poly(A)
tails at the 3 ′ termini of mRNAs play an important role
in their transport from the nucleus to the cytoplasm and
enhance their stability.
11.35 How does RNA editing contribute to protein diversity in
eukaryotes?
ANS: RNA editing sometimes leads to the synthesis of two or
more distinct polypeptides from a single mRNA.
11.36 How do the mechanisms by which the introns of tRNA
precursors, Tetrahymena rRNA precursors, and nuclear
pre-mRNAs are excised differ? In which process are
snRNAs involved? What role(s) do these snRNAs
play?
ANS: The introns of tRNA precursors, Tetrahymena rRNA
precursors, and nuclear pre-mRNAs are excised by com -
pletely different mechanisms. (1) Introns in tRNA are
excised by cleavage and joining events catalyzed by splic -
ing nucleases and ligases, respectively. (2) Introns in Tet-
rahymena rRNA precursors are excised autocatalytically.
(3) Introns of nuclear pre-mRNAs are excised by spli -
ceosomes. snRNAs are involved in nuclear pre-mRNA
splicing as structural components of spliceosomes. In
addition, snRNA U1 is required for the cleavage events
at the 5 ′ termini of introns; U1 is thought to base-pair
with a partially complementary consensus sequence at
this position in pre-mRNAs.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 44 8/14/2015 6:42:55 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 45 | Answers to All Questions and Problems WC -45
11.37 A mutation in an essential human gene changes the
5′ splice site of a large intron from GT to CC. Predict
the phenotype of an individual homozygous for this
mutation.
ANS: This zygote will probably be nonviable because the gene
product is essential, and the elimination of the 5 ′ splice
site will almost certainly result in the production of a
nonfunctional gene product.
11.38 T otal RNA was isolated from nuclei of human cells
growing in culture. This RNA was mixed with a purified,
denatured DNA fragment that carried a large intron of a
housekeeping gene (a gene expressed in essentially all
cells), and the RNA–DNA mixture was incubated for
12 hours under renaturation conditions. Would you
expect any RNA–DNA duplexes to be formed during the
incubation? If so, why? If not, why not? The same exper -
iment was then performed using total cytoplasmic RNA
from these cells. Would you expect any RNA–DNA
duplexes to be formed in this second experiment? If so,
why? If not, why not?
ANS: In the first experiment, yes, some hybridization would be
expected because not all of the RNA in the preparation
has been completely processed and will still contain the
intron sequence. However, if only cytoplasmic RNA is
used in the hybridization experiment, all of the mRNA in
the preparation will have been processed (because pro -
cessing occurs in the nucleus) and no hybridization will
be observed.
Chapter 12
12.1 In a general way, describe the molecular organization of
proteins and distinguish proteins from DNA, chemically
and functionally. Why is the synthesis of proteins of par -
ticular interest to geneticists?
ANS: Proteins are long chainlike molecules made up of amino
acids linked together by peptide bonds. Proteins are com -
posed of carbon, hydrogen, nitrogen, oxygen, and usually
sulfur. They provide the enzymatic capacity and much of
the structure of living organisms. DNA is composed
of phosphate, the pentose sugar 2-deoxyribose, and four
nitrogen-containing organic bases (adenine, cytosine,
guanine, and thymine). DNA stores and transmits the
genetic information in most living organisms. Protein
synthesis is of particular interest to geneticists because
proteins are the primary gene products—the key inter -
mediates through which genes control the phenotypes of
living organisms.
12.2 At what locations in the cell does protein synthesis occur?
ANS: Protein synthesis occurs on ribosomes. In eukaryotes,
most of the ribosomes are located in the cytoplasm and
are attached to the extensive membranous network of
endoplasmic reticulum. Some protein synthesis also
occurs in cytoplasmic organelles such as chloroplasts and
mitochondria. 12.3 Is the number of potential alleles of a gene directly
related to the number of nucleotide pairs in the gene? Is
such a relationship more likely to occur in prokaryotes or
in eukaryotes? Why?
ANS: It depends on how you define alleles. If every variation in
nucleotide sequence is considered to be a different allele,
even if the gene product and the phenotype of the organ -
ism carrying the mutation are unchanged, then the
number of alleles will be directly related to gene size.
However, if the nucleotide sequence change must pro -
duce an altered gene product or phenotype before it is
considered a distinct allele, then there will be a positive
correlation, but not a direct relationship, between the
number of alleles of a gene and its size in nucleotide
pairs. The relationship is more likely to occur in pro -
karyotes where most genes lack introns. In eukaryotic
genes, nucleotide sequence changes within introns are
usually neutral; that is, they do not affect the activity of
the gene product or the phenotype of the organism.
Thus, in the case of eukaryotic genes with introns, there
may be no correlation between gene size and number of
alleles producing altered phenotypes.
12.4 Why was it necessary to modify Beadle and T atum’s one
gene–one enzyme concept of the gene to one gene–one
polypeptide?
ANS: Several enzymes were shown to contain two or more dif -
ferent polypeptides, and these polypeptides were some -
times controlled by genes that mapped to different
chromosomes. Thus, the mutations clearly were not in
the same gene.
12.5 (a) Why is the genetic code a triplet code instead of a
singlet or doublet code? (b) How many different amino
acids are specified by the genetic code? (c) How many
different amino acid sequences are possible in a polypep -
tide 146 amino acids long?
ANS: (a) Singlet and doublet codes provide a maximum of
4 and (4)2 or 16 codons, respectively. Thus, neither code
would be able to specify all 20 amino acids. (b) 20.
(c) (20)146.
12.6 What types of experimental evidence were used to deci -
pher the genetic code?
ANS: Synthetic RNA molecules (polyuridylic acid molecules)
containing only the base uracil were prepared. When
these synthetic molecules were used to activate in vitro
protein synthesis systems, small polypeptide containing
only the amino acid phenylalanine (polyphenylalanine
molecules) was synthesized. Codons composed only of
uracil were thus shown to specify phenylalanine. Similar
experiments were carried out using synthetic RNA mol -
ecules with different base compositions. Later, in vitro
systems activated with synthetic RNA molecules with
known repeating base sequences were developed. Ulti -
mately, in vitro systems in which specific aminoacyl-
tRNAs where shown to bind to ribosomes activated with
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 45 8/14/2015 6:42:55 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 46 | 46-WC Answers to All Questions and Problems
specific mini-mRNAs, which were trinucleotides of
known base sequence, were developed and used in codon
identification.
12.7 In what sense and to what extent is the genetic code
(a) degenerate, (b) ordered, and (c) universal?
ANS: (a) The genetic code is degenerate in that all but 2 of the
20 amino acids are specified by two or more codons.
Some amino acids are specified by six different codons.
The degeneracy occurs largely at the third or 3 ′ base of
the codons. “Partial degeneracy” occurs where the third
base of the codon may be either of the two purines or
either of the two pyrimidines and the codon still specifies
the same amino acid. “Complete degeneracy” occurs
where the third base of the codon may be any one of the
four bases and the codon still specifies the same amino
acid. (b) The code is ordered in the sense that related
codons (codons that differ by a single base change) spec -
ify chemically similar amino acids. For example, the
codons CUU, AUU, and GUU specify the structurally
related amino acids leucine, isoleucine, and valine,
respectively. (c) The code appears to be almost com -
pletely universal. Known exceptions to universality
include strains carrying suppressor mutations that alter
the reading of certain codons (with low efficiencies in
most cases) and the use of UGA as a tryptophan codon in
yeast and human mitochondria.
12.8 The thymine analog 5-bromouracil is a chemical muta -
gen that induces single base-pair substitutions in DNA
called transitions (substitutions of one purine for another
purine and one pyrimidine for another pyrimidine).
Using the known nature of the genetic code (T able 12.1),
which of the following amino acid substitutions should
you expect to be induced by 5-bromouracil with the
highest frequency:
(a) Met → Val; (b) Met → Leu; (c) Lys → Thr; (d) Lys →
Gln; (e) Pro → Arg; or (f) Pro → Gln?
Why?
ANS: (a) Met → Val. This substitution occurs as a result of a
transition. All other amino acid substitutions listed would
require transversions.
12.9 Using the information given in Problem 12.8, would you
expect 5-bromouracil to induce a higher frequency of
His → Arg or His → Pro substitutions? Why?
ANS: Expect a higher frequency of His → Arg substitutions.
His → Arg results from a transition; His → Pro would
require a transversion (not induced by 5-bromouracil).
12.10 What is the minimum number of tRNAs required to rec -
ognize the six codons specifying the amino acid leucine?
ANS: Because of wobble (T able 12.2), one tRNA can recognize
both UUA and UUG codons for leucine. However, it
takes two more tRNAs to recognize CUU, CUC, CUA,
and CUG. Therefore, a minimum of three tRNAs are
required to recognize the six codons for leucine. 12.11 Characterize ribosomes in general as to size, location,
function, and macromolecular composition.
ANS: Ribosomes are from 10 to 20 nm in diameter. They are
located primarily in the cytoplasm of cells. In bacteria,
they are largely free in the cytoplasm. In eukaryotes,
many of the ribosomes are attached to the endoplasmic
reticulum in the cytoplasm. Ribosomes are complex
structures composed of over 50 different polypeptides
and three to five different RNA molecules. In both pro -
karyotes and eukaryotes, ribosomes are the site of
translation.
12.12 (a) Where in the cells of higher organisms do ribosomes
originate? (b) Where in the cells are ribosomes most
active in protein synthesis?
ANS: (a) The nucleus, specifically the nucleoli. (b) The cytoplasm.
12.13 Identify three different types of RNA that are involved in
translation and list the characteristics and functions of
each.
ANS: Messenger RNA (mRNA) molecules carry genetic
information from the chromosomes (where the informa -
tion is stored) to the ribosomes in the cytoplasm (where
the information is expressed during protein synthesis).
The linear sequence of triplet codons in an mRNA
molecule specifies the linear sequence of amino acids
in the polypeptide(s) produced during translation of
that mRNA. T ransfer RNA (tRNA) molecules are
small (about 80 nucleotides long) molecules that carry
amino acids to the ribosomes and provide the codon-
recognition specificity during translation. Ribosomal
RNA (rRNA) molecules provide part of the structure
and function of ribosomes; they represent an impor -
tant part of the machinery required for the synthesis of
polypeptides.
12.14. (a) How is messenger RNA related to polysome forma -
tion? (b) How does rRNA differ from mRNA and tRNA
in specificity? (c) How does the tRNA molecule differ
from that of DNA and mRNA in size and helical
arrangement?
ANS: (a) Polysomes are formed when two or more ribosomes
are simultaneously translating the same mRNA mole -
cule. Ribosomes are usually spaced about 90 nucleotides
apart on an mRNA molecule. Thus, polysome size is
determined by mRNA size. (b) A ribosome, which con -
tains rRNA molecules, can participate in the synthesis of
any polypeptide specified by the ribosome-associated
mRNA. In that sense, rRNA is nonspecific . Messenger
RNAs and tRNAs, in contrast, are specific , in directing the
synthesis of a particular polypeptide or set of polypep -
tides (mRNA) or in attaching to a particular amino acid
(tRNA). (c) T ransfer RNA molecules are much smaller
(about 80 nucleotides) than DNA or mRNA molecules.
They are single-stranded molecules but have complex
secondary structures because of the base pairing between
different segments of the molecules.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 46 8/14/2015 6:42:55 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 47 | Answers to All Questions and Problems WC -47
12.15 Outline the process of aminoacyl-tRNA formation.
ANS: A specific aminoacyl-tRNA synthetase catalyzes the forma -
tion of an amino acid-AMP complex from the appropriate
amino acid and ATP (with the release of pyro pho spha te).
The same enzyme then catalyzes the formation of the
aminoacyl-tRNA complex, with the release of AMP . Both
the amino acid-AMP and aminoacyl-tRNA linkages are
high-energy phosphate bonds.
12.16 How is translation (a) initiated and (b) terminated?
ANS: (a) T ranslation is initiated by a complex reaction involv -
ing mRNA, ribosomes, initiation factors (IF-1, IF-2, and
IF-3), GTP , the initiator codon AUG, and a special
initiator tRNA (rRNAfMet). It also appears to involve a
base-pairing interaction between a base sequence near
the 3 ′-end of the 16S rRNA and a base sequence in the
“leader sequence” of the mRNA. (b) T ranslation is
terminated by recognition of one or more of the chain-
termination codons (UAG, UAA, and UGA) by the
appropriate protein release factor (RF-1 or RF-2).
12.17 Of what significance is the wobble hypothesis?
ANS: Crick’s wobble hypothesis explains how the anticodon of
a given tRNA can base-pair with two or three different
mRNA codons. Crick proposed that the base-pairing
between the 5 ′ base of the anticodon in tRNA and the 3 ′
base of the codon in mRNA was less stringent than
normal and thus allowed some “wobble” at this site. As a
result, a single tRNA often recognizes two or three of
the related codons specifying a given amino acid (see
T able 12.2).
12.18 If the average molecular mass of an amino acid in a par -
ticular polypeptide is 100 daltons, about how many
nucleotides will be present in an mRNA coding sequence
specifying this polypeptide, which has a molecular mass
of 27,000 daltons?
ANS: At least 813 nucleotides [ = (270 aa × 3) + 3 nucleotides
for termination codon].
12.19 The bases A, G, U, C, I (inosine) all occur at the 5 ′ posi -
tions of anticodons in tRNAs.
(a) Which base can pair with three different bases at the
3′ positions of codons in mRNA? (b) What is the mini -
mum number of tRNAs required to recognize all codons
of amino acids specified by codons with complete
degeneracy?
ANS: (a) Inosine. (b) T wo.
12.20 Assume that in the year 2025, the first expedition of
humans to Mars discovers several Martian life forms
thriving in hydrothermal vents that exist below the plan -
et’s surface. Several teams of molecular biologists extract
proteins and nucleic acids from these organisms and
make some momentous discoveries. Their first discovery
is that the proteins in Martian life forms contain only 14
different amino acids instead of the 20 present in life forms on Earth. Their second discovery is that the DNA
and RNA in these organisms have only two different
nucleotides instead of the four nucleotides present in liv -
ing organisms on Earth. (a) Assuming that transcription
and translation work similarly in Martians and Earth -
lings, what is the minimum number of nucleotides that
must be present in the Martian codon to specify all the
amino acids in Martians? (b) Assuming that the Martian
code proposed above has translational start-and-stop
signals, would you expect the Martian genetic code to be
degenerate like the genetic code used on Earth?
ANS: (a) T wo nucleotides in all combinations of four (24) would
produce 16 codons. Therefore, the minimum number of
nucleotides comprising the Martian genetic code must
be four. (b) Sixteen codons would allow code words for
14 amino acids, one initiation codon, and a translational
termination codon. The Martian genetic code could not
be degenerate.
12.21 What are the basic differences between translation in
prokaryotes and in eukaryotes?
ANS: T ranslation occurs by very similar mechanisms in pro -
karyotes and eukaryotes; however, there are some differ -
ences. (1) In prokaryotes, the initiation of translation
involves base-pairing between a conserved sequence
(AGGAGG)—the Shine–Dalgarno box—in mRNA and
a complementary sequence near the 3 ′ end of the 16S
rRNA. In eukaryotes, the initiation complex forms at the
5′ end of the transcript when a cap-binding protein
interacts with the 7-methyl guanosine on the mRNA.
The complex then scans the mRNA processively and ini -
tiates translation (with a few exceptions) at the AUG
closest to the 5 ′ terminus. (2) In prokaryotes, the amino
group of the initiator methionyl-tRNAfMet is formylated;
in eukaryotes, the amino group of methionyl-tRNAiMet is
not formylated. (3) In prokaryotes, two soluble protein
release factors (RFs) are required for chain termination.
RF-1 terminates polypeptides in response to UAA and
UAG codons; RF-2 terminates chains in response to
UAA and UGA codons. In eukaryotes, one release factor
responds to all three termination codons.
12.22 What is the function of each of the following compo -
nents of the protein-synthesizing apparatus:
(a) Aminoacyl-tRNA synthetase. (b) Release factor 1.
(c) Peptidyl transferase. (d) Initiation factors. (e) Elonga -
tion factor G
ANS: (a) Attachment of an amino acid to the correct tRNA.
(b) Recognition of termination codons UAA and UAG and
release of the nascent polypeptide from the tRNA in the
P site of the ribosome. (c) Formation of a peptide bond
between the amino group of the aminoacyl-tRNA in the
A site and the carboxyl group of the growing polypeptide
on the tRNA in the P site. (d) Formation of the initiation
complex required for translation; all steps leading up to
peptide bond formation. (e) T ranslocation of the pepti -
dyl-tRNA from the A site on the ribosome to the P site.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 47 8/14/2015 6:42:56 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 48 | 48-WC Answers to All Questions and Problems
12.23 An E. coli gene has been isolated and shown to be 68 nm
long. What is the maximum number of amino acids that
this gene could encode?
ANS: Assuming 0.34 nm per nucleotide pair in B-DNA, a gene
68 nm long would contain 200 nucleotide pairs. Given
the triplet code, this gene would contain 200/3 = 66.7
triplets, one of which must specify chain termination.
Disregarding the partial triplet, this gene could encode a
maximum of 65 amino acids.
12.24 (a) What is the difference between a nonsense mutation
and a missense mutation? (b) Are nonsense or missense
mutations more frequent in living organisms? (c) Why?
ANS: (a) A nonsense mutation changes a codon specifying an
amino acid to a chain-termination codon, whereas a mis -
sense mutation changes a codon specifying one amino
acid to a codon specifying a different amino acid. (b)
Missense mutations are more frequent. (c) Of the 64
codons, only three specify chain termination. Thus, the
number of possible missense mutations is much larger
than the number of possible nonsense mutations. More -
over, nonsense mutations almost always produce non -
functional gene products. As a result, nonsense mutations
in essential genes are usually lethal in the homozygous
state.
12.25 The human a-globin chain is 141 amino acids long. How
many nucleotides in mRNA are required to encode
human a-globin?
ANS: 426 nucleotides—3 × 141 = 423 specifying amino acids
plus three (one codon) specifying chain termination.
12.26 What are the functions of the A, P, and E aminoacyl-
tRNA binding sites on the ribosome?
ANS: The incoming aminoacyl-tRNA enters the A site of
the ribosome, the nascent polypeptide-tRNA occupies
the P site, and the uncharged exiting tRNA occupies the
E site.
12.27 (a) In what ways does the order in the genetic code mini -
mize mutational lethality? (b) Why do base-pair changes
that cause the substitution of a leucine for a valine in the
polypeptide gene product seldom produce a mutant
phenotype?
ANS: (a) Related codons often specify the same or very similar
amino acids. As a result, single base-pair substitutions
frequently result in the synthesis of identical proteins
(degeneracy) or proteins with amino acid substitutions
involving very similar amino acids. (b) Leucine and valine
have very similar structures and chemical properties;
both have nonpolar side groups and fold into essentially
the same three-dimensional structures when present in
polypeptides. Thus, substitutions of leucine for valine or
valine for leucine seldom alter the function of a protein. 12.28 (a) What is the function of the Shine–Dalgarno sequence
in prokaryotic mRNAs? (b) What effect does the dele -
tion of the Shine–Dalgarno sequence from an mRNA
have on its translation?
ANS: (a) The Shine–Dalgarno sequence is a conserved
polypurine tract, consensus AGGAGG, that is located
about seven nucleotides upstream from the AUG initiation
codon in mRNAs of prokaryotes. It is complementary to,
and is believed to base-pair with, a sequence near the 5 ′
terminus of the 16S ribosomal RNA. (b) Prokaryotic
mRNAs with the Shine– Dalgarno sequence deleted are
either not translated or are translated inefficiently.
12.29 (a) In what ways are ribosomes and spliceosomes similar?
(b) In what ways are they different?
ANS: (a) Both ribosomes and spliceosomes play essential roles
in gene expression, and both are complex macromolecu -
lar structures composed of RNA and protein molecules.
(b) Ribosomes are located in the cytoplasm; spliceosomes
in the nucleus. Ribosomes are larger and more complex
than spliceosomes.
12.30 The 5 ′ terminus of a human mRNA has the following
sequence:
5′-GAAGAGACAAGGTCAUGGCCAUAUGC
UUGUUCCAAUCGUUAGCUGCGCAGGAUC -
GCCCUGGG . . . . . . 3 ′
When this mRNA is translated, what amino acid sequence
will be specified by this mRNA sequence?
ANS: NH2-Met-Ala-Ile-Cys-Leu-Phe-Gln-Ser-Leu-Ala-
Ala-Gln-Asp-Arg-Pro-Gly-COOH.
12.31 A partial (5 ′ subterminal) nucleotide sequence of a pro -
karyotic mRNA is as follows:
5′-.....AGGAGGCUCGAACAUGUCAAUAUG CUU
GUUCCAAUCGUUAGCUGCGCAGGACCGUCC
CG GA. . . . . . 3 ′
When this mRNA is translated, what amino acid
sequence will be specified by this portion of the mRNA?
ANS: Met-Ser-lle-Cys-Leu-Phe-Gln-Ser-Leu-Ala-Ala-
Gln-Asp-Arg-Pro-Gly
12.32 The following DNA sequence occurs in the nontem plate
strand of a gene in a bacterium (the promoter sequence
is located to the left but is not shown):
5′-GAATGTCAGAACTGCCATGCTTCATATGAA-
TAGACCTCTAG-3 ′
(a) What is the ribonucleotide sequence of the mRNA
molecule that is transcribed from this piece of DNA?
(b) What is the amino acid sequence of the polypeptide
encoded by this mRNA? (c) If the nucleotide indicated ↓
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 48 8/14/2015 6:42:56 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 49 | Answers to All Questions and Problems WC -49
by the arrow undergoes a mutation that changes T to A,
what will be the resulting amino acid sequence following
transcription and translation?
ANS: (a) 5′-GAAUGUCAGAACUGCCAUGCUUCAUAUG
AAUAGACCUCUAG-3 ′ (b) NH2-fMet-Ser-Glu-Leu-
Pro-Cys-Phe-Ile-COOH (c) NH2-fMet-Ser-Glu-Leu-
Pro-Cys-Phe-Ile-Arg-Ile-Asp-Leu-COOH.
12.33 Alan Garen extensively studied a particular nonsense
(chain-termination) mutation in the alkaline phospha -
tase gene of E. coli . This mutation resulted in the termi -
nation of the alkaline phosphatase polypeptide chain at a
position where the amino acid tryptophan occurred in
the wild-type polypeptide. Garen induced revertants (in
this case, mutations altering the same codon) of this
mutant with chemical mutagens that induced single
base-pair substitutions and sequenced the polypeptides
in the revertants. Seven different types of revertants
were found, each with a different amino acid at the tryp -
tophan position of the wild-type polypeptide (termina -
tion position of the mutant polypeptide fragment). The
amino acids present at this position in the various rever -
tants included tryptophan, serine, tyrosine, leucine, glu -
tamic acid, glutamine, and lysine. Did the nonsense
mutation studied by Garen contain a UAG, a UAA, or a
UGA nonsense mutation? Explain the basis of your
deduction.
ANS: (UAG). This is the only nonsense codon that is related to
tryptophan, serine, tyrosine, leucine, glutamic acid, glu -
tamine, and lysine codons by a single base-pair substitu -
tion in each case.
12.34 The following DNA sequence occurs in a bacterium
(the promoter sequence is located to the left but is not
shown).
↓
5′-CAATCATGGACTGCCATGCTTCATATGAATAGTTGACAT-3 ′
3′-GTTAGTACCTGACGGTACGAAGTATACTTATCAACTGTA-5 ′
(a) What is the ribonucleotide sequence of the mRNA
molecule that is transcribed from the template strand of
this piece of DNA? Assume that both translational start
and termination codons are present.
(b) What is the amino acid sequence of the polypeptide
encoded by this mRNA?
(c) If the nucleotide indicated by the arrow undergoes a
mutation that causes this C:G base pair to be deleted,
what will be the polypeptide encoded by the mutant
gene?
ANS: (a) 5′-CAAUCAUGGACUGCCAUGCUUCAUAUG
AAUAGUUGACAU-3 ′ (b) NH2-fMet-Asp-Cys-His-Ala-
Ser-T yr-Glu-COOH (c) NH2-fMet-Asp-Cys -Met-Leu-
His -Met-Asn-Ser- COOH.Chapter 13
13.1 Identify the following point mutations represented in
DNA and in RNA as (1) transitions, (2) transversions, or
(3) reading frameshifts. (a) A to G; (b) C to T; (c) C to G;
(d) T to A; (e) UAU ACC UAU to UAU AAC CUA;
(f) UUG CUA AUA to UUG CUG AUA.
ANS: (a) T ransition, (b) transition, (c) transversion, (d) trans -
version, (e) frameshift, (f) transition.
13.2 Of all possible missense mutations that can occur in a
segment of DNA encoding the amino acid tryptophan,
what is the ratio of transversions to transitions if
all single base-pair substitutions occur at the same
frequency?
ANS: 6:1. UGG transitions: UGA (nonsense), UAG (nonsense),
CGG (Arg). UGG transversions: UGC (Cys), UGU
(Cys), UCG (Ser), UUG (Leu), AGG (Arg), GGG (Gly).
13.3 Both lethal and visible mutations are expected to occur
in fruit flies that are subjected to irradiation. Outline a
method for detecting (a) X-linked lethals and (b) X-linked
visible mutations in irradiated Drosophila .
ANS: (a) ClB method, (b) attached X method (see Chapter 6).
13.4 H. J. Muller used the ClB technique to identify many
radiation-induced recessive lethal mutations on Dro-
sophila ’s X chromosome, which is now known to con -
tain more than a thousand genes. These mutations
could be propagated in stock cultures by keeping them
in heterozygous condition with the ClB chromosome.
Would you expect all these lethal mutations to be
alleles of one essential X-linked gene, or to be alleles
of different essential X-linked genes? Why couldn’t
H. J. Muller determine the answer to this question
experimentally?
ANS: The radiation-induced recessive lethal mutations that
Muller recovered in his experiments were likely
scattered across the entire X chromosome. Thus, they
likely affected different genes. However, Muller could
not study this issue because he could not carry out a
complementation test to determine if any of the lethal
mutations were alleles of the same gene. The reason is
that to perform the complementation test, Muller would
have had to cross females that carried a particular lethal
mutation balanced with the ClB chromosome to males
that carried a different lethal mutation. Because such
males are not viable, the required cross cannot be
performed.
13.5 Published spontaneous mutation rates for humans are
generally higher than those for bacteria. Does this indi -
cate that individual genes of humans mutate more fre -
quently than those of bacteria? Explain.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 49 8/14/2015 6:42:56 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 50 | 50-WC Answers to All Questions and Problems
ANS: Probably not. A human is larger than a bacterium, with
more cells and a longer life span. If mutation frequencies
are calculated in terms of cell generations, the rates for
human cells and bacterial cells are similar.
13.6 A precancerous condition (intestinal polyposis) in a par -
ticular human family group is caused by a single domi -
nant gene. Among the descendants of one woman who
died with cancer of the colon, 10 people have died with
the same type of cancer and 6 now have intestinal pol -
yposis. All other branches of the large kindred have been
carefully examined, and no cases have been found. Sug -
gest an explanation for the origin of the defective gene.
ANS: A dominant mutation presumably occurred in the woman
in whom the condition was first known.
13.7 Juvenile muscular dystrophy in humans depends on an
X-linked recessive gene. In an intensive study, 33 cases
were found in a population of some 800,000 people. The
investigators were confident that they had found all cases
that were well enough advanced to be detected at the
time the study was made. The symptoms of the disease
were expressed only in males. Most of those with the dis -
ease died at an early age, and none lived beyond 21 years
of age. Usually, only one case was detected in a family,
but sometimes two or three cases occurred in the same
family. Suggest an explanation for the sporadic occur -
rence of the disease and the tendency for the gene to
persist in the population.
ANS: The X-linked gene is carried by mothers, and the disease
is expressed in half of their sons. Such a disease is diffi -
cult to follow in pedigree studies because of the recessive
nature of the gene, the tendency for the expression to
skip generations in a family line, and the loss of the males
who carry the gene. One explanation for the sporadic
occurrence and tendency for the gene to persist is that,
by mutation, new defective genes are constantly being
added to the load already present in the population.
13.8 Products resulting from somatic mutations, such as the
navel orange and the Delicious apple, have become
widespread in citrus groves and apple orchards. However,
traits resulting from somatic mutations are seldom main -
tained in animals. Why?
ANS: Plants can be propagated vegetatively, but no such meth -
ods are available for widespread use in animals.
13.9 If a single short-legged sheep should occur in a flock,
suggest experiments to determine whether the short legs
are the result of a mutation or an environmental effect. If
due to a mutation, how can one determine whether the
mutation is dominant or recessive?
ANS: The sheep with short legs could be mated to unrelated
animals with long legs. If the trait is expressed in the first
generation, it could be presumed to be inherited and to
depend on a dominant gene. On the other hand, if it does
not appear in the first generation, F1 sheep could be crossed back to the short-legged parent. If the trait is
expressed in one-half of the backcross progeny, it is prob -
ably inherited as a simple recessive. If two short-legged
sheep of different sex could be obtained, they could be
mated repeatedly to test the hypothesis of dominance. In
the event that the trait is not transmitted to the progeny
that result from these matings, it might be considered to
be environmental or dependent on some complex genetic
mechanism that could not be identified by the simple test
used in the experiments.
13.10 How might enzymes such as DNA polymerase be in volved
in the mode of action of both mutator and antimutator
genes (mutant genes that increase and decrease, respec -
tively, mutation rates)?
ANS: Enzymes may discriminate among the different nucleo -
tides that are being incorporated. Mutator enzymes may
utilize a higher proportion of incorrect nucleotides,
whereas antimutator enzymes may select fewer incorrect
bases in DNA replication. In the case of the phage T4
DNA polymerase, the relative efficiencies of polymeriza -
tion and proofreading by the polymerase’s 3 ′ → 5′ exo-
nuclease activity play key roles in determining the
mutation rate.
13.11 How could spontaneous mutation rates be optimized by
natural selection?
ANS: If both mutators and antimutators operate in the same
living system, an optimum mutation rate for a particular
organism in a given environment may result from natu -
ral selection.
13.12 A mutator gene Dt in maize increases the rate at which
the gene for colorless aleurone ( a) mutates to the domi -
nant allele ( A), which yields colored aleurone. When
reciprocal crosses were made (i.e., seed parent dt/dt, a/a ×
Dt/Dt , a/a and seed parent Dt/Dt , a/a × dt/dt, a/a), the
cross with Dt/Dt seed parents produced three times as
many dots per kernel as the reciprocal cross. Explain
these results.
ANS: Dt is a mutator gene that induces somatic mutations in
developing kernels.
13.13 The deficiency Df(1)wrJ1 removes 16 contiguous bands
from a region near the left end of the Drosophila X chro-
mosome. Females homozygous for this deficiency die.
However, females heterozygous for it and a ClB chromo -
some are viable and fertile. If such females are mated to
males that carry wild-type X and Y chromosomes, what
kinds of progeny will appear and in what proportions?
ANS: The cross is Df(1)wrJ1/ClB females × +/Y (wild-type)
males. The genotypes of the daughters are Df(1)wrJ1/+
(phenotypically wild-type) and ClB/+ (bar-eyed). These
two classes of daughters will occur in equal proportions.
The sons inherit a Y chromosome and either the Df(1)
wrJ1 or ClB X chromosomes, both of which act as reces -
sive lethals. Thus, no sons will appear in the progeny.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 50 8/14/2015 6:42:56 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 51 | Answers to All Questions and Problems WC -51
13.14 In Drosophila , the Y chromosome Y· w+ has a small piece
of the X chromosome translocated to it; this piece con -
tains the wild-type alleles of all the genes missing in
Df(1)wrJ1 mentioned in Problem 13.13. If males carrying
Y·w+ and a wild-type X chromosome are crossed to Df(1)
wrJ1/ClB females, what kinds of progeny will appear, and
in what proportions? How would your answer change if
the wild-type X chromosome in the males carried a radi -
ation-induced recessive lethal mutation located within
the region that is missing in Df(1)wrJ1? How could these
unusual chromosomes be used to devise a scheme that
would allow you to carry out complementation tests
between two independently induced recessive lethal
mutations that map within this region?
ANS: In the cross Df(1)wrJ1/ClB females × +/Y·w+ (wild-type)
males, the daughters will be either Df(1)wrJ1/+ (pheno -
typically wild-type) or ClB/+ (bar-eyed); these two types
of daughters will appear in equal proportions. The sons
from the cross will be either Df(1)wrJ1/ Y·w+ (viable and
phenotypically wild-type because the small piece of the
X chromosome translocated to the Y chromosome con -
tains the genes that are missing in the deficiency Df(1)
wrJ1) or ClB/ Y·w+. This latter genotype will be viable if
the lethal mutation in the ClB chromosome resides in the
region defined by the deficiency Df(1)wrJ1. In that case,
bar-eyed males would appear and be as frequent as wild-
type males. If the lethal mutation in the ClB chromo -
some resides outside the region defined by Df(1)wrJ1,
then no bar-eyed males will appear among the progeny.
If the males in the cross carry a radiation-induced lethal
(ril) mutation in the region defined by Df(1)wrJ1—that is,
if the cross is Df(1)wrJ1/ClB females × ril/Y·w+ males
(viable because the small piece of the X chromosome
carried by the Y chromosome includes the wild-type
allele of ril)—there will not be any wild-type daughters
(genotype Df(1)wrJ1/ril) among the progeny. However,
bar-eyed daughters (genotypically ClB/ril should appear
unless the lethal mutation in the ClB chromosome is
allelic to ril.
An induced lethal mutation that lies within the region
defined by Df(1)wrJ1 could be tested for complementation
with another such lethal mutation. Let’s call the first
mutation lethal-1 and the second mutation lethal-2 . The
required cross for the complementation test is ClB/lethal-1
females × lethal-2 /Y·w+ males. This cross is possible
because the small piece of the X chromosome carried by
the Y· w+ chromosome contains the wild-type allele of
lethal- 2; thus, the lethal-2 /Y·w+ males are viable. Among
the progeny, we would look for daughters with the geno -
type lethal-1/lethal-2 , which, because they lack the ClB
chromosome, will have normal (non-bar) eyes. If these
females appear, we know that lethal-1 and lethal-2 comple -
ment one another; that is, they are mutations in different
genes. If these females do not appear, we can conclude that
lethal-1 and lethal-2 are alleles of the same gene. 13.15 If CTT is a DNA triplet (transcribed strand of DNA)
specifying glutamic acid, what DNA and mRNA base
triplet alterations could account for valine and lysine in
position 6 of the b-globin chain?
ANS:
Amino Acid
Glumatic acid
Valine GUA
Lysine AAA AAA
TTTCATGTACTT Transcribed strand
Mutation
MutationGAAmRNA DNA
GAA... .. ..
... .. ..
... .. ..
13.16 The bacteriophage T4 genome contains about 50
percent A:T base pairs and 50 percent G:C base pairs. The
base analog 2-aminopurine induces A:T → G:C and G:C
→ A:T base-pair substitutions by undergoing tautomeric
shifts. Hydroxylamine is a mutagenic chemical that reacts
specifically with cytosine and induces only G:C → A:T
substitutions. If a large number of independent muta -
tions were produced in bacteriophage T4 by treatment
with 2-aminopurine, what percentage of these mutations
should you expect to be induced to mutate back to the
wild-type genotype by treatment with hydroxylamine?
ANS: About half of the induced mutations would be expected
to mutate back to the wild-type genotype.
13.17 Assuming that the b-globin chain and the a-globin chain
shared a common ancestor, what mechanisms might
explain the differences that now exist in these two chains?
What changes in DNA and mRNA codons would
account for the differences that have resulted in unlike
amino acids at corresponding positions?
ANS: Mutations: transitions, transversions, and frameshifts.
13.18 In a given strain of bacteria, all of the cells are usually
killed when a specific concentration of streptomycin is
present in the medium. Mutations that confer resistance
to streptomycin occur. The streptomycin-resistant
mutants are of two types: some can live with or without
streptomycin; others cannot survive unless this drug is
present in the medium. Given a streptomycin-sensitive
strain of this species, outline an experimental procedure
by which streptomycin-resistant strains of the two types
could be established.
ANS: Irradiate the nonresistant strain and plate the irradiated
organisms on a medium containing streptomycin. Those
that survive and produce colonies are resistant. They
could then be replicated to a medium without strepto -
mycin. Those that survive would be of the first type;
those that can live with streptomycin but not without it
would be the second type.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 51 8/14/2015 6:42:56 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 52 | 52-WC Answers to All Questions and Problems
13.19 One stock of fruit flies was treated with 1000 roentgens
(r) of X-rays. The X-ray treatment increased the muta -
tion rate of a particular gene by 2 percent. What percent -
age increases in the mutation rate of this gene would be
expected if this stock of flies was treated with X-ray doses
of 1500 r, 2000 r, and 3000 r?
ANS: 3%; 4%; 6%.
13.20 Why does the frequency of chromosome breaks induced
by X-rays vary with the total dosage and not with the
rate at which it is delivered?
ANS: Each quantum of energy from the X-rays that is absorbed
in a cell has a certain probability of hitting and breaking
a chromosome. Hence, the greater the number of quanta
of energy or dosage, the more likely the breaks are to
occur. The rate at which this dosage is delivered does not
change the probability of each quantum inducing a
break.
13.21 A reactor overheats and produces radioactive tritium
(H3), radioactive iodine (I131), and radioactive xenon
(Xn133). Why should we be more concerned about radio -
active iodine than the other two radioactive isotopes?
ANS: Radioactive iodine is concentrated by living organisms
and food chains.
13.22 One person was in an accident and received 50 roentgens
(r) of X-rays at one time. Another person received 5 r in
each of 20 treatments. Assuming no intensity effect, what
proportionate number of mutations would be expected
in each person?
ANS: The person receiving a total of 100 r would be expected
to have twice as many mutations as the one receiving
50 r.
13.23 A cross was performed in Neurospora crassa between a
strain of mating type A and genotype x+ m+ z and a strain
of mating type a and genotype x m z+. Genes x, m, and z
are closely linked and are present in the order x–m–z on
the chromosome. An ascus produced from this cross
contained two copies (“identical twins”) of each of the
four products of meiosis. If the genotypes of the four
products of meiosis showed that gene conversion had
occurred at the m locus and that reciprocal recombina -
tion had occurred at the x and z loci, what might the
genotypes of the four products look like? In the paren -
theses below, write the genotypes of the four haploid
products of meiosis in an ascus showing gene conversion
at the m locus and reciprocal recombination of the flank -
ing markers (at the x and z loci).
Ascus Spore Pairs
1–2 3–4 5–6 7–8
( )( )( )( )
ANS: ( x+ m+ z) (x+ m+ z+) (x m+ z) (x m z+) or equivalent. 13.24 How does nitrous acid induce mutations? What specific
end results might be expected in DNA and mRNA from
the treatment of viruses with nitrous acid?
ANS: Nitrous acid brings about a substitution of an OH group
for an NH2 group in those bases (A, C, and G) having
NH2 side groups. In so doing, adenine is converted into
hypoxanthine, which base-pairs with cytosine, and cyto -
sine is converted into uracil, which base-pairs with ade -
nine. The net effects are GC ↔ AT base-pair substitutions
(see Figure 13.16).
13.25 Are mutational changes induced by nitrous acid more
likely to be transitions or transversions?
ANS: T ransitions.
13.26 You are screening three new pesticides for potential
mutagenicity by using the Ames test. T wo his− strains
resulting from either a frameshift or a transition muta -
tion were used and produced the following results (num -
ber of revertant colonies):
Strain 1Transition
Mutant
Control
(no chemical)Transion
Mutant
∙
ChemicalTransion Mutant
∙ Chemical
∙ Rat liver
Enzymes
Pesticide #1 21 180 19
Pesticide #2 18 19 17
Pesticide #3 25 265 270
Strain 2Frameshift
Mutant
Control
(no chemical)Frameshift
Mutant ∙
ChemicalFrameshift
Mutant ∙
Chemical ∙ Rat
liver Enzymes
Pesticide #1 5 4 5
Pesticide #2 7 5 93
Pesticide #3 6 9 7
What type of mutations, if any, do the three pesticides
induce?
ANS: P #1—Causes transition mutation. Liver enzymes convert
it into nonmutagen. Does not cause frameshift mutations.
P #2—Does not cause transition mutations. Liver enzymes
convert it into a frameshift mutagen. P #3—Causes
transition mutations. Liver enzymes have no effect on
mutagenicity. Does not cause frameshift mutations.
13.27 How does the action and mutagenic effect of 5-bromo -
uracil differ from that of nitrous acid?
ANS: Nitrous acid acts as a mutagen on either replicating or
nonreplicating DNA and produces transitions from A to
G or C to T, whereas 5-bromouracil does not affect non -
replicating DNA but acts during the replication process
causing GC ↔ AT transitions. 5-Bromouracil must be
incorporated into DNA during the replication process in
order to induce mispairing of bases and thus mutations.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 52 8/14/2015 6:42:57 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 53 | Answers to All Questions and Problems WC -53
13.28 Sydney Brenner and A. O. W. Stretton found that non -
sense mutations did not terminate polypeptide synthesis
in the rII gene of the bacteriophage T4 when these
mutations were located within a DNA sequence interval
in which a single nucleotide insertion had been made on
one end and a single nucleotide deletion had been made
on the other. How can this finding be explained?
ANS: The reading frame will be shifted between the two
frameshift mutations. This shift in reading frame does
not read the normal nonsense codon and termination
does not occur.
13.29 Seymour Benzer and Ernst Freese compared spontane -
ous and 5-bromouracil-induced mutants in the rII gene
of the bacteriophage T4; the mutagen increased the
mutation rate ( rII+ → rII) several hundred times above
the spontaneous mutation rate. Almost all (98 percent) of
the 5-bromouracil-induced mutants could be induced to
revert to wild-type ( rII → rII+) by 5-bromouracil treat -
ment, but only 14 percent of the spontaneous mutants
could be induced to revert to wild-type by this treatment.
Discuss the reason for this result.
ANS: 5-BU causes GC ↔ AT transitions. 5-BU can, therefore,
revert almost all of the mutations that it induces by
enhancing the transition event that is the reverse of the
one that produced the mutation. In contrast, the sponta -
neous mutations will include transversions, frameshifts,
deletions, and other types of mutations, including
transitions. Only the spontaneous transitions will show
enhanced reversion after treatment with 5-BU.
13.30 How do acridine-induced changes in DNA result in
inactive proteins?
ANS: Mutations induced by acridine dyes are primarily inser -
tions or deletions of single base-pairs. Such mutations
alter the reading frame (the in-phase triplets specifying
mRNA codons) for that portion of the gene distal (rela -
tive to the direction of transcription and translation) to
the mutation (see Figure 13.7 b). This would be expected
to totally change the amino acid sequences of polypep -
tides distal to the mutation site and produce inactive
polypeptides. In addition, such frameshift mutations fre -
quently produce in-frame termination codons that result
in truncated proteins.
Use the known codon-amino acid assignments (T able
12.1) to work the following problems.
13.31 Mutations in the genes encoding the α- and β-subunits
of hemoglobin lead to blood diseases such as thalassemia
and sickle-cell anemia. You have found a family in China
in which some members suffer from a new genetic form
of anemia. The DNA sequences at the 5 ′ end of the non -
template strand of the normal and mutant DNA encod -
ing the α subunit of hemoglobin are as follows:
Normal 5-ACGTTATGCCGTACTGCCAGCTAAC
TGCTAAAGAACAATTA……-3 Mutant 5-ACGTTATGCCCGTACTGCCAGCTAA
CTGCTAAAGAACAATTA….-3
(a) What type of mutation is present in the mutant hemo -
globin gene? (b) What are the codons in the translated
portion of the mRNA transcribed from the normal and
mutant genes? (c) What are the amino acid sequences of
the normal and mutant polypeptides?
ANS: (a) Frameshift due to the insertion of C at the 9th, 10th, or
11th nucleotide from the 5 ′ end. (b) Normal: 5 ′-AUGCC -
GUACUGCCAGCUAACUGCUAAAGAACAAUUA-3 ′.
Mutant: 5 ′-AUGCCCGUACUGCCAGCUAACUGC -
UAAAGAACAAUUA-3 ′. (c) Normal: NH2-Met-Pro-T yr-
Cys-Gln-Leu-Thr-Ala-Lys-Glu-Gln-Leu. Mutant: NH2-
Met-Pro-Val-Leu-Pro-Ala-Asn-Cys.
13.32 Bacteriophage MS2 carries its genetic information in
RNA. Its chromosome is analogous to a polygenic mol -
ecule of mRNA in organisms that store their genetic
information in DNA. The MS2 minichromosome
encodes four polypeptides (i.e., it has four genes). One of
these four genes encodes the MS2 coat protein, a poly -
peptide of 129 amino acids long. The entire nucleotide
sequence in the RNA of MS2 is known. Codon 112 of
the coat protein gene is CUA, which specifies the amino
acid leucine. If you were to treat a replicating population
of bacteriophage MS2 with the mutagen 5-bromouracil,
what amino acid substitutions would you expect to be
induced at position 112 of the MS2 coat protein (i.e.,
Leu → other amino acid)? ( Note: Bacteriophage MS2
RNA replicates using a complementary strand of RNA
and base-pairing as DNA.)
ANS: Proline and serine.
13.33 Would the different amino acid substitutions induced by
5-bromouracil at position 112 of the coat polypeptide
that you indicated in Problem 13.32 be expected to occur
with equal frequency? If so, why? If not, why not? Which
one(s), if any, would occur more frequently?
ANS: No. Leucine → proline would occur more frequently.
Leu (CUA) — 5-BU → Pro (CCA) occurs by a single
base-pair transition, whereas Leu (CUA) — 5-BU → Ser
(UCA) requires two base-pair transitions. Recall that
5-bromouracil (5-BU) induces only transitions (see
Figure 13.15).
13.34 Would such mutations occur if a nonreplicating suspen -
sion of MS2 phage was treated with 5-bromouracil?
ANS: No. 5-Bromouracil is mutagenic only to replicating
nucleic acids.
13.35 Recall that nitrous acid deaminates adenine, cytosine, and
guanine (adenine → hypoxanthine, which base-pairs with
cytosine; cytosine → uracil, which base-pairs with adenine;
and guanine → xanthine, which base-pairs with cytosine).
Would you expect nitrous acid to induce any mutations
that result in the substitution of another amino acid for a
glycine residue in a wild-type polypeptide (i.e., glycine →
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 53 8/14/2015 6:42:57 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 54 | 54-WC Answers to All Questions and Problems
another amino acid) if the mutagenesis were carried out
on a suspension of mature (nonreplicating) T4 bacterio -
phage? ( Note: After the mutagenic treatment of the phage
suspension, the nitrous acid is removed. The treated phage
is then allowed to infect E. coli cells to express any induced
mutations.) If so, by what mechanism? If not, why not?
ANS: Yes:
DNA:
mRNA:
Polypeptide:
orGGX
GGXHNO2
AGX
Gly Ser or Ar g
(depending on X)CCX'GGX
UCX'
DNA:
mRNA:
Polypeptide:
orGGX
GGXHNO2
GAX
Gly Asp or Glu
(depending on X)CCX'GGX
CUX'
DNA:
mRNA:
Polypeptide:GGX
GGXHNO2
AAX
Gly Asn or Lys
(depending on X)CCX'GGX
UUX'
Note: The X at the third position in each codon in mRNA
and in each triplet of base pairs in DNA refers to the fact
that there is complete degeneracy at the third base in the
glycine codon. Any base may be present in the codon,
and it will still specify glycine.
13.36 Keeping in mind the known nature of the genetic code,
the information given about phage MS2 in Problem
13.32, and the information you have learned about
nitrous acid in Problem 13.35, would you expect
nitrous acid to induce any mutations that would result
in amino acid substitutions of the type glycine →
another amino acid if the mutagenesis were carried out
on a suspension of mature (nonreplicating) MS2 bacte -
riophage? If so, by what mechanism? If not, why not?
ANS: No. The glycine codon is GGX, where X can be any one
of the four bases. Because of this complete degeneracy
at the third position of the glycine codon, changing X
to any other base will have no effect (i.e., the codon will
still specify glycine). Nitrous acid deaminates guanine
(G) to xanthine, but xanthine still base-pairs with cyto -
sine. Thus, guanine is not a target for mutagenesis by
nitrous acid.
13.37 Would you expect nitrous acid to induce a higher fre -
quency of T yr → Ser or T yr → Cys substitutions? Why?ANS: T yr → Cys substitutions; T yr to Cys requires a transition,
which is induced by nitrous acid. T yr to Ser would
require a transversion, and nitrous acid is not expected to
induce transversions.
13.38 Which of the following amino acid substitutions should
you expect to be induced by 5-bromouracil with the
highest frequency? (a) Met → Leu; (b) Met → Thr;
(c) Lys → Thr; (d) Lys → Gln; (e) Pro → Arg; or (f) Pro
→ Gln? Why?
ANS: (b) Met → Thr. 5-Bromouracil induces transitions, not
transversions. All other changes listed require transversions.
13.39 The wild-type sequence of part of a protein is
NH2-T rp-T rp-T rp-Met-Arg-Glu-T rp-Thr-Met
Each mutant in the following table differs from wild-
type by a single point mutation. Using this information,
determine the mRNA sequence coding for the wild-type
polypeptide. If there is more than one possible nucleo -
tide, list all possibilities.
Mutant Amino Acid Sequence of Polypeptide
1 T rp-T rp-T rp Met
2 T rp-T rp-T rp-Met-Arg-Asp-T rp-Thr-Met
3 T rp-T rp-T rp-Met-Arg-Lys-T rp-Thr-Met
4 T rp-T rp-T rp-Met-Arg-Glu-T rp-Met-Met
ANS: 5′-UGG-UGG-UGG-AUG-CGA(or AGA)-GAA(or
GAG)-UGG-AUG-3 ′
13.40 Acridine dyes such as proflavin are known to induce
primarily single base-pair additions and deletions. Sup -
pose that the wild-type nucleotide sequence in the
mRNA produced from a gene is
5′-AUGCCCUUUGGGAAAGGGUUUCCCUAA-3 ′
Also, assume that a mutation is induced within this gene by
proflavin, and, subsequently, a revertant of this mutation is
similarly induced with proflavin and shown to result from
a second-site suppressor mutation within the same gene. If
the amino acid sequence of the polypeptide encoded by
this gene in the revertant (double mutant) strain is
NH2-Met-Pro-Phe-Gly-Glu-Arg-Phe-Pro-COOH
what would be the most likely nucleotide sequence in the
mRNA of this gene in the revertant (double mutant)?
ANS: 5′-AUGCCCUUUGGGGAAAGGUUUCCCUAA-3 ′
13.41 Eight independently isolated mutants of E. coli , all of
which are unable to grow in the absence of histidine (his−),
were examined in all possible cis and trans heterozygotes
(partial diploids). All of the cis heterozygotes were able to
grow in the absence of histidine. The trans heterozygotes
yielded two different responses: some of them grew in the
absence of histidine; others did not. The experimental
results, using “ +” to indicate growth and “0” to indicate
no growth, are given in the accompanying table. How
many genes are defined by these eight mutations? Which
mutant strains carry mutations in the same gene(s)?
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 54 8/14/2015 6:42:57 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 55 | Answers to All Questions and Problems WC -55
Growth of Trans Heterozygotes (without Histidine)
Mutant 1 2 3 4 5 6 7 8
8 0 0 0 0 0 0 1 0
7 + + + + + + 0
6 0 0 0 0 0 0
5 0 0 0 0 0
4 0 0 0 0
3 0 0 0
2 0 0
1 0
ANS: T wo genes; mutations 1, 2, 3, 4, 5, 6, and 8 are in one
gene; mutation 7 is in a second gene.
13.42 Assume that the mutants described in Problem 13.41
yielded the following results. How many genes would
they have defined? Which mutations would have been in
the same gene(s)?
Mutant 1 2 3 4 5 6 7 8
8 + + + + + + 0 0
7 + + + + + + 0
6 + + + + 0 0
5 + + + + 0
4 + + 0 0
3 + + 0
2 0 0
1 0
ANS: Four genes; mutations 1 and 2 in one gene; mutations 3
and 4 in a second gene; mutations 5 and 6 in a third gene;
and mutations 7 and 8 in a fourth gene.
13.43 In Drosophila , white , white cherry , and vermilion are all sex-
linked mutations affecting eye color. All three mutations
are recessive to their wild-type allele(s) for red eyes. A
white-eyed female crossed with a vermilion-eyed male
produces white-eyed male offspring and red-eyed (wild-
type) female offspring. A white-eyed female crossed with
a white cherry-eyed male produces white-eyed sons and
light cherry-eyed daughters. Do these results indicate
whether or not any of the three mutations affecting eye
color are located in the same gene? If so, which
mutations?
ANS: The complementation test for allelism involves placing
mutations pairwise in a common protoplasm in the trans
configuration and determining whether the resulting
trans heterozygotes have wild-type or mutant pheno -
types. If the two mutations are in different genes, the
two mutations will complement each other, because the
wild-type copies of each gene will produce functional gene products (see Figure 13.21 a). However, if the two
mutations are in the same gene, both copies of the gene in
the trans heterozygote will produce defective gene prod -
ucts, resulting in a mutant phenotype (see Figure 13.21 b).
When complementation occurs, the trans heterozy -
gote will have the wild-type phenotype. Thus, the
complementation test allows one to determine whether
any two recessive mutations are located in the same gene
or in different genes. Because the mutations of interest
are sex-linked, all the male progeny will have the same
phenotype as the female parent. They are hemizygous,
with one X chromosome obtained from their mother. In
contrast, the female progeny are trans heterozygotes. In
the cross between the white-eyed female and the vermil -
ion-eyed male, the female progeny have red eyes, the
wild-type phenotype. Thus, the white and vermilion
mutations are in different genes, as illustrated in the
following diagram:
X chromosome
from par enttrans heter ozygote
X chromosome
from par ent
Complementation yields wild-type phenotype; both v+ and w+
gene pr oducts ar e produced in the trans heterozygote.vv+
w+v+ gene pr oduct
w+ gene pr oductw
In the cross between a white-eyed female and a white
cherry-eyed male, the female progeny have light cherry-
colored eyes (a mutant phenotype), not wild-type red
eyes as in the first cross. Since the trans heterozygote has
a mutant phenotype, the two mutations, white and white
cherry , are in the same gene:
trans heter ozygote
No w+ gene pr oduct; ther efore, mutant phenotype.wch No active ( w+)
gene pr oductw
X chromosome
from par entX chromosome
from par ent
13.44 The loz (lethal on Z) mutants of bacteriophage X are con -
ditional lethal mutants that can grow on E. coli strain
Y but cannot grow on E. coli strain Z. The results shown
in the following table were obtained when seven loz
mutants were analyzed for complementation by infect -
ing E. coli strain Z with each possible pair of mutants.
A “+” indicates that progeny phage were produced in
the infected cells, and a “0” indicates that no progeny
phage were produced. All possible cis tests were also
done, and all cis heterozygotes produced wild-type yields
of progeny phage.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 55 8/14/2015 6:42:58 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 56 | 56-WC Answers to All Questions and Problems
Mutant 1 2 3 4 5 6 7
7 + + 0 + 0 0 0
6 + + + + + 0
5 + + 0 + 0
4 0 0 + 0
3 + + 0
2 0 0
1 0
Propose three plausible explanations for the apparently
anomalous complementation behavior of loz mutant
number 7. (b) What simple genetic experiments can be
used to distinguish between the three possible explana -
tions? (c) Explain why specific outcomes of the proposed
experiments will distinguish between the three possible
explanations.
ANS: Mutations 1, 2, and 4 do not complement one another
and thus appear to be located in the same gene, as
do mutations 3 and 5. The anomaly is that mutation 7
does not complement mutations 3, 5, and 6, even
though mutation 6 does complement mutations 3 and
5. (a) There are three simple explanations of the seem -
ingly anomalous complementation behavior of muta -
tion 7. (1) It is a deletion spanning all or parts of two
genes. (2) It is a double mutation with defects in two
genes. (3) It is a polar mutation—a nonsense mutation
that interferes with the expression of downstream
genes—in the promoter-proximal gene of a multigenic
transcription unit. (b) Three simple genetic operations
will distinguish between these three possibilities.
(1) Reversion. Plate a large number of mutant 7 phage
on E. coli strain Z and look for wild-type revertants.
(2) Backcross mutant 7 to wild-type phage and test the
mutant progeny for the ability to complement muta -
tions 3 and 6. (3) Introduce F’s carrying tRNA non -
sense suppressor genes into E. coli strain Z and
determine whether any of them suppress the loz7
mutation. (c) If mutation 7 is a deletion, it will not
revert, and, if it is a double mutation, the reversion
rate will probably be below the level of detection in
your experiment. On the other hand, if it is a polar
nonsense mutation, loz+ revertants will be obtained. If
mutation 7 is a deletion, no new genotypes will be pro -
duced in the backcross to wild-type. However, if it is a
double mutation, some recombinant single-mutant
progeny will be produced in the backcross to wild-
type, and these single mutations will complement
either mutation 3 or mutation 6. If mutation 7 is a
polar nonsense mutation, it should be suppressed by
one or more of the tRNA suppressor genes introduced
into E. coli strain Z.Chapter 14
14.1 (a) In what ways is the introduction of recombinant DNA
molecules into host cells similar to mutation? (b) In what
ways is it different?
ANS: (a) Both introduce new genetic variability into the cell. In
both cases, only one gene or a small segment of DNA
representing a small fraction of the total genome is
changed or added to the genome. The vast majority of
the genes of the organism remain the same. (b) The
introduction of recombinant DNA molecules, if they
come from a very different species, is more likely to
result in a novel, functional gene product in the cell, if
the introduced gene (or genes) is capable of being
expressed in the foreign protoplasm. The introduction of
recombinant DNA molecules is more analogous to
duplication mutations (see Chapter 6) than to other
types of mutations.
14.2 Listed in this question are four different single strands of
DNA. Which of these, in their double-stranded form,
would you expect to be cleaved by a restriction
endonuclease?
(a) ACTCCAGAATTCACTCCG
(b) GCCTCATTCGAAGCCTGA
(c) CTCGCCAATTGACTCGTC
(d) ACTCCACTCCCGACTCCA
ANS: Restriction endonucleases cleave at palindromes in dou -
ble-stranded DNA. A palindrome (indicated in bold-
faced letters) can be found in all the double-stranded
sequences except d. Therefore, sequence d would not be
cleaved by a restriction endonuclease, whereas a, b,
and c could be cleaved by the appropriate enzyme.
(a) ACTCCAGAATTCACTCCG
TGCGGTCTTAAGTGAGGC
(b) GCCTCATTCGAAGCCTGA
CGGAGTAAGCTTCGGACT
(c) CTCGCCAATTGACTCGTC
GAGCGGTTAACTGAGCAG
(d) ACTCCACTCCCGACTCCA
TGAGGAGAGGGCTGAGGT
14.3 If the sequence of base pairs along a DNA molecule
occurs strictly at random, what is the expected frequency
of a specific restriction enzyme recognition sequence of
length (a) four and (b) six base pairs?
ANS: (a) (1/4)4 = 1/256; (b) (1/4)6 = 1/4096
14.4 In what ways do restriction endonucleases differ from
other endonucleases?
ANS: Restriction endonucleases recognize and cut specific
nucleotide sequences in DNA. Most other endonucleases
are not sequence-specific; many cut DNA sequences at
random.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 56 8/14/2015 6:42:58 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 57 | Answers to All Questions and Problems WC -57
14.5 Of what value are recombinant DNA and gene-cloning
technologies to geneticists?
ANS: Recombinant DNA and gene-cloning techniques allow
geneticists to isolate essentially any gene or DNA
sequence of interest and to characterize it structurally
and functionally. Large quantities of a given gene can be
obtained in pure form, which permits one to determine
its nucleotide-pair sequence (to “sequence it” in com -
mon lab jargon). From the nucleotide sequence and our
knowledge of the genetic code, geneticists can predict
the amino acid sequence of any polypeptide encoded by
the gene. By using an appropriate subclone of the gene as
a hybridization probe in northern blot analyses, geneti -
cists can identify the tissues in which the gene is
expressed. Based on the predicted amino acid sequence
of a polypeptide encoded by a gene, geneticists can syn -
thesize oligopeptides and use these to raise antibodies
that, in turn, can be used to identify the actual product of
the gene and localize it within cells or tissues of the
organism. Thus, recombinant DNA and gene-cloning
technologies provide very powerful tools with which to
study the genetic control of essentially all biological pro -
cesses. These tools have played major roles in the explo -
sive progress in the field of biology during the last three
decades.
14.6 What determines the sites at which DNA molecules will
be cleaved by a restriction endonuclease?
ANS: The nucleotide-pair sequence. Restriction endonucle -
ases recognize a specific nucleotide-pair sequence in
DNA regardless of the source of the DNA. In most cases,
this is a 4 or 6 nucleotide-pair sequence; in a few cases,
the recognition sequence is longer (e.g., 8 nucleotide
pairs). Most restriction enzymes cleave the two strands
of the DNA at a specific position (between the same two
adjacent nucleotides in each strand) within the recogni -
tion sequence. A few restriction enzymes bind at a spe -
cific recognition sequence but cut the DNA at a nearby
site outside of the recognition sequences. Some restric -
tion endonucleases cut both strands between the same
two nucleotide pairs (“blunt end” cutters), whereas oth -
ers cut the two strands at different positions and yield
complementary single-stranded ends (“sticky or stag -
gered end” cutters). See T able 14.1 for examples.
14.7 Restriction endonucleases are invaluable tools for biolo -
gists. However, genes encoding restriction enzymes
obviously did not evolve to provide tools for scientists.
Of what possible value are restriction endonucleases to
the microorganisms that produce them?
ANS: Restriction endonucleases are believed to provide a kind
of primitive immune system to the microorganisms
that produce them—protecting their genetic material
from “invasion” by foreign DNAs from viruses or other
pathogens or just DNA in the environment that might
be taken up by the microorganism. Obviously, these microorganisms do not have a sophisticated immune sys -
tem like that of higher animals (see Chapter 22).
14.8 Why is the DNA of a microorganism not degraded by a
restriction endonuclease that it produces, even though
its DNA contains recognition sequences normally
cleaved by the endonuclease?
ANS: Microorganisms that produce restriction endonucleases
also produce enzymes that modify one or more bases in
the recognition sequence for that endonuclease so that it
can no longer cleave the DNA at that site. In most cases,
the modifying enzyme is a methylase that attaches a
methyl group to one or more of the bases in the recogni -
tion sequence. For example, E. coli strains that produce
the restriction endonuclease EcoRI also produce EcoRI
methylase, an enzyme that transfers a methyl group from
S-adenosylmethionine to the second (most 3 ′) adenine
residue in each strand of the recognition sequence
(5-GAATCC-3) producing N6-methyladenines at these
positions. EcoRI cannot cleave DNA that contains
N6-methyladenine at these positions even if the EcoRI
recognition sequence is present in this DNA (see Figure
14.1). Thus, if one wishes to digest DNA with EcoRI, that
DNA must not be isolated from an E. coli strain that is
producing EcoRI methylase.
14.9 One of the procedures for cloning foreign DNA segments
takes advantage of restriction endonucleases such as Hin-
dIII (see T able 14.1) that produce complementary single-
stranded ends. These enzymes produce identical
complementary ends on cleaved foreign DNAs and on the
vector DNAs into which the foreign DNAs are inserted.
Assume that you have inserted your favorite gene into the
HindIII site in the polycloning region of the Bluescript
cloning vector with DNA ligase, have amplified the plas -
mid containing your gene in E. coli , and have isolated a
large quantity of gene/Bluescript DNA. How could you
excise your favorite gene from the Bluescript vector?
ANS: A foreign DNA cloned using an enzyme that produces
single-stranded complementary ends can always be
excised from the cloning vector by cleavage with the
same restriction enzyme that was originally used to clone
it. For example, the HindIII fragment carrying your
favorite can be excised from the Bluescript DNA by
cleavage with restriction endonuclease HindIII. The
human HindIII fragment will be flanked in the recombi -
nant plasmid DNA clone by HindIII cleavage sites.
14.10 You are working as part of a research team studying the
structure and function of a particular gene. Your job is to
clone the gene. A restriction map is available for the
region of the chromosome in which the gene is located;
the map is as follows:
XbaI PstIHindIII
EcoRI EcoRI HindIIISalI
GENE
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 57 8/14/2015 6:42:58 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 58 | 58-WC Answers to All Questions and Problems
Your first task is to prepare a genomic DNA library that
contains clones carrying the entire gene. Describe how
you would prepare such a library in plasmid vector
pBluescript II (see Figure 14.3), indicating which restric -
tion enzymes, media, and host cells you would use.
ANS: Step 1: Digest genomic DNA isolated from your research
organism with EcoRI. Step 2: T reat pBluescript II DNA
with EcoRI. Step 3: Mix the EcoRI-digested genomic and
vector DNAs under annealing conditions and incubate
with DNA ligase. Step 4: T ransform amp5 E. coli cells car -
rying the lacZM15 gene with the resulting ligation prod -
ucts. Step 5: Plate the transformed cells on nutrient agar
medium containing Xgal and ampicillin. Only trans -
formed cells will produce colonies in the presence of
ampicillin. Step 6: Prepare your genomic DNA library
by using bacteria from white colonies; these bacteria will
contain pBluescript II DNA with genomic DNA inserts.
Bacteria harboring Bluescript II plasmids with no insert
will produce blue colonies (see Figure 14.4).
14.11 Compare the nucleotide-pair sequences of genomic
DNA clones and cDNA clones of specific genes of higher
plants and animals. What is the most frequent difference
that you would observe?
ANS: Most genes of higher plants and animals contain non -
coding intron sequences. These intron sequences will be
present in genomic clones, but not in cDNA clones,
because cDNAs are synthesized using mRNA templates
and intron sequences are removed during the processing
of the primary transcripts to produce mature mRNAs.
14.12 Most of the genes of plants and animals that were cloned
soon after the development of recombinant DNA tech -
nologies were genes encoding products that are synthe -
sized in large quantities in specialized cells. For example,
about 90 percent of the protein synthesized in mature
red blood cells of mammals consists of α- and b-globin
chains, and the globin genes were among the first mam -
malian genes cloned. Why were genes of this type so
prevalent among the first eukaryotic genes that were
cloned?
ANS: Higher eukaryotes have very large genomes; for example,
the genomes of mammals contain approximately 3 × 109
nucleotide pairs. Thus, trying to identify a particular
single-copy gene from a clone library is like looking for
the proverbial “needle-in-a-haystack.” T o accomplish
this, one needs a nucleic acid hybridization probe specific
for the gene or an antibody probe specific for the gene
product. Given a specific cell or tissue type producing the
mRNA and/or the protein gene product in large amounts,
it was relatively easy to obtain pure mRNA or pure pro -
tein to use in making a hybridization or antibody probe,
respectively, with which to screen a library for the gene or
cDNA of interest. These approaches are much more dif -
ficult for the majority of the genes that encode products
that represent only a small proportion of the total gene
products in any given cell type. 14.13 Genomic clones of the chloroplastic glutamine synthe -
tase gene ( gln2) of maize are cleaved into two fragments
by digestion with restriction endonuclease HindIII,
whereas full-length maize gln2 cDNA clones are not cut
by HindIII. Explain these results.
ANS: The maize gln2 gene contains many introns, and one of
the introns contains a HindIII cleavage site. The intron
sequences (and thus the HindIII cleavage site) are not
present in mRNA sequences and thus are also not pres -
ent in full-length gln2 cDNA clones.
14.14 In the following illustration, the upper line shows a gene
composed of segments A–D. The lower circle shows a
mutant version of this gene, consisting of two fused
pieces (A-B, C-D), carried on a plasmid. You attempt a
targeted mutagenesis of a diploid cell by transforming
cells with the cloned mutant gene. The following dia -
gram shows the desired pairing of the plasmid and chro -
mosome just prior to recombination.
AB C
A' B' C'Probe
PlasmidD
D'x
x xx
You prepare DNA from the cells, digest it with an enzyme
that cuts at x, and hybridize the cleaved DNA with the
probe shown above. The following diagram shows a
Southern blot of possible results.
1 2 3 4 5
____ ____ ____ ____
____ ____
____
(a) Which lane shows fragments produced from DNA in
the cell before transformation? (b) Which lane shows
fragments produced from DNA in the cell in which the
anticipated targeted mutagenesis occurred?
(c) Which of these blot patterns might be expected if two
crossovers occurred, one between A and B, and the other
between C and D?
ANS: (a) 1 (b) 2 (c) 2
14.15 (a) What experimental procedure is carried out in South -
ern, northern, and western blot analyses? (b) What is the
major difference between Southern, northern, and west -
ern blot analyses?
ANS: (a) Southern, northern, and western blot procedures
all share one common step, namely, the transfer of
macromolecules (DNAs, RNAs, and proteins, respec -
tively) that have been separated by gel electrophoresis
to a solid support—usually a nitrocellulose or nylon
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 58 8/14/2015 6:42:59 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 59 | Answers to All Questions and Problems WC -59
membrane—for further analysis. (b) The major difference
between these techniques is the class of macromolecules
that are separated during the electrophoresis step: DNA
for Southern blots, RNA for northern blots, and protein
for western blots.
14.16 What major advantage does the polymerase chain reac -
tion (PCR) have over other methods for analyzing
nucleic acid structure and function?
ANS: The PCR technique has much greater sensitivity than
any other method available for analyzing nucleic acids.
Thus, PCR procedures permit analysis of nucleic acid
structure given extremely minute amounts of starting
material. DNA sequences can be amplified and structur -
ally analyzed from very small amounts of tissue like
blood or sperm in assault and rape cases. In addition,
PCR methods permit investigators to detect the pres -
ence of rare gene transcripts (e.g., in specific types of
cells) that could not be detected by less sensitive proce -
dures such as northern blot analyses or in situ hybridiza -
tion studies.
14.17 The cloning vectors in use today contain an origin of
replication, a selectable marker gene (usually an antibi -
otic-resistance gene), and one additional component.
What is this component, and what is its function?
ANS: All modern cloning vectors contain a “polycloning site”
or “multiple cloning site” (MCS)—a cluster of unique
cleavage sites for a number of different restriction endo -
nucleases in a nonessential region of the vector into
which the foreign DNA can be inserted. In general, the
greater the complexity of the MCS—that is, the more
restriction endonuclease cleavage sites that are present—
the greater the utility of the vector for cloning a wide
variety of different restriction fragments. For example,
see the MCS present in plasmid Bluescript II shown in
Figure 14.3.
14.18 The drawing in this problem shows a restriction map of
a segment of a DNA molecule. Eco refers to locations
where the restriction endonuclease EcoRI cuts the DNA,
and Pst refers to locations where the restriction enzyme
PstI cuts the DNA. Potential restriction sites are num -
bered 1–6. Distances between restriction sites are shown
on the bottom scale in base pairs (bp). The thick line
represents the part of the molecule that has homology
with a probe.
Eco
5000 bp 3000 bp 4000 bp 5000 bp 2000 bp1Pst
2Eco
3Pst
4Eco
5Pst
6
(a) Assume that individual 1 has restriction sites 1 through
6. If this individual’s DNA is digested with PstI, what are
the expected sizes of the DNA fragments that will
hybridize with the probe? (b) Assume that individual 2
has a mutation that eliminates site 4. If this individual’s DNA is digested with PstI, what are the expected sizes of
the DNA fragments that will hybridize with the probe?
(c) Assume that individual 3 has a mutation that elimi -
nates site 5. If the DNA of this individual is digested with
PstI, what are the expected sizes of the DNA fragments
that will hybridize with the probe? (d) If the DNA of
individual 1 is digested with both PstI and EcoRI, what
are the expected sizes of the DNA fragments that will
hybridize with the probe? (e) If the DNA of individual 3
is digested with both PstI and EcoRI, what are the
expected sizes of the DNA fragments that will hybridize
with the probe?
ANS: (a) 7000 bp + 7000 bp; (b) 14,000 bp; (c) 7000 bp + 7000
bp; (d) 4000 bp + 2000 bp + 5000 bp; (e) 4000 bp +
7000 bp.
14.19 The cystic fibrosis ( CF) gene (location: chromosome 7,
region q31) has been cloned and sequenced, and studies
of CF patients have shown that about 70 percent of them
are homozygous for a mutant CF allele that has a specific
three-nucleotide-pair deletion (equivalent to one codon).
This deletion results in the loss of a phenylalanine residue
at position 508 in the predicted CF gene product. Assume
that you are a genetic counselor responsible for advising
families with CF in their pedigrees regarding the risk of
CF among their offspring. How might you screen puta -
tive CF patients and their parents and relatives for the
presence of the CFDF508 mutant gene? What would the
detection of this mutant gene in a family allow you to say
about the chances that CF will occur again in the family?
ANS: Because the nucleotide-pair sequences of both the normal
CF gene and the CF∆508 mutant gene are known, labeled
oligonucleotides can be synthesized and used as hybridiza -
tion probes to detect the presence of each allele (normal
and ∆508). Under high-stringency hybridization condi -
tions, each probe will hybridize only with the CF allele that
exhibits perfect complementarity to itself. Since the
sequences of the CF gene flanking the ∆508 site are known,
oligonucleotide PCR primers can be synthesized and used
to amplify this segment of the DNA obtained from small
tissue explants of putative CF patients and their relatives
by PCR. The amplified DNAs can then be separated
by agarose gel electrophoresis, transferred to nylon
membranes, and hybridized to the respective labeled
oligonucleotide probes, and the presence of each CF allele
can be detected by autoradiography. For a demonstration
of the utility of this procedure, see Focus on Detection of
a Mutant Gene Causing Cystic Fibrosis. In the procedure
described there, two synthetic oligonucleotide probes—
oligo-N = 3′-CTTTTATAGTAGAAACCAC-5 ′ and
oligo- DF = 3′-TTCTTTTATAGTA—ACCACAA-5 ′
(the dash indicates the deleted nucleotides in the CFD508
mutant allele) were used to analyze the DNA of CF
patients and their parents. For confirmed CF families, the
results of these Southern blot hybridizations with the
oligo-N (normal) and oligo-DF ( CFD508) labeled probes
were often as follows:
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 59 8/14/2015 6:42:59 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 60 | 60-WC Answers to All Questions and Problems
Oligo- ∆F probe:Oligo-N pr obe:
Both parents were heterozygous for the normal CF allele
and the mutant CFD508 allele as would be expected for a
rare recessive trait, and the CF patient was homozygous for
the CFD508 allele. In such families, one-fourth of the chil -
dren would be expected to be homozygous for the D508
mutant allele and exhibit the symptoms of CF , whereas
three-fourths would be normal (not have CF). However,
two-thirds of these normal children would be expected to
be heterozygous and transmit the allele to their children.
Only one-fourth of the children of this family would be
homozygous for the normal CF allele and have no chance
of transmitting the mutant CF gene to their offspring.
Note that the screening procedure described here can be
used to determine which of the normal children are carri -
ers of the CFD508 allele: that is, the mutant gene can be
detected in heterozygotes as well as in homozygotes.
14.20 Cereal grains are major food sources for humans and
other animals in many regions of the world. However,
most cereal grains contain inadequate supplies of certain
of the amino acids that are essential for monogastric ani -
mals such as humans. For example, corn contains insuf -
ficient amounts of lysine, tryptophan, and threonine.
Thus, a major goal of plant geneticists is to produce corn
varieties with increased kernel lysine content. As a pre -
requisite to the engineering of high-lysine corn, molecu -
lar biologists need more basic information about the
regulation of the biosynthesis and the activity of the
enzymes involved in the synthesis of lysine. The first step
in the anabolic pathway unique to the biosynthesis of
lysine is catalyzed by the enzyme dihydrodipicolinate
synthase. Assume that you have recently been hired by a
major U.S. plant research institute and that you have
been asked to isolate a clone of the nucleic acid sequence
encoding dihydrodipicolinate synthase in maize. Briefly
describe four different approaches you might take in
attempting to isolate such a clone and include at least
one genetic approach.
ANS: You could attempt to isolate either a dihydropicolinate
synthase (DHPS) cDNA clone or a DHPS genomic
clone. Once you have isolated either DHPS clone, it can
be used as a hybridization probe to isolate the other
(genomic or cDNA) by screening an appropriate library
by in situ colony hybridization. Four approaches that
have proven effective in isolating other eukaryotic cod -
ing sequences of interest are the following: (1) You could
obtain a clone of the DHPS gene of a lower eukaryote
(a clone of the DHPS gene of Saccharomyces cerevisae
is available) or even a prokaryote and use it as a heter -
ologous hybridization probe to screen a maize cDNA library using low stringency conditions. Sometimes this
approach is successful; sometimes it is not successful.
Whether or not this approach works depends on how
similar the coding sequences of the specific gene of inter -
est are in the two species. (2) You could purify the DHPS
enzyme from corn and use the purified protein to pro -
duce an antibody to DHPS. This DHPS-specific anti -
body could then be used to screen a maize cDNA
expression library by a protocol analogous to the western
blot procedure. (An expression library contains the
cDNA coding sequences fused to appropriate transcrip -
tion and translation signals so that they are expressed in
E. coli or other host cells in which the cDNA library is
prepared.) (3) You could purify the DHPS enzyme from
maize and determine the amino acid sequence of its
NH2-terminus by microsequencing techniques. From
the amino acid sequence and the known genetic code,
you could predict the possible nucleotide sequences
encoding this segment of the protein. Because of the
degeneracy in the code, there would be a set of nucleo -
tide sequences that would all specify the same amino acid
sequence, and you would not know which one was pres -
ent in the maize DHPS gene. However, the synthesis of
oligonucleotides is now routine and quite inexpensive.
Thus, you could synthesize a mixture of oligonucleotides
containing all possible coding sequences and use this
mixture as a set of hybridization probes to screen an
appropriate library by in situ colony hybridization.
(4) Finally, you might try a simple and very quick genetic
approach based on the ability of cDNAs in an expression
library to rescue DHPS mutants of E. coli or other species
that can be transformed at high frequencies. You would
obtain a DHPS-deficient mutant of E. coli (available from
the E. coli Genetics Stock Center at Yale University),
transform it with your cDNA expression library, and
plate the transformed cells on medium lacking diami -
nopimelic acid (the product of DHPS). DHPS-deficient
E. coli mutants cannot grow in the absence of diaminopi -
melic acid; thus, any colonies that grow on your selection
plates should be the result of rescue of the DHPS mutant
bacteria by corn DHPS encoded by cDNAs in the library.
This entire screening procedure can be carried out in 3
or 4 days; thus, it is much simpler than the preceding
approaches. In fact, David A. Frisch first isolated a maize
DHPS cDNA by this simple, but powerful genetic
approach. However, that this approach would only be
expected to work in the case of enzymes that are active as
monomers or homomultimers; it is not applicable when
the active form of the enzyme is a heteromultimer.
14.21 You have just isolated a mutant of the bacterium Shigella
dysenteriae that is resistant to the antibiotic kanamycin,
and you want to characterize the gene responsible for
this resistance. Design a protocol using genetic selection
to identify the gene of interest.
ANS: Genetic selection is the most efficient approach to clon -
ing genes of this type. Prepare a genomic library in an
expression vector such as Bluescript (see Figure 14.3)
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 60 8/14/2015 6:42:59 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 61 | Answers to All Questions and Problems WC -61
using DNA from the kanamycin-resistant strain of Shi-
gella dysenteriae . Then, screen the library for the kanamy -
cin-resistance gene by transforming kanamycin-sensitive
E. coli cells with the clones in the library and plating the
transformed cells on medium containing kanamycin.
Only cells that are transformed with the kanamycin-
resistance gene will produce colonies in the presence of
kanamycin.
14.22 You have isolated a cDNA clone encoding a protein of
interest in a higher eukaryote. This cDNA clone is not
cleaved by restriction endonuclease EcoRI. When this
cDNA is used as a radioactive probe for blot hybridiza -
tion analysis of EcoRI-digested genomic DNA, three
radioactive bands are seen on the resulting Southern
blot. Does this result indicate that the genome of the
eukaryote in question contains three copies of the gene
encoding the protein of interest?
ANS: No. The genome of the species in question may contain
one, two, or three copies of the gene (or family of closely
related genes) encoding this protein. The possibilities
are as follows:
(1) One copy of the gene with two EcoRI cleavage sites
located within intron sequences. (2) T wo copies of the
gene with one EcoRI cleavage site located within an
intron sequence of one of the copies. (3) Three copies of
the gene with no EcoRI cleavage site in any of the copies,
that is, each copy present on a single EcoRI restriction
fragment.
14.23 A linear DNA molecule is subjected to single and double
digestions with restriction endonucleases, and the fol -
lowing results are obtained:
Enzymes Fragment Sizes (in kb)
EcoRI 2.9, 4.5, 7.4, 8.0
HindIII 3.9, 6.0, 12.9
EcoRI and HindIII 1.0, 2.0, 2.9, 3.5, 6.0, 7.4
Draw the restriction map defined by these data.
ANS: HH
E6.0 2.0 7.4 3.51.02.9
EE
14.24 A DNA molecule is subjected to single and double diges -
tions with restriction enzymes, and the products are sep -
arated by gel electrophoresis. The results are as follows
(fragment sizes are in kb):
EcoRIEcoRI
and
HindIII HindIII BamHIEcoRI
and
BamHIHindIII
and
BamHI
8 5 12 6 6 6
4 4 6 4 5
3 2 1
Draw the restriction map of this DNA molecule.ANS: H
B
B1
2
45
E
E
14.25 You are studying a circular plasmid DNA molecule of
size 10.5 kilobase pairs (kb). When you digest this plas -
mid with restriction endonucleases BamHI, EcoRI, and
HindIII, singly and in all possible combinations, you
obtain linear restriction fragments of the following sizes:
Enzymes Fragment Sizes (in kb)
BamHI 7.3, 3.2
EcoRI 10.5
HindIII 5.1, 3.4, 2.0
BamHI + EcoRI 6.7, 3.2, 0.6
BamHI + HindIII 4.6, 2.7, 2.0, 0.7, 0.5
EcoRI + HindIII 4.0, 3.4, 2.0, 1.1
BamHI + EcoRI + HindIII 4.0, 2.7, 2.0, 0.7, 0.6, 0.5
Draw a restriction map for the plasmid that fits your
data.
ANS: There are two possible restriction maps for these data as
shown below:
EB
H
B
HH4.0
2.00.72.70.50.6EB
H
BH
H4.0
2.70.72.00.50.6
Restriction enzyme cleavage sites for BamHI, EcoRI, and
HindIII are denoted by B, E, and H, respectively. The
numbers give distances in kilobase pairs.
14.26 The automated DNA sequencing machines utilize fluo -
rescent dyes to detect the nascent DNA chains synthe -
sized in the presence of the four dideoxy (ddX) chain
terminators, each labeled with a different fluorescent
dye. The dyes fluoresce at different wavelengths, which
are recorded by a photocell as the products of the reac -
tions are separated based on length by capillary gel elec -
trophoresis (see Figure 14.17). In the standard sequencing
reaction, the chains terminating with ddG fluoresce dark
blue (peaks appear black in computer printout), those
terminating with ddC fluoresce light blue, those termi -
nating with ddA fluoresce green, and those terminating
with ddT fluoresce red. The computer printout for the
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 61 8/14/2015 6:43:00 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 62 | 62-WC Answers to All Questions and Problems
sequence of a short segment of DNA is shown as
follows.
First
nucleotide
Last
nucleotide
What is the nucleotide sequence of the nascent strand of
DNA?
What is the nucleotide sequence of the DNA template
strand?
ANS: Nascent strand:
5′-AGTTCTAGAGCGGCCGCCACCGCGTGGAGCTCCAGCTTTTGTTCCCTTT-3 ′
T emplate strand:
3′-TCAAGATCTCGCCGGCGGTGGCGCACCTCGAGGTCGAAAACAAGGGAAA-5 ′
14.27 T en micrograms of a decanucleotide-pair HpaI restriction
fragment were isolated from the double-stranded DNA
chromosome of a small virus. Octanucleotide poly(A)
tails were then added to the 3 ′ ends of both strands using
terminal transferase and dATP; that is,
5′-X X X X X X X X X X-3 ′
3′-X′ X′ X′ X′ X′ X′ X′ X′ X′ X′-5′
↓ terminal transferase, dATP
5′-X X X X X X X X X X A A A A A A A A-3 ′
3′-A A A A A A A A X ′ X′ X′ X′ X′ X′ X′ X′ X′ X′-5′
where X and X ′ can be any of the four standard nucleo -
tides, but X ′ is always complementary to X.
The two complementary strands (“Watson” strand and
“Crick” strand) were then separated and sequenced by
the 2 ′,3′-dideoxyribonucleoside triphosphate chain-ter -
mination method. The reactions were primed using a
synthetic poly(T) octamer; that is,
Watson strand
3′-A A A A A A A A X ′ X′ X′ X′ X′ X′ X′ X′ X′ X′-5′
5′-T T T T T T T T-OH
Crick strand
5′-X X X X X X X X X X A A A A A A A A-3 ′
HO-T T T T T T T T -5′
T wo DNA sequencing reactions were carried out.
Reaction 1 contained the Watson strand template/primer
shown above; reaction 2 contained the Crick strand
template/primer. Both sequencing reactions contained
DNA polymerase and all other substrates and compo -
nents required for DNA synthesis in vitro plus the
standard four 2 ′,3′-dideoxyribonucleoside triphosphate chain-terminators—ddGTP , ddCTP , ddATP , and ddTTP—
each labeled with a different fluorescent dye. The dyes
fluoresce at different wavelengths, which are recorded by
a photocell as the products of the reactions are separated
by capillary gel electrophoresis (see Figure 14.17). In the
standard sequencing reaction, the chains terminating with
ddG fluoresce dark blue (peaks appear black in the com -
puter printouts), those terminating with ddC fluoresce
light blue, those terminating with ddA fluoresce green,
and those terminating with ddT fluoresce red. The com -
puter printout for sequencing reaction 1, which contained
the Watson strand as template, is shown as follows.
11 0 Nucleotide:
Draw the predicted computer printout for reaction
2, which contained the Crick strand as template, in the
following box. Remember that all DNA synthesis occurs
in the 5 ′ → 3′ direction and that the sequence of
the nascent strand reads 5 ′ to 3 ′ from left to right in the
printout.
11 0 Nucleotide:
ANS:
11 0 Nucleotide:
Chapter 15
15.1 Distinguish between a genetic map, a cytogenetic map,
and a physical map. How can each of these types of maps
be used to identify a gene by positional cloning?
ANS: Genetic map distances are determined by crossover fre -
quencies. Cytogenetic maps are based on chromosome
morphology or physical features of chromosomes. Physi -
cal maps are based on actual physical distances—the
number of nucleotide pairs (0.34 nm per base pair)—
separating genetic markers. If a gene or other DNA
sequence of interest is shown to be located near a mutant
gene, a specific band on a chromosome, or a particular
DNA restriction fragment, that genetic or physical
marker (mutation, band, or restriction fragment) can be
used to initiate a chromosome walk to the gene of
interest.
15.2 In the technique of positional cloning, a researcher
begins with a DNA library and selects a clone that is
tightly linked to the gene of interest. That clone, or a
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 62 8/14/2015 6:43:00 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 63 | Answers to All Questions and Problems WC -63
piece of it, is then used as a probe to isolate an overlap -
ping clone from a different DNA library. The second
clone is used to isolate a third overlapping clone from
the first library, and so on, until the researcher has
“walked” along the chromosome to the desired locus. (a)
How can the researcher walk consistently in the same
direction along the chromosome during the cloning pro -
cess? (b) What could happen if a long repetitive DNA
sequence such as a transposon was situated between the
starting clone and the gene of interest?
ANS: (a) T o ensure that the researcher “walks” in the same
direction along the chromosome to the desired locus, it is
necessary to check at each step in the process, usually by
blot hybridization with subclones, which end of the clone
used as a probe overlaps with the next recovered clone.
(b) A long repetitive sequence could present a problem in
chromosome walking because if that sequence is used as a
probe to isolate a new clone, it will hybridize with restric -
tion fragments from all over the genome, and thereby
thwart the effort to walk systematically in one direction
along a single chromosome. T o overcome this problem, a
researcher would have to “jump over” the repetitive ele -
ment and use a piece of unique DNA beyond the element
as a probe in the next step of the walking procedure.
15.3 What is a contig? What is an RFLP? What is a VNTR?
What is an STS? What is an EST? How is each of these
used in the construction of chromosome maps?
ANS: A contig ( contig uous clones) is a physical map of a chro -
mosome or part of a chromosome prepared from a set of
overlapping genomic DNA clones. An RFLP ( restriction
fragment length polymorphism) is a variation in the
length of a specific restriction fragment excised from a
chromosome by digestion with one or more restriction
endonucleases. A VNTR ( variable number tandem
repeat) is a short DNA sequence that is present in the
genome as tandem repeats and in highly variable copy
number. An STS ( sequence tagged site) is a unique DNA
sequence that has been mapped to a specific site on a
chromosome. An EST ( expressed sequence tag) is a cDNA
sequence—a genomic sequence that is transcribed. Con -
tig maps permit researchers to obtain clones harboring
genes of interest directly from DNA Stock Centers—to
“clone by phone.” RFLPs are used to construct the high-
density genetic maps that are needed for positional clon -
ing. VNTRs are especially valuable RFLPs that are used
to identify multiple sites in genomes. STSs and EST s
provide molecular probes that can be used to initiate
chromosome walks to nearby genes of interest.
15.4 The following is a Southern blot of EcoRI-digested DNA
of rye plants from two different inbred lines, A and B.
Developed autoradiogram I shows the bands resulting
from probing the blot with 32P-labeled cDNA1. Autora -
diogram II shows the same Southern blot after it was
stripped of probe and reprobed with 32P-labeled cDNA2. I II
A B A B
a1 b1
b2
a2
a3 b3
a4
(a) Which bands would you expect to see in the autora -
diogram of a similarly probed Southern blot prepared
using EcoRI-digested DNA from F1 hybrid plants pro -
duced by crossing the two inbred lines? (b) What can you
conclude about the gene(s) represented by band a1 on
blot I in the two inbreds? (c) The F1 plants were crossed
to plants possessing only bands a1, a4, and b3. DNA was
isolated from several individual progeny and digested
with EcoRI. The resulting DNA fragments were sepa -
rated by gel electrophoresis, transferred to a nylon mem -
brane, and hybridized with radioactive cDNA1 and
cDNA2 probes. The following table summarizes the
bands present in autoradiograms obtained using DNA
from individual progeny.
Plant
No. Bands Present
a1 a2 a3 a4 b1 b2 b3
1 + + + + +
2 + + + + +
3 + + + + +
4 + + + + +
5 + + + + + + +
6 + + + + +
7 + + + + +
8 + + + + +
9 + + + + +
10 + + +
Interpret these data. Do the data provide evidence for
RFLPs? At how many loci? Are any of the RFLPs
linked? If so, what are the linkage distances defined by
the data?
ANS: (a) a1, a2, a3, a4, b1, b2, and b3. (b) Band a1 represents a
locus whose DNA is homologous to cDNA1. Since the
marker is not polymorphic in the parents used, it cannot
be mapped in this cross. (c) The cDNA1 probe detects
one RFLP locus with alleles that are visualized as band
a4 and bands a2/a3. The cDNA2 detects a second RFLP
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 63 8/14/2015 6:43:01 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 64 | 64-WC Answers to All Questions and Problems
locus with alleles that are visualized as band b3 and bands
b1/b2. The two loci are linked with 20% recombination
observed in this cross.
15.5 As part of the Human Genome Mapping Project, you are
trying to clone a gene involved in colon cancer. Your first
step is to localize the gene using RFLP markers. In the
following table, RFLP loci are defined by STS number
(e.g., STS1), and the gene for colon cancer is designated C.
Loci% Recombi -
nation Loci% Recombi -
nation
C, STS1 50 STS1, STS5 10
C, STS2 15 STS2, STS3 30
C, STS3 15 STS2, STS4 14
C, STS4 1 STS2, STS5 50
C, STS5 40 STS3, STS4 16
STS1, STS2 50 STS3, STS5 25
STS1, STS3 35 STS4, STS5 41
STS1, STS4 50
(a) Given the percentage recombination between differ -
ent RFLP loci and the gene for colon cancer shown in the
table, draw a genetic map showing the order and genetic
distances between adjacent RFLP markers and the gene
for colon cancer. (b) Given that the human genome con -
tains approximately 3.3 × 109 base pairs of DNA and that
the human genetic map contains approximately 3300 cM,
approximately how many base pairs of DNA are located
along the stretch of chromosome defined by this RFLP
map? ( Hint: First figure how many base pairs of DNA are
present per cM in the human genome.) (c) How many
base pairs of DNA are present in the region between the
colon cancer gene and the nearest STS?
ANS: (a) 10 cM 25 cM 15 cM 1 cM 14 cM
STS1 STS5 STS3 C STS4 STS2
(b) 3.3 × 109 bp/3.3 × 103 cM = 1 × 106 bp/cM. The
total map length is 65 cM, which equates to about 65 ×
106 or 65 million bp.
(c) The cancer gene ( C) and STS4 are separated by 1 cM
or about 1 million base pairs.
15.6 What are STRs? Why are they sometimes called
microsatellites?
ANS: STRs are polymorphic tandem repeats of sequences of
only two to four nucleotide pairs. They are called micro -
satellites because they are short in length and are compo -
nents of the highly repetitive satellite DNAs of eukaryotes
(see Chapter 9).
15.7 You have cloned a previously unknown human gene.
What procedure will allow you to position this gene on
the cytological map of the human genome without per -
forming any pedigree analyses? Describe how you would
carry out this procedure.ANS: With a clone of the gene available, fluorescent in situ
hybridization (FISH) can be used to determine which
human chromosome carries the gene and to localize the
gene on the chromosome. Single-stranded copies of the
clone are coupled to a fluorescent probe and hybridized
to denatured DNA in chromosomes spread on a slide.
After hybridization, free probe is removed by washing,
and the location of the fluorescent probe is determined
by photography using a fluorescence microscope (see
Focus on: In Situ Hybridization).
15.8 You have identified a previously unknown human EST.
What must be done before this new EST can be called
an STS?
ANS: An EST must be placed on the physical map of a chro -
mosome before it can be called an STS. If it is also posi -
tioned on the genetic map of the chromosome, then it is
called an anchor marker.
15.9 VNTRs and STRs are specific classes of polymorphisms.
What is the difference between a VNTR and an STR?
ANS: Variable number tandem repeats (VNTRs) are com -
posed of repeated sequences of 10–80 nucleotide pairs,
and short tandem repeats (STRs) are composed of
repeated sequences of 2–10 nucleotide pairs.
15.10 An RFLP and a mutant allele that causes albinism in
humans cannot be shown to be separated by recombina-
tion based on pedigree analysis or by radiation hybrid
mapping. Do these observations mean that the RFLP
occurs within or overlaps the gene harboring the muta -
tion that causes albinism? If so, why? If not, why not?
ANS: The resolution of genetic mapping in humans is quite
low—in the range of 1–10 million base pairs. Radiation
hybrid mapping provides higher resolution—to about
50 kb. However, even with 50-kb resolution, there could
be several genes separating the RFLP from the mutation
responsible for albinism.
15.11 A cloned 6-kb fragment of DNA from human chromo -
some 9 contains a single site recognized by the restric -
tion enzyme EcoRI. This cloned fragment is demarcated
by sites for the restriction enzyme BamHI. There are no
other BamHI recognition sites within the clone.
A researcher has collected DNA samples from 10 people.
He digests each sample with a combination of EcoRI and
BamHI enzymes. The doubly digested DNA is then frac -
tionated by gel electrophoresis and blotted to a mem -
brane. After fixing the DNA to the membrane, the
researcher hybridizes it with a radioactive probe made
from the entire cloned BamHI fragment. The autoradio -
gram obtained by exposing an X-ray film to this mem -
brane yielded the following results. Three of the DNA
samples contained a 4-kb fragment and a 2-kb fragment
that hybridize with the probe, three of the DNA samples
contained a 6-kb DNA fragment that hybridizes with the
probe, and four of the DNA samples contain 6-, 4-, and
2-kb DNA fragments that hybridize with the probe.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 64 8/14/2015 6:43:01 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 65 | Answers to All Questions and Problems WC -65
What has this analysis revealed? What are the genotypes
of the three different types of DNA samples?
ANS: The results of this analysis reveal that the EcoRI cleavage
site within the original 6-kb BamHI clone is polymorphic—
that is, it is present in some chromosomes 9 but absent in
others. We can represent these two types of chromo -
somes 9 as BEB (with the EcoRI site between flanking
BamHI sites) and B-B (without the EcoRI site). The first
three samples came from people who were homozygous
for the BEB version of chromosome 9, the next three
samples came from people who were homozygous for
the B-B version, and the last four samples came from
people who where heterozygous for the two versions—
that is, they had the genotype BEB/B-B . In the human
population that was sampled, the EcoRI site is therefore
the basis for a restriction fragment length polymorphism
(RFLP).
15.12 Both an RFLP and a mutation that causes deafness in
humans map to the same location on the same chromo -
some. How can you determine whether or not the
RFLP overlaps with the gene containing the deafness
mutation?
ANS: You can start a chromosome walk using the hybridization
probe that detects the RFLP . However, if a physical map
of this region of the chromosome already exists (see
Figure 15.5), a chromosome walk might not be neces -
sary. cDNAs can be used to locate candidate genes in the
region covered by the chromosome walk, and the
sequences of genes in individuals with this form of inher -
ited deafness can be compared with the sequences of
homologous genes of individuals with normal hearing,
looking for changes that would be expected to cause a
loss of gene function. The overall process is illustrated in
Figure 15.6.
15.13 What were the goals of the Human Genome Project?
What impact has achieving these goals had on the prac -
tice of medicine to date? What are some of the predicted
future impacts? What are some of the possible misuses of
human genome data?
ANS: The goals of the Human Genome Project were to pre -
pare genetic and physical maps showing the locations of
all the genes in the human genome and to determine the
nucleotide sequences of all 24 chromosomes in the
human genome. These maps and nucleotide sequences
of the human chromosomes helped scientists identify
mutant genes that result in inherited diseases. Hopefully,
the identification of these mutant disease genes will lead
to successful treatments, including gene therapies, for at
least some of these diseases in the future. Potential mis -
uses of these data include invasions of privacy by govern -
ments and businesses—especially employment agencies
and insurance companies. Individuals must not be denied
educational opportunities, employment, or insurance
because of inherited diseases or mutant genes that result
in a predisposition to mental or physical abnormalities. 15.14 What difficulty does repetitive DNA pose for the assem -
bly of whole genome shotgun sequences by computer
analysis?
ANS: Repetitive DNA can make it difficult to assemble long
stretches of DNA sequence from the sequences of DNA
fragments that contain these sequences. The reason is
that in the computer analysis, a repetitive sequence in
one DNA fragment will match with the same repetitive
sequence in another DNA fragment even if the two
DNA fragments are not contiguous in the genome. The
effort to determine which short DNA fragments are
authentic neighbors (contiguous to each other) can
therefore be thrown off by these spurious matches.
15.15 Which type of molecular marker, RFLP or EST, is most
likely to mark a disease-causing mutant gene in humans?
Why?
ANS: An EST is more likely than an RFLP to occur in a dis -
ease-causing human gene. All EST s correspond to
expressed sequences in a genome. RFLPs occur through -
out a genome, in both expressed and unexpressed
sequences. Because less than 2 percent of the human
genome encodes proteins, most RFLPs occur in noncod -
ing DNA.
15.16 Bacteriophage ΦX174 contains 11 genes in a genome of
5386 bp; E. coli has a predicted 4288 genes in a genome
of about 4.639 kb; S. cerevisiae has about 6000 genes in a
genome of size 12.1 mb; C. elegans has about 19,000
genes present in a genome of about 100 mb; and H. sapi -
ens has an estimated 22,000 genes in its 3000-mb genome.
Which genome has the highest gene density? Which
genome has the lowest gene density? Does there appear
to be any correlation between gene density and develop -
mental complexity? If so, describe the correlation.
ANS: The bacteriophage ΦX174 genome has the highest gene
density—one gene per 490 nucleotide pairs. The human
genome has the lowest gene density—about one gene
per 100 kb. In the species mentioned in this question,
there is a striking correlation between genome size and
developmental complexity. With some exceptions,
including species with polyploid genomes, there does
appear to be a rough correlation between genome size
and developmental complexity.
15.17 A contig map of one segment of chromosome 3 of Arabi-
dopsis is as follows.
A1234 5Chromosome segment
6789 10
BH
CG
EDFGenomic clones in
YAC vectors
(a) If an EST hybridizes with genomic clones C, D, and
E, but not with the other clones, in which segment of
chromosome 3 is the EST located? (b) If a clone of gene
ARA hybridizes only with genomic clones C and D, in
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 65 8/14/2015 6:43:01 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 66 | 66-WC Answers to All Questions and Problems
which chromosome segment is the gene located? (c) If a
restriction fragment hybridizes with only one of the
genomic clones shown above, in which chromosome
segment(s) could the fragment be located?
ANS: (a) Segment 5; (b) segment 4; (c) segment 1, 6, or 10.
15.18 Eight human–Chinese hamster radiation hybrids were
tested for the presence of six human EST s designated A
through F . The results are shown in the following table,
where a plus indicates that a marker was present and a
minus indicates that it was absent.
12345678
–– ––
–– ––
– –––
–– ––
–– ––
–A
B
C
D
E
F–++ ++
++ ++
+++ +
++ ++
++ ++
+ ++++ –Radiation hybridMarker
Based on these data, do any of the EST s appear to be
closely linked? Which ones? What would be needed for
you to be more certain of your answer?
ANS: EST markers D and E appear to be closely linked. The
eight human–Chinese hamster radiation hybrids contain
either both D and E or neither marker. More radiation
hybrids would need to be tested for the presence of these
EST s to obtain convincing evidence of this linkage.
15.19 What is the major advantage of gene chips as a microar -
ray hybridization tool?
ANS: The major advantage of gene chips as a microarray
hybridization tool is that a single gene chip can be used
to quantify thousands of distinct nucleotide sequences
simultaneously. The gene-chip technology allows
researchers to investigate the levels of expression of a
large number of genes more efficiently than was possible
using earlier microarray procedures.
15.20 What major advantage does the green fluorescent pro -
tein of the jellyfish have over other methods for studying
protein synthesis and localization?
ANS: The green fluorescent protein (GFP) can be used to study
protein localization and movement over time in living
cells. Most other procedures for studying protein localiza -
tion require that cells be permeabilized and/or fixed and
exposed to antibodies coupled to radioactive or fluores -
cent compounds prior to visualization. As a result, these
procedures only provide information about the location
of a protein at a single time point. In contrast, GFP-tagged
proteins can be used to study the synthesis and movement
of proteins in living cells over time (hours to days).
15.21 You are given chromosome-specific cDNA libraries for
all 24 human chromosomes. How might these libraries
be used to study chromosome evolution in primates?ANS: The DNA sequences in human chromosome-specific
cDNA libraries can be coupled to fluorescent dyes and
hybridized in situ to the chromosomes of other primates.
The hybridization patterns can be used to detect changes
in genome structure that have occurred during the evo -
lution of the various species of primates from common
ancestors (see Figure 6.4). Such comparisons are espe -
cially effective in detecting new linkage relationships
resulting from translocations and centric fusions.
15.22 Of the cereal grass species, only maize contains two cop -
ies of each block of linked genes. What does this duplica -
tion of sets of maize genes indicate about the origin of
this agronomically important species?
ANS: The presence of two copies of each block of genes in the
corn genome indicates that maize has evolved from a tet -
raploid ancestor. The presence of one set of genes pri -
marily in the large chromosomes and the second set
largely in the small chromosomes suggests that maize
has evolved from an allotetraploid (see Chapter 6) pro -
duced by combining the diploid genomes of two ances -
tral cereal grass species.
15.23 Five human genomic DNA clones present in PAC vec -
tors were tested by hybridization for the presence of six
sequence-tagged sites designated STS1 through STS6.
The results are given in the following table: a plus indi -
cates the presence of the STS, and a minus indicates the
absence of the STS.
123456
++ +
–– +
–– +
++ –
–– +A
B
C
D
E–– –
+ ––
–++
–– –
– +–STSYAC clone
(a) What is the order of the STS sites on the
chromosome?
(b) Draw the contig map defined by these data.
ANS: (a) Order of STS sites: 2-5-1-4-3-6.
(b)
A25143 6
B C
DESTS markers:
YAC
clones
15.24 The complete sequences of six mitochondrial genomes
of H. neanderthalensis have been available for some time;
the first H. neanderthalensis mtDNA sequence was pub -
lished in 2008. How similar are the sequences of the
mtDNAs of H. neanderthalensis and H. sapiens ? Are the
genomes similar in size? Is the amount of diversity
observed in the mtDNAs of Neanderthals and humans
the same? If not, what might this tell us about the sizes of
Neanderthal and human populations? How many genes
are present in the H. neanderthalensis mitochondrial
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 66 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 67 | Answers to All Questions and Problems WC -67
genome? How many of these genes encode proteins?
How many specify structural RNA molecules? Are there
any pseudogenes in H. neanderthalensis mtDNA? All of
these questions can be answered by visiting the http://
www.ncbi.nlm.nih.gov/ web site.
ANS: The mtDNAs of Homo neanderthalensis and H. sapiens are
very similar, both in size and in nucleotide sequence. The
H. neanderthalensis mtDNA contains 16,565 nucleotide
pairs, whereas the H. sapiens mtDNA contains 16,569
nucleotide pairs, and the two DNAs exhibit 99 percent
sequence identity. There is less sequence diversity in the
mtDNAs of Neanderthals than in the mtDNAs of
humans, which is consistent with Neanderthal popula -
tions being smaller than human populations. There are
37 genes in the Neanderthal mtDNA: 13 encode pro -
teins and 24 specify structural RNAs (tRNAs and
rRNAs). The Neanderthal mitochondrial genome does
not contain any pseudogenes.
15.25 Assume that you have just sequenced a small fragment of
DNA that you had cloned. The nucleotide sequence of
this segment of DNA is as follows.
aagtagtcgaaaccgaattccgtagaaacaactcgcacgctccggtttc
gtgttgcaacaaaataggcattcccatcgcggcagttagaatcaccga
gtgcccagagtcacgttcgtaagcaggcgcagtttacaggcagca
gaaaaatcgattgaacagaaatggctggcggtaaagcaggcaagga
ttcgggcaaggccaaggcgaaggcggtatcgcgttccgcgcgcgcggg
In an attempt to learn something about the identity or
possible function of this DNA sequence, you decide to
perform a BLAST (nucleotide blast) search on the NCBI
web site (http://www.ncbi.nlm.nih.gov). Paste or type
this sequence into the query sequence box. Run the
search and examine the sequences most closely related to
your query sequence. Are they coding sequences? What
proteins do they encode? Repeat the BLAST search with
only half of your sequence as the query sequence. Do you
still identify the same sequences in the databases? If you
use one-fourth of your sequence as a query, do you still
retrieve the same sequences? What is the shortest DNA
sequence that you can use as a query and still identify the
same sequences in the databanks?
ANS: All of the sequences identified by the megablast search
encode histone H2a proteins. The query sequence is
identical to the coding sequence of the Drosophila
melanogaster histone H2aV gene (a member of the gene
family encoding histone H2a proteins). The query
sequence encodes a Drosophila histone H2a polypeptide
designated variant V . The same databank sequences are
identified when one-half or one-fourth of the given
nucleotide sequence is used as the query in the megablast
search. Query sequences as short as 15–20 nucleotides
can be used to identify the Drosophila gene encoding the
histone H2a variant. However, the results will vary
depending on the specific nucleotide sequence used as
the query sequence. 15.26 The NCBI web site (http://www.ncbi.nlm.nih.gov) can
also be used to search for protein sequences. Instead of
performing a BLAST search with a nucleic acid query,
one performs a protein blast with a polypeptide (amino
acid sequence) query. Assume that you have the follow -
ing partial sequence of a polypeptide:
GYDVEKNNSRIKLGLKSL VSKGIL VQTKGT
GASGSFKLNKKAASGEAKPQAKKAGAAKA
Go to the NCBI web site and access the BLAST tool.
Then click on protein blast and enter the query sequence
in the box at the top. Then click BLAST. What is the
identity of your query sequence?
ANS: Your query sequence is a portion of histone H1.2 of the
mouse ( Mus musculus ). This portion of the mouse histone
H1.2 polypeptide differs by one amino acid from the
corresponding part of the human H1 histone.
15.27 The sequence of a gene in Drosophila melanogaster that
encodes a histone H2A polypeptide is as follows:
aagtagtcgaaaccgaattccgtagaaacaactcgcacgctccggtttc
gtgttgcaacaaaataggcattcccatcgcggcagttagaatcacc
gagtgcccagagtcacgttcgtaagcaggcgcagtttacaggcagcag
aaaaatcgattgaacagaaatggctggcggtaaagcaggcaagg
attcgggcaaggccaaggcgaaggcggtatcgcgttccgcgcg
cgcgggtcttcagttccccgtgggtcgcatccatcgtcatctcaag
agccgcactacgtcacatggacgcgtcggagccactgcagccgtg
tactccgctgccatattggaatacctgaccgccgaggtcctggagtt
ggcaggcaacgcatcgaaggacttgaaagtgaaacgtatcactcc
tcgccacttacagctcgccattcgcggagacgaggagctggacag
cctgatcaaggcaaccatcgctggtggcggtgtcattccgcacata
cacaagtcgctgatcggcaaaaaggaggaaacggtgcaggatccgc
agcggaagggcaacgtcattctgtcgcaggcctactaagccagtcgg
caatcggacgccttcgaaacatgcaacactaatgtttaattcagattt
cagcagagacaagctaaaacaccgacgagttgtaatcatttctgtgcg
ccagcatatatttcttatatacaacgtaatacataattatgtaattctagca
tctccccaacactcacatacatacaaacaaaaaatacaaacacacaaaac
gtatttacccgcacgcatccttggcgaggttgagtatgaaacaaa
aacaaaacttaatttagagcaaagtaattacacgaataaatttaataa
aaaaaactataataaaaacgcc.
Let’s use the translation software available on the Inter -
net at http://www.expasy.org/tools/dna.html to translate
this gene in all six possible reading frames and see which
reading frame specifies histone H2A. Just type or paste
the DNA sequence in the “ExPASy T ranslate” tool box
and click TRANSLATE SEQUENCE. The results will
show the products of translation in all six reading frames
with Met’s and Stop ’s boldfaced to highlight potential
open-reading frames. Which reading frame specifies his -
tone H2A?
ANS: Reading frame 5 ′ → 3′ number 1 has a large open read -
ing frame with a methionine codon near the 5 ′ end. You
can verify that this is the correct reading frame by using
the predicted translation product as a query to search
one of the protein databases (see Problem 15.26).
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 67 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 68 | 68-WC Answers to All Questions and Problems
Chapter 16
16.1 What are CpG islands? Of what value are CpG islands in
positional cloning of human genes?
ANS: CpG islands are clusters of cytosines and guanines that
are often located just upstream (5 ′) from the coding
regions of human genes. Their presence in nucleotide
sequences can provide hints as to the location of genes in
human chromosomes.
16.2 Why is the mutant gene that causes Huntington’s disease
called huntingtin ? Why might this gene be renamed in
the future?
ANS: The gene was named huntingtin after the disease that it
causes when defective. The gene will probably be
renamed after the function of its gene product has been
determined.
16.3 How was the nucleotide sequence of the CF gene used to
obtain information about the structure and function of
its gene product?
ANS: The CF gene was identified by map position-based clon -
ing, and the nucleotide sequences of CF cDNAs were
used to predict the amino acid sequence of the CF gene
product. A computer search of the protein data banks
revealed that the CF gene product was similar to several
ion channel proteins. This result focused the attention of
scientists studying cystic fibrosis on proteins involved in
the transport of salts between cells and led to the discov -
ery that the CF gene product was a transmembrane con -
ductance regulator—now called the CFTR protein.
16.4 How might the characterization of the CF gene and its
product lead to the treatment of cystic fibrosis by
somatic-cell gene therapy? What obstacles must be over -
come before cystic fibrosis can be treated successfully by
gene therapy?
ANS: Once the function of the CF gene product has been
established, scientists should be able to develop proce -
dures for introducing wild-type copies of the CF gene
into the appropriate cells of cystic fibrosis patients to
alleviate the devastating effects of the mutant gene. A
major obstacle to somatic-cell gene-therapy treatment of
cystic fibrosis is the size of the CF gene—about 250 kb,
which is too large to fit in the standard gene transfer vec -
tors. Perhaps a shortened version of the gene constructed
from the CF cDNA—about 6.5 kb—can be used in place
of the wild-type gene. A second major obstacle is getting
the transgene into enough of the target cells of the cystic
fibrosis patient to alleviate the symptoms of the disease.
A third challenge is to develop an expression vector con -
taining the gene that will result in long-term expression
of the introduced gene in transgenic cells. Another con -
cern is how to avoid possible side effects caused by over -
expression or inappropriate expression of the transgene
in cystic fibrosis patients. Despite these obstacles, many
scientists are optimistic that cystic fibrosis will be effec -
tively treated by somatic-cell gene therapy in the future. 16.5 Myotonic dystrophy (MD), occurring in about 1 of 8000
individuals, is the most common form of muscular
dystrophy in adults. The disease, which is characterized
by progressive muscle degeneration, is caused by a domi -
nant mutant gene that contains an expanded CAG repeat
region. Wild-type alleles of the MD gene contain 5–30
copies of the trinucleotide. Mutant MD alleles contain
50 to over 2000 copies of the CAG repeat. The complete
nucleotide sequence of the MD gene is available. Design
a diagnostic test for the mutant gene responsible for
myotonic dystrophy that can be carried out using
genomic DNA from newborns, fetal cells obtained by
amniocentesis, and single cells from eight-cell pre-
embryos produced by in vitro fertilization.
ANS: Oligonucleotide primers complementary to DNA
sequences on both sides (upstream and downstream) of the
CAG repeat region in the MD gene can be synthesized and
used to amplify the repeat region by PCR. One primer
must be complementary to an upstream region of the tem -
plate strand, and the other primer must be complementary
to a downstream region of the nontemplate strand. After
amplification, the size(s) of the CAG repeat regions can be
determined by gel electrophoresis (see Figure 16.2). T ri -
nucleotide repeat lengths can be measured by including
repeat regions of known length on the gel. If fewer than 30
copies of the trinucleotide repeat are present on each chro -
mosome, the newborn, fetus, or pre-embryo is homozy -
gous for a wild-type MD allele or heterozygous for two
different wild-type MD alleles. If more than 50 copies of
the repeat are present on each of the homologous chromo -
somes, the individual, fetus, or cell is homozygous for a
dominant mutant MD allele or heterozygous for two dif -
ferent mutant alleles. If one chromosome contains less
than 30 copies of the CAG repeat and the homologous
chromosome contains more than 50 copies, the newborn,
fetus, or pre-embryo is heterozygous, carrying one
wild-type MD allele and one mutant MD allele.
16.6 In humans, the absence of an enzyme called purine
nucleoside phosphorylase (PNP) results in a severe
T-cell immunodeficiency similar to that of severe com -
bined immunodeficiency disease (SCID). PNP deficiency
exhibits an autosomal recessive pattern of inheritance,
and the gene encoding human PNP has been cloned and
sequenced. Would PNP deficiency be a good candidate
for treatment by gene therapy? Design a procedure for
the treatment of PNP deficiency by somatic-cell gene
therapy.
ANS: Yes. A somatic-cell gene therapy procedure similar to
that used for X-linked SCID (see Figure 16.7) might be
effective in treating purine nucleoside phosphorylase
(PNP) deficiency. White blood cells could be isolated
from the patient, transfected with a vector carrying a
wild-type PNP gene, grown in culture and assayed for
the expression of the PNP transgene, and then infused
back into the patient after the expression of the trans -
gene had been verified.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 68 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 69 | Answers to All Questions and Problems WC -69
16.7 Human proteins can now be produced in bacteria such as
E. coli . However, one cannot simply introduce a human
gene into E. coli and expect it to be expressed. What steps
must be taken to construct an E. coli strain that will
produce a mammalian protein such as human growth
hormone?
ANS: The transcription initiation and termination and transla -
tion initiation signals or eukaryotes differ from those of
prokaryotes such as E. coli . Therefore, to produce a
human protein in E. coli , the coding sequence of the
human gene must be joined to appropriate E. coli regula -
tory signals—promoter, transcription terminator, and
translation initiator sequences. Moreover, if the gene
contains introns, they must be removed or the coding
sequence of a cDNA must be used, because E. coli does
not possess the spliceosomes required for the excision of
introns from nuclear gene transcripts. In addition, many
eukaryotic proteins undergo posttranslational process -
ing events that are not carried out in prokaryotic cells.
Such proteins are more easily produced in transgenic
eukaryotic cells growing in culture.
16.8 You have constructed a synthetic gene that encodes an
enzyme that degrades the herbicide glyphosate. You wish
to introduce your synthetic gene into Arabidopsis plants
and test the transgenic plants for resistance to glypho -
sate. How could you produce a transgenic Arabidopsis
plant harboring your synthetic gene by A. tumefaciens -
mediated transformation?
ANS: You would first construct a chimeric gene containing
your synthetic gene fused to a plant promoter such as the
35S promoter of cauliflower mosaic virus and a plant
transcription termination and polyadenylation signal
such as the one from the nos gene of the Ti plasmid. This
chimeric gene would then be inserted into the T-DNA
of a Ti plasmid carrying a dominant selectable marker
gene (e.g., 35S/NPTII/ nos, which confers resistance to
kanamycin to host cells) and introduced into Agrobacte-
rium tumefaciens cells by transformation. Tissue explants
from Arabidopsis plants would be co-cultivated with A.
tumefaciens cells harboring the recombinant Ti plasmid,
and plant cells that carry T-DNAs inserted into their
chromosomes would be selected by growth on medium
containing the appropriate selective agent (e.g., kanamy -
cin). T ransgenic plants would then be regenerated from
the transformed cells and tested for resistance to
glyphosate.
16.9 A human STR locus contains a tandem repeat (TAGA)n,
where n may be any number between 5 and 15. How
many alleles of this locus would you expect to find in the
human population?
ANS: Eleven, ranging in multiples of 3, from 15 to 45 nucleo -
tides long.
16.10 A group of bodies are found buried in a forest. The police
suspect that they may include the missing Jones family
(two parents and two children). They extract DNA from bones and examine (using PCR) genes A and B, which
are known to contain tandem triplet repeats of variable
length. They also analyze DNA from two other men.
The results are shown below where the numbers indi -
cate the number of copies of a tandem repeat in a par -
ticular allele; for example, male 1 has one allele with 8
and another allele with 9 copies of a tandem repeat in
gene A.
Gene A Gene B
Male 1 8/9 5/7
Male 2 6/8 5/5
Male 3 7/10 7/7
Woman 8/8 3/5
Child 1 7/8 5/7
Child 2 8/8 3/7
Could the woman have been the mother of both chil -
dren? Why or why not? Which man, if any, could have
been the father of child 1?
ANS: The woman could be the mother of both children, hav -
ing passed alleles A 8 and B 5 to child 1 and A 8 and B 3
to child 2. Male 3 could have been the father of child 1.
If so, he contributed alleles A 7 and B 7.
16.11 DNA profiles have played central roles in many rape and
murder trials. What is a DNA profile? What roles do
DNA profiles play in these forensic cases? In some cases,
geneticists have been concerned that DNA profile data
were being used improperly. What were some of their
concerns, and how can these concerns be properly
addressed?
ANS: DNA profiles are the specific patterns (1) of peaks pres -
ent in electropherograms of chromosomal STRs or
VNTRs amplified by PCR using primers tagged with
fluorescent dyes and separated by capillary gel electro -
phoresis (see Figures 16.11 and 16.12) or (2) of bands on
Southern blots of genomic DNAs that have been digested
with specific restriction enzymes and hybridized to
appropriate STR or VNTR sequences (see Figure 16.10).
DNA profiles, “like” epidermal fingerprints, are used as
evidence for identity or nonidentity in forensic cases.
Geneticists have expressed concerns about the statistical
uses of DNA profile data. In particular, they have ques -
tioned some of the methods used to calculate the proba-
bility that DNA from someone other than the suspect
could have produced an observed profile. These con -
cerns have been based in part on the lack of adequate
DNA profile databases for various human subpopula -
tions and the lack of precise information about the
amount of variability in DNA profiles for individuals of
different ethnic backgrounds. These concerns have been
addressed by the acquisition of data on profile frequen -
cies in different populations and ethnic groups from
throughout the world.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 69 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 70 | 70-WC Answers to All Questions and Problems
16.12 The DNA profiles shown in this problem were prepared
using genomic DNA from blood cells obtained from a
woman, her daughter, and three men who all claim to be
the girl’s father.
MC F1 F2 F3
Based on the DNA profiles, what can be determined
about paternity in this case?
ANS: Neither F1 nor F2 could be the girl’s biological father;
only individual F3 could be the child’s father.
16.13 Most forensic experts agree that profiles of DNA from
blood samples obtained at crime scenes and on personal
items can provide convincing evidence for murder con -
victions. However, the defense attorneys sometimes
argue successfully that sloppiness in handling blood sam -
ples results in contamination of the samples. What prob -
lems would contamination of blood samples present in
the interpretation of DNA profiles? Would you expect
such errors to lead to the conviction of an innocent per -
son or the acquittal of a guilty person?
ANS: Contamination of blood samples would introduce more
variability into DNA profiles. This would lead to a lack
of allelic matching of profiles obtained from the blood
samples and from the defendant. Mixing errors would be
expected to lead to the acquittal of a guilty person and
not to the conviction of an innocent person. Only the
mislabeling of samples could implicate someone who is
innocent.
16.14 The Ti plasmid contains a region referred to as T-DNA.
Why is this region called T-DNA, and what is its
significance?
ANS: The T in T-DNA is an abbreviation for “transferred.”
The T-DNA region of the Ti plasmid is the segment
that is transferred from the Ti plasmid of the bacterium
to the chromosomes of the plant cells during Agrobacte-
rium tumefaciens -mediated transformation. 16.15 The generation of transgenic plants using A. tumefaciens -
mediated transformation often results in multiple sites of
insertion. These sites frequently vary in the level of
transgene expression. What approaches could you use to
determine whether or not transgenic plants carry more
than one transgene and, if so, where the transgenes are
inserted into chromosomes?
ANS: Probing Southern blots of restriction enzyme-digested
DNA of the transgenic plants with 32P-labeled transgene
may provide evidence of multiple insertions but would
not reveal the genomic location of the inserts. Fluores -
cence in situ hybridization (FISH) is a powerful proce -
dure for determining the genomic location of gene
inserts. FISH is used to visualize the location of trans -
genes in chromosomes.
16.16 Disarmed retroviral vectors can be used to introduce
genes into higher animals including humans. What
advantages do retroviral vectors have over other kinds of
gene-transfer vectors? What disadvantages?
ANS: Disarmed retroviruses are lacking genes essential for
reproduction in host cells but can still integrate into the
DNA of the host cell in the proviral state. The retroviral
genomes are small enough to allow them to be manipu -
lated easily in vitro and yet will accept foreign DNA
inserts of average gene size. The retroviruses contain
strong promoters in their long terminal repeats that can
be used to drive high levels of transcription of the for -
eign gene insert.
16.17 T ransgenic mice are now routinely produced and studied
in research laboratories throughout the world. How are
transgenic mice produced? What kinds of information
can be obtained from studies performed on transgenic
mice? Does this information have any importance to the
practice of medicine? If so, what?
ANS: T ransgenic mice are usually produced by microinjecting
the genes of interest into pronuclei of fertilized eggs or
by infecting pre-implantation embryos with retroviral
vectors containing the genes of interest. T ransgenic mice
provide invaluable tools for studies of gene expression,
mammalian development, and the immune system of
mammals. T ransgenic mice are of major importance in
medicine; they provide the model system most closely
related to humans. They have been, and undoubtedly
will continue to be, of great value in developing the tools
and technology that will be used for human gene therapy
in the future.
16.18 T wo men claim to be the father of baby Joyce Doe. Joyce’s
mother had her CODIS STR DNA profile analyzed and
was homozygous for allele 8 at the TPOX locus (allele 8
contains 8 repeats of the GAAT sequence at this poly -
morphic locus). Baby Joyce is heterozygous for alleles 8
and 11 at this locus. In an attempt to resolve the disputed
paternity, the two men were tested for their STR DNA
profiles at the TPOX locus on chromosome 2. Putative
father 1 was heterozygous for alleles 8 and 11 at the
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 70 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 71 | Answers to All Questions and Problems WC -71
TPOX locus, and putative father 2 was homozygous for
allele 11 at this locus. Can these results resolve this case
of disputed paternity. If so, who is the biological father? If
not, why not?
ANS: The results cannot resolve the case of disputed paternity.
Baby Joyce received allele 8 at the TPOX locus from her
mother. Given that baby Joyce is heterozygous for alleles
8 and 11 at the TPOX locus, she must have received
allele 11 from her father. However, both of the putative
fathers carry allele 11 and could have passed it on to baby
Joyce.
16.19 Many valuable human proteins contain carbohydrate or
lipid components that are added posttranslationally. Bac -
teria do not contain the enzymes needed to add these
components to primary translation products. How might
these proteins be produced using transgenic animals?
ANS: Posttranslationally modified proteins can be produced in
transgenic eukaryotic cells growing in culture or in
transgenic plants and animals. Indeed, transgenic sheep
have been produced that secrete human blood-clotting
factor IX and a1-antitrypsin in their milk. These sheep
were produced by fusing the coding sequences of the
respective genes to a DNA sequence that encodes the
signal peptide required for secretion and introducing
this chimeric gene into fertilized eggs that were then
implanted and allowed to develop into transgenic ani -
mals. In principle, this approach could be used to pro -
duce any protein of interest.
16.20 Richard Meagher and coworkers have cloned a family of
10 genes that encode actins (a major component of the
cytoskeleton) in Arabidopsis thaliana . The 10 actin gene
products are similar, often differing by just a few amino
acids. Thus, the coding sequences of the 10 genes are
also very similar, so that the coding region of one gene
will cross-hybridize with the coding regions of the other
nine genes. In contrast, the noncoding regions of the 10
genes are quite divergent. Meagher has hypothesized
that the 10 actin genes exhibit quite different temporal
and spatial patterns of expression. You have been hired
by Meagher to test this hypothesis. Design experiments
that will allow you to determine the temporal and spatial
pattern of expression of each of the 10 actin genes in
Arabidopsis .
ANS: You can subclone the 3 ′ noncoding regions (sequences
between the translation-termination codons and the 3 ′
termini of the transcripts) of the actin genes and use
these sequences as gene-specific hybridization probes,
after verifying their specificity (no cross-hybridization to
the other genes in the gene family). This procedure has
worked elegantly for the 15 tubulin genes and the 10
actin genes of Arabidopsis , because the transcript
sequences are very divergent in the 5 ′ and 3 ′ noncoding
regions. You cannot, of course, use intron sequences
because they are excised during pre-mRNA processing.
These 3 ′ noncoding gene-specific hybridization probes are then used to measure individual gene transcript lev -
els in various organs and tissues of developing plants by
either northern blot or in situ hybridization experiments.
Alternatively, the 5 ′ and 3 ′ noncoding regions can be
used to design gene-specific PCR primers, and reverse
transcription PCR (RT-PCR) can be used to measure
individual gene transcript levels in organs and tissues.
Indeed, Meagher and colleagues have already used this
approach to document the striking temporal and tissue-
specific patterns of actin gene expression in Arabidopsis .
16.21 The first transgenic mice resulted from microinjecting
fertilized eggs with vector DNA similar to that dia -
grammed in Figure 16.15 except that it contained a pro -
moter for the mammalian metallothionein gene linked to
the HGH gene. The resulting transgenic mice showed
elevated levels of HGH in tissues of organs other than the
pituitary gland—for example, in heart, lung, and liver—
and the pituitary gland underwent atrophy. How might
the production of HGH in transgenic animals be better
regulated, with expression restricted to the pituitary gland?
ANS: The vector described contains the HGH gene; however,
it does not contain a mammalian HGH promoter that
will regulate the expression of the transgene in the
appropriate tissues. Construction of vectors containing a
properly positioned mammalian HGH-promoter
sequence should result in transgenic mice in which
HGH synthesis is restricted to the pituitary gland.
16.22 How do the reverse genetic approaches used to dissect
biological processes differ from classical genetic
approaches?
ANS: Classical genetic approaches use mutational dissection to
probe the functions of genes. Mutant alleles that produce
altered phenotypes are identified and used to investigate
the functions of the wild-type alleles. Comparative
molecular analyses of mutant and wild-type organisms
sometimes allow researchers to determine the precise
function of a gene. Reverse genetic approaches use the
known nucleotide sequences of genes to design proce -
dures to either produce null mutations in them or inhibit
their expression. RNA interference protocols are used to
block the expression of specific genes. T-DNA and trans -
poson insertion protocols are used to produce null muta -
tions (to “knock out” the function) of specific genes.
Basically, in classical genetics, you start with mutant
alleles and hope to uncover the wild-type gene function;
in reverse genetics, you start with the wild-type gene and
generate mutant alleles.
16.23 How can RNAi gene silencing be used to determine the
function of genes?
ANS: RNAi involves the use of double-stranded RNAs, where
one strand is complementary to the mRNA and the
other strand is equivalent to the mRNA, to silence the
expression of target genes. RNAi makes use of the
RNA-induced silencing complex (RISC) to block gene
expression (see Figure 16.23).
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 71 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 72 | 72-WC Answers to All Questions and Problems
16.24 How do insertional mutagenesis approaches differ from
other reverse genetic approaches?
ANS: Insertional mutagenesis approaches produce mutant
alleles—usually null alleles, or “knockouts,”—by the
insertion of foreign DNA into genes. Other reverse
genetic approaches, for example, RNA interference,
inhibit the expression of the genes but leave them struc -
turally intact.
16.25 Insertional mutagenesis is a powerful tool in both plants
and animals. However, when performing large-scale
insertional mutagenesis, what major advantage do plants
have over animals?
ANS: Plants have an advantage over animals in that once inser -
tional mutations are induced they can be stored for long
periods of time and distributed to researchers as dormant
seeds.
16.26 We discussed the unfortunate effects of insertional muta -
genesis in the four boys who developed leukemia after
treatment of X-linked severe combined immunodefi -
ciency disease by gene therapy. How might this conse -
quence of gene therapy be avoided in the future? Do you
believe that the use of somatic-cell gene therapy to treat
human diseases can ever be made 100 percent risk-free?
Why? Why not?
ANS: The vectors used in somatic-cell gene therapy must not
insert themselves preferentially into important genes,
especially proto-oncogenes. Ideally, the vectors should
insert themselves into unessential regions of the human
genome. However, such vectors may not exist. At the
minimum, however, vectors should be used that insert
into the genome at random sites so that their chance of
inserting into an important regulatory gene such as a
proto-oncogene is very low. Gene therapy will probably
never be completely risk-free, because anomalous inser -
tion events will always occur at some low frequency. No
biological process is 100 percent accurate. However, the
potential benefits of gene therapy must outweigh the
potential risks before the procedure will become an
accepted tool for treating inherited diseases.
16.27 One strand of a gene in Arabidopsis thaliana has the fol -
lowing nucleotide sequence:
atgagtgacgggaggaggaagaagagcgtgaacggaggt
gcaccggcgcaaacaatcttggatgatcggagatctagtcttccgga
agttgaagcttctccaccggctgggaaacgagctgttatcaagagtgc
cgatatgaaagatgatatgcaaaaggaagctatcgaaatcgccatct
ccgcgtttgagaagtacagtgtggagaaggatatagctgagaatataa
agaaggagtttgacaagaaacatggtgctacttggcattgcattgttgg
tcgcaactttggttcttatgtaacgcatgagacaaaccatttcgtttacttct
acctcgaccagaaagctgtgctgctcttcaagtcgggttaa
The function(s) of this gene is still uncertain. (a) How
might insertional mutagenesis be used to investigate the
function(s) of the gene? (b) Design an experiment using
RNA interference to probe the function(s) of the gene.ANS: (a) You would first want to check the Salk Institute’s
Genome Analysis Laboratory web site to see if a T-DNA
or transposon insertion has already been identified in
this gene (see Problem 16.28). If so, you can simply order
seeds of the transgenic line from the Arabidopsis Biologi -
cal Resource Center at Ohio State University. If no
insertion is available in the gene, you can determine
where it maps in the genome and use transposons that
preferentially jump to nearby sites to identify a new
insertional mutation (see http://www.arabidopsis.org/
abrc/ima/jsp). (b) You can construct a gene that has sense
and antisense sequences transcribed to a single mRNA
molecule (see Figure 16.23 b), introduce it into Arabidop-
sis plants by A. tumefaciens -mediated transformation, and
study its effect(s) on the expression of the gene and the
phenotype of transgenic plants. The transcript will form
a partially base-paired hairpin that will enter the RISC
silencing pathway and block the expression of the gene
(see Figure 16.23 b).
16.28 Let’s check the Salk Institute’s Genome Analysis Labora -
tory web site (http://signal.salk.edu/cgi-bin/tdnaexpress)
to see if any of their T-DNA lines have insertions in the
gene shown in the previous question. At the SIGnAL
web site, scroll down to “Blast” and paste or type the
sequence in the box. The resulting map will show the
location of mapped T-DNA insertions relative to
the location of the gene (green rectangle at the top). The
blue arrows at the top right will let you focus on just the
short region containing the gene or relatively long
regions of chromosome 4 of Arabidopsis . Are there any
T-DNA insertions in the gene in question? Near the
gene?
ANS: A search of the Salk Institute’s Genome Analysis Labora -
tory (SIGnAL) web site reveals that there are numerous
T-DNA insertions (Salk T-DNA insertions and several
others) located in the promoter region of this gene.
Moreover, there are two insertion lines (FLAG_177C02
and FLAG_216D01) in the collection at the Institute of
Agronomic Research in Versailles, France, with inserts in
the coding region of this gene. All of these insertion lines
in these collections are available to researchers on
request. Thus, the function of this gene can be studied by
using these insertion lines.
16.29 The CRISPR/Cas9 anti-phage immunity system in Strep -
tococcus pyogenes deploys a variety of crRNAs derived from
the spacer and repeat sequences in the CRISPR array in
the S. pyogenes genome. In combination with the transac -
tivating RNA (tracrRNA), these crRNAs guide the Cas9
endonuclease to complementary sequences in infecting
phage genomes, whereupon Cas9 cleaves the phage DNA.
A requirement for cleavage is that the targeted phage
DNA sequence be immediately upstream of a protospacer
adjacent motif (PAM), which in the S. pyogenes system is
5′-NGG-3 ′. Why is it important that the CRISPR array
in the S. pyogenes genome not contain this PAM?
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 72 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 73 | Answers to All Questions and Problems WC -73
ANS: It is important that the CRISPR array in the S. pyogenes
genome does not contain the PAM 5 ′NGG-3 ′ because if
it did, crRNAs generated from the array could target the
Cas9 endonuclease to the array and cleave it, resulting in
breakage of the S. pyogenes chromosome.
16.30 The Streptococcus pyogenes Cas9 endonuclease can be tar -
geted to a specific genomic DNA sequence by an sgRNA
that at its 5 ′ end has 20 nucleotides complementary to the
target sequence. If this target sequence is immediately
upstream of the protospacer adjacent motif (PAM)
5′NGG-3 ′, Cas9 will cleave the target DNA. Suppose you
have chosen a 20-nucleotide target sequence in the genome
of Drosophila melanogaster and that this sequence is next to
the required PAM. How could you determine if Cas9 will
cleave only this sequence in the Drosophila genome?
ANS: You could use the 20-nucleotide sequence as a query in
BLAST to scan the sequenced portion of the Drosophila
genome to see if all or part of the target sequence is pres -
ent anywhere else. If this sequence is present elsewhere,
then you could check to see if the PAM 5 ′-NGG-3 ′ is
immediately downstream of the sequence. If it is, then
the Cas9 endonuclease will cleave at this site as well as at
the intended target site.
16.31 How could the CRISPR/Cas9 system be used to create a
translocation between two autosomes in cultured human
cells?
ANS: Create two sgRNAs, one to target a sequence on a par -
ticular autosome and the other to target a sequence
on a different autosome. Then introduce these sgRNAs
and the Cas9 endonuclease into cultured cells to induce
breakage at the two target sites. The broken DNA mol -
ecules may be repaired by the NHEJ pathway, and if they
are, the broken pieces of different autosomes could be
joined covalently, creating a reciprocal translocation.
Chapter 17
17.1 How can inducible and repressible enzymes of microor -
ganisms be distinguished?
ANS: By studying the synthesis or lack of synthesis of the
enzyme in cells grown on chemically defined media. If
the enzyme is synthesized only in the presence of a cer -
tain metabolite or a particular set of metabolites, it is
probably inducible. If it is synthesized in the absence but
not in the presence of a particular metabolite or group of
metabolites, it is probably repressible.
17.2 Distinguish between (a) repression and (b) feedback
inhibition caused by the end-product of a biosynthetic
pathway. How do these two regulatory phenomena com -
plement each other to provide for the efficient regula -
tion of metabolism?
ANS: Repression occurs at the level of transcription during
enzyme synthesis. The end-product, or a derivative of
the end-product, of a repressible system acts as an effector molecule that usually, if not always, combines
with the product of one or more regulator genes to turn
off the synthesis of the enzymes in the biosynthetic path -
way. Feedback inhibition occurs at the level of enzyme
activity; it usually involved the first enzyme of the bio -
synthetic pathway. Feedback inhibition thus brings about
an immediate arrest of the biosynthesis of the end-
product. All together, feedback inhibition and repression
rapidly and efficiently turn off the synthesis of both the
enzymes and the end-products that no longer need to be
synthesized by the cell.
17.3 In the lactose operon of E. coli , what is the function of
each of the following genes or sites: (a) regulator, (b)
operator, (c) promoter, (d) structural gene Z, and (e)
structural gene Y?
ANS: Gene or Regulatory
Element Function
(a) Regulator gene Encodes the repressor
(b) Operator Binding site of repressor
(c) Promoter Binding site of RNA
polymerase and CAP-cAMP
complex
(d) Structural gene Z Encodes b-galactosidase
(e) Structural gene Y Encodes b-galactoside
permease
17.4 What would be the result of inactivation by mutation of
the following genes or sites in the E. coli lactose operon:
(a) regulator, (b) operator, (c) promoter, (d) structural
gene Z, and (e) structural gene Y?
ANS: (a) Constitutive synthesis of the lac enzymes.
(b) Constitutive synthesis of the lac enzymes.
(c) Uninducibility of the lac enzymes.
(d) No b-galactosidase activity.
(e) No b-galactoside permease activity.
17.5 Groups of alleles associated with the lactose operon are
as follows (in order of dominance for each allelic series):
repressor, Is (superrepressor), I+ (inducible), and I− (con -
stitutive); operator, Oc (constitutive, cis− dominant) and
O+ (inducible, cis-dominant); structural, Z+ and Y+. (a)
Which of the following genotypes will produce b-galac-
tosidase and b-galactoside permease if lactose is present:
(1) I+O+Z+Y+, (2) I−OcZ+Y+, (3) IsOcZ+Y+, (4) IsO+Z+Y+,
and (5) I−O+Z+Y+? (b) Which of the above genotypes
will produce b-galactosidase and b-galactoside permease
if lactose is absent? Why?
ANS: (a) 1, 2, 3, and 5. Genotype 1 is wild-type and inducible,
whereas genotypes 2, 3, and 5 are constitutive; all except 4
will produce b-galactosidase and b-galactoside permease in
the presence of lactose. However, genotype 4 has a super -
repressor mutation ( Is) and is uninducible with normal
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 73 8/14/2015 6:43:02 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 74 | 74-WC Answers to All Questions and Problems
levels of lactose. (b) 2, 3, and 5. In genotypes 2 and 3, the
repressor cannot bind to Oc and in genotype 5, no repressor
is made; both situations render the operon constitutive.
17.6 Assume that you have discovered a new strain of E. coli
that has a mutation in the lac operator region that causes
the wild-type repressor protein to bind irreversibly
to the operator. You have named this operator mutant
Osb for “ superbinding” operator. (a) What phenotype
would a partial diploid of genotype I+OsbZ−Y+/I+O+Z+Y−
have with respect to the synthesis of the enzymes
b-galactosidase and b-galactoside permease? (b) Does
your new Osb mutation exhibit cis or trans dominance in
its effects on the regulation of the lac operon?
ANS: (a) b-Galactosidase will be produced only when lactose is
present. Permease will not be produced at all. (b) cis
dominance.
17.7 Why is the Oc mutation in the E. coli lac operon epistatic
to the Is mutation?
ANS: The Oc mutant prevents the repressor from binding to
the operator. The Is mutant repressor cannot bind to Oc.
The Is mutant protein has a defect in the allosteric site
that binds allolactose but has a normal operator binding
site. Therefore, because the single Oc mutant would have
the same phenotype as the Oc Is double mutant, the Oc
mutation is, by definition, epistatic to Is.
17.8 For each of the following partial diploids indicate
whether enzyme synthesis is constitutive or inducible
(see Problem 17.5 for dominance relationships):
(a) I+O+Z+Y+/I+O+Z+Y+, (b) I+O+Z+Y+/I+OcZ+Y+,
(c) I+OcZ+Y+/I+OcZ+Y+, (d) I+O+Z+Y+/I−O+Z+Y+,
(e) I−O+Z+Y+/I−O+Z+Y+.
Why?
ANS: (a) Inducible, this is the wild-type genotype and
phenotype.
(b) Constitutive, the Oc mutation produces an operator
that is not recognized by the lac repressor.
(c) Constitutive, same as for (b).
(d) Inducible, I+ is dominant to I−.
(e) Constitutive, no active repressor is synthesized in this
bacterium.
17.9 Write the partial diploid genotype for a strain that will
(a) produce b-galactosidase constitutively and permease
inducibly and (b) produce b-galactosidase constitutively
but not permease either constitutively or inducibly, even
though a Y+ gene is known to be present.
ANS: (a) I+ Oc Z+ Y−/I+ O+ Z+ Y+ (b) I+ Oc A+ Y−/Is O+ Z+ Y+
17.10 As a genetics historian, you are repeating some of the
classic experiments conducted by Jacob and Monod with
the lactose operon in E. coli . You use an F plasmid to construct several E. coli strains that are partially diploid
for the lac operon. You construct strains with the follow -
ing genotypes: (1) I+OcZ+Y−/I+O+Z−Y+, (2) I+OcZ−Y+/
I+O+Z+Y−, (3) I−O+Z+Y+/I+O+Z−Y−, (4) IsO+Z−Y−/
I+O+Z+Y+, and (5) I+OcZ+Y+/IsO+Z−Y+. (a) Which of
these strains will produce functional b-galactosidase in
both the presence and absence of lactose? (b) Which of
these strains will exhibit constitutive synthesis of func -
tional b-galactoside permease? (c) Which of these strains
will express both gene Z and gene Y constitutively and
will produce functional products ( b-galactosidase and
b-galactoside permease) of both genes? (d) Which of
these strains will show cis dominance of lac operon regu-
latory elements? (e) Which of these strains will exhibit
trans dominance of lac operon regulatory elements?
ANS: (a) 1, 5.
(b) 2, 5.
(c) 5.
(d) 1, 2, 5.
(e) 3, 4.
17.11 Constitutive mutations produce elevated enzyme levels
at all times; they may be of two types: Oc or I−. Assume
that all other DNA present is wild-type. Outline how the
two constitutive mutants can be distinguished with
respect to (a) map position, (b) regulation of enzyme
levels in Oc/O+ versus I−/I+ partial diploids, and (c) the
position of the structural genes affected by an Oc muta -
tion versus the genes affected by an I− mutation in a par -
tial diploid.
ANS: (a) The Oc mutations map very close to the Z structural
gene; I− mutations map slightly farther from the struc -
tural gene (but still very close by; see Figure 17.5).
(b) An I+O+Z+Y+/I+OcZ+Y+ partial diploid would exhibit
constitutive synthesis of b-galactosidase and b-galacto-
side permease, whereas an I+O+Z+Y+/I−O+Z+Y+ partial
diploid would be inducible for the synthesis of these
enzymes.
(c) The Oc mutation is cis-dominant; the I− mutation is
trans -recessive.
17.12 How could the tryptophan operon in E. coli have devel -
oped and been maintained by evolution?
ANS: The system could have developed from a series of tan -
dem duplications of a single ancestral gene. Mutational
changes that make the system more efficient and, there -
fore, favored by natural selection could have brought the
system to its present level of efficiency.
17.13 Of what biological significance is the phenomenon of
catabolite repression?
ANS: Catabolite repression has apparently evolved to assure
the use of glucose as a carbon source when this carbohy -
drate is available, rather than less efficient energy sources.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 74 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 75 | Answers to All Questions and Problems WC -75
17.14 How might the concentration of glucose in the medium
in which an E. coli cell is growing regulate the intracel -
lular level of cyclic AMP?
ANS: Possibly by directly or indirectly inhibiting the enzyme
adenylcyclase, which catalyzes the synthesis of cyclic
AMP from ATP .
17.15 Is the CAP–cAMP effect on the transcription of the lac
operon an example of positive or negative regulation? Why?
ANS: Positive regulation; the CAP–cAMP complex has a posi -
tive effect on the expression of the lac operon. It func -
tions in turning on the transcription of the structural
genes in the operon.
17.16 Would it be possible to isolate E. coli mutants in which
the transcription of the lac operon is not sensitive to
catabolite repression? If so, in what genes might the
mutations be located?
ANS: Yes; in the gene encoding CAP . Some mutations in this
gene might result in a CAP that binds to the promoter in
the absence of cAMP . Also, mutations in the gene (or
genes) coding for the protein (or proteins) that regulate
the cAMP level as a function of glucose concentration.
17.17 Using examples, distinguish between negative regulatory
mechanisms and positive regulatory mechanisms.
ANS: Negative regulatory mechanisms, such as that involving
the repressor in the lactose operon, block the transcrip -
tion of the structural genes of the operon, whereas posi -
tive mechanisms, such as the CAP–cAMP complex in the
lac operon, promote the transcription of the structural
genes of the operon.
17.18 The following table gives the relative activities of the
enzymes b-galactosidase and b-galactoside permease in
cells with different genotypes at the lac locus in E. coli .
The level of activity of each enzyme in wild-type E. coli
not carrying F’s was arbitrarily set at 100; all other values
are relative to the observed levels of activity in these
wild-type bacteria. Based on the data given in the table
for genotypes 1 through 4, fill in the levels of enzyme
activity that would be expected for the fifth genotype.
𝛃-Galactoside𝛃-Galactosidase
Permease
Genotype - Inducer + Inducer - Inducer + Inducer
1. I+O+Z+Y+ 0.1 100 0.1 100
2. I−O+Z+Y+ 100 100 100 100
3. I+OcZ+Y+ 25 100 25 100
4. I−O+Z+Y−/
F′ I−O+Z+Y+200 200 100 100
5. I−OcZ−Y+/
F′ I+O+Z+Y+
ANS: 0.1; 100; 25.1; 200. 17.19 The rate of transcription of the trp operon in E. coli
is controlled by both (1) repression/derepression and
(2) attenuation. By what mechanisms do these two regu-
latory processes modulate trp operon transcript levels?
ANS: Repression/derepression of the trp operon occurs at the
level of transcription initiation, modulating the fre -
quency at which RNA polymerase initiates transcription
from the trp operon promoters. Attenuation modulates
trp transcript levels by altering the frequency of termina -
tion of transcription within the trp operon leader region
(trpL).
17.20 What effect will deletion of the trpL region of the trp
operon have on the rates of synthesis of the enzymes
encoded by the five genes in the trp operon in E. coli cells
growing in the presence of tryptophan?
ANS: Deletion of the trpL region would result in the levels of
the tryptophan biosynthetic enzymes in cells growing in
the presence of tryptophan being increased about 10-fold
because attenuation would no longer occur if this region
were absent.
17.21 By what mechanism does the presence of tryptophan in
the medium in which E. coli cells are growing result in
premature termination or attenuation of transcription of
the trp operon?
ANS: First, remember that transcription and translation are
coupled in prokaryotes. When tryptophan is present in
cells, tryptophan-charged tRNATr p is produced. This
allows translation of the trp leader sequence through the
two UGG T rp codons to the trp leader sequence UGA
termination codon. This translation of the trp leader
region prevents base-pairing between the partially com -
plementary mRNA leader sequences 75–83 and 110–121
(see Figure 17.15 b), which in turn permits formation of
the transcription–termination “hairpin” involving leader
sequences 110–121 and 126–134 (see Figure 17.15 c).
17.22 Suppose that you used site-specific mutagenesis to mod-
ify the trpL sequence such that the two UGG T rp codons
at positions 54–56 and 57–60 (see Figure 17.14) in the
mRNA leader sequence were changed to GGG Gly
codons. Will attenuation of the trp operon still be regu -
lated by the presence or absence of tryptophan in the
medium in which the E. coli cells are growing?
ANS: No. Attenuation of the trp operon would now be con -
trolled by the presence or absence of Gly-tRNAGly.
17.23 What do trp attenuation and the lysine riboswitch have
in common?
ANS: Both trp attenuation and the lysine riboswitch turn off
gene expression by terminating transcription upstream
from the coding regions of the regulated genes. Both
involve the formation of alternative mRNA secondary
structures—switching between the formation of antiter -
minator and transcription–terminator hairpins—in
response to the presence or absence of a specific
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 75 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 76 | 76-WC Answers to All Questions and Problems
metabolite (compare Figure 17.15 and Figure 2 in the
Focus On The Lysine Riboswitch).
17.24 Would attenuation of the type that regulates the level of
trp transcripts in E. coli be likely to occur in eukaryotic
organisms?
ANS: No. Since transcription (nucleus) and translation (cyto -
plasm) are no coupled in eukaryotes, attenuation of the
type occurring in prokaryotes would not be possible.
Chapter 18
18.1 Operons are common in bacteria but not in eukaryotes.
Suggest a reason why.
ANS: In multicellular eukaryotes, the environment of an indi -
vidual cell is relatively stable. There is no need to respond
quickly to changes in the external environment. In addi -
tion, the development of a multicellular organism
involves complex regulatory hierarchies composed of
hundreds of different genes. The expression of these
genes is regulated spatially and temporally, often through
intricate intercellular signaling processes.
18.2 In bacteria, translation of an mRNA begins before the
synthesis of that mRNA is completed. Why is this “cou -
pling” of transcription and translation not possible in
eukaryotes?
ANS: Coupling of transcription and translation is not possible
in eukaryotes because these two processes take place in
different cellular compartments—transcription in the
nucleus and translation in the cytoplasm.
18.3 Muscular dystrophy in humans is caused by mutations in
an X-linked gene that encodes a protein called dystro -
phin. What techniques could you use to determine if this
gene is active in different types of cells, say skin cells,
nerve cells, and muscle cells?
ANS: Activity of the dystrophin gene could be assessed by blot -
ting RNA extracted from the different types of cells and
hybridizing it with a probe from the gene (northern
blotting); or the RNA could be reverse transcribed into
cDNA using one or more primers specific to the dystro-
phin gene and the resulting cDNA could be amplified by
the polymerase chain reaction (RT-PCR). Another tech -
nique would be to hybridize dystrophin RNA in situ —that
is, in the cells themselves—with a probe from the gene.
It would also be possible to check each cell type for pro-
duction of dystrophin protein by using anti-dystrophin
antibodies to analyze proteins from the different cell
types on western blots or analyze the proteins in the cells
themselves—that is, in situ .
18.4 Why do steroid hormones interact with receptors inside
the cell, whereas peptide hormones interact with recep -
tors on the cell surface?
ANS: Steroid hormones are small, lipid-soluble molecules that
have little difficulty passing through the cell membrane. Peptide hormones are typically too large to pass through
the cell membrane freely; rather, their influence must be
mediated by a signaling system that begins with a mem -
brane-bound receptor protein that binds the hormone.
18.5 In the polytene chromosomes of Drosophila larvae (Chap -
ter 6), some bands form large “puffs” when the larvae are
subjected to high temperatures. How could you show
that these puffs contain genes that are vigorously tran -
scribed in response to this heat shock treatment?
ANS: One procedure would be to provide larvae with radioac -
tively labeled UTP , a building block of RNA, under dif -
ferent conditions—with and without heat shock. Then
prepare samples of polytene cells from these larvae for
autoradiography. If the heat shock-induced puffs contain
genes that are vigorously transcribed, the radioactive sig -
nal should be abundant in the puffs.
18.6 How would you distinguish between an enhancer and a
promoter?
ANS: An enhancer can be located upstream, downstream, or
within a gene, and it functions independently of its ori -
entation. A promoter is almost always immediately
upstream of a gene and it functions only in one direction
with respect to the gene.
18.7 T ropomyosins are proteins that mediate the interaction
of actin and troponin, two proteins involved in muscle
contractions. In higher animals, tropomyosins exist as a
family of closely related proteins that share some amino
acid sequences but differ in others. Explain how these
proteins could be created from the transcript of a single
gene.
ANS: By alternate splicing of the transcript.
18.8 A polypeptide consists of three separate segments of
amino acids, A—B—C. Another polypeptide contains
segments A and C but not segment B. How might you
determine if these two polypeptides are produced by
translating alternately spliced versions of RNA from a
single gene or by translating mRNA from two different
genes?
ANS: Southern blotting of genomic DNA digested with an
appropriate restriction enzyme, followed by hybridiza -
tion of the blot with a probe containing the DNA encod -
ing segments A and B, or B and C, or at least parts of
these adjacent segments. If one DNA fragment is
detected on the blot, the two polypeptides are encoded
by a single gene whose RNA is alternately spliced to pro -
duce two mRNAs. If two DNA fragments are detected,
the two polypeptides are encoded by two different genes.
18.9 What techniques could be used to show that a plant gene
is transcribed when the plant is illuminated with light?
ANS: Northern blotting of RNA extracted from plants grown
with and without light, or PCR amplification of cDNA
made by reverse transcribing these same RNA extracts.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 76 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 77 | Answers to All Questions and Problems WC -77
18.10 When introns were first discovered, they were thought
to be genetic “junk”—that is, sequences without any use -
ful function. In fact, they appeared to be worse than junk
because they actually interrupted the coding sequences
of genes. However, among eukaryotes, introns are perva -
sive and anything that is pervasive in biology usually has
a function. What function might introns have? What
benefit might they confer on an organism?
ANS: Introns make it possible for genes to encode different—
but related—polypeptides by alternate splicing of their
RNA transcripts.
18.11 The GAL4 transcription factor in yeast regulates two
adjacent genes, GAL1 and GAL10 , by binding to DNA
sequences between them. These two genes are tran -
scribed in opposite directions on the chromosome, one
to the left of the GAL4 protein’s binding site and the
other to the right of this site. What property of enhanc -
ers does this situation illustrate?
ANS: That enhancers can function in either orientation.
18.12 Using the techniques of genetic engineering, a researcher
has constructed a fusion gene containing the heat-shock
response elements from a Drosophila hsp70 gene and the
coding region of a jellyfish gene ( gfp) for green fluores -
cent protein. This fusion gene has been inserted into the
chromosomes of living Drosophila by the technique of
transposon-mediated transformation (Chapter 21 on the
Instructor Companion site). Under what conditions will
the green fluorescent protein be synthesized in these
genetically transformed flies? Explain.
ANS: The green fluorescent protein will be made after the flies
are heat shocked.
18.13 Suppose that the segment of the hsp70 gene that was used
to make the hsp70/gfp fusion in the preceding problem
had mutations in each of its heat-shock response ele -
ments. Would the green fluorescent protein encoded by
this fusion gene be synthesized in genetically trans -
formed flies?
ANS: Probably not unless the promoter of the gfp gene is recog -
nized and transcribed by the Drosophila RNA polymerase
independently of the heat-shock response elements.
18.14 The polypeptide products of two different genes, A and
B, each function as transcription factors. These polypep -
tides interact to form dimers: AA homodimers, BB
homodimers, and AB heterodimers. If the A and B poly -
peptides are equally abundant in cells, and if dimer for -
mation is random, what is the expected ratio of
homodimers to heterodimers in these cells?
ANS: With equal abundance of the A and B polypeptides, AA
homodimers should constitute 1/4 of the total dimers
formed, BB homodimers should constitute 1/4 of the
total, and AB heterodimers should constitute 1/2 of the
total. The expected ratio of homodimers to heterodimers
is therefore (1/4 + 1/4):(1/2) = 1:1. 18.15 A particular transcription factor binds to enhancers in 40
different genes. Predict the phenotype of individuals homo -
zygous for a frameshift mutation in the coding sequence of
the gene that specifies this transcription factor.
ANS: The mutation is likely to be lethal in homozygous condi -
tion because the transcription factor controls so many
different genes, and a frameshift mutation in the coding
sequence will almost certainly destroy the transcription
factor’s function.
18.16 The alternately spliced forms of the RNA from the Dro-
sophila doublesex gene encode proteins that are needed to
block the development of one or the other set of sexual
characteristics. The protein that is made in female ani -
mals blocks the development of male characteristics, and
the protein that is made in male animals blocks the
development of female characteristics. Predict the phe -
notype of XX and XY animals homozygous for a null
mutation in the doublesex gene.
ANS: Both XX and XY animals would develop as intersexes
because neither of the forms of the doublesex protein
will be able to block sexual development. In these ani -
mals, both developmental pathways will be carried out,
leading to tissues that have both male and female
characteristics.
18.17 The RNA from the Drosophila Sex-lethal (Sxl) gene is
alternately spliced. In males, the sequence of the mRNA
derived from the primary transcript contains all eight
exons of the Sxl gene. In females, the mRNA contains
only seven of the exons because during splicing exon 3 is
removed from the primary transcript along with its
flanking introns. The coding region in the female’s
mRNA is therefore shorter than it is in the male’s mRNA.
However, the protein encoded by the female’s mRNA is
longer than the one encoded by the male’s mRNA. How
might you explain this paradox?
ANS: Exon 3 contains an in-frame stop codon. Thus, the pro -
tein translated from the Sxl mRNA in males will be
shorter than the protein translated from the shorter Sxl
mRNA in females.
18.18 In Drosophila , expression of the yellow gene is needed for
the formation of dark pigment in many different tissues;
without this expression, a tissue appears yellow in color.
In the wings, the expression of the yellow gene is con -
trolled by an enhancer located upstream of the gene’s
transcription initiation site. In the tarsal claws, expres -
sion is controlled by an enhancer located within the
gene’s only intron. Suppose that by genetic engineering,
the wing enhancer is placed within the intron and the
claw enhancer is placed upstream of the transcription
initiation site. Would a fly that carried this modified yel-
low gene in place of its natural yellow gene have darkly
pigmented wings and claws? Explain.
ANS: Yes. Enhancers are able to function in different positions
in and around a gene.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 77 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 78 | 78-WC Answers to All Questions and Problems
18.19 A researcher suspects that a 550-bp-long intron contains
an enhancer that drives expression of an Arabidopsis gene
specifically in root tip tissue. Outline an experiment to
test this hypothesis.
ANS: The intron could be placed in a GUS expression vector,
which could then be inserted into Arabidopsis plants. If
the intron contains an enhancer that drives gene expres -
sion in root tips, transgenic plants should show GUS
expression in their root tips. See the Problem-Solving
Skills feature in Chapter 18 for an example of this type of
analysis.
18.20 What is the nature of each of the following classes of
enzymes? What does each type of enzyme do to chroma -
tin? (a) HAT s, (b) HDACs, (c) HMT s.
ANS: (a) HAT s, histone acetyl transferases, transfer acetyl
groups to the amino acid lysine in histones; (b) HDACs,
histone deacetylases, remove acetyl groups from these
lysines; (c) HMT s, histone methyl transferases, transfer
methyl groups to lysine, arginine, and histidine in
histones.
18.21 In Drosophila larvae, the single X chromosome in males
appears diffuse and bloated in the polytene cells of the
salivary gland. Is this observation compatible with the
idea that X-linked genes are hyperactivated in Drosophila
males?
ANS: Yes. The diffuse, bloated appearance indicates that the
genes on this chromosome are being transcribed
vigorously—the chromatin is “open for business.”
18.22 Suppose that the LCR of the b-globin gene cluster was
deleted from one of the two chromosomes 11 in a man.
What disease might this deletion cause?
ANS: The LCR regulates the expression of all the genes linked
to it. Deletion of the LCR would ablate or impair globin
gene expression from one of the two chromosomes 11.
With less b-globin being produced, the individual would
likely suffer from anemia.
18.23 Would double-stranded RNA derived from an intron be
able to induce RNA interference?
ANS: Short interfering RNAs target messenger RNA mole -
cules, which are devoid of introns. Thus, if siRNA were
made from double-stranded RNA derived from an
intron, it would be ineffective against an mRNA target.
18.24 An RNA interference-like phenomenon has been impli -
cated in the regulation of transposable elements. In Dro-
sophila , two of the key proteins involved in this regulation
are encoded by the genes aubergine and piwi. Flies that
are homozygous for mutant alleles of these genes are
lethal or sterile, but flies that are heterozygous for them
are viable and fertile. Suppose that you have strains of
Drosophila that are heterozygous for aubergine or piwi
mutant alleles. Why might the genomic mutation rate in
these mutant strains be greater than the genomic muta -
tion rate in a wild-type strain?ANS: The aubergine and piwi gene products mediate the RNAi-
like response. Reduction in the amount of aubergine or
piwi protein would likely impair the organism’s ability to
mount this response, and without a vigorous capacity for
regulation, transposable elements would be more likely
to move in the genome. This movement would likely
cause mutations because the transposons could insert
into genes and inactivate them. Thus, Drosophila that are
heterozygous for mutations in aubergine or piwi might
experience higher mutation rates than Drosophila lacking
these mutations.
18.25 Suppose that female mice homozygous for the a allele of
the Igf2 gene are crossed to male mice homozygous for
the b allele of this gene. Which of these two alleles will
be expressed in the F1 progeny?
ANS: The paternally contributed allele ( b) will be expressed in
the F1 progeny.
18.26 Epigenetic states are transmitted clonally through cell
division. What kinds of observations indicate that these
states can be reversed or reset?
ANS: Here are two observations that show reversal or resetting
of an epigenetic state: (1) For imprinted genes in mam -
mals, the epigenetic state can be reset when the gene
passes through the germ line of the opposite sex.
(2) Genes on the inactive X chromosome in mammals
are reactivated in the female germ line.
18.27 A researcher hypothesizes that in mice gene A is actively
transcribed in liver cells, whereas gene B is actively tran -
scribed in brain cells. Describe procedures that would
allow the researcher to test this hypothesis.
ANS: RNA could be isolated from liver and brain tissue.
Northern blotting or RT-PCR with this RNA could
then establish which of the genes ( A or B) is transcribed
in which tissue. For northern blotting, the RNA samples
would be fractionated in a denaturing gel and blotted to
a membrane and then the RNA on the membrane would
be hybridized with gene-specific probes, first for one
gene, then for the other (or the researcher could prepare
two separate blots and hybridize each one with a differ -
ent probe). For RT-PCR, the RNA samples would be
reverse transcribed into cDNA using primers specific for
each gene; then the cDNA molecules would be amplified
by standard PCR and the products of the amplifications
would be fractionated by gel electrophoresis to deter -
mine which gene’s RNA was present in the original
samples.
18.28 Suppose that the hypothesis mentioned in the previous
question is correct and that gene A is actively transcribed
in liver cells, whereas gene B is actively transcribed in
brain cells. The researcher now extracts equivalent
amounts of chromatin from liver and brain tissues and
treats these extracts separately with DNase I for a lim -
ited period of time. If the DNA that remains after the
treatments is then fractionated by gel electrophoresis,
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 78 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 79 | Answers to All Questions and Problems WC -79
transferred to a membrane by Southern blotting, and
hybridized with a radioactively labeled probe specific for
gene A, which sample (liver or brain) will be expected to
show the greater signal on the autoradiogram? Explain
your answer.
ANS: The sample of chromatin from brain tissue would be
expected to show the greater signal on a Southern blot
hybridized with a probe specific for gene A. The reason
is that this gene is not so well transcribed in brain cells;
consequently, it will be more resistant to digestion with
DNase I in chromatin derived from brain cells than in
chromatin derived from liver cells in which it is actively
transcribed (and therefore more open to digestion with
DNase I).
18.29 Why do null mutations in the msl gene in Drosophila have
no effect in females?
ANS: The msl gene is not functional in females.
18.30 Suppose that a woman carries an X chromosome in
which the XIST locus has been deleted. The woman’s
other X chromosome has an intact XIST locus. What
pattern of X-inactivation would be observed throughout
the woman’s body?
ANS: The X chromosome containing the intact XIST locus
will be silenced in all cases because that locus is located
with the X inactivation center (XIC) and aids in silencing
the inactive X.
18.31 In Drosophila , the variegated phenotype of the white mot -
tled allele is suppressed by a dominant autosomal muta -
tion that knocks out the function of the gene for
heterochromatin protein 1 (HP1), an important factor in
heterochromatin formation. Flies with the white mottled
allele and the suppressor mutation have an almost uni -
form red color in their eyes; without the suppressor
mutation, the eyes are mosaics of red and white tissue.
Can you suggest an explanation for the effect of the sup -
pressor mutation?
ANS: HP1, the protein encoded by the wild-type allele of the
suppressor gene, is involved in chromatin organization.
Perhaps this heterochromatic protein spreads from the
region near the inversion breakpoint in the chromosome
that carries the white mottled allele and brings about the
“heterochromatization” of the white locus. When HP1 is
depleted by knocking out one copy of the gene encoding
it—that is, by putting the suppressor mutation into the
fly’s genotype, the “heterochromatization” of the white
locus would be less likely to occur, and perhaps not occur
at all. The white locus would then function fully in all
eye cells, producing a uniform red eye color.
18.32 The sheep Dolly (Chapter 2) was the first cloned mam -
mal. Dolly was created by implanting a nucleus from a
cell taken from the udder of a female sheep into an enu -
cleated egg. This nucleus had two X chromosomes, and
because it came from a differentiated cell, one of them
must have been inactivated. If the udder cell was heterozygous for at least one X-linked gene whose
expression you could assay, how could you determine if
all of Dolly’s cells had the same X chromosome inacti -
vated? If, upon testing, Dolly’s cells prove to be mosaic
for X chromosome activity—that is, different X’s are
active in different clones of cells—what must have hap -
pened during her embryological development?
ANS: T ake samples of cells from Dolly and determine if the
products of both alleles of the X-linked gene are present
in them. If the products of both alleles are present, then
Dolly must be a genetic mosaic for X chromosome
activity. Thus, during her development, the pattern of
X-inactivation that existed in the udder cell from which
she was derived must have been reset. If only one of the
gene’s products is detected—and if the sample of cells is
representative of all Dolly’s cells—then Dolly must have
maintained the pattern of X-inactivation that existed in
the udder cell from which she was derived.
Chapter 19
19.1 If heart disease is considered to be a threshold trait, what
genetic and environmental factors might contribute to
the underlying liability for a person to develop this
disease?
ANS: Some of the genes implicated in heart disease are listed
in T able 19.2. Environmental factors might include diet,
amount of exercise, and whether or not the person
smokes.
19.2 A wheat variety with red kernels (genotype A′A′ B′B′)
was crossed with a variety with white kernels (genotype
AA BB ). The F1 were intercrossed to produce an F2. If
each primed allele increases the amount of pigment in
the kernel by an equal amount, what phenotypes will be
expected in the F2? Assuming that the A and B loci assort
independently, what will the phenotypic frequencies be?
ANS: 1/16 red; 4/16 = 1/4 dark pink; 6/16 pink; 4/16 = 1/4
light pink; 1/16 white.
19.3 For alcoholism, the concordance rate for monozygotic
twins is 55 percent, whereas for dizygotic twins, it is
28 percent. Do these data suggest that alcoholism has a
genetic basis?
ANS: The concordance for monozygotic twins is almost twice
as great as that for dizygotic twins. Monozygotic twins
share twice as many genes as dizygotic twins. The data
strongly suggest that alcoholism has a genetic basis.
19.4 The height of the seed head in wheat at maturity is deter -
mined by several genes. In one variety, the head is just
9 inches above the ground; in another, it is 33 inches
above the ground. Plants from the 9-inch variety were
crossed to plants from the 33-inch variety. Among the F1,
the seed head was 21 inches above the ground. After self-
fertilization, the F1 plants produced an F2 population in
which 9-inch and 33-inch plants each appeared with a
frequency of 1/256. (a) How many genes are involved in
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 79 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 80 | 80-WC Answers to All Questions and Problems
the determination of seed head height in these strains of
wheat? (b) How much does each allele of these genes
contribute to seed head height? (c) If a 21-inch F1 plant
were crossed to a 9-inch plant, how often would you
expect 18-inch wheat to occur in the progeny?
ANS: (a) 4; (b) 3 inches; (c) frequency of 1/4.
19.5 Assume that size in rabbits is determined by genes with
equal and additive effects. From a total of 2012 F2 prog -
eny from crosses between true-breeding large and small
varieties, eight rabbits were as small as the small variety
and eight were as large as the large variety. How many
size-determining genes were segregating in these
crosses?
ANS: Because 8/2012 is approximately 1/256 = (1/4)4, it appears
that four size-determining genes were segregating in the
crosses.
19.6 A sample of 20 plants from a population was measured in
inches as follows: 18, 21, 20, 23, 20, 21, 20, 22, 19, 20, 17,
21, 20, 22, 20, 21, 20, 22, 19, and 23. Calculate (a) the
mean, (b) the variance, and (c) the standard deviation.
ANS: (a) The mean is 20.45 inches. (b) The variance is 2.37
inches2. (c) The standard deviation is 1.54 inches.
19.7 Quantitative geneticists use the variance as a measure of
scatter in a sample of data; they calculate this statistic by
averaging the squared deviations between each measure -
ment and the sample mean. Why don’t they simply mea -
sure the scatter by computing the average of the
deviations without bothering to square them?
ANS: Because S(Xi − mean) = 0.
19.8 T wo inbred strains of corn were crossed to produce an
F1, which was then intercrossed to produce an F2. Data
on ear length from a sample of F1 and F2 individuals gave
phenotypic variances of 15.2 cm2 and 27.6 cm2, respec -
tively. Why was the phenotypic variance greater for the
F2 than for the F1?
ANS: For the F1, Vg = 0 because they are all genetically identi -
cal and heterozygous; for the F2, Vg > 0 because genetic
differences result from the segregation and independent
assortment of genes. Thus, in the F2, the phenotypic
variance has a pronounced genetic component.
19.9 A study of quantitative variation for abdominal bristle
number in female Drosophila yielded estimates of VT =
6.08, Vg = 3.17, and Ve = 2.91. What was the broad-sense
heritability?
ANS: 3.17/6.08 = 0.52
19.10 A researcher has been studying kernel number on ears of
corn. In one highly inbred strain, the variance for kernel
number is 426. Within this strain, what is the broad-
sense heritability for kernel number?
ANS: The broad-sense heritability within a highly inbred
strain is expected to be zero because there is no genetic
variability. 19.11 Measurements on ear length were obtained from three
populations of corn—two inbred varieties and a ran -
domly pollinated population derived from a cross
between the two inbred strains. The phenotypic vari -
ances were 9.2 cm2 and 9.6 cm2 for the two inbred variet -
ies and 26.4 cm2 for the randomly pollinated population.
Estimate the broad-sense heritability of ear length for
these populations.
ANS: Ve is estimated by the average of the variances of the
inbreds: 9.4 cm2. Vg is estimated by the difference between
the variances of the randomly pollinated population and
the inbreds: (26.4 − 9.4) = 17.0 cm2. The broad-sense
heritability is H2 = Vg /VT = 17.0/26.4 = 0.64.
19.12 Figure 19.4 summarizes data on maturation time in pop -
ulations of wheat. Do these data provide any insight as to
whether or not this trait is influenced by dominance?
Explain.
ANS: Because the F1 plants have maturation times midway
between those of the parental strains, there seems to be
little or no dominance for this trait.
19.13 A quantitative geneticist claims that the narrow-sense
heritability for body mass in human beings is 0.7, while
the broad-sense heritability is only 0.3. Why must there
be an error?
ANS: Broad-sense heritability must be greater than narrow-
sense heritability because H2 = Vg /VT > Va /VT = h2.
19.14 The mean value of a trait is 100 units, and the narrow-
sense heritability is 0.4. A male and a female measuring
124 and 126 units, respectively, mate and produce a large
number of offspring, which are reared in an average
environment. What is the expected value of the trait
among these offspring?
ANS: (125 − 100)(0.4) + 100 = 110 units.
19.15 The narrow-sense heritability for abdominal bristle
number in a population of Drosophila is 0.3. The mean
bristle number is 12. A male with 10 bristles is mated to
a female with 20 bristles, and a large number of progeny
are scored for bristle number. What is the expected num -
ber of bristles among these progeny?
ANS: (15 − 12)(0.3) + 12 = 12.9 bristles.
19.16 A breeder is trying to decrease the maturation time in a
population of sunflowers. In this population, the mean
time to flowering is 100 days. Plants with a mean flower -
ing time of only 90 days were used to produce the next
generation. If the narrow-sense heritability for flowering
time is 0.2, what will the average time to flowering be in
the next generation?
ANS: (90 − 100)(0.2) + 100 = 98 days.
19.17 A fish breeder wishes to increase the rate of growth in a
stock by selecting for increased length at 6 weeks after
hatching. The mean length of 6-week-old fingerlings is
currently 10 cm. Adult fish that had a mean length of
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 80 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 81 | Answers to All Questions and Problems WC -81
15 cm at 6 weeks of age were used to produce a new gen -
eration of fingerlings. Among these, the mean length was
12.5 cm. Estimate the narrow-sense heritability of fin -
gerling length at 6 weeks of age and advise the breeder
about the feasibility of the plan to increase growth rate.
ANS: h2 = R/S = (12.5 − 10)/(15 − 10) = 0.5; selection for
increased growth rate should be effective.
19.18 Leo’s IQ is 86 and Julie’s IQ is 110. The mean IQ in the
population is 100. Assume that the narrow-sense herita -
bility for IQ is 0.4. What is the expected IQ of Leo and
Julie’s first child?
ANS: (98 − 100)(0.4) + 100 = 99.2.
19.19 One way to estimate a maximum value for the narrow-
sense heritability is to calculate the correlation between
half-siblings that have been reared apart and divide it by
the fraction of genes that half-siblings share by virtue of
common ancestry. A study of human half-siblings found
that the correlation coefficient for height was 0.14. From
this result, what is the maximum value of the narrow-
sense heritability for height in this population?
ANS: Half-siblings share 25 percent of their genes. The maxi -
mum value for h2 is therefore 0.14/0.25 = 0.56.
19.20 A selection differential of 40 mg per generation was used
in an experiment to select for increased pupa weight in
Tribolium . The narrow-sense heritability for pupa weight
was estimated to be 0.3. If the mean pupa weight was
initially 2000 mg and selection was practiced for 10 gen -
erations, what was the mean pupa weight expected to
become?
ANS: The response to selection in one generation is R = h2 S =
(0.3)(40 mg) = 12 mg. The cumulative effect over 10 gen -
erations is therefore 10 × 12 mg = 120 mg. Thus, the
mean pupa weight should become 2120 mg.
19.21 On the basis of the observed correlations for personality
traits shown in T able 19.5, what can you say about the
value of the environmentality ( C2 in T able 19.3)?
ANS: The correlations for MZT are not much different from
those for MZA. Evidently, for these personality traits,
the environmentality ( C2 in T able 19.3) is negligible.
19.22 Correlations between relatives provide estimates of the
broad and narrow-sense heritabilities on the assumption
that the genetic and environmental factors influencing
quantitative traits are independent of each other and that
they do not interact in some peculiar way. In Chapter 18,
we considered epigenetic modifications of chromatin
that regulate genes and noted the possibility that some of
these modifications might be induced by environmental
factors. How could epigenetic influences on complex
traits be incorporated into the basic theory of quantita -
tive genetics?
ANS: We might represent the value of a quantitative trait, T, as
m + g + e + eg, where m is the mean of the population, g is
the deviation due to genetic factors, e is the deviation due to environmental factors, and eg is the deviation due to
epigenetic factors arising from the interaction of genetic
and environmental factors.
Chapter 20
20.1 The following data for the M–N blood types were
obtained from native villages in Central and North
America:
Group Sample Size M MN N
Central American 86 53 29 4
North American 278 78 61 139
Calculate the frequencies of the LM and LN alleles for the
two groups.
ANS: Frequency of LM in Central American population: p = (2 ×
53 + 29)/(2 × 86) = 0.78; q = 0.22. Frequency of LM in
North American population: p = (2 × 78 + 61)/(2 × 278) =
0.39; q = 0.61.
20.2 The frequency of an allele in a large randomly mating
population is 0.2. What is the frequency of heterozygous
carriers?
ANS: 2pq = 2(0.2)(0.8) = 0.32.
20.3 The incidence of recessive albinism is 0.0004 in a human
population. If mating for this trait is random in the pop -
ulation, what is the frequency of the recessive allele?
ANS: q2 = 0.0004; q = 0.02.
20.4 In a sample from an African population, the frequencies
of the LM and LN alleles were 0.78 and 0.22, respec -
tively. If the population mates randomly with respect to
the M–N blood types, what are the expected frequencies
of the M, MN, and N phenotypes?
ANS: Phenotype Hardy–Weinberg Frequency
M (0.78)2 = 0.61
MN 2(0.78)(0.22) = 0.34
N (0.22)2 = 0.05
20.5 Human beings carrying the dominant allele T can taste
the substance phenylthiocarbamide (PTC). In a popula -
tion in which the frequency of this allele is 0.4, what is
the probability that a particular taster is homozygous?
ANS: Frequency of tasters (genotypes TT and Tt): (0.4)2 + 2
(0.4)(0.6) = 0.64. Frequency of TT tasters among all
tasters: (0.4)2/(0.64) = 0.25.
20.6 A gene has three alleles, A1, A2, and A3, with frequencies
0.6, 0.3, and 0.1, respectively. If mating is random, pre -
dict the combined frequency of all the heterozygotes in
the population.
ANS: Frequency of heterozygotes combined = 2[(0.6)(0.3) +
(0.3)(0.1) + ((0.6)(0.1)] = 0.54.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 81 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 82 | 82-WC Answers to All Questions and Problems
20.7 Hemophilia is caused by an X-linked recessive allele. In a
particular population, the frequency of males with hemo -
philia is 1/4000. What is the expected frequency of
females with hemophilia?
ANS: (0.00025)2 = 6.25 × 10−8.
20.8 In Drosophila , the ruby eye phenotype is caused by a
recessive, X-linked mutant allele. The wild-type eye
color is red. A laboratory population of Drosophila is
started with 25 percent ruby-eyed females, 25 percent
homozygous red-eyed females, 5 percent ruby-eyed
males, and 45 percent red-eyed males. (a) If this popula -
tion mates randomly for one generation, what is the
expected frequency of ruby-eyed males and females? (b)
What is the frequency of the recessive allele in each of
the sexes?
ANS: (a) Half the males will be ruby-eyed and 5 percent (0.50 ×
0.10 × 100 percent) of the females will be ruby-eyed.
(b) Among males, the frequency of the recessive allele
will be 0.5, which was its frequency among females in the
previous generation; among females, the frequency of
the recessive allele will be (0.5 + 0.1)/2 = 0.3, which is
the average of the frequencies of this allele in males and
females in the previous generation.
20.9 A trait determined by an X-linked dominant allele shows
100 percent penetrance and is expressed in 36 percent of
the females in a population. Assuming that the popula -
tion is in Hardy–Weinberg equilibrium, what proportion
of the males in this population express the trait?
ANS: In females, the frequency of the dominant phenotype is
0.36. The frequency of the recessive phenotype is 0.64 = q2;
thus, q = 0.8 and p = 0.2. The frequency of the dominant
phenotype in males is therefore p = 0.2.
20.10 A phenotypically normal couple has had one normal
child and a child with cystic fibrosis, an autosomal reces -
sive disease. The incidence of cystic fibrosis in the popu -
lation from which this couple came is 1/500. If their
normal child eventually marries a phenotypically normal
person from the same population, what is the risk that
the newlyweds will produce a child with cystic fibrosis?
ANS: The probability that the unaffected child of the couple is
a carrier of the mutant allele for cystic fibrosis is 2/3. The
probability that the mate of this individual is a carrier can
be determined by using the population incidence of the
disease. The mutant allele frequency is the square root of
the incidence—0.045—and the frequency of heterozy -
gotes under the assumption of random mating is 2 ×
0.045 × (1 − 0.045) = 0.086. If both individuals are car -
riers, the chance that they will have an affected child is
1/4. Putting all this analysis together, the risk for the
child to have cystic fibrosis is therefore 2/3 × 0.086 ×
1/4 = 0.014, which is seven times the incidence in the
population at large. 20.11 What frequencies of alleles A and a in a randomly mating
population maximize the frequency of heterozygotes?
ANS: Frequency of heterozygotes = H = 2pq = 2p(1 − p).
Using calculus, take the derivative of H and set the result
to zero to solve for the value of p that maximizes H: dH/
dp = 2 − 4p = 0 implies that p = 2/4 = 0.5.
20.12 In an isolated population, the frequencies of the IA, IB,
and i alleles of the A–B–O blood type gene are, respec -
tively, 0.15, 0.25, and 0.60. If the genotypes of the A–B–O
blood type gene are in Hardy–Weinberg proportions,
what fraction of the people who have type A blood in this
population is expected to be homozygous for the IA
allele?
ANS: In a Hardy–Weinberg population, the frequency of IAIA
homozygotes is (0.15)2 = 0.0335 and the frequency of IAi
heterozygotes is 2 × 0.15 × 0.60 = 0.18. The sum of
these frequencies—0.2025—is the frequency of individ -
uals with type A blood. Thus, the frequency of IAIA
homozygotes among all individuals with type A blood is
0.0225/0.2025 = 0.1111.
20.13 In a survey of moths collected from a natural population,
a researcher found 51 dark specimens and 49 light speci -
mens. The dark moths carry a dominant allele, and the
light moths are homozygous for a recessive allele. If the
population is in Hardy–Weinberg equilibrium, what is
the estimated frequency of the recessive allele in the
population? How many of the dark moths in the sample
are likely to be homozygous for the dominant allele?
ANS: Under the assumption that the population is in Hardy–
Weinberg equilibrium, the frequency of the allele for
light coloration is the square root of the frequency of
recessive homozygotes. Thus, q = √0.49 = 0.7, and the
frequency of the allele for dark color is 1 − q = p = 0.3.
From p2 = 0.09, we estimate that 0.09 × 100 = 9 of
the dark moths in the sample are homozygous for the
dominant allele.
20.14 A population of Hawaiian Drosophila is segregating two
alleles, P1 and P2, of the phosphoglucose isomerase ( PGI)
gene. In a sample of 100 flies from this population, 30
were P1P1 homozygotes, 60 were P1P2 heterozygotes, and
10 were P2P2 homozygotes. (a) What are the frequencies
of the P1 and P2 alleles in this sample? (b) Perform
a chi-square test to determine if the genotypes in the
sample are in Hardy–Weinberg proportions. (c) Assum -
ing that the sample is representative of the population,
how many generations of random mating would be
required to establish Hardy–Weinberg proportions in
the population?
ANS: (a) P1 = 0.6 and P2 = 0.4. (b) Predict H–W proportions
by multiplying the expected genotype frequencies by the
sample size and compare these values with the observed
genotype frequencies using a chi-square test:
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 82 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 83 | Answers to All Questions and Problems WC -83
Genotype H–W Frequency Predicted Number
P1P10.62 = 0.36 0.36 × 100 = 36
P1P22(0.6)(0.4) = 0.48 0.28 × 100 = 48
P2P20.42 = 0.16 0.16 × 100 = 16
c2 = (30 − 36)2/36 + (60 − 48)2/48 + (10 − 16)2/16 = 6.25,
df = 1; 6.25 is greater than 3.841; therefore, the observed
genotypes are not in agreement with H–W.
20.15 In a large population that reproduces by random mating,
the frequencies of the genotypes GG, Gg, and gg are 0.04,
0.32, and 0.64, respectively. Assume that a change in the
climate induces the population to reproduce exclusively
by self-fertilization. Predict the frequencies of the geno-
types in this population after many generations of
self-fertilization.
ANS: Ultimate frequency of GG is 0.2; ultimate frequency of
gg is 0.8.
20.16 The frequencies of the alleles A and a are 0.6 and 0.4,
respectively, in a particular plant population. After many
generations of random mating, the population goes
through one cycle of self-fertilization. What is the
expected frequency of heterozygotes in the progeny of
the self-fertilized plants?
ANS: 2pq(1 − F) = 2(0.6)(0.4)(1 − 0.5) = 0.24.
20.17 Each of two isolated populations is in Hardy–Weinberg
equilibrium with the genotype frequencies shown below:
Genotype: AA Aa Aa
Frequency in
Population 1:0.04 0.32 0.64
Frequency in
Population 2:0.64 0.32 0.04
(a) If the populations are equal in size and they merge to
form a single large population, predict the allele and
genotype frequencies in the large population immedi -
ately after merger.
(b) If the merged population reproduces by random mat -
ing, predict the genotype frequencies in the next
generation.
(c) If the merged population continues to reproduce by
random mating, will these genotype frequencies remain
constant?
ANS: (a) Frequency of A in merged population is 0.5 and that
of a is also 0.5; (b) 0.25 ( AA), 0.50 ( Aa), and 0.25 ( aa);
(c) frequencies in (b) will persist.
20.18 A population consists of 25 percent tall individuals
(genotype TT), 25 percent short individuals (genotype
tt), and 50 percent individuals of intermediate height (genotype Tt). Predict the ultimate phenotypic and
genotypic composition of the population if, generation
after generation, mating is strictly assortative (i.e., tall
individuals mate with tall individuals, short individuals
mate with short individuals, and intermediate individuals
mate with intermediate individuals).
ANS: Ultimately, all members of the population will either be
TT or tt, each 50% of the total.
20.19 In controlled experiments with different genotypes of
an insect, a researcher has measured the probability of
survival from fertilized eggs to mature, breeding
adults. The survival probabilities of the three geno -
types tested are 0.92 (for GG), 0.90 (for Gg), and 0.56
(for gg). If all breeding adults are equally fertile, what
are the relative fitnesses of the three genotypes? What
are the selection coefficients for the two least fit
genotypes?
ANS: The relative fitnesses can be obtained by dividing each of
the survival probabilities by the largest probability (0.92).
Thus, the relative fitnesses are 1 for GG, 0.98 = 1 − 0.02
for Gg, and 0.61 = 1 − 0.39 for gg. The selection coef -
ficients are s1 = 0.02 for Gg and s2 = 0.39 for gg.
20.20 In a large randomly mating population, 0.84 of the indi -
viduals express the phenotype of the dominant allele A
and 0.16 express the phenotype of the recessive allele a.
(a) What is the frequency of the dominant allele? (b) If
the aa homozygotes are 5 percent less fit than the other
two genotypes, what will the frequency of A be in the
next generation?
ANS: Frequency of a is q = 0.4; (a) thus p = 1 − q = 0.6;
(b) use the following scheme:
Genotype AA Aa Aa
Hardy–Weinberg frequency 0.36 0.48 0.16
Relative fitness 1 1 0.95
Relative contribution to
next generation0.36 0.48 0.152
Proportional contribution
to next generation0.363 0.484 0.153
Thus, the frequency of the A allele in the next generation
will be (0.363 + 0.484/2) = 0.605.
20.21 Because individuals with cystic fibrosis die before they
can reproduce, the coefficient of selection against them
is s = 1. Assume that heterozygous carriers of the
recessive mutant allele responsible for this disease are as
fit as wild-type homozygotes and that the population
frequency of the mutant allele is 0.02. (a) Predict the
incidence of cystic fibrosis in the population after one
generation of selection. (b) Explain why the incidence of
cystic fibrosis hardly changes even with s = 1.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 83 8/14/2015 6:43:03 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 84 | 84-WC Answers to All Questions and Problems
ANS: (a) Use the following scheme:
Genotype CC Cc cc
Hardy–Weinberg (0.98)2 = 2(0.98)(0.02) = (0.02)2 =
frequency 0.9604 0.0392 0.0004
Relative fitness 1 1 0
Relative (0.9604) × 1 (0.0392) × 1 0
contribution
to next generation
Proportional 0.9604/0.9996 0.0392/0.9996 0
contribution = 0.9608 = 0.0392
The new frequency of the allele for cystic fibrosis is (0.5)
(0.0392) = 0.0196; thus, the incidence of the disease will
be (0.0196)2 = 0.00038, which is very slightly less than
the incidence in the previous generation. (b) The inci -
dence of cystic fibrosis does not change much because
selection can only act against the recessive allele when it
is in homozygotes, which are rare in the population.
20.22 For each set of relative fitnesses for the genotypes AA,
Aa, and aa, explain how selection is operating. Assume
that 0 < t < s < 1.
AA Aa aa
Case 1 1 1 1 - s
Case 2 1 - s1 - s1
Case 3 1 1 - t1 - s
Case 4 1 - s1 1 - t
ANS: Case 1: selection is operating against a deleterious
recessive allele. Case 2: selection is operating against a
deleterious dominant allele. Case 3: selection is operat -
ing against a deleterious allele that has some expression
in heterozygotes, that is, it is partially dominant. Case 4:
selection is operating against both alleles in homozygous
condition; this is a case of balancing selection.
20.23 The frequency of newborn infants homozygous for a
recessive lethal allele is about 1 in 25,000. What is the
expected frequency of carriers of this allele in the
population?
ANS: q2 = 4 × 10−5; thus q = 6.3 × 10−3 and 2 pq = 0.0126.
20.24 A population of size 50 reproduces in such a way that
the population size remains constant. If mating is ran -
dom, how rapidly will genetic variability, as measured by
the frequency of heterozygotes, be lost from this
population?
ANS: The frequency of heterozygotes will decrease by a
1/(2N) = 1/100 = 0.01 per generation.
20.25 A population is segregating three alleles, A1, A2, and A3,
with frequencies 0.2, 0.5, and 0.3, respectively. If these
alleles are selectively neutral, what is the probability that
A2 will ultimately be fixed by genetic drift? What is the
probability that A3 will ultimately be lost by genetic drift?ANS: Probability of ultimate fixation of A2 is 0.5; probability of
ultimate loss of A3 is 1 − 0.3 = 0.7.
20.26 A small island population of mice consists of roughly
equal numbers of males and females. The Y chromo -
some in one-fourth of the males is twice as long as the
Y chromosome in the other males because of an expan -
sion of heterochromatin. If mice with the large Y chro -
mosome have the same fitness as mice with the small
Y chromosome, what is the probability that the large
Y chromosome will ultimately be fixed in the mouse
population?
ANS: 0.25.
20.27 In some regions of west Africa, the frequency of the
HBBS allele is 0.2. If this frequency is the result of a
dynamic equilibrium due to the superior fitness of
HBBSHBBA heterozygotes, and if HBBSHBBS homozy -
gotes are essentially lethal, what is the intensity of selec -
tion against the HBBAHBBA homozygotes?
ANS: p = 0.2; at equilibrium, p = t/(s + t). Because s = 1, we
can solve for t; t = 0.25.
20.28 Mice with the genotype Hh are twice as fit as either of
the homozygotes HH and hh. With random mating, what
is the expected frequency of the h allele when the mouse
population reaches a dynamic equilibrium because of
balancing selection?
ANS: The relative fitnesses of the genotypes HH, Hh, and hh
are 0.5, 1, and 0.5, respectively. At equilibrium, the fre -
quency of h will be s/(t + s) = (0.5)/(0.5 + 0.5) = 0.5.
20.29 A completely recessive allele g is lethal in homozygous
condition. If the dominant allele G mutates to g at a rate
of 10−6 per generation, what is the expected frequency of
the lethal allele when the population reaches mutation–
selection equilibrium?
ANS: At mutation–selection equilibrium
qu s == = // 10 10 .001.−6
20.30 Individuals with the genotype bb are 20 percent less fit
than individuals with the genotypes BB or Bb. If B
mutates to b at a rate of 10−6 per generation, what is the
expected frequency of the allele b when the population
reaches mutation–selection equilibrium?
ANS: qu s == =2.2× // (0.2) 10 10−−63.
Chapter 21
21.1 Which of the following pairs of DNA sequences could
qualify as the terminal repeats of a bacterial IS element.
Explain.
(a) 5′-GAATCCGCA-3 ′ and 5 ′-ACGCCTAAG-3 ′
(b) 5 ′-GAATCCGCA-3 ′ and 5 ′-CTTAGGCGT-3 ′
(c)5′-GAATCCGCA-3 ′ and 5 ′-GAATCCGCA-3 ′
(d) 5 ′-GAATCCGCA-3 ′ and 5 ′-TGCGGATTC-3 ′.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 84 8/14/2015 6:43:05 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 85 | Answers to All Questions and Problems WC -85
ANS: The pair in (d) are inverted repeats and could therefore
qualify.
21.2 Which of the following pairs of DNA sequences could
qualify as target site duplications at the point of an IS 50
insertion? Explain.
(a) 5′-AATTCGCGT-3 ′ and 5 ′-AATTCGCGT-3 ′
(b) 5 ′-AATTCGCGT-3 ′ and 5 ′-TGCGCTTAA-3 ′
(c) 5′-AATTCGCGT-3 ′ and 5 ′-TTAAGCGCA-3 ′
(d) 5 ′-AATTCGCGT-3 ′ and 5 ′-ACGCGAATT-3 ′.
ANS: The pair in (a) are direct repeats and could therefore
qualify.
21.3 One strain of E. coli is resistant to the antibiotic strepto -
mycin, and another strain is resistant to the antibiotic
ampicillin. The two strains were cultured together and
then plated on selective medium containing streptomy -
cin and ampicillin. Several colonies appeared, indicating
that cells had acquired resistance to both antibiotics.
Suggest a mechanism to explain the acquisition of dou -
ble resistance.
ANS: Resistance for the second antibiotic was acquired by con -
jugative gene transfer between the two types of cells.
21.4 What distinguishes IS and Tn 3 elements in bacteria?
ANS: Tn3 elements carry a gene that is not essential for
transposition.
21.5 The circular order of genes on the E. coli chromosome is
*A B C D E F G H *, with the * indicating that the ends of
the chromosome are attached to each other. T wo copies
of an IS element are located in this chromosome: one
between genes C and D, and the other between genes D
and E. A single copy of this element is also present in the
F plasmid. T wo Hfr strains were obtained by selecting
for integration of the F plasmid into the chromosome.
During conjugation, one strain transfers the chromo -
somal genes in the order D E F G H A B C , whereas the
other transfers them in the order D C B A H G F E .
Explain the origin of these two Hfr strains. Why do they
transfer genes in different orders? Does the order of
transfer reveal anything about the orientation of the IS
elements in the E. coli chromosome?
ANS: In the first strain, the F factor integrated into the chro -
mosome by recombination with the IS element between
genes C and D. In the second strain, it integrated by
recombination with the IS element between genes D and
E. The two strains transfer their genes in different orders
because the two chromosomal IS elements are in oppo -
site orientation.
21.6 The composite transposon Tn 5 consists of two IS 50 ele-
ments, one on either side of a group of three genes for
antibiotic resistance. The entire unit IS 50L kanr bler strr
IS50R can transpose to a new location in the E. coli chro -
mosome. However, of the two IS 50 elements in this transposon, only IS 50R produces the catalytically active
transposase. Would you expect IS 50R to be able to be
excised from the Tn 5 composite transposon and insert
elsewhere in the chromosome? Would you expect IS 50L
to be able to do this?
ANS: Both IS 50 elements should be able to excise from the
transposon and insert elsewhere in the chromosome,
because even though IS 50L does not produce its own
transposase, IS 50R provides a source of this enzyme.
21.7 By chance, an IS 1 element has inserted near an IS 2 ele-
ment in the E. coli chromosome. The gene between them,
sug+, confers the ability to metabolize certain sugars.
Will the unit IS 1 sug+ IS2 behave as a composite trans -
poson? Explain.
ANS: No. IS 1 and IS 2 are mobilized by different transposases.
21.8 A researcher has found a new Tn 5 element with the
structure IS 50L strr bler kanr IS50L. What is the most
likely origin of this element?
ANS: IS50L inserted on each side of the cluster of antibiotic
resistance genes.
21.9 Would a Tn 3 element with a frameshift mutation early
in the tnpA gene be able to form a cointegrate? Would a
Tn3 element with a frameshift mutation early in the
tnpR gene be able to form a cointegrate?
ANS: The tnpA mutation: no; the tnpR mutation: yes.
21.10 What enzymes are necessary for replicative transposition
of Tn 3? What are their respective functions?
ANS: T wo enzymes, transposase and resolvase, are needed for
replicative transposition. These enzymes are encoded by
genes of Tn 3. T ransposase catalyzes formation of a coin -
tegrate between donor and recipient plasmids. During
this process, Tn 3 is replicated so that there is a copy of it
at each junction in the cointegrate. Resolvase catalyzes
the site-specific recombination between the two Tn 3
elements and thereby resolves the cointegrate, generat -
ing two molecules each with a copy of the transposon.
Resolvase also represses the synthesis of both the trans -
posase and resolvase enzymes.
21.11 What is the medical significance of bacterial transposons?
ANS: Many bacterial transposons carry genes for antibiotic
resistance, and it is relatively simple for these genes to
move from one DNA molecule to another. DNA mole -
cules that acquire resistance genes can be passed to other
cells in a bacterial population, both vertically (by descent)
and horizontally (by conjugative transfer). Over time,
continued exposure to an antibiotic will select for cells
that have acquired a gene for resistance to that antibiotic.
The antibiotic will therefore no longer be useful in com -
bating these bacteria.
21.12 Describe the structure of the Ac transposon in maize. In
what ways do the Ds transposons differ structurally and
functionally from the Ac transposon?
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 85 8/14/2015 6:43:05 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 86 | 86-WC Answers to All Questions and Problems
ANS: The Ac element consists of 4563 nucleotide pairs
bounded by inverted repeats that are 11 nucleotide pairs
long. The Ac element is flanked by direct repeats of eight
nucleotide pairs long; however, these repeats are created
at the time the element is inserted into a chromosome
(target site duplications) and are therefore not consid -
ered to be integral parts of the element itself. Ds ele-
ments possess the same terminal inverted repeats as Ac,
but their internal sequences vary. Some residue of the Ac
sequence may be present, or non- Ac sequences may be
present; sometimes, one Ds element is contained within
another Ds element.
21.13 In homozygous condition, a deletion mutation of the c
locus, cn, produces colorless (white) kernels in maize; the
dominant wild-type allele, C, causes the kernels to be
purple. A newly identified recessive mutation of the c
locus, cm, has the same phenotype as the deletion muta -
tion (white kernels), but when cmcm and cncn plants are
crossed, they produce white kernels with purple stripes.
If it is known that the cncn plants harbor Ac elements,
what is the most likely explanation for the cm mutation?
ANS: The cm mutation is due to a Ds or an Ac insertion.
21.14 In maize, the O2 gene, located on chromosome 7, con -
trols the texture of the endosperm, and the C gene,
located on chromosome 9, controls its color. The gene
on chromosome 7 has two alleles, a recessive, o2, which
causes the endosperm to be soft, and a dominant, O2,
which causes it to be hard. The gene on chromosome 9
also has two alleles, a recessive, c, which allows the endo -
sperm to be colored, and a dominant, CI, which inhibits
coloration. In one homozygous CI strain, a Ds element is
inserted on chromosome 9 between the C gene and the
centromere. This element can be activated by introduc -
ing an Ac element by appropriate crosses. Activation of
Ds causes the CI allele to be lost by chromosome break -
age. In CI/c/c kernels, such loss produces patches of col -
ored tissue in an otherwise colorless background.
A geneticist crosses a strain with the genotype o2/o2; CI
Ds/CI Ds to a strain with the genotype O2/o2; c/c. The
latter strain also carries an Ac element somewhere in the
genome. Among the offspring, only those with hard
endosperm show patches of colored tissue. What does
this tell you about the location of the Ac element in the
O2/o2; c/c strain?
ANS: The Ac element must be tightly linked to the O2 allele.
21.15 In maize, the recessive allele bz (bronze ) produces a lighter
color in the aleurone than does the dominant allele, Bz.
Ears on a homozygous bz/bz plant were fertilized by pol -
len from a homozygous Bz/Bz plant. The resulting cobs
contained kernels that were uniformly dark except for a
few on which light spots occurred. Suggest an
explanation.
ANS: The paternally inherited Bz allele was inactivated by a
transposable element insertion. 21.16 The X-linked singed locus is one of several in Drosophila
that controls the formation of bristles on the adult cuti -
cle. Males that are hemizygous for a mutant singed allele
have bent, twisted bristles that are often much reduced in
size. Several P element insertion mutations of the singed
locus have been characterized, and some have been
shown to revert to the wild-type allele by excision of the
inserted element. What conditions must be present to
allow such reversions to occur?
ANS: The P transposase to catalyze excision and the absence of
P-specific piRNAs that would repress excision.
21.17 Dysgenic hybrids in Drosophila have elevated mutation
rates as a result of P element transposition. How could
you take advantage of this situation to obtain P element
insertion mutations on the X chromosome?
ANS: Cross dysgenic (highly mutable) males carrying a wild-
type X chromosome to females homozygous for a bal -
ancer X chromosome; then cross the heterozygous F1
daughters individually to their brothers and screen the
F2 males that lack the balancer chromosome for mutant
phenotypes, including failure to survive (lethality). Muta -
tions identified in this screen are probably due to P ele-
ment insertions in X-linked genes.
21.18 If DNA from a P element insertion mutation of the Dro-
sophila white gene and DNA from a wild-type white gene
were purified, denatured, mixed with each other, rena -
tured, and then viewed with an electron microscope,
what would the hybrid DNA molecules look like?
ANS: P element DN A
White gene DNA
(Should see a single-stranded DNA loop corresponding
to the insertion.)
21.19 When complete P elements are injected into embryos
from an M strain, they transpose into the chromosomes
of the germ line, and progeny reared from these embryos
can be used to establish new P strains. However, when
complete P elements are injected into embryos from
insects that lack these elements, such as mosquitoes, they
do not transpose into the chromosomes of the germ line.
What does this failure to insert in the chromosomes of
other insects indicate about the nature of P element
transposition?
ANS: Factors made by the fly’s genome are required for trans -
position; other insects apparently lack the ability to pro -
vide these factors.
21.20 (a) What are retroviruslike elements? (b) Give examples
of retroviruslike elements in yeast and Drosophila .
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 86 8/14/2015 6:43:05 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 87 | Answers to All Questions and Problems WC -87
(c) Describe how retroviruslike elements transpose.
(d) After a retroviruslike element has been inserted into
a chromosome, is it ever expected to be excised?
ANS: (a) Retroviruslike elements resemble integrated retrovi -
ruses in overall structure and behavior. (b) Examples
include the T y 1 element in yeast and the copia element in
Drosophila . (c) Retroviruslike elements transpose using
an RNA intermediate. The element DNA is transcribed
into single-stranded RNA, which is reverse-transcribed
into double-stranded DNA (cDNA). The double-
stranded cDNA is then inserted into a site in the genome.
(d) No. However, the L TRs could pair and recombine to
excise all but one L TR.
21.21 Sometimes, solitary copies of the L TR of T y 1 elements
are found in yeast chromosomes. How might these soli -
tary L TRs originate?
ANS: Through crossing over between the L TRs of a T y 1
element.
21.22 Would you ever expect the genes in a retrotransposon to
possess introns? Explain.
ANS: No. The intron sequences would be removed by RNA
processing prior to reverse transcription into DNA.
21.23 Suggest a method to determine whether the TART
retroposon is situated at the telomeres of each of the
chromosomes in the Drosophila genome.
ANS: In situ hybridization to polytene chromosomes using a
TART probe.
21.24 It has been proposed that the hobo transposable elements in
Drosophila mediate intrachromosomal recombination—
that is, two hobo elements on the same chromosome pair
and recombine with each other. What would such a
recombination event produce if the hobo elements were
oriented in the same direction on the chromosome?
What if they were oriented in opposite directions?
ANS: Same orientation: a deletion; opposite orientation: an
inversion.
21.25 What evidence suggests that some transposable elements
are not simply genetic parasites?
ANS: TART and HeT-A replenish the ends of Drosophila
chromosomes.
21.26 Approximately half of all spontaneous mutations in Dro-
sophila are caused by transposable element insertions. In
human beings, however, the accumulated evidence sug -
gests that the vast majority of spontaneous mutations are
not caused by transposon insertions. Propose a hypothe -
sis to explain this difference.
ANS: The transposition rate in humans may be very much less
than it is in Drosophila .
21.27 Z. Ivics, Z. Izsvák, and P . B. Hackett have “resurrected” a
nonmobile member of the Tc1/mariner family of trans -
posable elements isolated from the DNA of salmon. These researchers altered 12 codons within the coding
sequence of the transposase gene of the salmon element
to restore the catalytic function of its transposase. The
altered element, called Sleeping Beauty , is being tested as
an agent for the genetic transformation of vertebrates
such as mice and zebra fish (and possibly humans).
Suppose that you have a bacterial plasmid containing the
gene for green fluorescent protein ( gfp) inserted between
the ends of a Sleeping Beauty element. How would you
go about obtaining mice or zebra fish that express the
gfp gene?
ANS: The Sleeping Beauty element could be used as a transfor -
mation vector in vertebrates much like the P element has
been used in Drosophila . The gfp gene could be inserted
between the ends of the Sleeping Beauty element and
injected into eggs or embryos along with an intact Sleep-
ing Beauty element capable of encoding the element’s
transposase. If the transposase that is produced in the
injected egg or embryo acts on the element that contains
the gfp gene, it might cause the latter to be inserted into
genomic DNA. Then, if the egg or embryo develops into
an adult, that adult can be bred to determine if a Sleeping
Beauty/gfp transgene is transmitted to the next genera -
tion. In this way, it would be possible to obtain strains of
mice or zebra fish that express the gfp gene.
21.28 The human genome contains about 5000 “processed
pseudogenes,” which are derived from the insertion of
DNA copies of mRNA molecules derived from many
different genes. Predict the structure of these pseudo -
genes. Would each type of processed pseudogene be
expected to found a new family of retrotransposons
within the human genome? Would the copy number of
each type of processed pseudogene be expected to
increase significantly over evolutionary time, as the copy
number of the Alu family has? Explain your answers.
ANS: The processed pseudogenes will, in the best of cases,
contain sequences from the transcription start site to the
poly-A tail of the transcript (if there is one); however,
they will not contain the gene’s promoter or any of its
introns. Because these pseudogenes will not have a pro -
moter, they are not likely to found new retrotransposon
families. Without a promoter, they will not be tran -
scribed; hence, they will not produce RNA to be reverse
transcribed into DNA for insertion into other sites in the
genome. Most likely, the copy number of each of these
processed pseudogenes will not increase as the copy
number of the Alu element has. The Alu element con -
tains an “internal” promoter recognized by RNA poly -
merase III. Each insertion of the Alu element contains
this promoter and can therefore be transcribed into
RNA, which can subsequently be reverse transcribed
into DNA. The L1 element also contains an “internal”
promoter, but this promoter is recognized by RNA poly -
merase II. Most protein-coding genes contain an “exter -
nal” promoter—that is, one that is not transcribed—and
this promoter is recognized by RNA polymerase II.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 87 8/14/2015 6:43:05 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 88 | 88-WC Answers to All Questions and Problems
Chapter 22
22.1 During oogenesis, what mechanisms enrich the cyto -
plasm of animal eggs with nutritive and determinative
materials?
ANS: Unequal division of the cytoplasm during the meiotic
divisions; transport of substances into the oocyte from
surrounding cells such as the nurse cells in Drosophila .
22.2 Predict the phenotype of a fruit fly that develops from an
embryo in which the posterior pole cells had been
destroyed by a laser beam.
ANS: The fly will be sterile because the posterior pole cells
form the germ line in adults of both sexes.
22.3 Outline the main steps in the genetic analysis of develop -
ment in a model organism such as Drosophila .
ANS: Collect mutations with diagnostic phenotypes; map the
mutations and test them for allelism with one another;
perform epistasis tests with mutations in different genes;
clone individual genes and analyze their function at the
molecular level.
22.4 Why is the early Drosophila embryo a syncytium?
ANS: Mitotic division is so rapid that there is not enough time
for membranes to form between cells.
22.5 In Drosophila , what larval tissues produce the external
organs of the adult?
ANS: Imaginal discs.
22.6 Like dorsal , bicoid is a strict maternal-effect gene in Dro-
sophila ; that is, it has no zygotic expression. Recessive
mutations in bicoid (bcd) cause embryonic death by pre -
venting the formation of anterior structures. Predict the
phenotypes of (a) bcd/bcd animals produced by mating
heterozygous males and females; (b) bcd/bcd animals pro -
duced by mating bcd/bcd females with bcd/+ males;
(c) bcd/+ animals produced by mating bcd/bcd females
with bcd/+ males; (d) bcd/bcd animals produced by mating
bcd/+ females with bcd/bcd males; (e) bcd/+ animals pro -
duced by mating bcd/+ females with bcd/bcd males.
ANS: (a) Wild-type; (b) embryonic lethal; (c) embryonic lethal;
(d) wild-type; (e) wild-type.
22.7 Why do women, but not men, who are homozygous for
the mutant allele that causes phenylketonuria produce
children that are physically and mentally retarded?
ANS: In homozygous condition, the mutation that causes phe -
nylketonuria has a maternal effect. Women homozygous
for this mutation influence the development of their
children in utero .
22.8 In Drosophila , recessive mutations in the dorsal–ventral
axis gene dorsal (dl) cause a dorsalized phenotype in
embryos produced by dl/dl mothers; that is, no ventral
structures develop. Predict the phenotype of embryos
produced by females homozygous for a recessive muta -
tion in the anterior–posterior axis gene nanos.ANS: Some structures fail to develop in the posterior portion
of the embryo.
22.9 A researcher is planning to collect mutations in mater -
nal-effect genes that control the earliest events in
Drosophila development. What phenotype should the
researcher look for in this search for maternal-effect
mutations?
ANS: Female sterility. Females affected by these mutations will
lay abnormal eggs that will not develop into viable
embryos.
22.10 A researcher is planning to collect mutations in the gap
genes, which control the first steps in the segmentation
of Drosophila embryos. What phenotype should the
researcher look for in this search for gap gene
mutations?
ANS: Screen for lethal mutations that prevent regions of the
embryo from developing normally.
22.11 How do the somatic cells that surround a developing
Drosophila egg in the ovary influence the formation of
the dorsal–ventral axis in the embryo that will be pro -
duced after the egg is fertilized?
ANS: The somatic cells surrounding a developing Drosophila
egg in the ovary determine where the spätzle protein,
which is the ligand for the T oll receptor protein, will be
cleaved. This cleavage will eventually occur on the ven -
tral side of the developing embryo.
22.12 What events lead to a high concentration of hunchback
protein in the anterior of Drosophila embryos?
ANS: The hunchback mRNA is translated into protein only in
the anterior region of the developing embryo. This
RNA is supplied to the egg by the nurse cells and it is
also synthesized after fertilization by transcription of
the hunchback gene. This zygotic transcription is stimu -
lated by a transcription factor encoded by maternally
supplied bicoid mRNA, which is located in the anterior
of the egg. Thus, hunchback mRNA is concentrated in
the anterior of the embryo. In addition, the hunchback
mRNA that is located in the posterior of the embryo is
bound by nanos protein and then degraded. The nanos
protein is concentrated in the posterior of the embryo
because maternally supplied nanos mRNA is preferen -
tially localized there.
22.13 Diagram a pathway that shows the contributions of the
sevenless (sev) and bride of sevenless (boss) genes to the dif -
ferentiation of the R7 photoreceptor in the ommatidia of
Drosophila eyes. Where would eyeless (ey) fit in this
pathway?
ANS: ey → boss → sev → R7 differentiation
22.14 The sevB4 allele is temperature sensitive; at 22.7°C, flies
that are homozygous for it develop normal R7 photore -
ceptors, but at 24.3°C, they fail to develop these photo -
receptors. sos2A is a recessive, loss-of-function mutation
in the son of sevenless (sos) gene. Flies with the genotype
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 88 8/14/2015 6:43:05 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 89 | Answers to All Questions and Problems WC -89
sevB4/sevB4; sos2A/+ fail to develop R7 photoreceptors
if they are raised at 22.7°C. Therefore, sos2A acts as
a dominant enhancer of the sevB4 mutant phenotype
at this temperature. Based on this observation, where
is the protein product of the wild-type sos gene—
called SOS—likely to act in the pathway for R7
differentiation?
ANS: If the SEV protein is activated—either by the BOSS
ligand or by a gain-of-function mutation in the sev gene,
a faulty effector protein could stop it from inducing the
R7 cell to differentiate. The SOS protein is likely to be a
downstream effector in the pathway for R7 differentia -
tion because when it is depleted by mutating one copy of
the sos gene, flies that have a partially functional SEV
protein show a mutant phenotype—that is, transmission
of the developmental signal through SEV and its down -
stream effector proteins is weakened.
20.15 When the mouse Pax6 gene, which is homologous to the
Drosophila eyeless gene, is expressed in Drosophila , it pro -
duces extra compound eyes with ommatidia, just like
normal Drosophila eyes. If the Drosophila eyeless gene were
introduced into mice and expressed there, what effect
would you expect? Explain.
ANS: Because the Pax6 gave the same phenotype in flies as
overexpression of the eyeless gene, the genes must be
functionally homologous, as well as structurally homolo -
gous. Therefore, expect extra mouse eyes or eye pri -
morida when expressing eyeless in the mouse.
22.16 Would you expect to find homologues of Drosophila ’s
BX-C and ANT-C genes in animals with radial symme -
try such as sea urchins and starfish? How could you
address this question experimentally?
ANS: Maybe these organisms would not have homologues of
the BX-C and ANT-C genes because they do not have
segmented bodies with bilateral symmetry as Drosophila
does. T o see if homologues to these genes are present,
use Drosophila BX-C and ANT-C DNA as probes to
hybridize with starfish or sea urchin genomic DNA on a
Southern blot. The hybridization would have to be done
under conditions that allow DNA that is not a perfect
match to form a duplex—that is, under conditions of low
stringency. Usually, hybridizations of this type are car -
ried out at lower temperatures than typical Southern
hybridizations. If the probes stick to the DNA on the
blot, there is evidence for homologues to the BX-C and
ANT-C genes in the genomic DNA. Follow-up experi -
ments might endeavor to clone this DNA and, ultimately,
to sequence it to determine just how close a match it is to
the Drosophila probe DNA.
22.17 How might you show that two mouse Hox genes are
expressed in different tissues and at different times dur -
ing development?
ANS: Northern blotting of RNA extracted from the tissues at
different times during development. Hybridize the blot
with gene-specific probes. 22.18 Distinguish between therapeutic and reproductive
cloning.
ANS: Therapeutic cloning involves the creation of an embryo
by implanting the nucleus of a somatic cell into an enu -
cleated egg and stimulating the egg to divide. Stem cells
are then taken from the embryo to differentiate into spe -
cific tissues in the individual from which the somatic cell
was taken. These tissues will be genetically identical to
the other tissues of the individual—thus, they are unlikely
to be rejected by the individual’s immune system. Repro -
ductive cloning involves the creation of an embryo by
implanting the nucleus of a somatic cell into an enucle -
ated egg and then allowing the egg to develop into an
entire individual.
22.19 What is the scientific significance of reproductive
cloning?
ANS: Reproductive cloning of mammals such as sheep, mice,
and cats indicates that somatic cell nuclei have all the
genetic information to direct the development of a com -
plete, viable organism. It also shows that epigenetic
modifications of chromatin, such as X chromosome inac -
tivation, can be reset.
22.20 The methylation of DNA, the acetylation of histones,
and the packaging of DNA into chromatin by certain
kinds of proteins are sometimes referred to as epigenetic
modifications of the DNA. These modifications portend
difficulties for reproductive cloning. Do they also por -
tend difficulties for therapeutic cloning and for the use of
stem cells to treat diseases or injuries that involve the loss
of specific cell types?
ANS: Methylation of DNA, acetylation of histones, and pack -
aging of DNA into chromatin by certain kinds of pro -
teins all portend difficulties for therapeutic cloning as
well as for reproductive cloning. These epigenetic modi -
fications of somatic cell DNA would have to be “repro -
grammed” in the oocyte or they could affect how the
stem cells derived from the oocyte would develop.
22.21 Assume that an animal is capable of producing 100 mil -
lion different antibodies and that each antibody contains
a light chain of 220 amino acids long and a heavy chain
of 450 amino acids. How much genomic DNA would be
needed to accommodate the coding sequences of these
genes?
ANS: If each antibody consists of one kind of light chain and
one kind of heavy chain, and if light and heavy chains can
combine freely, the potential to produce 100 million dif -
ferent antibodies implies the existence of 10,000 light
chain genes and 10,000 heavy chain genes (10,000 ×
10,000 = 100 million). If each light chain is 220 amino
acids long, each light chain gene must comprise 3 × 220 =
660 nucleotides because each amino acid is specified by a
triplet of nucleotides; similarly, each heavy chain gene
must comprise 3 × 450 = 1350 nucleotides. Therefore,
the genome must contain 10,000 × 660 = 6.6 million
nucleotides devoted to light chain production and
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 89 8/14/2015 6:43:05 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 90 | 90-WC Answers to All Questions and Problems
10,000 × 1,350 = 13.5 million nucleotides devoted to
heavy chain production. Altogether, then, the genome
must contain 19.5 million nucleotides dedicated to
encoding the amino acids of the various antibody chains.
22.22 Each LkVk gene segment in the kappa light chain locus on
chromosome 2 consists of two coding exons, one for the
leader peptide and one for the variable portion of the
kappa light chain. Would you expect to find a stop codon
at the end of the coding sequence in the second
(Vk) exon?
ANS: No, because the Vk coding sequence must be joined to
the coding sequence of the constant region to encode a
complete kappa light chain.
Chapter 23
23.1 Many cancers seem to involve environmental factors.
Why, then, is cancer called a genetic disease?
ANS: Cancer has been called a genetic disease because it results
from mutations of genes that regulate cell growth and
division. Nonhereditary forms of cancer result from
mutations in somatic cells. These mutations, however,
can be induced by environmental factors including
tobacco smoke, chemical pollutants, ionizing radiation,
and UV light. Hereditary forms of cancer also frequently
involve the occurrence of environmentally induced
somatic mutations.
23.2 Both embryonic cells and cancer cells divide quickly.
How can these two types of cells be distinguished from
each other?
ANS: Cancer cells do not display contact inhibition—they pile
up on top of each other—whereas embryonic cells spread
out in flat sheets. Cancer cells are frequently aneuploid;
embryonic cells are euploid.
23.3 Most cancer cells are aneuploid. Suggest how aneuploidy
might contribute to deregulation of the cell cycle.
ANS: Aneuploidy might involve the loss of functional copies of
tumor suppressor genes, or it might involve the inappro -
priate duplication of proto-oncogenes. Loss of tumor sup -
pressor genes would remove natural brakes on cell division,
and duplication of proto-oncogenes would increase the
abundance of factors that promote cell division.
23.4 Would you ever expect to find a tumor-inducing retrovi -
rus that carried a processed cellular tumor suppressor
gene in its genome?
ANS: No. A virus that carried a processed copy of a tumor sup -
pressor gene would not be expected to induce tumor for -
mation because the product of the tumor suppressor
gene would help to restrain cell growth and division.
23.5 How do we know that normal cellular oncogenes are not
simply integrated retroviral oncogenes that have acquired
the proper regulation?
ANS: They possess introns. 23.6 How might the absence of introns in a retroviral onco -
gene explain that gene’s overexpression in the tissues of
an infected animal?
ANS: The absence of introns might speed up the expression of
the gene’s protein product because there would be no
need for splicing. In addition, some introns contain
sequences called silencers that negatively regulate tran -
scription. Removal of these sequences might cause tran -
scription to occur when it otherwise would not.
23.7 When cellular oncogenes are isolated from different ani -
mals and compared, the amino acid sequences of the
polypeptides they encode are found to be very similar.
What does this suggest about the functions of these
polypeptides?
ANS: The products of these genes play important roles in cell
activities.
23.8 The majority of the c-ras oncogenes obtained from can -
cerous tissues have mutations in codon 12, 59, or 61 in
the coding sequence. Suggest an explanation.
ANS: Mutations in these codons cause amino acid changes that
activate the Ras protein.
23.9 When a mutant c-H-ras oncogene with a valine for gly -
cine substitution in codon 12 is transfected into cultured
NIH 3T3 cells, it transforms those cells into cancer cells.
When the same mutant oncogene is transfected into cul -
tured embryonic cells, it does not transform them. Why?
ANS: The cultured NIH 3T3 cells probably carry other muta -
tions that predispose them to become cancerous; trans -
fection of such cells with a mutant c-H-ras oncogene may
be the last step in the process of transforming the cells
into cancer cells. Cultured embryonic cells probably do
not carry the predisposing mutations needed for them to
become cancerous; thus, when they are transfected with
the mutant c-H-ras oncogene, they continue to divide
normally.
23.10 A mutation in the ras cellular oncogene can cause cancer
when it is in heterozygous condition, but a mutation in
the RB tumor suppressor gene can cause cancer only
when it is in homozygous condition. What does this dif -
ference between dominant and recessive mutations
imply about the roles that the ras and RB gene products
play in normal cellular activities?
ANS: Ras protein is an activator of cell division, whereas RB
protein is a suppressor of cell division.
23.11 Explain why individuals who develop nonhereditary reti -
noblastoma usually have tumors in only one eye, whereas
individuals with hereditary retinoblastoma usually
develop tumors in both eyes.
ANS: Retinoblastoma results from homozygosity for a loss-of-
function (recessive) allele. The sporadic occurrence of
retinoblastoma requires two mutations of this gene in
the same cell or cell lineage. Therefore, retinoblastoma
is rare among individuals who, at conception, are
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 90 8/14/2015 6:43:05 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 91 | Answers to All Questions and Problems WC -91
homozygous for the wild-type allele of the RB gene. For
such individuals, we would expect the frequency of
tumors in both eyes to be the square of the frequency of
tumors in one eye. Individuals who are heterozygous for
a mutant RB allele require only one somatic mutation to
occur for them to develop retinoblastoma. Because there
are millions of cells in each retina, there is a high prob -
ability that this somatic mutation will occur in at least
one cell in each eye, causing both eyes to develop tumors.
23.12 Approximately 5 percent of the individuals who inherit
an inactivated RB gene do not develop retinoblastoma.
Use this statistic to estimate the number of cell divisions
that form the retinal tissues of the eye. Assume that the
rate at which somatic mutations inactivate the RB gene is
one mutation per 106 cell divisions.
ANS: The probability that a carrier does not develop retino -
blastoma is 0.05, which is equal to the probability that
the wild-type RB allele is not mutationally inactivated
during the cell divisions that form the retinas of the eyes.
If the rate of mutational inactivation is u = 10−6 per cell
division, and n is the number of cell divisions, then 0.05 =
(1 − u)n. If we take logarithms of both sides, log(0.05) =
nlog(1 − u), which to a good approximation, is equal to
nlog (u). After substituting 10−6 for u and solving, we find
that n = 1.3 × 106.
23.13 Inherited cancers like retinoblastoma show a dominant
pattern of inheritance. However, the underlying genetic
defect is a recessive loss-of-function mutation—often
the result of a deletion. How can the dominant pattern of
inheritance be reconciled with the recessive nature of the
mutation?
ANS: At the cellular level, loss-of-function mutations in the RB
gene are recessive; a cell that is heterozygous for such a
mutation divides normally. However, when a second
mutation occurs, that cell becomes cancerous. If the first
RB mutation was inherited, there is a high probability
that the individual carrying this mutation will develop
retinoblastoma because a second mutation can occur any
time during the formation of the retinas in either eye.
Thus, the individual is predisposed to develop retino -
blastoma, and it is this predisposition that shows a domi -
nant pattern of inheritance.
23.14 The following pedigree shows the inheritance of familial
ovarian cancer caused by a mutation in the BRCA1 gene.
Should II-1 be tested for the presence of the predispos -
ing mutation? Discuss the advantages and disadvantages
of testing.
Ovarian cancer
NormalI
II
III
ANS: II-1 should be tested for the BRCA1 mutation that appar -
ently was involved in the ovarian cancer that developed
in her mother and sister. If she is found to carry this mutation, a prophylactic oophorectomy can be pre -
scribed to reduce the chance that she will develop
cancer. If she is found to be free of the mutation carried
by her mother and sister, then she is not more likely to
develop ovarian cancer than a woman in the general
population.
23.15 In what sense is pRB a negative regulator of E2F tran -
scription factors?
ANS: By binding to E2F transcription factors, pRB prevents
those transcription factors from activating their target
genes—which encode proteins involved in progression
of the cell cycle; pRB is therefore a negative regulator of
transcription factors that stimulate cell division.
23.16 A particular E2F transcription factor recognizes the
sequence TTTCGCGC in the promoter of its target
gene. A temperature-sensitive mutation in the gene
encoding this E2F transcription factor alters the ability
of its protein product to activate transcription; at 25°C,
the mutant protein activates transcription normally, but
at 35°C, it fails to activate transcription at all. However,
the ability of the protein to recognize its target DNA
sequence is not impaired at either temperature. Would
cells heterozygous for this temperature-sensitive muta -
tion be expected to divide normally at 25°C? at 35°C?
Would your answers change if the E2F protein functions
as a homodimer?
ANS: At 25°, cell division should be normal—the same as for
cells homozygous for a wild-type allele of the E2F gene.
At 35°, division would be expected to be impaired either
because the mutant E2F protein binds unproductively to
the sequence in its target gene or because a mutant E2F
polypeptide dimerizes with a wild-type E2F polypeptide
and abolishes the activation function of the wild-type
polypeptide.
23.17 During the cell cycle, the p16 protein is an inhibitor of
cyclin/CDK activity. Predict the phenotype of cells
homozygous for a loss-of-function mutation in the gene
that encodes p16. Would this gene be classified as a
proto-oncogene or as a tumor suppressor gene?
ANS: Cells homozygous for a loss-of-function mutation in the
p16 gene might be expected to divide in an uncontrolled
manner because the p16 protein would not be able to
inhibit cyclin-CDK activity during the cell cycle. The
p16 gene would therefore be classified as a tumor sup -
pressor gene.
23.18 The BCL-2 gene encodes a protein that represses the
pathway for programmed cell death. Predict the pheno -
type of cells heterozygous for a dominant activating
mutation in this gene. Would the BCL-2 gene be classi -
fied as a proto-oncogene or as a tumor suppressor gene?
ANS: Cells heterozygous for a dominant activating mutation
in the BCL-2 gene would be expected to be unable to
execute the programmed cell death pathway in response
to DNA damage induced by radiation treatment.
Such cells would continue to divide and accumulate
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 91 8/14/2015 6:43:06 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 92 | 92-WC Answers to All Questions and Problems
mutations; ultimately they would have a good chance of
becoming cancerous. The BCL-2 gene would therefore
be classified as a proto-oncogene.
23.19 The protein product of the BAX gene negatively regu -
lates the protein product of the BCL-2 gene—that is,
BAX protein interferes with the function of the BCL-2
protein. Predict the phenotype of cells homozygous for a
loss-of-function mutation in the BAX gene. Would this
gene be classified as a proto-oncogene or as a tumor sup -
pressor gene?
ANS: Cells homozygous for a loss-of-function mutation in the
BAX gene would be unable to prevent repression of the
programmed cell death pathway by the BCL-2 gene
product. Consequently, these cells would be unable to
execute that pathway in response to DNA damage
induced by radiation treatment. Such cells would
continue to divide and accumulate mutations; ultimately,
they would have a good chance of becoming cancerous.
The BAX gene would therefore be classified as a tumor
suppressor gene.
23.20 Cancer cells frequently are homozygous for loss-of-
function mutations in the TP53 gene, and many of these
mutations map in the portion of TP53 that encodes the
DNA-binding domain of p53. Explain how these muta -
tions contribute to the cancerous phenotype of the cells.
ANS: Loss-of-function mutations in the DNA-binding
domain of p53 abolish the ability of that protein to acti -
vate transcription of target genes whose products are
involved in the restraint of cell division or in the promo -
tion of programmed cell death. Without restraint of cell
division or promotion of programmed cell death, cells
accumulate damage to their DNA and ultimately become
cancerous.
23.21 Suppose that a cell is heterozygous for a mutation that
caused p53 to bind tightly and constitutively to the DNA
of its target genes. How would this mutation affect the
cell cycle? Would such a cell be expected to be more or
less sensitive to the effects of ionizing radiation?
ANS: If a cell were heterozygous for a mutation that caused
p53 to bind tightly and constitutively to the DNA of its
target genes, its growth and division might be retarded,
or it might be induced to undergo apoptosis. Such a cell
would be expected to be more sensitive to the effects of
ionizing radiation because radiation increases the expres -
sion of p53, and in this case, the p53 would be predis -
posed to activate its target genes, causing the cell to
respond vigorously to the radiation treatment.
23.22 Mice homozygous for a knockout mutation of the TP53
gene are viable. Would they be expected to be more or
less sensitive to the killing effects of ionizing radiation?
ANS: Homozygous TP53 knockout mice might actually be less
sensitive to the killing effects of ionizing radiation
because p53 would be unable to mediate the apoptotic
response to the radiation treatment. 23.23 Would cancer-causing mutations of the APC gene be
expected to increase or decrease the ability of pAPC to
bind b-catenin?
ANS: They would probably decrease the ability of pAPC to
bind b-catenin.
23.24 Mice that are heterozygous for a knockout mutation in
the RB gene develop pituitary and thyroid tumors. Mice
that are homozygous for this mutation die during embry -
onic development. Mice that are homozygous for a
knockout mutation in the gene encoding the p130
homologue of RB and heterozygous for a knockout
mutation in the gene encoding the p107 homologue of
RB do not have a tendency to develop tumors. However,
homozygotes for knockout mutations in both of these
genes die during embryonic development. What do
these findings suggest about the roles of the RB, p139 ,
and p107 genes in embryos and adults?
ANS: All three genes ( RB, p130, and p107) are essential for
embryonic development, although by themselves, p130
and p107 are dispensable, possibly because their products
are functionally redundant. (Both gene products must be
inactivated before any deleterious effect is seen.) In
adults, only pRB appears to play a role in suppressing
tumor formation.
23.25 It has been demonstrated that individuals with diets poor
in fiber and rich in fatty foods have an increased risk to
develop colorectal cancer. Fiber-poor, fat-rich diets may
irritate the epithelial lining of the large intestine. How
could such irritation contribute to the increased risk for
colorectal cancer?
ANS: The increased irritation to the intestinal epithelium
caused by a fiber-poor, fat-rich diet would be expected to
increase the need for cell division in this tissue (to replace
the cells that were lost because of the irritation), with a
corresponding increase in the opportunity for the occur -
rence of cancer-causing mutations.
23.26 Messenger RNA from the KAI1 gene is strongly
expressed in normal prostate tissues but weakly expressed
in cell lines derived from metastatic prostate cancers.
What does this finding suggest about the role of the
KAI1 gene product in the etiology of prostate cancer?
ANS: The KAI1 gene is a prostate tumor suppressor gene.
Functional inactivation of this gene allows prostate
tumors to develop.
23.27 The p21 protein is strongly expressed in cells that have
been irradiated. Researchers have thought that this strong
expression is elicited by transcriptional activation of the
p21 gene by the p53 protein acting as a transcription factor.
Does this hypothesis fit with the observation that p21
expression is induced by radiation treatment in mice homo -
zygous for a knockout mutation in the TP53 gene? Explain.
ANS: No. Apparently there is another pathway—one not medi -
ated by p53—that leads to the activation of the p21 gene.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 92 8/14/2015 6:43:06 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 93 | Answers to All Questions and Problems WC -93
Chapter 24
24.1 What was some of the evidence that led Charles Darwin
to argue that species change over time?
ANS: Among other things, Darwin observed species on islands
that were different from each other and from continental
species but were still similar enough to indicate that they
were related. He also observed variation within species,
especially within domesticated breeds, and saw how the
characteristics of an organism could be changed by selec -
tive breeding. His observations of fossilized organisms
indicated that some species have become extinct.
24.2 Darwin stressed that species evolve by natural selection.
What was the main gap in his theory?
ANS: Darwin did not understand the mechanism of inheri -
tance; he did not know of Mendel’s principles.
24.3 Using the data in T able 24.1, and assuming that mating is
random with respect to the blood type, predict the fre -
quencies of the three genotypes of the Duffy blood-type
locus in a South African and an English population.
ANS: The frequency of the a allele is 0.06 in the South African
population and 0.42 in the English population. The pre -
dicted genotype frequencies under the assumption of
random mating are as follows:
Genotype South Africa England
aa (0.06)2 = 0.004 (0.42)2 = 0.18
ab 2(0.06)(0.94) = 0.11 2(0.42)(0.58) = 0.49
bb (0.94)2 = 0.88 (0.58)2 = 0.33
24.4 Theodosius Dobzhansky and his collaborators studied
chromosomal polymorphisms in Drosophila pseudoobscura
and its sister species in the western United States. In one
study of polymorphisms in chromosome III of D. pseu -
doobscura sampled from populations at different locations
in the Yosemite region of the Sierra Nevada, Dobzhan -
sky (1948, Genetics 33: 158–176) recorded the following
frequencies of the Standard (ST) banding pattern:
Location Frequency STElevation
(in feet)
Jacksonville 0.46 850
Lost Claim 0.41 3,000
Mather 0.32 4,600
Aspen 0.26 6,200
Porcupine 0.14 8,000
T uolumne 0.11 8,600
Timberline 0.10 9,900
Lyell Base 0.10 10,500
What is interesting about these data?ANS: The frequency of the ST banding pattern declines with
increasing altitude. Thus, the data indicate that this
chromosomal polymorphism exhibits an altitudinal
cline.
24.5 In a survey of electrophoretically detectable genetic vari -
ation in the alcohol dehydrogenase gene of Drosophila
melanogaster , a researcher found two allozymes, denoted
F (fast) and S (slow) in a population; 32 individuals were
homozygous for the F allele of the gene, 22 were homo -
zygous for the S allele, and 46 were heterozygous for the
F and S alleles. Are the observed frequencies of the three
genotypes consistent with the assumption that the popu -
lation is in Hardy–Weinberg equilibrium?
ANS: In the sample, the frequency of the F allele is (2 × 32 +
46)/(2 × 100) = 0.55 and the frequency of the S allele is
1 − 0.55 = 0.45. The predicted and observed genotype
frequencies are as follows:
Genotype Observed Hardy–Weinberg Predicted
FF 32 100 × (0.55)2 = 30.25
FS 46 100 × 2(0.55)(0.45) = 49.5
SS 22 100 × (0.45)2 = 20.25
T o test for agreement between the observed and pre -
dicted values, we compute a chi-square statistic with
1 degree of freedom: c2 = S(obs. − pred.)2/pred. = 0.50,
which is not significant at the 5 percent level. Thus, the
population appears to be in Hardy–Weinberg equilib -
rium for the alcohol dehydrogenase locus.
24.6 A researcher has been studying genetic variation in fish
populations by using PCR to amplify microsatellite
repeats at a particular site on a chromosome (see Chap -
ter 16). The diagram below shows the gel-fractionated
products of amplifications with DNA samples from 10
different fish. How many distinct alleles of this microsat -
ellite locus are evident in the gel?
ANS: There are four alleles.
24.7 Within the coding region of a gene, where would you
most likely find silent polymorphisms?
ANS: In the third position of some of the codons. Due to the
degeneracy of the genetic code, different codons can
specify the same amino acid. The degeneracy is most
pronounced in the third position of many codons, where
different nucleotides can be present without changing
the amino acid that is specified.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 93 8/14/2015 6:43:06 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 94 | 94-WC Answers to All Questions and Problems
24.8 Why are the nucleotide sequences of introns more poly -
morphic than the nucleotide sequences of exons?
ANS: Introns do not encode amino acids; most exons do.
Many—perhaps most—of the nucleotides within an
intron can be changed without impairing the expression
of the gene or the integrity of its polypeptide product.
By contrast, many of the nucleotides within exons—
especially the first and second positions of codons—are
functionally constrained by the amino acids specified.
24.9 DNA and protein molecules are “documents of evolu -
tionary history.” Why aren’t complex carbohydrate mol -
ecules such as starch, cellulose, and glycogen considered
“documents of evolutionary history”?
ANS: Complex carbohydrates are not “documents of evolu -
tionary history” because, although they are polymers,
they are typically made of one subunit incorporated rep -
etitiously into a chain. Such a polymer has little or no
“information content.” Thus, there is little or no oppor -
tunity to distinguish a complex carbohydrate obtained
from two different organisms. Moreover, complex carbo -
hydrates are not part of the genetic machinery; their for -
mation is ultimately specified by the action of enzymes,
which are gene products, but they themselves are not
genetic material or the products of the genetic material.
24.10 A geneticist analyzed the sequences of a gene cloned
from four different individuals. The four clones were
identical except for a few base pair differences, a deletion
(gap), and a transposable element (TE) insertion:
Sequences
1TEG
C
2TEA
T
T
A
G
CC
G3C
G
4A
T
Using this information, compute the minimum number
of mutations required to explain the derivation of the
four sequences (1, 2, 3, and 4) in the following phyloge -
netic trees:
12 43 12 34
Tree AT ree BT ree C34 21
Which of these trees provides the most parsimonious
explanation for the evolutionary history of the four DNA
sequences?
ANS: The tree on the right would require nine mutations.
These mutations are a deletion in the branch leading to the common ancestor of sequences 1, 2, and 3; a TE
insertion in the branch leading to the common ancestor
of sequences 1 and 2; and seven base-pair changes: one
leading to sequence 1, another leading to sequence 2, two
leading to sequence 3 and three leading to sequence 4.
The tree in the middle would also require nine mutations.
In this tree, we regard the gap as ancestral—which means
that sequence 4 has acquired an “insertion” at the posi -
tion of the gap. The other mutations are a TE insertion
in the branch leading to the common ancestor of
sequences 1 and 2, and seven base-pair changes: one
leading to sequence 1, another to sequence 2, two lead -
ing to sequence 3, and three leading to sequence 4.
The tree on the right would also require nine mutations.
Here again we regard the gap as ancestral; evidently, an
insertion occurred at the position of the gap in the
branch leading to sequence 4. The TE insertion can also
be regarded as ancestral, with loss occurring in the
branch leading to the common ancestor of sequences
3 and 4. There are also seven base-pair changes in this
tree: one leading to sequence 1, another leading to
sequence 2, two leading to sequence 3 and three leading
to sequence 4. These interpretations of the data assume
that insertions and deletions (gaps) are reversible and
that there is no way of telling which way the sequence
evolved—that is, through insertion or deletion. How -
ever, if we know, for example, that the TE is a retrotrans -
poson incapable of excision, then we would need more
than nine mutations to explain the tree on the right. The
TE insertions must have occurred independently in the
branches leading to sequences 1 and 2, and there is no
need to postulate excision of the TE in the branch lead -
ing to the common ancestor of sequences 3 and 4. Thus,
on the assumption that the TE is not excisable, 10 muta -
tions are needed to explain the tree on the right. Given
this reservation, the left and middle trees provide the
most parsimonious explanations for the evolution of the
four sequences.
24.11 The heme group in hemoglobin is held in place by histi -
dines in the globin polypeptides. All vertebrate globins
possess these histidines. Explain this observation in terms
of the Neutral Theory of Molecular Evolution.
ANS: The histidines are rigorously conserved because they
perform an important function—anchoring the heme
group in hemoglobin. Because these amino acids are
strongly constrained by natural selection, they do not
evolve by mutation and random genetic drift.
24.12 During the early evolutionary history of the vertebrates,
a primordial globin gene was duplicated to form the
α- and b-globin genes. The rate of evolution of the poly -
peptides encoded by these duplicate genes has been
estimated to be about 0.9 amino acid substitutions per
site every billion years. By comparing the human α- and
b-globins, the average number of amino acid substitu -
tions per site has been estimated to be 0.800. From this
estimate, calculate when the duplication event that
produced the α- and b-globin genes must have occurred.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 94 8/14/2015 6:43:07 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 95 | Answers to All Questions and Problems WC -95
ANS: The total elapsed evolutionary time is 0.800/0.9 = 880
million years, which must be apportioned equally to the
α and β gene lineages by dividing by 2; thus, the time
since the duplication event is estimated to be 440 million
years.
24.13 Ribonuclease, a protein that degrades RNA, is 124 amino
acids long. A comparison between the amino acid
sequences of cow and rat ribonucleases reveals 40 differ -
ences. What is the average number of amino acid substi -
tutions that have occurred per site in these two
evolutionary lineages? If the cow and the rat lineages
diverged from a common ancestor 80 million years ago,
what is the rate of ribonuclease evolution?
ANS: Estimate the average number of substitutions per site in
the ribonuclease molecule as −ln(S), where S = (124 −
40)/124 = 0.68, the proportion of amino acids that are
the same in the rat and cow molecules. The average
number of substitutions per site since the cow and rat
lineages diverged from a common ancestor is therefore
0.39. The evolutionary rate in the cow and rat lineages is
0.39/(2 × 80 million years) = 2.4 substitutions per site
every billion years.
24.14 If a randomly mating population is segregating n selec -
tively neutral alleles of a gene and each allele has the
same frequency, what is the frequency of all the homozy -
gotes in the population?
ANS: With n alleles having equal frequency, the frequency of
any one allele is 1/ n. Under random mating, the fre -
quency of homozygotes for a particular allele is (1/ n)2.
The frequency of all the homozygotes is therefore
∑(1/n)2 = n(1/n)2 = 1/n.
24.15 If the evolutionary rate of amino acid substitution in a
protein is K, what is the average length of time between
successive amino acid substitutions in this protein?
ANS: The reciprocal of the rate, that is, 1/ K.
24.16 The coding sequence of the alcohol dehydrogenase
(Adh) gene of D. melanogaster consists of 765 nucleo -
tides (255 codons); 192 of these nucleotides are func -
tionally silent—that is, they can be changed without
changing an amino acid in the Adh polypeptide. In a
study of genetic variation in the Adh gene, Martin
Kreitman observed that 13 of the 192 silent nucleo -
tides were polymorphic. If the same level of polymor -
phisms existed among the nonsilent nucleotides of the
Adh gene, how many amino acid polymorphisms
would Kreitman have observed in the populations he
studied?
ANS: The fraction of polymorphic sites among the silent
nucleotides is 13/192 = 0.068. If the same level of poly -
morphism existed among the nonsilent sites, the number
of amino acid polymorphisms would be 225 × 0.067 =
17.2. Kreitman actually observed only one amino acid
polymorphism—evidence that amino acid changes in
alcohol dehydrogenase are deleterious. 24.17 How might you explain the 1000-fold difference in the
evolutionary rates of fibrinopeptide and histone 3?
ANS: The protein with the higher evolutionary rate is not as
constrained by natural selection as the protein with the
lower evolutionary rate.
24.18 A geneticist has studied the sequence of a gene in each of
three species, A, B, and C. Species A and species B are
sister species; species C is more distantly related. The
geneticist has calculated the ratio of nonsynonymous
(NS) to synonymous (S) nucleotide substitutions in the
coding region of the gene in two ways—first, by compar -
ing the gene sequences of species A and C, and second,
by comparing the gene sequences of species B and C.
The NS:S ratio for the comparison of species B and C is
five times greater than it is for the comparison of species
A and C. What might this difference in the NS:S ratios
suggest?
ANS: The difference in the NS:S ratios suggests that in at least
one lineage, positive selection has been operating to
change nucleotides in the gene.
24.19 Dispersed, repetitive sequences such as transposable ele -
ments may have played a role in duplicating short regions
in a genome. Can you suggest a mechanism? ( Hint: See
Chapter 21 on the Instructor Companion site.)
ANS: Repetitive sequences that are near each other can medi -
ate displaced pairing during meiosis. Exchange involving
the displaced sequences can duplicate the region between
them.
24.20 Exon shuffling is a mechanism that combines exons from
different sources into a coherent sequence that can
encode a composite protein—one that contains peptides
from each of the contributing exons. Alternate splicing is
a mechanism that allows exons to be deleted during the
expression of a gene; the mRNAs produced by alternate
splicing may encode different, but related, polypeptides
(see Chapter 18). What bearing do these two mecha -
nisms have on the number of genes in a eukaryotic
genome? Do these mechanisms help to explain why the
gene number in the nematode Caenorabditis elegans is not
too different from the gene number in Homo sapiens ?
ANS: Exon shuffling is a way of creating genes that have pieces
from disparate sources. Through exon shuffling, the
number of genes in a genome could be increased without
having to evolve the genes “from scratch.” However, the
genome sequencing projects indicate that the gene num -
ber in complex, multicellular vertebrates is not much dif -
ferent from the gene number in simple, multicellular
invertebrates or in plants. If, judging from their pheno -
types, multicellular vertebrates need more gene products
than phenotypically simpler invertebrates such as C. ele -
gans, alternate splicing could provide some of these gene
products without increasing the number of genes.
24.21 Drosophila mauritiana inhabits the island of Mauritius in
the Indian Ocean. Drosophila simulans , a close relative, is
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 95 8/14/2015 6:43:07 PM |
https://www.press.muni.cz/media/3019066/answers_to_all_questions.pdf | 96 | 96-WC Answers to All Questions and Problems
widely distributed throughout the world. What experi -
mental tests would you perform to determine if D. mau -
ritiana and D. simulans are genetically different species?
ANS: Cross D. mauritiana with D. simulans and determine if
these two species are reproductively isolated. For
instance, can they produce offspring? If they can, are the
offspring fertile?
24.22 Distinguish between allopatric and sympatric modes of
speciation.
ANS: Allopatric speciation occurs when populations diverge
genetically while they are geographically separated.
Sympatric speciation occurs when populations diverge
genetically while they inhabit the same territory.
24.23 The prune gene (symbol pn) is X-linked in Drosophila
melanogaster . Mutant alleles of this gene cause the eyes to
be brown instead of red. A dominant mutant allele of
another gene located on a large autosome causes
hemizygous or homozygous pn flies to die; this dominant
mutant allele is therefore called Killer of prune (symbol
Kpn). How could mutants such as these play a role in
the evolution of reproductive isolation between
populations?
ANS: The Kpn–pn interaction is an example of the kind of neg -
ative epistasis that might prevent populations that have
evolved separately from merging into one panmictic
population. The Kpn mutation would have evolved in
one population and the pn mutation in another, geo -
graphically separate population. When the populations
merge, the two mutations can be brought into the same fly by interbreeding. If the combination of these muta -
tions is lethal, then the previously separate populations
will not be able to exchange genes, that is, they will be
reproductively isolated.
24.24 A segment of DNA in an individual may differ at several
nucleotide positions from a corresponding DNA seg -
ment in another individual. For instance, one individual
may have the sequence …A…G…C… and another indi -
vidual may have the sequence …T…A…A…. These two
DNA segments differ in three nucleotide positions.
Because the nucleotides within each segment are tightly
linked, they will tend to be inherited together as a unit,
that is, without being scrambled by recombination.
We call such heritable units DNA haplotypes. Through
sampling and DNA sequencing, researchers can deter -
mine which DNA haplotypes are present in a particular
population. When this kind of analysis is performed on
human populations by sequencing, for example, a seg -
ment of mitochondrial DNA, it is found that samples
from Africa exhibit more haplotype diversity than sam -
ples from other continents. What does this observation
tell us about human evolution?
ANS: More haplotype diversity refers to the number of differ -
ent haplotypes that are found in a population. If African
populations of humans have the greatest haplotype
diversity, then these populations appear to have had a
longer time to accumulate different haplotypes—that is,
they are older than other populations. Greater haplotype
diversity in African populations of humans is therefore
evidence that African populations were at the root of the
modern human evolutionary tree.
ONLINE_AnswerstoOddNumberedQuestionsandProblems.indd 96 8/14/2015 6:43:07 PM |
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 1 |
Genetics 301 Sample Final Examination
Spring 2003
50 Multiple Choice Questions -(Choose the best answer)
1. A cross between two true breeding lines one with dark blue flowers and one with bright
white flowers produces F1 offspring that are light blue. When the F1 progeny are
selfed a 1:2:1 ratio of dark blue to light blue to white flowers is observed. What genetic
phenomenon is consistent with these results?
a. epistasis
b. incomplete dominance
c. codominance
d. inbreeding depression
e. random mating
2. Mutations which occur in body cells which do not go on to form gametes can be classified as:
a. auxotrophic mutations
b. somatic mutations
c. morphological mutations
d. oncogenes
e. temperature sensitive mutations
3. What would be the freque ncy of AABBCC individuals from a mating of two AaBbCc
individuals?
a.. 1/64
b. 1/32
c. 1/16
d. 1/8
e. 3/16
f. 1/4
4. The stage of meiosis in which chromosomes pair and cross over is:
a. prophase I
b. metaphase I
c. prophase II
d. met aphase II
e. anaphase II
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 2 | 25. Polyploidy refers to:
a. extra copies of a gene adjacent to each other on a chromosome
b. an individual with complete extra sets of chromosomes
c. a chromosome which has replicated but not divided
d. multiple ribosomes present on a single mRNA
e. an inversion which does not include the centromere
6. A gene showing codominance -
a. has both alleles independently expressed in the heterozygote
b. has one allele dominant to the other
c. has alleles tightly linked on the same chromosome
d. has alleles expressed at the same time in development
e. has alleles that are recessive to each other
7. The phenomenon of “independent assortment” refers to:
a. expression at the same stage of development
b. unlinked transmission of genes in crosses resulting from being locat ed on
different chromsomes, or far apart on the same chromosome .
c. association of an RNA and a protein implying related function
d. independent location of genes from each other in an interphase cell
e. association of a protein and a DNA sequence im plying related function
8. Mendel’s law of segregation, as applied to the behavior of chromosomes in meiosis, means
that:
a. pairing of homologs will convert one allele into the other, leading to separation of the
types.
b. alleles of a gene separate fro m each other when homologs separate in meiosis I,
or in meiosis II if there is a single crossover between the gene and the
centromere.
c. genes on the same chromosome will show 50% recombination
d. alleles of a gene will be linked and passed on together through meiosis
9. Which component of transcribed RNA in eukaryotes is present in the initial transcript but is
removed before translation occurs:
a. Intron
b. 3’ Poly A tail
c. Ribosome binding site
d. 5’ cap
e. codons coding for the pr otein to be produced
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 3 | 310. Choose the correct statement about the genetic code.
a. includes 61 codons for amino acids and 3 stop codons
b. almost universal; exactly the same in most genetic systems
c. three bases per codon
d. some amino acids are coded by multiple codons
e. all of the above
11. X -chromosome inactivation
a. normally takes place in males but not females
b. is the cause of the Y chromosome being genetically inactive
c. takes place in humans so that the same X chromosome is inactive in all of the cells
of a female
d. occurs in fruit flies but not in mammals
e. results in genetically turning off one of the two X chromosomes in female
mammals
12. DNA ligase is:
a. an enzyme that joins fragments in nor mal DNA replication
b. an enzyme involved in protein synthesis
c. an enzyme of bacterial origin which cuts DNA at defined base sequences
d. an enzyme that facilitates transcription of specific genes
e. an enzyme which limits the level to which a particular nutrient reaches
13. An Hfr strain of E. coli contains:
a. a vector of yeast or bacterial origin which is used to make many copies of a
particular DNA sequence
b. a bacterial chromosome with a human gene inserted
c. a bacterial chromosome with the F factor inser ted
d. a human chromosome with a transposable element inserted
e. a bacterial chromosome with a phage inserted
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 4 | 414. An experiment was conducted in E. coli to map the following genes (pro, his, bio, met, phe
and trp) on a circular map using 3 different Hfr strai ns.
Strain 1 Order of transfer (early to late): trp met his pro
Strain 2 Order of transfer (early to late): his met trp bio
Strain 3 Order of transfer (early to late): pro phe bio trp
Based on the results what is the most likely map?
a. b.
c. d.
15. Generation of antibody diversity in vertebrate animals takes place through:
a. the presence of as many genes in the germ line as there are types of antibodies
possible.
b. infection with bacteria carrying antibody genes
c. infection with viruses carrying antibody genes
d. polyploidy in antibody -forming cells
e. rearrangement of DNA in tissues that go on to produce antibodies
16. Replication of DNA:
a. takes place in a “conservative” manner
b. takes place in a “dispersive” manner
c. takes place in a “semi -conservative” manner
d. usually involves one origin of replication per chromosome in eukaryotes
e. takes place only in the 3’ to 5’ direction
trp
pro
his phe met bio trp
pro
bio met phe his
phe
met
bio pro trp his trp
pro
met bio phe his |
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 5 | 517. A duplication is:
a. an exchange between non -homologous chromosomes, resulting in chromosomes
with new genes adjacent to each other.
b. loss of genes in part of a chromosome
c. an extra copy of the genes on part of a chromosome
d. a reversal of order of genes on a chromosome
e. an extra set of chromosome s in an organism
18. What is the co -transduction frequency for the A and B genes, from the following dataset?
(Assume that there has been selection for the A+ form of the A gene).
Genotype Number
A+B+ C+ 10
A+B+ C - 30
A+ B - C+ 20
A+ B - C- 40
a. .10
b. .20
c. .30
d. .40
e. .50
19. A mutation in a codon leads to the substitution of one amino acid with another. What is the
name for this type of mutation?
a. nonsense mutation
b. missense mutation
c. frameshift mutation
d. promoter muttion
e. operator mutation
20. Mapping of human chromosomes:
a. has been restricted to the sex chromosomes because of small family sizes
b. proceeded much more successfully as large numbers of DNA markers became
available.
c. has determined that the number of linkage groups is about twi ce the number of
chromosomes
d. has demonstrated that almost all of the DNA is involved in coding for genes
e. has shown that there are more genes on the Y than on the X chromosome
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 6 | 621. Homeobox sequences
a. are present in the genome of many anima l species
b. are found in prokaryotes but not in eukaryotes
c. were identified as the integration sites for bacterial viruses
d. represent integration sites for transposable elements
e. represent the termination signals for transcription
22. Tracin g of a cell lineage during development means that:
a. the cells giving rise to and derived from a specific cell are known
b. the sequence of the enhancers for developmental genes is known
c. the regulatory genes for the organism have been genetically mappe d
d. cell components in the membrane involved in signaling have been isolated
e. cell components in the nucleus involved in signaling have been isolated
23. Zinc finger proteins and helix -turn-helix proteins are:
a. types of DNA -binding proteins
b.involved in the control of translation
c.components of ribosomes
d.part of the hemoglobin in blood cells
e.bound to transfer RNA during replication
24. Transcriptional activator proteins:
a. transcribe a messenger off a DNA template
b. bind to ribosomes to activate the pro duction of specific proteins
c. are produced during an infection of bacteria by a phage
d. are essential to function of transfer RNAs during translation
e. bind regions near a eukaryotic gene and allow an RNA polymerase to
transcribe a gene
25.Differential distrib ution of substances in the egg most typically results in:
a. differences in gene expression which may establish a pattern in the embryo as
the cells divide
b. amplification of specific genes during development
c.development of polyploid tissues
d.loss of specific genes during development
e.dominance of genes derived from the father
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 7 | 726. Arabidopsis is advantageous for plant genetic research because:
a. it is commercially important as a food crop
b. it is an endangered species
c. it is the closest to humans of any exi sting plant
d. it is a small plant with a small genome size which can be raised inexpensively
e. it is a close relative of corn and results with this species can be applied to problems
in corn
27. A homeotic mutation is one which:
a. is present in only one form in an i ndividual
b. substitutes one body part for another in development
c. results in development of a tumor
d. is wild type at one temperature and abnormal at another
e. leads to increased body size in an organism
28. Assuming that the level of glucose is low, a mutation in the repressor of the lac operon in E.
coli, preventing binding of the repressor to the operator, should result in:
a. constitutive expression of the lac operon genes
b. lack of expression or reduced expression of the lac operon genes under all
circumsta nces
c. expression of the genes only when lactose is present
d. expression of the genes only when lactose is absent
29. Assuming that the level of glucose is low, a mutation in the repressor associated with the lac
operon of E. coli which prevents binding of the repressor to lactose should result in:
a. constitutive expression of the lac operon genes
b. lack of expression or reduced expression of the lac operon genes under all
circumstances
c. expression of the genes only when lactose is present
d. expression of the genes only when lactose is absent
30. RFLP analysis is a technique that
a. uses hybridization to detect specific DNA restriction fragments in genomic DNA
b. is used to determine whether a gene is transcribed in specific cells
c. me asures the transfer frequency of genes during conjugation
d. is used to detect genetic variation at the protein level.
e. is used to amplify genes for producing useful products
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 8 | 831.Plasmid vectors for cloning
a. can generally accommodate larger inserts tha n phage vectors can
b. grow within bacteria, and are present in bacterial colonies on an agar plate
c. can accommodate inserts of over 100 kilobases
d. include centromeres to allow propagation in yeast
e. burst bacteria and form plaques on a “lawn” of bacteria
32.Sim ple tandem repeat polymorphisms in humans are most useful for:
a. solving criminal and paternity cases
b. reconstructing the relationships of humans and chimps.
c. estimating relationships of humans and Neanderthals
d. transferring disease resistanc e factors into bone marrow cells
e. estimating matches for blood transfusions
33.The polymerase chain reaction or PCR is a technique that
a. was used to demonstrate DNA as the genetic material
b. is used to determine the content of minerals in a soil sample
c. uses short DNA primers and a thermostable DNA polymerase to replicate
specific DNA sequences in vitro .
d. measures the ribosome transfer rate during translation
e. detects the level of polymerases involved in replication
34.Positional clonin g refers to:
a. using a selection procedure to clone a cDNA
b. cloning a portion of a gene using PCR
c. isolating a gene by PCR using primers from another species
d. isolating a gene from a specific tissue in which it is being expressed
e. mapping a gene to a chromosomal region and then identifying and cloning a
genomic copy of the gene from the region
35.Large quantities of useful products can be produced through genetic engineering involving:
a. bacteria containing recombinant plasmids
b. yeast carrying foreign genes
c. transgenic plants
d. mammals producing substances in their milk
e. all of the above
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 9 | 936.On average, how many fragments would a restriction enzyme which recognizes a specific 4
base sequence in DNA be expected to cleave a double -stranded bacteriop hage with a
genome size of 5,000 bp into?
a. about 2
b. about 4
c. about 20
d. about 50
e. about 1250
37.The “sticky ends” generated by restriction enzymes allow:
a. selection for plasmids lacking antibiotic resistance
b. easy identification of plasmids which carry an insert
c. replication of transfer RNA within the bacterial cell
d. insertion of centromeres into ribosomes lacking them
e. pieces of DNA from different sources to hybridize to each other and to be
joined together
38.QTL analysis is used to:
a. ident ify RNA polymerase binding sites
b. map genes in bacterial viruses
c. determine which genes are expressed at a developmental stage
d. identify chromosome regions associated with a complex trait in a genetic
cross
e. determine the most rapidly -evolving parts of genes
39.Assuming Hardy -Weinberg equilibrium, the genoypte frequency of heterozygotes, if the
frequency of the two alleles at the gene being studied are 0.6 and 0.4, will be:
a. 0.80
b. 0.64
c. 0.48
d. 0.32
e. 0.16
40.The likelihood of an individual in a population carrying two specific alleles of a human DNA
marker, each of which has a frequency of 0.2, will be:
a. 0.4
b. 0.32
c. 0.16
d. 0.08
e. 0.02
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 10 | 1041.A threshold trait is one which:
a. is expressed on a continuous scale ( such as blood pressure)
b. is present in a few discrete classes, but is influenced by both genetics and the
environment (such as diabetes or schizophrenia)
c. is caused by only a single gene, with no environmental influence
d. is present in a very low f requency in the population
e. is associated with superior survival of the heterozygote
42. Mitochondrial DNA is advantageous for evolutionary studies because:
a. it is inherited only through the female parent and thus evolves in a way that
allows trees of relationship to be easily constructed
b. it is inserted into the X chromosome
c. it first appeared in humans and is not found in other animals
d. it evolves more slowly than the genes in the nucleus
e. it was derived from the globin genes as an extra copy
43.What are the assumptions of Hardy Weinberg equilibrium?
a. Small population size, random mating, no selection, no migration, no mutation
b. large population size, random mating, no selection, no migration, no mutation
c. large population size, random mating, heterozygotes survive the best, no migration, no
mutation
d. large population size, like individuals mate, no selection, no migration, no mutation
e. large population size, random mating, no selection, migrants enter from other
populations, no mutation
44.Twin studies in hum ans are useful because:
a. they allow more refined estimates of chromosome location to be made
b. twins have a greater likelihood of being heterozygous
c. they allow improved expression of genes
d. cloning of genes is facilitated by the presence of extra copies.
e. they allow genetic as opposed to environmental influences on variation in a
trait to be estimated
45.Which of the following statements about heritability are true?
a. is a measure of level of gene linkage
b. is a measure of inbreedin g
c. is a measure of proportion of repeated DNA in an organism
d. is a measure of the level of heterozygotes in a population
e. is a measure of the proportion of variation that is due to genetic causes
|
https://public.wsu.edu/~thorglab/biol301/exams/finalkey.pdf | 11 | 1146.The allele associated with sickle cell anem ia apparently reached a high frequency in some
human populations due to:
a. random mating
b. superior fitness of heterozygotes in areas where malaria was present
c. migration of individuals with the allele into other populations
d. a high mutation rate at that specific gene
e. genetic drift
47.An increase in the inbreeding coefficient, F,is likely to result in:
a. reduced likelihood of heterozygotes being present in a population
b. higher proportion of genes that show linkage
c. high er proportion of genes with introns
d. lower level of difference between proteins in two daughter cells
e. higher level of difference between RNA molecules in two daughter cells
48.Most new mutations appear to be:
a. beneficial
b. neutral or deleterious
c. present in homozygotes rather than heterozygotes
d. detectable using allozyme studies (protein electrophoresis)
e. present within pericentric inversions
49.If the frequency of males affected with an X -linked recessive condition in a human
population is .10 (one i n ten), what will be the expected frequency of affected females?
a.0001
b. .001
c. .02
d. .01
e. .05
50. The following genotypes are found in a population:
AA Aa aa
70 50 20
What are the allele frequencies of A and a?
a. A = 0.86 and a = 0.14
b. A = 0.68 and a = 0.32
c. A = 0.63 and a = 0.36
d. A = 0.32 and a = 0.68
e. A = 0.36 and a = 0.63
|
https://people.bu.edu/msoren/BI515_2014/Exam1key.pdf | 1 | Population Genetics — BI 515 — Exam 1, Spring 2014 Answer the following questions. Do you own work. Please type your answers in this document and submit electronically. All of the questions can be answered with one or a few sentences and/or numerical results. 1. Early doubters of Mendelian genetics pointed to the general lack of 3:1 phenotypic ratios in natural populations as evidence that Mendel’s results on peas were not generally applicable. Why is this argument flawed?
A
3:1
phenotypic
ratio
is
predicted
for
the
offspring
produced
by
a
pair
of
heterozygous
parents
or
for
a
population
with
an
overall
allele
frequency
of
0.5
(assuming
in
both
cases
that
there
are
two
alleles,
one
fully
dominant,
the
other
recessive),
but
this
prediction
does
not
apply
generally
to
population-‐level
data
because
allele
frequencies
other
than
0.5
will
generate
different
ratios
of
phenotypes
at
the
population
level.
(E.g.,
suppose
A
is
at
frequency
0.2,
we
predict
0.04
AA
genotypes
plus
0.32
Aa
genotypes,
so
a
64:36
ratio
of
the
recessive
phenotype
to
dominant
phenotype.)
2. Provide a simple verbal explanation for why the probability of fixation for a new, neutral mutation is 1/(2N).
In
a
population
of
finite
size,
the
process
of
coalescence
ultimately
leads
to
a
single
ancestral
allele
in
the
past.
Assuming
constant
population
size,
that
allele
was
one
of
the
2N
alleles
in
an
ancestral
population.
Moving
forward
in
time,
any
of
those
2N
alleles
might
have
been
the
one
to
survive
and
go
to
fixation,
assuming
no
differences
in
fitness
(selection).
3. Explain the subtle distinction between the terms autozygous and homozygous.
An
individual
is
autozygous
(and
also
homozygous)
if
the
two
alleles
at
a
locus
are
identical
by
descent.
The
individual
is
homozygous
(but
not
necessarily
autozygous)
if
the
two
alleles
at
a
locus
are
identical
in
state.
4. What factors influence effective population size in natural populations and what is the direction of their effects? 1)
Variation
in
population
size
over
time,
2)
variation
among
individuals
in
offspring
production
(i.e.,
greater
variation
than
expected
under
a
Poisson
process),
3)
a
difference
in
the
effective
number
of
breeding
males
and
females,
4)
differences
in
ploidy
(e.g.,
sex
chromosomes,
mtDNA),
and
5)
populations
structure.
The
first
3
reduce
effective
population
size
relative
to
census
population
size.
Reduced
ploidy
also
reduces
effective
population
size
(assuming
equal
variance
in
male
and
female
reproductive
success),
whereas
population
structure
increases
effective
population
size
(it’s
unlikely
that
subpopulations
will
all
drift
in
the
same
direction,
resulting
in
longer
than
expected
maintenance
of
diversity
in
the
overall
population).
5. We have not yet considered models of natural selection, but you should be able to solve this problem using basic Mendelian and Hardy-Weinberg logic. Strong selection is one possible reason for a population deviating from Hardy-Weinberg equilibrium. Suppose that a gene has a dominant allele (A) and a recessive allele (a) and that survival during early life stages for individuals homozygous for the recessive allele is only 80% as high as for individuals with the dominant phenotype. |
https://people.bu.edu/msoren/BI515_2014/Exam1key.pdf | 2 | Population Genetics — BI 515 — Exam 1, Spring 2014 a) If the population allele frequency is 0.7 A and 0.3 a in generation 1 adults, what are the expected proportions of the three genotypes in generation 2 zygotes? AA
=
0.49;
Aa
=
0.42;
aa
=
0.09
b) What are the allele frequencies and expected proportions of the three genotypes in generation 2 adults? (Assume that a very large number of offspring is produced and that 20% of aa individuals dies immediately, before a random sample of the remaining individuals is selected to form the adult population for the next generation.) 20%
mortality
reduces
aa
from
0.09
to
0.072,
so
new
frequencies
are:
AA
=
0.49/0.982
=
0.49898
Aa
=
0.42/0.982
=
0.42770
aa
=
0.072/0.982
=
0.07332
freq
A
=
(2*0.49898+0.41752)/2
=
0.71283
freq
a
=
(2*0.07332+0.41752)/2
=
0.28717
c) Would a sample size of 1000 adults be enough to detect a significant deviation from Hardy-Weinberg equilibrium in the generation 2 adults? Short
answer:
“No”
Suppose
499
AA,
428
Aa
and
73
aa
individuals.
Observed
allele
frequencies
are:
A
=
(2*499+428)/2000
=
0.713
a
=
(2*73+428)/2000
=
0.287
Expected
genotype
frequencies:
AA
=
0.7132
x
1000
=
508.369
Aa
=
2*0.713*0.287
x
1000
=
409.262
aa
=
0.2872
x
1000
=
82.369
(observed
–
expected)2/expected:
-‐9.3692/508.369
=
0.1727
18.7382/409.262
=
0.8579
-‐9.3692/82.369
=
1.0657
chi-‐squared
=
2.0963,
not
significant
at
p
<
0.05 6. The table below shows the genotypes for one individual at nine microsatellite loci as well as the population level allele frequencies for the allele(s) present in this individual. Using the data in this table, calculate the probability that a randomly selected individual from the same population would match the genotype show in the table at right: a) Probability: _2.82147E-‐13_ b) This genotype was derived from a blood smear at a crime scene. If a suspect, who happens to be Asian, had a matching genotype, how would you argue the case if you were the prosecutor? Using
one
the
most
basic
principles
of
population
genetics
and
statistics,
we
can
calculate
that
the
probability
of
an
individual
exactly
matching
the
genotype
at
all
10
of
these
microsatellite
loci
is
only
hints: critical value for the χ2 distribution with 1 df and p-value = 0.05 is 3.84 |
https://people.bu.edu/msoren/BI515_2014/Exam1key.pdf | 3 | Population Genetics — BI 515 — Exam 1, Spring 2014
€ Ft=12N+1−12N# $ % & ' ( Ft−12.82147E-‐13.
Put
another
way,
there
is
only
a
1
in
3.544
trillion
chance
that
a
randomly
selected
person
would
match
this
genotype
by
chance!
We
can
be
certain
he’s
guilty.
c) Likewise, if you were the defense attorney? 1)
We
are
provided
no
information
about
the
population
from
which
these
allele
frequencies
were
derived.
For
all
we
know
the
table
provides
data
for
a
Caucasian
population
and
therefore
the
calculation
of
any
statistical
probability
of
a
match
is
completely
invalid.
For
all
we
know,
the
alleles
in
this
genotype
are
common
Asian
alleles
and
there
may
be
less
diversity
in
these
loci
in
the
Asian
population,
making
a
random
match
far
more
likely.
2)
Mistakes
in
the
lab
(including
sample
mix-‐ups,
cross
contamination,
genotyping
errors).
3)
Just
because
the
defendants
blood
was
at
the
crime
scene
does
not
mean
he’s
guilty
of
the
crime.
4)
How
do
we
know
the
defendant
does
not
have
an
identical
twin
(or
other
close
relative,
for
that
matter,
who
would
have
a
higher
probability
of
matching).
Locus
Allele
1
Allele
2
Allele
1:
Population
Frequency
Allele
2:
Population
Frequency
D3S1358
15
15
0.24
—
vWA
17
19
0.49
0.11
D21S11
30
32
0.02
0.23
D18S51
13
16
0.29
0.09
D13S317
11
11
0.10
—
FGA
20
24
0.39
0.05
D8S1179
13
13
0.30
—
D5S818
11
12
0.39
0.24
D7S820
9
12
0.06
0.12
7. The equation for Wright’s fixation index for a random-breeding population of size N is as follows: a) Explain in words the basic logic of this equation.
The
equation
includes
two
parts,
the
first
being
the
probability
that
two
randomly
selected
alleles
are
identical
copies
from
the
prior
generation
(1/2N)
and
the
second
being
the
probability
that
two
alleles
are
identical
copies
from
an
earlier
generation,
which
is
expressed
as
the
probability
that
the
two
alleles
are
not
identical
from
the
previous
generation
(1-‐1/2N)
times
the
fixation
index
for
the
previous
generation.
b) Assuming F0 (F at time zero) = 0, what is the expected value of F after 100 generations for a population of size 250 (2N = 500)? F100
=
0.181433195
c) The equation above assumes no mutation. Write the equation for Ft when mutation is possible. |
https://people.bu.edu/msoren/BI515_2014/Exam1key.pdf | 4 | Population Genetics — BI 515 — Exam 1, Spring 2014 d) What is the equilibrium value of F if the per locus mutation rate is 0.0001?
ˆF=11+4Nµ=0.909090909
e) Explain in words why the population reaches an equilibrium value of F and stays there. An
equilibrium
is
reached
when
the
rate
at
which
diversity
is
lost
through
genetic
drift
is
equal
to
the
introduction
of
new
diversity
due
to
mutation.
8. Consider the following sample of 6 gene sequences, with the alignment below showing only the variable positions along a sequence of 1000 bases. a) Calculate the number of segregating sites (S) and nucleotide diversity (∏ = the average number of pairwise mismatches)? S
=
10
∏
=
(3
x
2
x
4
+
2
x
5
x
1
+
5
x
3
x
3)/15
=
5.267 b) Give two estimates of θ that can be derived from these data? θ
=
∏
=
5.267
θ
=
S/(1
+
½
+
1/3
+
¼
+
1/5)
=
4.380
c) Why might the two estimates of θ not match? The
theory
showing
that
both
of
these
quantities
estimate
θ
(=
4Nµ)
assumes
constant
population
size.
Changes
in
population
size
affect
the
shape
of
coalescent
trees
and
thus
the
patterns
of
nucleotide
diversity
observed
in
DNA
sequences.
In
a
growing
population,
for
example,
we
expect
to
see
relatively
more
segregating
sites,
leading
to
a
higher
value
for
θS
than
θΠ Sample1 A A G C C T G T G T Sample2 A A G C C T G T A T Sample3 A A G C T T G T A T Sample4 A G A T T T A C A C Sample5 T A A T T C A C A C Sample6 T A A T T C A C A C 9. Briefly describe the Wright-Fisher model of random genetic drift.
In
the
Wright-‐Fisher
model,
a
population
of
N
individuals
with
2N
alleles
produces
a
very
large
number
of
gametes
(effectively
infinite,
equivalent
to
sampling
with
replacement),
from
which
2N
alleles
are
randomly
drawn
to
form
the
next
generation
of
N
adults.
(There
is
no
accounting
of
different
sexes
such
that
it
is
possible
(with
probability
1/2N)
that
the
two
randomly
selected
gametes
selected
to
form
a
€ Ft=12N" # $ % & ' 1−µ()2+1−12N" # $ % & ' 1−µ()2Ft−1 |
https://people.bu.edu/msoren/BI515_2014/Exam1key.pdf | 5 | Population Genetics — BI 515 — Exam 1, Spring 2014 new
diploid
individuals
are
identical
copies
from
the
previous
generation
–
this
doesn’t
happen
in
organisms
with
separate
sexes
and
sexual
reproduction,
but
a
proper
diploid
sexual
model
yields
essentially
the
same
results.)
a) An classic experimental study using Drosophila randomly selected 8 males and 8 females to produce each successive generation, thus maintaining a constant population size of 2N = 32. We looked at the expected and observed results for this experiment in lecture (see PowerPoints). There is, overall, a reasonably good fit between observation and theory, but drift appears to have proceeded more quickly than expected in the experimental populations. What is a likely explanation for the discrepancy?
Drift
likely
proceeded
more
quickly
because
the
variance
in
reproduction
among
males
and/or
females
in
the
experimental
populations
was
higher
than
expected
under
a
random
Poisson
process,
thus
reducing
the
effective
population
size.
10. (Fill in the blank!) In generations, the average time to coalescence for two randomly sampled alleles is the reciprocal of the probability of coalescence in a single generation (= __2N___ generations). Now consider the case where k alleles have been sampled. Explain in as simple terms as possible why it makes sense that the average time until 2 of the k alleles coalesce is € 4Nk(k−1)? Hint: It may be helpful to focus on how the probability of coalescence changes with increasing k. You may want to use both words and simple equations in your answer. With
k
alleles,
there
are
“k
choose
2”
pairs
of
alleles
that
might
coalesce
in
each
preceding
generation.
“k
choose
2”
equals
k(k-‐1)/2
–
given
more
chances
for
coalescence
every
generation,
the
time
until
the
first
pair
of
alleles
coalescence
is
proportionally
shorter:
11. Download a new version of the coalescent simulation codes from the course web page (CoalSim3.py) and test whether the code is producing results that are consistent with theoretical expectations (note that this code adds the simulation of mutations on the coalescent tree, necessary for the next question below). Specifically, how does tree height and tree length vary with k and N? A perfect answer will be two graphs: 1) one graph showing tree height as a function of N with multiple lines showing the result for different values of k. Plot both the simulated results with standard errors and the theoretical expectations. You can calculate the mean and standard error in Excel using, for example, =AVERAGE(A1:A100) and =STDEV(A1:A100)/SQRT(100); and 2) the same for total tree length. I
should
have
instructed
you
to
plot
tree
height
and
total
tree
length
against
k
with
different
lines
for
N,
easier
to
see
the
results
that
way
–
see
next
page. 2Nkk−1()/2=4Nkk−1() |
https://people.bu.edu/msoren/BI515_2014/Exam1key.pdf | 6 | Population Genetics — BI 515 — Exam 1, Spring 2014
12. Use the same python code (CoalSim3.py) to answer the following question: If you’re going to collect twice as much data to get a better estimate of θ for a given population (assuming that the population has been at constant size and affected only by drift and mutation), is it better to collect data for twice as many samples, twice as many loci, or twice the length of DNA sequence per locus? Start the simulation with k = 10, nloci = 10, seq_len = 500, N = 10000, and mu = 0.0000001. Then double each parameter (k, nloci, seq_len) one at a time to generate estimates of θ based on the number of segregating sites (S) and nucleotide diversity (∏). A better estimate is one that is subject to less variation, and a good way to compare variability is with the coefficient of variation. You can calculate this in Excel using, for example, =STDEV(A1:A100)/AVERAGE(A1:A100). Does doubling the sample size, doubling the number of loci, or doubling the length of each locus results in the greatest improvement in the coefficient of variation of the θ estimates? Explain why this is the case. A table would work well to summarize your results. Model
k,
n_loci,
seq_length
θS CV θπ CV 10,
10,
500
2.0094
0.1937
2.0141
0.2242
20,
10,
500
1.9931
0.1655
1.9961
0.2139
10,
20,
500
2.0056
0.1324
2.0017
0.1520
10,
10,
1000
4.0045
0.1765
4.0028
0.2008
Any
increase
in
the
size
of
the
data
set
(more
samples,
more
loci,
longer
sequences)
improves
both
estimates
of
theta
(i.e.,
reduces
the
coefficient
of
variation),
but
increasing
the
number
of
loci
has
the
largest
effect.
In
other
words,
if
you
have
the
opportunity
to
double
the
size
of
your
data
set,
your
time
and
money
is
best
invested
in
doubling
the
number
of
loci.
Adding
samples
only
marginally
increases
the
historical
information
at
a
given
locus,
because
most
of
the
coalescent
history
at
a
given
locus
is
captured
by
a
small
number
of
samples;
adding
more
sequence
improves
the
genealogical
estimate
for
a
given
locus
but
does
not
increase
the
number
of
coalescent
events
represented
by
the
data;
increasing
the
number
of
loci
increases
the
number
of
independent
estimates
of
the
history,
as
each
locus
has
it’s
own
coalescent
history.
Thus,
adding
more
loci
adds
the
greatest
additional
information
about
history.
100#1000#10000#100000#1000000#
0#5#10#15#20#Tree$Height$Number$of$Samples$(k)$N=100#N=1000#N=10000#N=100000#expected#expected#expected#expected#
100#1000#10000#100000#1000000#10000000#
0#5#10#15#20#Total&Tree&Length&Number&of&Samples&(k)&N=100#N=1000#N=10000#N=100000#expected#expected#expected#expected# |
https://people.bu.edu/msoren/BI515_2014/Exam1key.pdf | 7 | Population Genetics — BI 515 — Exam 1, Spring 2014 ** Note: the results you need to answer the two questions above will be saved to the file “CoalSimResults.out” – you can change the name of this file at line 12 of the code if that makes it easier to keep track of the results from different runs. You can open the output file(s) in Excel to summarize the results across runs. If you want, you can increase the number of replicate runs (line 15 of the code) to get a better estimate of the average outcomes. If you know what you need to do but are not sure about how to do it, I’m happy to give you some help with Python, etc. |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 1 | 1 Name ____________ _KEY ____________________
Biology 201 (Genetics)
Exam # 1
21 September 2004
• Read the question carefully before answering. Think before you write. Be concise.
• You will have up to 85 minutes hour to take this exam. After that, you M UST stop no matter
where you are in the exam.
• If I can not read your handwriting, I will count the question wrong.
• Sign the honor pledge if applicable.
• Good luck!
I pledge that I have neither given nor received unauthorized assistance during the c ompletion of this
work.
Signature: _________________________________________________________
|
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 2 | 2
1. Albinism (lack of skin pigment) was thought to be caused solely by one recessive mutation in the
gene encoding tyrosinase. However, a study from 1952 repor ted that two albino parents produced
three normally pigmented children.
How would you explain this phenomenon at a genetic level. In your answer, make sure you indicate
how pigment formation is inherited based on the data from the study cited above. (Although it may
be formally possible, gi ve me an answer other than “the albino male was not the biological father of
the children ”!).
The best answer is that this is an example of two genes controlling skin color and duplicative recessive
epistasis . Gene A is for the tyrosinase and Gene B is for another gene required for pigment formation.
Recessive mutations in either gene cause albinism. Parent 1 was aaBB and parent 2 was AAbb . Thus,
children were AaBb (non -albino). I als o accepted that this was an example of a mutation distinct from
the earlier described recessive mutation in the tyrosinase gene . In this case, the mutation (AD) is
behaving in a dominant fashion to the wildtype allele A . Both parents are AAD and so the kids can be
AA, although the chance of this occurring is (1/4) 3.
2. Explain how one would determine whether an organism expressing a dominant trait is heterozygous
or homozygous?
You would do a test cross. Cross the individual of unknown genotype with an individual expressing the
recessive phenotype. If the prog eny all have the dominant phenotype, than the individual of unknown
genotype was homozygous dominant. If the ½ of the progeny are have the dominant phenotype and ½
of the progeny are have the recessive phenotype , than the individual of unknown genotype was
heterozygous .
Imagine an individual with the genotype AaDdgg, where each of these genes is on a different
chromosome.
a. How many different gametes types can be formed by this individual? 4
b. What are the gametes? ADG, Adg, aDg, adg
c. Now imagine an individual with the genotype AaDdggRr, where each of these genes is on
a different chromosome. How many different gametes types can be formed by this
individual? 8
6 pts.
6 pts.
8 pts. |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 3 | 3 3. Consider three independently assorting gene pairs , which control three different characters . A is
dominant to a, B is dominant to b, and D is do minant to d.
For a cross between parents that are Aa BbDD and AABbDd, write the answer to the questions
below in the blank to the left of the question .
a. what is the probability of obta ining an offspring that is AABbDd ?
b. what is the probability of obtaining an offspring that is purebreeding for all three
dominant traits?
c. what is the probability of obtaining an offspring that will express all three dom inant
traits?
9 pts.
_____ 1/8_____
_
___1/16_____
_____ 3/4____ |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 4 | 4 4. From a highly watched soap opera: Monica had a baby and there was some question as to whether
the father of the child was Monica's husband (Alan) or Monica’s fellow doctor friend ( Rick ).
Monica's blood type is A, Alan's is AB, and Rick's is O. The baby’ s blood type is O. The potential
pedig ree is shown below , along with the blood types of each individual .
Based on what you have learned about blood group genetics , answer the questions below .
As a reminder:
v The I gene controls which sugar gets added to H substance on the red blood cell surface. There
are three alleles of the I gene (IA, IB, and i) - where IA and IB are codominant, IA is dominant to
i (O blood ), and I B is dominant to i (O bloo d).
v The H allele ( whic h allows H substance to be made) is dominant to h allele ( which is defective in
making h substance ).
v The h allele is epistatic to the alleles at the I locus
a) Could Alan be the father? Why or why not?
Yes. If Alan is heterozygous for the H substance gene (Hh) and Monica is heterozygous for the H
substance gene (Hh) , they would have a ¼ chance of producing a child that was hh. Since the
recessive h allele is epistatic to the I gene, the genotype at the I locus is now irrelevant. The child
would not have an h s ubstance and thus would appear to have O blood, since the sugars controlled by
the I gene could not be added to the surface of the red blood cell.
b) Could Rick be the father? Why or why not?
Yes. The most likely answer is that Rick is ii and Monica is IA i. Thus, they have a ¼ chance o f
having a child that is ii (blood group O). The answer from (a) could also have occ urred , but it is less
likely tha n the gen otypes g iven for (b) .8 pts. |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 5 | 5
5. Normal hedgehogs have straight fur and long whiskers . Mutant hedgehogs have been isolated with
either kinked fur or short whiskers . The genes for each of these characters are on different
chromosomes . You capture some hedgeho gs and mate them and get the following data.
Number of progeny
mating genotypes straight fur and
long whiskers straight fur and
short whiskers kinked fur and
long whiskers kinked fur and
short whiskers
Straight, short
X
Straight, short AaBb
AaBb 30 90 10 30
Kinked, long
X
Straight, short aabb
AaBb 40 40 40 40
Kinked, short
X
straight, short aaBb
AABb 40 120 0 0
a) For each mutation, indicate whether it is dominant or recessive by filling in the blanks below
with the word dominant or recessive.
The allele for kin ked fur is ____ RECESSIVE ___________ to the allele for straight fur.
The allele for short whiskers is ___DOMINANT ____________ to the allele for long whiskers.
b) Provide a legend for each trait (using A/a for fur type and B/b for whisker type).
A = straight
a = kink
B = short
b = long
c) In the table above in the column labeled genotype , write the genotypes of the parents for each
cross. 9 pts. |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 6 | 6 6. A purebreeding variety of opium poppy having leaves that are irregularly shaped (lacerate) was
crossed with a variety that has normal leaves. All the F 1 had normal leaves. Two F 1 plants were
interbred to produce the F 2. Of the F 2, 145 had normal leaves and 9 had lacerate leaves. These
crosses are shown in the figure below.
Figure 1:
P
generation lacerate
__aabb __ X normal
__AABB __
F1
generation Normal leaves __AaBb__
F2
generation 145 normal leaves __A-B-; A-bb; aaB -
9 lacerate leave s
__aabb __
a) Explain how inheritance of lacerate leaves is determined in the opium poppy?
There are two genes that control leaf shape and epistasis is occurring since the F2 atio is in 16ths
(15:1) . Specifically, a dominant allele in either of two genes is sufficient to get normal shaped
leaves. Perhaps the genes encode proteins of similar function , so having the dominant form of either
allele is sufficient to get normal leaves. In other words, for lacerate leaves to appear, both genes
must be present in the recessive form.
b) Give the possible genotypes that correspond to each phenotype for the plants in the P, F 1, and F 2
generations by putting the genotype s in the blanks in the figure above . You can use a dash to
indicate either of two alleles is possible for the same phenotype (ie A- = AA or Aa).
Cross F1 plants 8 pts. |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 7 | 7 7. In the pedigree s below (they are all the same) , a trait is determined by a single gene and affected
individuals are shaded. State whether is would be possible for the trait to be inherited in each of the
following ways by wr iting YES or NO in the blank to the left of each inheritance pattern .
a. autosomal r ecessive
b. X-linked recessive
c. autosomal dominant
d. X-linked dominant
8 pts.
______ YES ____
_
_____ NO______
_
______ NO_____
_ ____NO_______
_ |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 8 | 8 8. Two genes are located on separate autosomes. One gene pair determines hair color in foxes where
AA is lethal before birth , Aa is platinum hair, and aa is silver hair . A second gene pair (B/b)
determines hair length where short hair is dominant to long hair. A platinum fox that was pure
breeding for short hair length is crossed with a silver fox with long hair. The F1 contained foxes that
were platinum and others that were silver. Two of the platinum F1 foxes were mated. Give the
phenotypes and expected phenotypic ratios for the foxes in the F2 generation using either a branch
diagram or statistics to do the problem.
Note that the problem asks for ratios of the F2 generat ion. Since the AA progeny die before birth, they
are not counted in th e frequencies.
9. Below are chromosomes in prophase of mitosis in an organisms with a diploid number of 4.
a. Label the homologous chromo somes by indicating which belong in the same pair.
b. Label the sister chromatids.
c. How many individual molecules of DNA are present in the cell at prophase of mitosis? 8
2/3 platinum 3/4 short
1/4 short 6/12 platinum, short
2/12 platinum, long
1/3 silver 3/4 short
1/4 short 3/12 silver, short
1/12 silver, long
sister chromatids homologous chromosomes
homologous chromosomes 8 pts.
6 pts. |
https://facultystaff.richmond.edu/~lrunyenj/bio201/04bio201%20exam%201%20key.pdf | 9 | 9
Multiple choice section: ( 24 points total – 4 points per question )
Write your answer in the blank provided to the left. IF you want to explain your answer, you can do so
next to the question
1. Imagine a cell with a diploid number of 6. If one of the chromosome s has a centromere that is
absent , the effect on mitosis would be:
a. There would be no effect because centromeres are only important in meiosis.
b. One daughter cell has 8 chromosomes and the other daughter cell has 4 chromosomes .
c. One daughter cell has 7 chromosomes and the other daughter cell has 5 c hromosomes .
d. One daughter cell has 12 chromosomes and the other daughter cell has 0 chromosomes .
e. None of the above (if you consider mitosis would probably arrest at cell cycle checkpoint ).
2. The following have entirely identical DNA sequences :
a. Sister chromatids
b. Homologous chromosomes
c. Chromatin
d. All X chromosomes
e. A and B
3. Which o f the types of chromo somes below are found in all human diploid cells ?
a. Sex chromosomes
b. Autosomes
c. Centrosomic chromosomes
d. Both a and b
e. All of the above
4. A baby was karotyped as 47, XX , +21 . This genotype could have arisen as a result of ONE
nondisjunction event :
a. in the egg during meiosis II before fertilization .
b. in the sperm during meiosis II before fertilization.
c. in the egg during meiosis I before fertilization .
d. either a or c.
e. either a or b or c .
5. Which of Mendel’s Laws is NOT exemplified in a monohybrid cross
a. Unit factors occur in pairs
b. One unit factor in a pair can be dominant to another
c. Law of Equal S egragation
d. Law of Independent Assortment
e. None of the above (ie all of the above do apply in a monohybrid cross).
6. The most fundamental feature of that t wo members of a homologous chromosome p air share is that
they have
a. the same length .
b. the same banding pattern .
c. the same centromere position .
d. alleles of the same genes at the same loci, where the chromosomes are genetically
identical.
e. alleles of the same gen es at the same loci, where the chromosomes are genetically similar
but not necessarily genetically identical . C or E
__A___
______
___D__
______
___E__
______
__D___
______
___E__
______ |
https://www.usabo-trc.org/sites/default/files/images/pdf/exams/semifinal-answers/2011-semifinal-answers.pdf | 1 | 1
USABO SEMIFINAL EXAMINATION
March 16 to 25, 2011
2011 USABO Semifinal Exam DRAFT
Part A
Cell and Molecular Biology (20%) 12 questions 1 -12
Plant Anatomy and Physiology (15%) 9 questions 13 -21
Animal Anatomy and Physiology (25%) 15 questions 2 2-36
Ethology (5%) 3 questions 37 -39
Genetics and Evolution (20%) 12 questions 40 -51
Ecology (10%) 6 questions 52 -57
Biosystematics (5%) 3 questions 58 -60
Part A
CELL AND MOLECULAR QUESTIONS 1 to 12
1. If you extract the genetic material of th e Bacteriophage ( X174), you will find that
its composition is 25% A, 33% T, 24% G, and 18% C. How would you interpret
these results?
A. The experiment's results must be erroneous; something went wrong
B. We could admit that the %A approximately equals that of T, and the same is true for
C and G. Consequently, Chargaff's rules are followed and the DNA is double
stranded
C. Because the %A does not equal the %T, nor does the %G equal the %C, the DNA
is single -stranded; it is replicated by special enzymes, following a particular
replication pattern, with the single -stranded chain as a template
D. Because the %A does not equal the %T, nor does the %G equal the %C, the DNA
must be single -stranded; It replicates by synthesizing a complementary strand and
uses the double st randed form as a template
E. Bacteriophage ( X174) is an RNA virus
Answer D
|
https://www.usabo-trc.org/sites/default/files/images/pdf/exams/semifinal-answers/2011-semifinal-answers.pdf | 2 | 2 2. The diagrams below refer to variation in the amount of DNA (y -axis) as a function
of time (x -axis) during cell division. (The units are arbitrary.) Which of these
diagrams de pict what happens during meiosis and mitosis, respectively?
A. 1 and 2
B. 1 and 3
C. 2 and 3
D. 3 and 4
E. 4 and 1
Answer E
3. Which of the following cellular proteins make direct contact with chromosomes?
A. Centrosomes and microtubule -associated pr oteins
B. Kinesins, myosins, and actin microfilaments
C. Histones, condensins, and synaptonemal complexes
D. All of the above
E. None of the above
Answer C
4. Your colleague’s PCR reaction failed to amplify the human rhodopsin gene. Her
lab notebook indicates that s he added dNTPs, the Rhodopsin template gene,
complementary DNA primers, buffer, and an E. Coli DNA polymerase and ran
the reaction under the proper conditions. How would you advise her to fix the
reaction?
A. Add a bacterial promoter to the Rhodopsin templat e
B. Add extra ATP so there is enough energy to catalyze the reaction
C. Add dNTPs to facilitate elongation
D. Use a different polymerase
E. Use RNA primers instead
Answer: D
5. For a constant concentration of an enzyme, which of the following is true of a
noncomp etitive inhibitor?
A. km is lowered; vmax remains constant
B. km is increased; vmax remains constant
C. km remains constant; vmax is lowered
D. km remains constant; vmax is increased |
https://www.usabo-trc.org/sites/default/files/images/pdf/exams/semifinal-answers/2011-semifinal-answers.pdf | 3 | 3 E. km remains constant; vmax remains constant
Answer C
6. The mitoch ondrion has more than three stop codons. Which biological principle
does this violate?
A. Central dogma
B. Endosymbiotic theory
C. Conservation DNA replication
D. Complementary base -pairing
E. Universal genetic code
Answer : E
7. Which of the following structures and processes can e xist in eukaryotic cells and
in all prokaryotic cells?
I. Nuclear envelope
II. Ribosomes
III. Introns
IV. ATP synthesis
V. rRNA 18S
VI. Cell membrane
VII. DNA polymerase
VIII. Cytoskeletal elements
A. I, II, III and VIII
B. II, IV, VI and VIII
C. I, III, V and VII
D. II, IV, V and VI
E. II, III, VI and VIII
Answer : D
8. Comparing the effect of an inhibitor with an uncoupler of oxidative
phosphorylation, the:
A. inhibitor would allow electrons to pass through the electron transport chain
B. inhibitor would increase the pumping of protons by the electron t ransport chain
C. uncoupler would increase heat production by the mitochondria
D. uncoupler would inhibit the reduction of oxygen by the electron transport chain
E. uncoupler would stop the oxidation of NADH by the electron transport chain
Answer: C
9. Three di fferent genes (B, D, and W) are found on a small region of chromosome
1. Each gene has two alleles. In order to determine the recombination frequency
between these three genes, sperm were isolated from a male heterozygous for all
three genes. The male h ad all dominant alleles on his maternal copy of
chromosome 1, but only recessive alleles on his paternal copy of chromosome 1.
Each sperm was isolated individually and PCR amplified in the BDW region. |
https://www.usabo-trc.org/sites/default/files/images/pdf/exams/semifinal-answers/2011-semifinal-answers.pdf | 4 | 4 The amplified products were spotted on a nitrocellulo se membrane and
radioactive allele specific probes were hybridized with the samples. The
resulting audioradiograph is shown below where a dark spot indicates successful
hybridization of the probe with the membrane.
What is the recombination freque ncy between B and W?
A. 1:2
B. 1:3
C. 1:4
D. 5:6
E. 1:1
Answer: B
10. You order a degenerate probe designed from the following hemoglobin protein
sequence:
Trp – Gly – Lys – Val – Asn
TGG GGC AAA GTC AAT
T G T C
A A
G G
How many different probe sequences would be returned to you? How many
would be specific to you r gene of interest?
A. 25 total, 1 specific to gene
B. 25 total, 5 specific to gene
C. 32 total, 1 speci fic to gene
D. 64 total, 1 specific to gene
E. 64 total, 5 specific to gene |
https://www.usabo-trc.org/sites/default/files/images/pdf/exams/semifinal-answers/2011-semifinal-answers.pdf | 5 | 5
Answer: D
11. A yeast extract contains all the enzymes required for alcohol production. The
extract is incubated under anaerobic conditions in 1 liter of media containing: 200
mM gl ucose, 20 mM ADP, 40 mM ATP, 2 mM NADH, 2 mM NAD+ and 20 mM
Pi (inorganic phosphates). What is the maximum amount of ethanol that can be
produced in these conditions?
A: 2 mM
B. 20 mM
C. 40 mM
D. 200 mM
E. 400 mM
Answer: B
12. The concentration of i ons inside an amoeba is expressed below as ion -units per
milliliter. The composition of the extra -cellular environment (ECE) is given for
comparison. Assume the amoeba has been in the environment for some time.
Na+ K+ Cl- HCO3-
Amoeba 1 42 3 119
ECE 21 16 41 119
Simple diffusion alone could account for which ionic concentration inside the
amoeba: [Assume the membrane is permeable in some degree to all of the above
ions.]
A. Na+
B. HCO3-
C. Na+, K+, Cl- and HCO3-
D. Na+, Cl- and HCO3-
E. K+
Answer B
PLANT ANATOM Y AND PHYSIOLOGY
13. You find a plant that appears to have parallel veined leaves. Examination of its
root indicates a single layered pericycle, primary xylem in the center of the root,
and an active vascular cambium. The plant most likely belongs to whic h of the
following groups?
A. Conifer
B. Dicot
C. Fern
D. Gnetum
E. Monocot |
Subsets and Splits