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Chapter 20

20.1 Operons are common in bacteria but not in eukaryotes. Suggest a reason why.

ANS: In multicellular eukaryotes, the environment of an individual cell is relatively


stable. There is no need to respond quickly to changes in the external environment. In
addition, 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.
FEEDBACK: 20.6
DIFFICULTY: easy

20.2. In bacteria, translation of an mRNA begins before the synthesis of that mRNA is
completed. Why is this “coupling” 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.
FEEDBACK: 20.1
DIFFICULTY: easy

20.3 Muscular dystrophy in humans is caused by mutations in an X-linked gene that


encodes a protein called dystrophin. 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 blotting 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 dystrophin gene and the resulting cDNA could be amplified by the
polymerase chain reaction (RT-PCR). Another technique 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 production of dystrophin protein by
using anti-Dystrophin antibodies to analyze proteins from the different cell types on
western blots, or to analyze the proteins in the cells themselves—that is, in situ.
FEEDBACK: 20.1
DIFFICULTY: medium

20.4. Why do steroid hormones interact with receptors inside the cell, whereas peptide
hormones interact with receptors 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 membrane-bound receptor protein that binds the hormone.
FEEDBACK: 20.1
DIFFICULTY: easy

20.5 How could you use the polytene chromosomes of Dipteran insects to study the
regulation of transcription?

ANS: By monitoring puffs in response to environmental signals, such as heat shock, or


to hormonal signals.
FEEDBACK: 20.1
DIFFICULTY: easy

20.6. 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 orientation. A promoter is almost always immediately
upstream of a gene and it functions only in one direction with respect to the gene.
FEEDBACK: 20.2
DIFFICULTY: easy

20.7 Tropomyosins 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.


FEEDBACK: 20.2
DIFFICULTY: easy
20.8. 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 hybridization of the blot with a probe containing the DNA encoding
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 produce two mRNAs. If two DNA fragments are
detected, the two polypeptides are encoded by two different genes.
FEEDBACK: 20.2
DIFFICULTY: medium

20.9 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.
FEEDBACK: 20.2
DIFFICULTY: medium

20.10. When introns were first discovered, they were thought to be genetic “junk”—that
is, sequences without any useful function. In fact, they appeared to be worse than junk
because they actually interrupted the coding sequences of genes. However, among
eukaryotes, introns are pervasive 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.
FEEDBACK: 20.2
DIFFICULTY: medium

20.11 Why does it make sense for the photosynthetic enzyme ribulose 1,5-bisphosphate
carboxylase (RBC) to be synthesized specifically when plants are exposed to light?

ANS: This enzyme plays an important role in photosynthesis, a light-dependent process.


Thus, it makes sense that its production should be triggered by exposure to light.
FEEDBACK: 20.2
DIFFICULTY: medium

20.12. 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 fluorescent protein. This fusion gene has
been inserted into the chromosomes of living Drosophila by the technique of transposon-
mediated transformation (Chapter 18). 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.
FEEDBACK: 20.3
DIFFICULTY: medium

20.13 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
elements. Would the green fluorescent protein encoded by this fusion gene be
synthesized in genetically transformed flies?

ANS: Probably not unless the promoter of the gfp gene is recognized and transcribed by
the Drosophila RNA polymerase independently of the heat shock response elements.
FEEDBACK: 20.3
DIFFICULTY: medium

20.14. The polypeptide products of two different genes, A and B, each function as
transcription factors. These polypeptides interact to form dimers: AA homodimers, BB
homodimers, and AB heterodimers. If the A and B polypeptides are equally abundant in
cells, and if dimer formation 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.
FEEDBACK: 20.3
DIFFICULTY: hard

20.15 A particular transcription factor binds to enhancers in 40 different genes. Predict


the phenotype of individuals homozygous 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 condition 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.
FEEDBACK: 20.3
DIFFICULTY: medium

20.16. The alternately spliced forms of the RNA from the Drosophila 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 animals blocks the development of
male characteristics, and the protein that is made in male animals blocks the development
of female characteristics. Predict the phenotype of XX and XY animals homozygous for a
null mutation in the doublesex gene.

ANS: Both XX and XY animals would develop as intersexes.


FEEDBACK: 20.3
DIFFICULTY: medium

20.17 The protein product of the Drosophila Sex-lethal gene is needed in females but
not in males. Predict the phenotype of XY Drosophila that are hemizygous for a null
mutation in the X-linked Sex-lethal gene.

ANS: The flies would be phenotypically normal males.


FEEDBACK: 20.3
DIFFICULTY: medium

20.18. 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 controlled by an enhancer located
upstream of the gene’s transcription initiation site. In the tarsal claws, expression 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
yellow 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.
FEEDBACK: 20.3
DIFFICULTY: medium
20.19 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
expression in root tips, transgenic plants should show GUS expression in their root tips.
See the Focus on Problem Solving in Chapter 20 for an example of this type of analysis.
FEEDBACK: 20.3
DIFFICULTY: hard

20.20. What is the nature of each of the following classes of enzymes? What does each
type of enzyme do to chromatin? (a) HATs, (b) HDACs, (c) HMTs.

ANS: (a) HATs, histone acetyl transferases, transfer acetyl groups to the amino acid
lysine in histones; (b) HDACs, histone deacetylases, remove acetyl groups from these
lysines; (c) HMTs, histone methyl transferases, transfer methyl groups to lysine, arginine,
and histidine in histones.
FEEDBACK: 20.5
DIFFICULTY: easy

20.21 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.
FEEDBACK: 20.5
DIFFICULTY: medium

20.22. Suppose that the LCR of the β -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 β -globin being produced, the individual would likely suffer from anemia.
FEEDBACK: 20.5
DIFFICULTY: medium

20.23 Would double-stranded RNA derived from an intron be able to induce RNA
interference?
ANS: Short interfering RNAs target messenger RNA molecules, 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.
FEEDBACK: 20.4
DIFFICULTY: medium

20.24. RNA interference has been implicated in the regulation of transposable elements.
In Drosophila, two of the key proteins involved in RNA interference 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 mutation rate in a wild-type strain?

ANS: The aubergine and piwi gene products mediate the RNAi response. Reduction in
the amount of aubergine or piwi protein would likely impair the organism’s ability to
mount an RNAi response, and without a vigorous capacity for RNAi, 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.
FEEDBACK: 20.4
DIFFICULTY: medium

20.25 Suppose 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.
FEEDBACK: 20.5
DIFFICULTY: medium

20.26. In trypanosomes, what mechanisms lead to the expression of a different variant


surface glycoprotein?

ANS: Although trypanosomes contain over 1000 varient surface glycoprotein (vsg)
genes, all but the one vsg gene located within the expression site (ES) are kept silent.
The trypanosome’s glycoprotein surface coat can change by several mechanisms
regulating vsg gene expression: (1) the ES currently being transcribed can be silent, and
another ES activated; (2) one of the silent vsg genes can be copied into the ES that is
currently being transcribed; or (3) a crossover event can exchange the active vsg gene for
an inactive one—once the inactive gene becomes linked to the promoter of the
transcribed ES, it becomes active.
FEEDBACK: 20.5
DIFFICULTY: medium

20.27 A researcher hypothesizes that in mice gene A is actively transcribed in liver cells,
whereas gene B is actively transcribed 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 different 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 determine
which gene’s RNA was present in the original samples.
FEEDBACK: 20.1
DIFFICULTY: medium

20.28. 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 limited period of time. If
the DNA that remains after the treatments is then fractionated by gel electrophoresis,
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 DNaseI).
FEEDBACK: 20.5
DIFFICULTY: medium
20.29 Why do null mutations in the mle gene in Drosophila have no effect in females?

ANS: The mle gene is not functional in females.


FEEDBACK: 20.6
DIFFICULTY: easy

20.30. 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.
FEEDBACK: 20.6
DIFFICULTY: medium