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Chapter 30

Multiple Choice
1. RNA generally functions as a regulator by
a. base-pairing with a single-stranded region.
b. influencing ribosomal actiity.
c. recruiting proteins to gene promoters.
d. cataly!ing biochemical reactions.
e. participating in chromatin remodeling.
Ans" a
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&. 'he mRNA of the Neurospora gene NMT1
a. cataly!es a reaction inoling its own product.
b. base-pairs with other mRNAs to regulate their e(pression.
c. has two domains) one is a coding se*uence and the other is a ribo!yme.
d. is only transcribed when the substrate of its product is present.
e. is alternatiely spliced depending on the concentration of a metabolite of itamin +1.
Ans" e
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3. ,hich of the following is generally not a way that antisense RNA might inhibit gene
e(pression-
a. .t might preent translation.
b. .t might affect RNA processing.
c. .t might affect stability of the protein product.
d. .t might preent transcription.
e. All of the aboe are ways that antisense RNA might inhibit gene e(pression.
Ans" c
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/. ,hat types of genes are e(pected to e(perience transcriptional interference-
a. paralogous genes
b. nested genes
c. genes encoding subunits of the same protein
d. ad0acent genes
e. alleles on homologous chromosomes
Ans" b
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2. +acterial regulator RNAs are called
a. C3's.
b. CR.4#Rs.
c. #R5M#'s.
d. sRNAs.
e. siRNAs.
Ans" d
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6. 7777777777777777777 are a special class of eu8aryotic miRNAs that are actie in
germ cells.
a. CR.4#Rs.
b. C3's.
c. piRNAs
d. siRNAs.
e. sRNAs.
Ans" c
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$. :u8aryotic siRNAs originate from
a. iral infection.
b. siRNA-encoding genes that produce a transcript that is processed into many small
RNAs.
c. degraded messenger RNAs.
d. siRNA-encoding genes that produce a transcript that folds to become double-stranded.
e. introns remoed during mRNA processing.
Ans" a
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%. 'he regulation of e(pression of the C. elegans gene lin14 by lin4 was one of the first
8nown animal e(amples of
a. a gain-of-function mutation.
b. nested genes.
c. a riboswitch.
d. an antisense gene.
e. RNA interference.
Ans" e
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9. .n mammals and other animals1 the e(pression of a specific gene can be turned off by
the introduction of
a. long ds;NA.
b. short dsRNA.
c. short ds;NA.
d. short ss;NA.
e. long ds;NA.
Ans" b
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10. .n yeast1 heterochromatin formation and transcriptional repression can be facilitated
by transcripts of
a. telomeric simple se*uence satellites.
b. intronic se*uences.
c. histone genes.
d. centromeric simple se*uence satellites.
e. nested genes.
Ans" d
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4hort Answer
11. ;escribe two ways that the formation of a double helical region between an RNA
regulator and its target can affect the target.
Ans" <ormation of a double helical region may protect the target from protein binding or
it may hae the opposite effect. ;uple( formation may also preent the target from
adopting a particular secondary structure.
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1&. ,hat is a riboswitch-
Ans" A riboswitch is an RNA molecule whose secondary structure can change to control
its actiity.
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13. .n what ways can riboswitches function-
Ans" A riboswitch may assume alternate base-pairing configurations =with the presence of
a ligand or an enironmental change> that affect translation of an mRNA. .t can be a
ribo!yme1 or it can interfere with ribosome binding.
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1/. ?ow can artificial antisense genes be constructed-
Ans" Artificial antisense genes can be constructed by reersing the orientation of a gene
with respect to its promoter. 'his results in transcription of an antisense RNA that is
complementary to the mRNA of the original gene1 so that they can base-pair and suppress
the mRNA@s translation or affect its stability.
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12. .n transcriptional interference1 how may transcription of a noncoding RNA suppress
transcription of a downstream target-
Ans" .nitiation at the promoter of the noncoding RNA leads to RNA polymerase actiity
that continues through the downstream promoter. 'his readthrough preents initiation at
the downstream target@s promoter1 perhaps through disruption of chromosomal structure.
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16. .n light of our recent 8nowledge of the sources of regulatory RNA1 ealuate the idea
that ast stretches of the eu8aryotic genome are A0un8B ;NA.
Ans" Recent e(periments inoling whole-genome tiling arrays or whole-cell RNA
se*uencing hae shown that the ma0ority of the eu8aryotic genome is transcribed. Many
of these transcripts must act as regulatory RNAs1 probably as antisense RNAs that
regulate the e(pression of other genes. .t now appears that much of the noncoding portion
of the eu8aryotic genome is functional1 not A0un8.B
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1$. ,hat are C3's and #R5M#'s-
Ans" Cryptic unstable transcripts1 or C3's1 are noncoding antisense RNAs in yeast that
recruit histone deacetylases to result in locally remodeled chromatin and shut off
transcription of a particular gene. #romoter upstream transcripts1 or #R5M#'s1 hae
similar effects in human ?eCa cells.
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1%. .n bacteria1 what is the function of oxyS-
Ans" oxyS is transcribed to an sRNA that affects the e(pression of a number of genes. .t
acts by complementary base-pairing with RNA transcripts1 either actiating or repressing
e(pression. .n the case of the flhA gene transcript1 base-pairing of the oxyS transcript
preents ribosomal binding and represses translation.
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19. ,hat are CR.4#Rs-
Ans" Clusters of regularly interspersed short palindromic repeats =CR.4#Rs> are found in
pro8aryotes1 where they proide a defense against iral infection. A long transcript is
produced and processed into many small RNAs that presumably base-pair with phage
;NA and interfere with its e(pression.
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&0. ;escribe how microRNAs are produced in C. elegans and other eu8aryotes.
Ans" 'he microRNA gene is transcribed and a double-stranded region is formed in the
RNA. 'his region is recogni!ed by the ;icer nuclease which cleaes the RNA1 forming
the actie miRNA.
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&1. ,hat is the role of the R.4C comple( in RNAi-
Ans" 'he R.4C comple( contains the proteins and siRNA re*uired for cleaage of the
target mRNA. 'he siRNA base pairs with the target mRNA after a helicase unwinds the
siRNA.
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&&. ,hat is unusual about the role of miRNA in e(pression of the tumor necrosis factor-
D ='N<-D> gene-
Ans" miRNA actually activates translation of the mRNA for this gene1 when miRNA
normally represses gene e(pression. 3nder conditions of serum staration1 a different set
of proteins is recruited to the mRNA1 so that R.4C and its associated miRNA function to
facilitate translation.
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&3. ?ow does the C. elegans gene lin4 control the e(pression of lin14-
Ans" lin4 is transcribed to an miRNA that is complementary to1 and base-pairs with1 the
3E 3'R of the lin14 transcript1 inhibiting its e(pression.
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&/. ,hy were early attempts to use RNAi unsuccessful in mammalian cells-
Ans" 'he double-stranded RNA fragments1 which were greater than &6 nucleotides in
length1 triggered the actiation of en!ymes that shut down protein synthesis and degraded
all mRNAs. 'he discoery that shorter double-stranded RNA fragments did not hae this
effect led to successful implementation of the techni*ue.
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&2. ,hat is the role of RNA-dependent RNA polymerase in transcription repression in
the yeast S. pombe-
Ans" 4e*uences within the centromeric heterochomatin are transcribed and conerted to
dsRNA by RNA-dependent RNA polymerase. 'he dsRNAs are processed into siRNAs
that are recruited by an RNA-induced transcriptional silencing comple( =R.'4>.
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