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2009 Garland Science P!li"#in$
Fr%& DNA '% RNA
7-1 RNA in cells differs from DNA in that ___________________.
(a) it contains the base uracil, which pairs with cytosine
(b) it is single-stranded and cannot form base pairs
(c) it is single-stranded and can fold up into a ariety of structures
(d) the sugar ribose contains fewer o!ygen atoms than does deo!yribose
7-2 "ranscription is similar to DNA replication in that ___________________.
(a) an RNA transcript is synthesi#ed discontinuously and the pieces are then
$oined together
(b) it uses the same en#yme as that used to synthesi#e RNA primers during
DNA replication
(c) the newly synthesi#ed RNA remains paired to the template DNA
(d) nucleotide polymeri#ation occurs only in the %&-to-'& direction
7-3 (or each of the following sentences, fill in the blan)s with the best word or phrase
selected from the list below. Not all words or phrases will be used* use each word
or phrase only once.
(or a cell+s genetic material to be used, the information is first
copied from the DNA into the nucleotide se,uence of RNA in a
process called __________________. -arious )inds of RNA are
produced, each with different functions. __________________
molecules code for proteins, __________________ molecules act
as adaptors for protein synthesis, __________________ molecules
are integral components of the ribosome, and
__________________ molecules are important in the splicing of
RNA transcripts.
incorporation rRNA transmembrane
pRNA transcription proteins
7-4 .atch the following structures with their names.
(igure /0-1
7-5 2hich of the following statements is false3
(a) A new RNA molecule can begin to be synthesi#ed from a gene before the
preious RNA molecule+s synthesis is completed.
(b) 4f two genes are to be e!pressed in a cell, these two genes can be
transcribed with different efficiencies.
(c) RNA polymerase is responsible for both unwinding the DNA heli! and
cataly#ing the formation of the phosphodiester bonds between nucleotides.
(d) 5nli)e DNA, RNA uses a uracil base and a deo!yribose sugar.
7-6 2hich one of the following is the main reason that a typical eucaryotic gene is
able to respond to a far greater ariety of regulatory signals than a typical
procaryotic gene or operon3
(a) 6ucaryotes hae three types of RNA polymerase.
(b) 6ucaryotic RNA polymerases re,uire general transcription factors.
(c) "he transcription of a eucaryotic gene can be influenced by proteins that
bind far from the promoter.
(d) 7rocaryotic genes are pac)aged into nucleosomes.
7-7 .atch the following types of RNA with the main polymerase that transcribes
7-8 8ist three ways in which the process of eucaryotic transcription differs from the
process of bacterial transcription.
7-9 (or each of the following sentences, fill in the blan)s with the best word or phrase
selected from the list below. Not all words or phrases will be used* each word or
phrase should be used only once.
4n eucaryotic cells, general transcription factors are re,uired for the
actiity of all promoters transcribed by RNA polymerase 44. "he
assembly of the general transcription factors begins with the
binding of the factor __________________ to DNA, causing a
mar)ed local distortion in the DNA. "his factor binds at the DNA
se,uence called the __________________ bo!, which is typically
located 9% nucleotides upstream from the transcription start site.
:nce RNA polymerase 44 has been brought to the promoter DNA,
it must be released to begin ma)ing transcripts. "his release
process is facilitated by the addition of phosphate groups to the tail
of RNA polymerase by the factor __________________. 4t must
be remembered that the general transcription factors and RNA
polymerase are not sufficient to initiate transcription in the cell and
are affected by proteins bound thousands of nucleotides away from
the promoter. 7roteins that lin) the distantly bound transcription
regulators to RNA polymerase and the general transcription factors
include the large comple! of proteins called
the__________________. "he pac)ing of DNA into chromatin
also affects transcriptional initiation, and histone
__________________ is an en#yme that can render the DNA less
accessible to the general transcription factors.
actiator lac "(44A
;A7 ligase "(44D
deacetylase mediator "(44<
enhancer "A"A
7-10 =ou hae a piece of DNA that includes the following se,uence>
2hich of the following RNA molecules could be transcribed from this piece of
(a) %&-5A5;;?5AA?;5A??;;5A5?;5A-'&
(b) %&-A5A??;A55;?A5;;??A5A?;A5-'&
(c) %&-5A;?A5A??;;5A?;55A;??A5A-'&
(d) none of the aboe
7-11 =ou hae a segment of DNA that contains the following se,uence>
4f you )now that the RNA transcribed from this segment contains the following
2hich of the following choices best describes how transcription occurs3
(a) "he top strand is the template strand* RNA polymerase moes along this
strand from %& to '&.
(b) "he top strand is the template strand* RNA polymerase moes along this
strand from '& to %&.
(c) "he bottom strand is the template strand* RNA polymerase moes along
this strand from %& to '&.
(d) "he bottom strand is the template strand* RNA polymerase moes along
this strand from '& to %&.
7-12 2hich of the following molecules of RNA would you predict to be the most li)ely
to fold into a specific structure as a result of intramolecular base pairing3
(a) %&-
(b) %&-
(c) %&-
(d) %&-
7-13 4magine that an RNA polymerase is transcribing a segment of DNA that contains
the following se,uence>
'&-";A?A";;?"?A;" %&
A. 4f the polymerase is transcribing from this segment of DNA from left to
right, which strand (top or bottom) is the template3
A. 2hat will be the se,uence of that RNA (be sure to label the %& and '& ends
of your RNA molecule)3
7-14 "he sigma subunit of bacterial RNA polymerase ___________________.
(a) contains the catalytic actiity of the polymerase
(b) remains part of the polymerase throughout transcription
(c) recogni#es promoter sites in the DNA
(d) recogni#es transcription termination sites in the DNA
7-15 2hich of the following might decrease the transcription of only one specific gene
in a bacterial cell3
(a) a decrease in the amount of sigma factor
(b) a decrease in the amount of RNA polymerase
(c) a mutation that introduced a stop codon into the DNA that precedes the
gene+s coding se,uence
(d) a mutation that introduced e!tensie se,uence changes into the DNA that
precedes the gene+s transcription start site
7-16 "here are seeral reasons why the primase used to ma)e the RNA primer for
DNA replication is not suitable for gene transcription. 2hich of the statements
below is not one of those reasons3
(a) 7rimase initiates RNA synthesis on a single-stranded DNA template.
(b) 7rimase can initiate RNA synthesis without the need for a base-paired
(c) 7rimase synthesi#es only RNAs of about %@9B nucleotides in length.
(d) "he RNA synthesi#ed by primase remains base-paired to the DNA
7-17 =ou hae a bacterial strain with a mutation that remoes the transcription
termination signal from the Abd operon. 2hich of the following statements
describes the most li)ely effect of this mutation on Abd transcription3
(a) "he Abd RNA will not be produced in the mutant strain.
(b) "he Abd RNA from the mutant strain will be longer than normal.
(c) Cigma factor will not dissociate from RNA polymerase when the Abd
operon is being transcribed in the mutant strain.
(d) RNA polymerase will moe in a bac)wards fashion at the Abd operon in
the mutant strain.
7-18 "ranscription in bacteria differs from transcription in a eucaryotic cell because
(a) RNA polymerase (along with its sigma subunit) can initiate transcription
on its own
(b) RNA polymerase (along with its sigma subunit) re,uires the general
transcription factors to assemble at the promoter before polymerase can
begin transcription
(c) "he sigma subunit must associate with the appropriate type of RNA
polymerase to produce mRNAs
(d) RNA polymerase must be phosphorylated at its ;-terminal tail for
transcription to proceed
7-19 2hich of the following does not occur before a eucaryotic mRNA is e!ported
from the nucleus3
(a) "he ribosome binds to the mRNA.
(b) "he mRNA is polyadenylated at its '& end.
(c) 0-methyl-? is added in a %& to %& lin)age to the mRNA.
(d) RNA polymerase dissociates.
7-20 5se the numbers in the choices below to indicate where in the schematic diagram
of a eucaryotic cell ((igure /0-9B) those processes ta)e place.
(igure /0-9B
D. transcription
9. translation
'. RNA splicing
1. polyadenylation
%. RNA capping
7-21 "otal nucleic acids are e!tracted from a culture of yeast cells and are then mi!ed
with resin beads to which the polynucleotide %&-
"""""""""""""""""""""""""-'& has been coalently attached. After a
short incubation, the beads are then e!tracted from the mi!ture. 2hen you
analy#e the cellular nucleic acids that hae stuc) to the beads, which of the
following is most abundant3
(a) DNA
(b) tRNA
(c) rRNA
(d) mRNA
7-22 Name three coalent modifications that can be made to an RNA molecule in
eucaryotic cells before the RNA molecule becomes a mature mRNA.
7-23 2hich of the following statements about RNA splicing is false3
(a) ;onentional introns are not found in bacterial genes.
(b) (or a gene to function properly, eery e!on must be remoed from the
primary transcript in the same fashion on eery mRNA molecule produced
from the same gene.
(c) Cmall RNA molecules in the nucleus perform the splicing reactions
necessary for the remoal of introns.
(d) Cplicing occurs after the %& cap has been added to the end of the primary
7-24 "he length of a particular gene in human DNA, measured from the start site for
transcription to the end of the protein-coding region, is DB,BBB nucleotides,
whereas the length of the mRNA produced from this gene is 1BBB nucleotides.
2hat is the most li)ely reason for this difference3
7-25 2hy is the old dogma Eone geneFone proteinG not always true for eucaryotic
7-26 4s this statement true or false3 6!plain your answer.
ECince introns do not contain protein coding information, they do not hae
to be remoed precisely (meaning, a nucleotide here and there should not
matter) from the primary transcript during RNA splicing.G
7-27 =ou hae discoered a gene ((igure /0-90A) that is alternatiely spliced to
produce seeral forms of mRNA in arious cell types, three of which are shown in
(igure /0-90A. "he lines connecting the e!ons that are included in the mRNA
indicate the splicing. (rom your e!periments, you )now that protein translation
begins in e!on D. (or all forms of the mRNA, the encoded protein se,uence is the
same in the regions of the mRNA that correspond to e!ons D and DB. 6!ons 9 and
' are alternatie e!ons used in different mRNA, as are e!ons 0 and H. 2hich of
the following statements about e!ons 9 and ' is the most accurate3 6!plain your
(igure /0-90
(a) 6!ons 9 and ' must hae the same number of nucleotides.
(b) 6!ons 9 and ' must contain an integral number of codons (that is, the
number of nucleotides diided by ' must be an integer).
(c) 6!ons 9 and ' must contain a number of nucleotides that when diided by
', leaes the same remainder (that is, B, D, or 9).
(d) 6!ons 9 and ' must hae different numbers of nucleotides.
Fr%& RNA '% Pr%'ein
7-28 2hich of the following statements about the genetic code is correct3
(a) All codons specify more than one amino acid.
(b) "he genetic code is redundant.
(c) All amino acids are specified by more than one codon.
(d) All codons specify an amino acid.
NOTE: The following codon table i to be !ed fo" #"oble$ %7-29 to %7-36& %7-43&
and %7-47'
7-29 "he piece of RNA below includes the region that codes the binding site for the
initiator tRNA needed in translation.
2hich amino acid will be on the tRNA that is the first to bind to the A-site of the
(a) methionine
(b) arginine
(c) cystine
(d) aline
7-30 "he following DNA se,uence includes the beginning of a se,uence coding for a
protein. 2hat would be the result of a mutation that changed the ; mar)ed by an
asteris) to an A3
7-31 2hich amino acid would you e!pect a tRNA with the anticodon %&-;55-'& to
(a) lysine
(b) glutamic acid
(d) leucine
(d) phenylalanine
7-32 2hich of the following pairs of codons might you e!pect to be read by the same
tRNA as a result of wobble3
(a) ;55 and 555
(b) ?A5 and ?AA
(c) ;A; and ;A5
(d) AA5 and A?5
7-33 Aelow is a segment of RNA from the middle of an mRNA.
4f you were told that this segment of RNA was part of the coding region of an
mRNA for a large protein, gie the amino acid se,uence for the protein that is
encoded by this segment of mRNA. 2rite your answer using the one-letter amino
acid code.
7-34 Aelow is the se,uence from the '& end of an mRNA.
4f you were told that this se,uence contains the stop codon for the protein encoded
by this mRNA, what is the anticodon on the tRNA in the 7-site of the ribosome
when release factor binds to the A-site3
(a) %&-;;A-'&
(b) %&-;;?-'&
(c) %&-5??-'&
(d) %&-55A-'&
7-35 :ne strand of a section of DNA isolated from the bacterium E. coli reads>
A. Cuppose that an mRNA is transcribed from this DNA using the
complementary strand as a template. 2hat will be the se,uence of the
mRNA in this region (ma)e sure you label the %& and '& ends of the
A. <ow many different peptides could potentially be made from this
se,uence of RNA, assuming that translation initiates upstream of this
;. 2hat are these peptides3 (?ie your answer using the one-letter amino
acid code.)
7-36 A strain of yeast translates mRNA into protein inaccurately. 4ndiidual molecules
of a particular protein isolated from this yeast hae ariations in the first DD amino
acids compared with the se,uence of the same protein isolated from normal yeast
cells, as listed in (igure /0-'K. 2hat is the most li)ely cause of this ariation in
protein se,uence3
(igure /0-'K
(a) a mutation in the DNA coding for the protein
(b) a mutation in the anticodon of the isoleucine tRNA (tRNA
(c) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to
distinguish between different amino acids
(d) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to
distinguish between different tRNA molecules
7-37 2hich of the following statements is true3
(a) Ribosomes are large RNA structures composed solely of rRNA.
(b) Ribosomes are synthesi#ed entirely in the cytoplasm.
(c) rRNA contains the catalytic actiity that $oins amino acids together.
(d) A ribosome binds one tRNA at a time.
7-38 (igure /0-'HA shows the stage in translation when an incoming aminoacyl-tRNA
has bound to the A-site on the ribosome. 5sing the components shown in (igure
/0-'HA as a guide, show on (igure /0-'HA and /0-'H; what happens in the
ne!t two stages to complete the addition of the new amino acid to the growing
polypeptide chain.
(igure /0-'H
7-39 A poison added to an in vitro translation mi!ture containing mRNA molecules
with the se,uence %&-A5?AAAAAAAAAAAA5AA-'& has the following effect>
the only product made is a .et-8ys dipeptide that remains attached to the
ribosome. 2hat is the most li)ely way in which the poison acts to inhibit protein
(a) 4t inhibits peptidyl transferase actiity.
(b) 4t inhibits moement of the small subunit relatie to the large subunit.
(c) 4t inhibits release factor.
(d) 4t mimics release factor.
7-40 4n eucaryotes, but not in procaryotes, ribosomes find the start site of translation by
(a) binding directly to a ribosome-binding site preceding the initiation codon
(b) scanning along the mRNA from the %& end
(c) recogni#ing an A5? codon as the start of translation
(d) binding an initiator tRNA
7-41 2hich of the following statements about procaryotic mRNA molecules is false3
(a) A single procaryotic mRNA molecule can be translated into seeral
(b) Ribosomes must bind to the %& cap before initiating translation.
(c) mRNAs are not polyadenylated.
(d) Ribosomes can start translating an mRNA molecule before transcription is
7-42 (igure /0-19 shows an mRNA molecule.
(igure /0-19
A. .atch the labels gien in the list below with the label lines in (igure /0-
(a) ribosome-binding site
(b) initiator codon
(c) stop codon
(d) untranslated '& region
(e) untranslated %& region
(f) protein-coding region
A. 4s the mRNA shown procaryotic or eucaryotic3 6!plain your answer.
7-43 A mutation in the tRNA for the amino acid lysine results in the anticodon
se,uence %&-5A5-'& (instead of %&-555-'&). 2hich of the following aberrations
in protein synthesis might this tRNA cause3 ()efe" to the codon table *"o+ided
abo+e %7-29',
(a) read-through of stop codons
(b) substitution of lysine for isoleucine
(c) substitution of lysine for tyrosine
(d) substitution of lysine for phenylalanine
7-44 =ou hae discoered a protein that inhibits translation. 2hen you add this
inhibitor to a mi!ture capable of translating human mRNA and centrifuge the
mi!ture to separate polyribosomes and single ribosomes, you obtain the results
shown in (igure /0-11. 2hich of the following interpretations is consistent with
these obserations3
(igure /0-11
(a) "he protein binds to the small ribosomal subunit and increases the rate of
initiation of translation.
(b) "he protein binds to se,uences in the %& region of the mRNA and inhibits
the rate of initiation of translation.
(c) "he protein binds to the large ribosomal subunit and slows down
elongation of the polypeptide chain.
(d) "he protein binds to se,uences in the '& region of the mRNA and preents
termination of translation.
7-45 "he concentration of a particular protein L in a normal human cell rises gradually
from a low point, immediately after cell diision, to a high point, $ust before cell
diision, and then drops sharply. "he leel of its mRNA in the cell remains fairly
constant throughout this time. 7rotein L is re,uired for cell growth and surial,
but the drop in its leel $ust before cell diision is essential for diision to
proceed. =ou hae isolated a line of human cells that grow in si#e in culture but
cannot diide, and on analy#ing these mutants, you find that leels of L mRNA in
the mutant cells are normal. 2hich of the following mutations in the gene for L
could e!plain these results3
(a) the introduction of a stop codon that truncates protein L at the fourth
amino acid
(b) a change of the first A"? codon to ;;A
(c) the deletion of a se,uence that encodes sites at which ubi,uitin can be
attached to the protein
(d) a change at a splice site that preents splicing of the RNA
7-46 (or each of the following sentences, fill in the blan)s with the best word or phrase
selected from the list below. Not all words or phrases will be used* use each word
or phrase only once.
:nce an mRNA is produced, its message can be decoded on
ribosomes. "he ribosome is composed of two subunits> the
__________________ subunit, which cataly#es the formation of
the peptide bonds that lin) the amino acids together into a
polypeptide chain, and the __________________ subunit, which
matches the tRNAs to the codons of the mRNA. During the chain
elongation process of translating an mRNA into protein, the
growing polypeptide chain attached to a tRNA is bound to the
__________________-site of the ribosome. An incoming
aminoacyl-tRNA carrying the ne!t amino acid in the chain will
bind to the __________________-site by forming base pairs with
the e!posed codon in the mRNA. "he __________________
en#yme cataly#es the formation of a new peptide bond between the
growing polypeptide chain and the newly arriing amino acid. "he
end of a protein-coding message is signaled by the presence of a
stop codon, which binds the __________________ called release
factor. 6entually, most proteins will be degraded by a large
comple! of proteolytic en#ymes called the __________________.
A medium proteasome
central 7 RNA
DNA peptidyl transferase small
6 polymerase "
large protein ubi,uitin
7-47 After treating cells with a mutagen, you isolate two mutants. :ne carries alanine
and the other carries methionine at a site in the protein that normally contains
aline. After treating these two mutants again with mutagen, you isolate mutants
from each that now carry threonine at the site of the original aline (see (igure
/0-10). Assuming that all mutations caused by the mutagen are due to single
nucleotide changes, deduce the codons that are used for aline, alanine,
methionine, and threonine at the affected site. ()efe" to the codon table
*"o+ided abo+e %7-29',
(igure /0-10
7-48 2hich of the following methods is not used by cells to regulate the amount of a
protein in the cell3
(a) ?enes can be transcribed into mRNA with different efficiencies.
(b) .any ribosomes can bind to a single mRNA molecule.
(c) 7roteins can be tagged with ubi,uitin, mar)ing them for degradation.
(d) Nuclear pore comple!es can regulate the speed at which newly
synthesi#ed proteins are e!ported from the nucleus into the cytoplasm.
7-49 2hich of the following statements about the proteasome is false3
(a) 5bi,uitin is a small protein that is coalently attached to proteins to mar)
them for deliery to the proteasome.
(b) 7roteases reside in the central cylinder of a proteasome.
(c) .isfolded proteins are deliered to the proteasome, where they are
se,uestered from the cytoplasm and can attempt to refold.
(d) "he protein stoppers that surround the central cylinder of the proteasome
use the energy from A"7 hydrolysis to moe proteins into the proteasome
inner chamber.
RNA and '#e Ori$in" %( Li(e
7-50 2hich of the following molecules is thought to hae arisen first during eolution3
(a) protein
(b) DNA
(c) RNA
(d) All came to be at the same time.
7-51 According to current thin)ing, the minimum re,uirement for life to hae
originated on 6arth was the formation of a _______________.
(a) molecule that could proide a template for the production of a
complementary molecule
(b) double-stranded DNA heli!
(c) molecule that could direct protein synthesis
(d) molecule that could cataly#e its own replication
7-52 Ribo#ymes cataly#e which of the following reactions3
(a) DNA synthesis
(b) transcription
(c) RNA splicing
(d) protein hydrolysis
7-53 =ou are studying a disease that is caused by a irus, but when you purify the irus
particles and analy#e them you find they contain no trace of DNA. 2hich of the
following molecules are li)ely to contain the genetic information of the irus3
(a) high-energy phosphate groups
(b) RNA
(c) lipids
(d) carbohydrates
7-54 ?ie a reason why DNA ma)es a better material than RNA for the storage of
genetic information, and e!plain your answer.
H%) We *n%): Crac+in$ '#e Gene'ic C%de
7-55 =ou hae discoered an alien life form that surprisingly uses DNA as its genetic
material, ma)es RNA from DNA, and reads the information from RNA to ma)e
protein using ribosomes and tRNAs, which read triplet codons. Aecause it is your
$ob to decipher the genetic code for this alien, you synthesi#e some artificial RNA
molecules and e!amine the protein products produced from these RNA molecules
in a cell-free translation system using purified alien tRNAs and ribosomes. =ou
obtain the results shown in "able /0-%%.
"able /0-%%
(rom this information, which of the following peptides can be produced from
poly 5A5;3
(a) 4le-7he--al-"yr
(b) "yr-Cer-7he-Ala
(c) 4le-8ys-<is-"yr
(d) ;ys-7ro-8ys-Ala
7-56 An e!traterrestrial organism (6") is discoered whose basic cell biology seems
pretty much the same as that of terrestrial organisms e!cept that it uses a different
genetic code to translate RNA into protein. =ou set out to brea) the code by
translation e!periments using RNAs of )nown se,uence and cell-free e!tracts of
6" cells to supply the necessary protein-synthesi#ing machinery. 4n e!periments
using the RNAs below, the following results were obtained when the 9B possible
amino acids were added either singly or in different combinations of two or three>
RNA D> %&-?;?;?;?;?;?;?;?;?;?;?;?;?;?;-'&
RNA 9> %&-?;;?;;?;;?;;?;;?;;?;;?;;?;;?;;-'&
5sing RNA D, a polypeptide was produced only if alanine and aline were added
to the reaction mi!ture. 5sing RNA 9, a polypeptide was produced only if leucine
and serine and cysteine were added to the reaction mi!ture. Assuming that protein
synthesis can start anywhere on the template, that the 6" genetic code is
nonoerlapping and linear, and that each codon is the same length (li)e the
terrestrial triplet code), how many nucleotides does an 6" codon contain3
(a) 9
(b) '
(c) 1
(d) %
(e) K
7-57 NACA has discoered an alien life form. =ou are called in to help NACA
scientists to deduce the genetic code for this alien. Curprisingly, this alien life
form shares many similarities with life on 6arth> this alien uses DNA as its
genetic material, ma)es RNA from DNA, and reads the information from RNA to
ma)e protein using ribosomes and tRNAs. 6en more ama#ing, this alien uses the
same 9B amino acids, li)e the organisms found on 6arth, and also codes for each
amino acid by a triplet codon. <oweer, the scientists at NACA hae found that
the genetic code used by the alien life form differs from that used by life on 6arth.
NACA scientists drew this conclusion after creating a cell-free protein synthesis
system from alien cells and adding an mRNA made entirely of uracil (poly 5).
"hey found that poly 5 directs the synthesis of a peptide containing only glycine.
NACA scientists hae synthesi#ed a poly A5 mRNA and obsere that it codes for
a polypeptide of alternating serine and proline amino acids. (rom these
e!periments, can you determine which codons code for serine and proline3
-on! .!etion' ;an you propose a mechanism for how the alien+s physiology is
altered so that it uses a different genetic code from life on 6arth, despite all the