7
FROM DNA TO PROTEIN: HOW CELLS READ THE GENOME
 2009 Garland Science Publishing
From DNA to 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 variety of structures
(d)
the sugar ribose contains fewer oxygen atoms than does deoxyribose
7-2
Transcription is similar to DNA replication in that ___________________.
(a)
an RNA transcript is synthesized discontinuously and the pieces are then
joined together
(b)
it uses the same enzyme as that used to synthesize RNA primers during
DNA replication
(c)
the newly synthesized RNA remains paired to the template DNA
(d)
nucleotide polymerization occurs only in the 5′-to-3′ direction
7-3
For each of the following sentences, fill in the blanks 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.
For a cell’s genetic material to be used, the information is first
copied from the DNA into the nucleotide sequence of RNA in a
process called transcription. Various kinds of RNA are produced,
each with different functions. mRNA molecules code for proteins,
tRNA __ molecules act as adaptors for protein synthesis in a
process called translation,
rRNA _ molecules are integral components of the ribosome, and
snRNA_ molecules are important in the splicing of RNA
transcripts.
incorporation
transmembrane
pRNA
proteins
7-4
Match the following structures with their names.
4.A ADENİN
1.C URASİL
2-B DEOXYRİBOSE
3-D RİBOSE
Figure Q7-4
7-5
Which of the following statements is false?
(a)
A new RNA molecule can begin to be synthesized from a gene before the
previous RNA molecule’s synthesis is completed.
(b)
If two genes are to be expressed in a cell, these two genes can be
transcribed with different efficiencies.
(c)
RNA polymerase is responsible for both unwinding the DNA helix and
catalyzing the formation of the phosphodiester bonds between nucleotides.
(d)
Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.
7-6
Which one of the following is the main reason that a typical eucaryotic gene is
able to respond to a far greater variety of regulatory signals than a typical
procaryotic gene or operon?
(a)
Eucaryotes have three types of RNA polymerase.
(b)
Eucaryotic RNA polymerases require general transcription factors.
(c)
The transcription of a eucaryotic gene can be influenced by proteins
that bind far from the promoter.
(d)
Procaryotic genes are packaged into nucleosomes.
7-7
Match the following types of RNA with the main polymerase that transcribes
them.
1- A
2-E D
3-C B
7-9
For each of the following sentences, fill in the blanks 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.
In eucaryotic cells, general transcription factors are required for the
activity of all promoters transcribed by RNA polymerase II. The
assembly of the general transcription factors begins with the
binding of the factor TFIID __ to DNA, causing a marked local
distortion in the DNA. This factor binds at the DNA sequence
called the TATA _box, which is typically located 25 nucleotides
upstream from the transcription start site. Once RNA polymerase II
has been brought to the promoter DNA, it must be released to
begin making transcripts. This release process is facilitated by the
addition of phosphate groups to the tail of RNA polymerase by the
factor TFIIH. It 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. Proteins that
link the distantly bound transcription regulators to RNA
polymerase and the general transcription factors include the large
complex of proteins called the activator _..The packing of DNA
into chromatin also affects transcriptional initiation, and histone
deacetylase _ is an enzyme that can render the DNA less
accessible to the general transcription factors.
CAP
lac
ligase
mediator
TFIIA
enhancer
7-10
You have a piece of DNA that includes the following sequence:
5′-ATAGGCATTCGATCCGGATAGCAT-3′
3′-TATCCGTAAGCTAGGCCTATCGTA-5′
Which of the following RNA molecules could be transcribed from this piece of
DNA?
(a)
(b)
(c)
(d)
5′-UAUCCGUAAGCUAGGCCUAUGCUA-3′
5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′
5′-UACGAUAGGCCUAGCUUACGGAUA-3′
none of the above
7-11
You have a segment of DNA that contains the following sequence:
5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′
3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′
If you know that the RNA transcribed from this segment contains the following
sequence:
5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA–3′
Which of the following choices best describes how transcription occurs?
(a)
The top strand is the template strand; RNA polymerase moves along this
strand from 5′ to 3′.
(b)
The top strand is the template strand; RNA polymerase moves along this
strand from 3′ to 5′.
(c)
The bottom strand is the template strand; RNA polymerase moves along
this strand from 5′ to 3′.
(d)
The bottom strand is the template strand; RNA polymerase moves
along this strand from 3′ to 5′.
7-12
Which of the following molecules of RNA would you predict to be the most likely
to fold into a specific structure as a result of intramolecular base pairing?
(a)
(b)
(c)
(d)
7-14
5′CCCUAAAAAAAAAAAAAAAAUUUUUUUUUUUUUUUUAGGG3′
5′UGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG-3′
5′AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′
5′GGAAAAGGAGAUGGGCAAGGGGAAAAGGAGAUGGGCAAGG-3′
The sigma subunit of bacterial RNA polymerase ___________________.
(a)
contains the catalytic activity of the polymerase
(b)
remains part of the polymerase throughout transcription
(c)
recognizes promoter sites in the DNA
(d)
recognizes transcription termination sites in the DNA
7-15
Which of the following might decrease the transcription of only one specific gene
in a bacterial cell?
(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 sequence
(d)
a mutation that introduced extensive sequence changes into the DNA
that precedes the gene’s transcription start site
7-16
There are several reasons why the primase used to make the RNA primer for DNA
replication is not suitable for gene transcription. Which of the statements below is
not one of those reasons?
(a)
Primase initiates RNA synthesis on a single-stranded DNA template.
(b)
Primase can initiate RNA synthesis without the need for a base-paired
primer.
(c)
Primase synthesizes only RNAs of about 5–20 nucleotides in length.
(d)
The RNA synthesized by primase remains base-paired to the DNA
template.
7-17
You have a bacterial strain with a mutation that removes the transcription
termination signal from the Abd operon. Which of the following statements
describes the most likely effect of this mutation on Abd transcription?
(a)
The Abd RNA will not be produced in the mutant strain.
(b)
The Abd RNA from the mutant strain will be longer than normal.
(c)
Sigma factor will not dissociate from RNA polymerase when the Abd
operon is being transcribed in the mutant strain.
(d)
RNA polymerase will move in a backwards fashion at the Abd operon in
the mutant strain.
7-18
Transcription 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) requires the general
transcription factors to assemble at the promoter before polymerase can
begin transcription
(c)
The sigma subunit must associate with the appropriate type of RNA
polymerase to produce mRNAs
(d)
RNA polymerase must be phosphorylated at its C-terminal tail for
transcription to proceed
7-19
Which of the following does not occur before a eucaryotic mRNA is exported
from the nucleus?
(a)
The ribosome binds to the mRNA.
(b)
The mRNA is polyadenylated at its 3′ end.
(c)
(d)
7-methyl-G is added in a 5′ to 5′ linkage to the mRNA.
RNA polymerase dissociates.
7-20
Use the numbers in the choices below to indicate where in the schematic diagram
of a eucaryotic cell (Figure Q7-20) those processes take place.
7-21
Total nucleic acids are extracted from a culture of yeast cells and are then mixed
with resin beads to which the polynucleotide 5′TTTTTTTTTTTTTTTTTTTTTTTTT-3′ has been covalently attached. After a
short incubation, the beads are then extracted from the mixture. When you
analyze the cellular nucleic acids that have stuck to the beads, which of the
following is most abundant?
(a)
DNA
(b)
tRNA
(c)
rRNA
(d)
mRNA
7-22
Name three covalent modifications that can be made to an RNA molecule in
eucaryotic cells before the RNA molecule becomes a mature mRNA.
7-23
Which of the following statements about RNA splicing is false?
(a)
Conventional introns are not found in bacterial genes.
(b)
For a gene to function properly, every exon must be removed from the
primary transcript in the same fashion on every mRNA molecule
produced from the same gene.
(c)
Small RNA molecules in the nucleus perform the splicing reactions
necessary for the removal of introns.
(d)
Splicing occurs after the 5′ cap has been added to the end of the primary
transcript.
From RNA to Protein
7-28
Which of the following statements about the genetic code is correct?
(a)
All codons specify more than one amino acid.
(b)
The genetic code is redundant.
(c)
(d)
All amino acids are specified by more than one codon.
All codons specify an amino acid.
NOTE: The following codon table is to be used for Problems Q7-29 to Q7-36, Q7-43,
and Q7-47.
7-29
The piece of RNA below includes the region that codes the binding site for the
initiator tRNA needed in translation.
5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′
Which amino acid will be on the tRNA that is the first to bind to the A-site of the
ribosome?
(a)
methionine
(b)
arginine
(c)
cystine
(d)
valine
7-31
Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to
carry?
(a)
lysine
(b)
glutamic acid
(d)
leucine
(d)
phenylalanine
7-32
Which of the following pairs of codons might you expect to be read by the same
tRNA as a result of wobble?
(a)
CUU and UUU
(b)
GAU and GAA
(c)
CAC and CAU
(d)
AAU and AGU
7-34
Below is the sequence from the 3′ end of an mRNA.
5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′
If you were told that this sequence contains the stop codon for the protein encoded
by this mRNA, what is the anticodon on the tRNA in the P-site of the ribosome
when release factor binds to the A-site?
(a)
5′-CCA-3′
(b)
5′-CCG-3′
(c)
5′-UGG-3′
(d)
5′-UUA-3′
7-36
A strain of yeast translates mRNA into protein inaccurately. Individual molecules
of a particular protein isolated from this yeast have variations in the first 11 amino
acids compared with the sequence of the same protein isolated from normal yeast
cells, as listed in Figure Q7-36. What is the most likely cause of this variation in
protein sequence?
Figure Q7-36
(a)
(b)
(c)
(d)
a mutation in the DNA coding for the protein
a mutation in the anticodon of the isoleucine tRNA (tRNAIle)
a mutation in the isoleucyl-tRNA synthetase that decreases its ability
to distinguish between different amino acids
a mutation in the isoleucyl-tRNA synthetase that decreases its ability to
distinguish between different tRNA molecules
7-37
Which of the following statements is true?
(a)
Ribosomes are large RNA structures composed solely of rRNA.
(b)
Ribosomes are synthesized entirely in the cytoplasm.
(c)
rRNA contains the catalytic activity that joins amino acids together.
(d)
A ribosome binds one tRNA at a time.
7-38
Figure Q7-38A shows the stage in translation when an incoming aminoacyl-tRNA
has bound to the A-site on the ribosome. Using the components shown in Figure
Q7-38A as a guide, show on Figure Q7-38B and Q7-38C what happens in the
next two stages to complete the addition of the new amino acid to the growing
polypeptide chain.
Figure Q7-38
7-39
A poison added to an in vitro translation mixture containing mRNA molecules
with the sequence 5′-AUGAAAAAAAAAAAAUAA-3′ has the following effect:
the only product made is a Met-Lys dipeptide that remains attached to the
ribosome. What is the most likely way in which the poison acts to inhibit protein
synthesis?
(a)
It inhibits peptidyl transferase activity.
(b)
It inhibits movement of the small subunit relative to the large subunit.
(c)
It inhibits release factor.
(d)
It mimics release factor.
7-40
In 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 5′ end
(c)
recognizing an AUG codon as the start of translation
(d)
binding an initiator tRNA
7-41
Which of the following statements about procaryotic mRNA molecules is false?
(a)
A single procaryotic mRNA molecule can be translated into several
proteins.
(b)
Ribosomes must bind to the 5′ cap before initiating translation.
(c)
mRNAs are not polyadenylated.
(d)
Ribosomes can start translating an mRNA molecule before transcription is
complete.
7-42
Figure Q7-42 shows an mRNA molecule.
Figure Q7-42
A.
Match the labels given in the list below with the label lines in Figure Q742.
(a)
ribosome-binding site 3
(b)
initiator codon
2
(c)
stop codon
4
(d)
untranslated 3′ region 6
(e)
untranslated 5′ region 1
(f)
protein-coding region 5
7-43
A mutation in the tRNA for the amino acid lysine results in the anticodon
sequence 5′-UAU-3′ (instead of 5′-UUU-3′). Which of the following aberrations
in protein synthesis might this tRNA cause? (Refer to the codon table provided
above Q7-29.)
(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
You have discovered a protein that inhibits translation. When you add this
inhibitor to a mixture capable of translating human mRNA and centrifuge the
mixture to separate polyribosomes and single ribosomes, you obtain the results
shown in Figure Q7-44. Which of the following interpretations is consistent with
these observations?
Figure Q7-44
(a)
(b)
(c)
(d)
7-45
The protein binds to the small ribosomal subunit and increases the rate of
initiation of translation.
The protein binds to sequences in the 5′ region of the mRNA and
inhibits the rate of initiation of translation.
The protein binds to the large ribosomal subunit and slows down
elongation of the polypeptide chain.
The protein binds to sequences in the 3′ region of the mRNA and prevents
termination of translation.
The concentration of a particular protein X in a normal human cell rises gradually
from a low point, immediately after cell division, to a high point, just before cell
division, and then drops sharply. The level of its mRNA in the cell remains fairly
constant throughout this time. Protein X is required for cell growth and survival,
but the drop in its level just before cell division is essential for division to
proceed. You have isolated a line of human cells that grow in size in culture but
cannot divide, and on analyzing these mutants, you find that levels of X mRNA in
the mutant cells are normal. Which of the following mutations in the gene for X
could explain these results?
(a)
the introduction of a stop codon that truncates protein X at the fourth
amino acid
(b)
a change of the first ATG codon to CCA
(c)
the deletion of a sequence that encodes sites at which ubiquitin can be
attached to the protein
(d)
a change at a splice site that prevents splicing of the RNA
7-46
For each of the following sentences, fill in the blanks 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.
Once an mRNA is produced, its message can be decoded on
ribosomes. The ribosome is composed of two subunits: the large
subunit, which catalyzes the formation of the peptide bonds that
link the amino acids together into a polypeptide chain, and the
small _ 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 ________P__________-site of the
ribosome. An incoming aminoacyl-tRNA carrying the next amino
acid in the chain will bind to the _________A_________-site by
forming base pairs with the exposed codon in the mRNA.
The peptidyl transferase ___ enzyme catalyzes the formation of
a new peptide bond between the growing polypeptide chain and the
newly arriving amino acid. The end of a protein-coding message is
signaled by the presence of a stop codon, which binds the protein
called release factor. Eventually, most proteins will be degraded by
a large complex of proteolytic enzymes called the proteasome __.
medium
central
DNA
E
7-47
RNA
polymerase
T
ubiquitin
After treating cells with a mutagen, you isolate two mutants. One carries alanine
and the other carries methionine at a site in the protein that normally contains
valine. After treating these two mutants again with mutagen, you isolate mutants
from each that now carry threonine at the site of the original valine (see Figure
Q7-47). Assuming that all mutations caused by the mutagen are due to single
nucleotide changes, deduce the codons that are used for valine, alanine,
methionine, and threonine at the affected site. (Refer to the codon table
provided above Q7-29.)
Figure Q7-47
7-48
Which of the following methods is not used by cells to regulate the amount of a
protein in the cell?
(a)
Genes can be transcribed into mRNA with different efficiencies.
(b)
Many ribosomes can bind to a single mRNA molecule.
(c)
Proteins can be tagged with ubiquitin, marking them for degradation.
(d)
Nuclear pore complexes can regulate the speed at which newly
synthesized proteins are exported from the nucleus into the cytoplasm.
7-49
Which of the following statements about the proteasome is false?
(a)
Ubiquitin is a small protein that is covalently attached to proteins to mark
them for delivery to the proteasome.
(b)
Proteases reside in the central cylinder of a proteasome.
(c)
Misfolded proteins are delivered to the proteasome, where they are
sequestered from the cytoplasm and can attempt to refold.
(d)
The protein stoppers that surround the central cylinder of the proteasome
use the energy from ATP hydrolysis to move proteins into the proteasome
inner chamber.
RNA and the Origins of Life
7-50
Which of the following molecules is thought to have arisen first during evolution?
(a)
protein
(b)
DNA
(c)
RNA
(d)
All came to be at the same time.
7-51
According to current thinking, the minimum requirement for life to have
originated on Earth was the formation of a _______________.
(a)
molecule that could provide a template for the production of a
complementary molecule
(b)
double-stranded DNA helix
(c)
molecule that could direct protein synthesis
(d)
molecule that could catalyze its own replication
7-52
Ribozymes catalyze which of the following reactions?
(a)
DNA synthesis
(b)
transcription
(c)
RNA splicing
(d)
protein hydrolysis
7-53
You are studying a disease that is caused by a virus, but when you purify the virus
particles and analyze them you find they contain no trace of DNA. Which of the
following molecules are likely to contain the genetic information of the virus?
(a)
high-energy phosphate groups
(b)
RNA
(c)
lipids
(d)
carbohydrates
How We Know: Cracking the Genetic Code
7-55
You have discovered an alien life form that surprisingly uses DNA as its genetic
material, makes RNA from DNA, and reads the information from RNA to make
protein using ribosomes and tRNAs, which read triplet codons. Because it is your
job to decipher the genetic code for this alien, you synthesize some artificial RNA
molecules and examine the protein products produced from these RNA molecules
in a cell-free translation system using purified alien tRNAs and ribosomes. You
obtain the results shown in Table Q7-55.
Table Q7-55
From this information, which of the following peptides can be produced from
poly UAUC?
(a)
Ile-Phe-Val-Tyr
(b)
Tyr-Ser-Phe-Ala
(c)
Ile-Lys-His-Tyr
(d)
Cys-Pro-Lys-Ala
7-56
An extraterrestrial organism (ET) is discovered whose basic cell biology seems
pretty much the same as that of terrestrial organisms except that it uses a different
genetic code to translate RNA into protein. You set out to break the code by
translation experiments using RNAs of known sequence and cell-free extracts of
ET cells to supply the necessary protein-synthesizing machinery. In experiments
using the RNAs below, the following results were obtained when the 20 possible
amino acids were added either singly or in different combinations of two or three:
RNA 1: 5′-GCGCGCGCGCGCGCGCGCGCGCGCGCGC-3′
RNA 2: 5′-GCCGCCGCCGCCGCCGCCGCCGCCGCCGCC-3′
Using RNA 1, a polypeptide was produced only if alanine and valine were added
to the reaction mixture. Using RNA 2, a polypeptide was produced only if leucine
and serine and cysteine were added to the reaction mixture. Assuming that protein
synthesis can start anywhere on the template, that the ET genetic code is
nonoverlapping and linear, and that each codon is the same length (like the
terrestrial triplet code), how many nucleotides does an ET codon contain?
(a)
2
(b)
3
(c)
4
(d)
5
(e)
6