CHAPTER 9
HOW GENES AND GENOMES EVOLVE
 2009 Garland Science Publishing
Generating Genetic Variation
9-1
Which of the following statements is false?
(a)
A mutation that arises in a mother’s somatic cell often causes a disease in
her daughter.
(b)
All mutations in an asexually reproducing single-celled organism are
passed on to progeny.
(c)
In an evolutionary sense, somatic cells exist only to help propagate germline cells.
(d)
A mutation is passed on to offspring only if it is present in the germ line.
9-2
Your friend works in a lab that is studying why a particular mutant strain of
Drosophila grows an eye on its wing. Your friend discovers that this mutant strain
of Drosophila is expressing a transcription factor incorrectly. In the mutant
Drosophila, this transcription factor, which is normally expressed in the
primordial eye tissue, is now misexpressed in the wing primordial wing tissue,
thus turning on transcription of the set of genes required to produce an eye in the
wing primordial tissue. If this hypothesis is true, which of the following types of
genetic change would most likely lead to this situation?
(a)
a mutation within the transcription factor gene that leads to a premature
stop codon after the third amino acid
(b)
a mutation within the transcription factor gene that leads to a substitution
of a positively charged amino acid for a negatively charged amino acid
(c)
a mutation within an upstream enhancer of the gene
(d)
a mutation in the TATA box of the gene
9-3
Match the type of phenotypic change below with the type of genetic change most
likely to cause it. Each type of genetic change may be used more than once, or
may not be used at all.
Phenotypic changes:
1.
A protein normally localized in the nucleus is now localized in the
cytoplasm. _________
2.
A protein acquires a DNA binding domain. _________
3.
Tandem copies of a gene are found in the genome. _________
4.
A copy of a bacterial gene is now found integrated on a human
chromosome. _________
5.
A protein becomes much more unstable. _________
6.
A protein normally expressed only in the liver is now expressed in blood
cells. _________
Types of genetic change:
A.
mutation within a gene
B.
gene duplication
C.
mutation in a regulatory region
D.
exon shuffling
E.
horizontal gene transfer
9-4
For each of the following sentences, fill in the blanks with the best word or phrase
in the list below. Not all words or phrases will be used; use each word or phrase
only once.
Sexual reproduction in a multicellular organism involves
specialized reproductive cells, called __________________s,
which come together to form a __________________ that will
divide to produce both reproductive and __________________
cells. A point mutation in the DNA is considered a
__________________ mutation if it changes a nucleotide that
leads to no phenotypic consequence; a point mutation is considered
__________________ if it changes a nucleotide within a gene and
causes the protein to be non-functional.
common
gamete
homologous
deleterious
unequal
somatic
neutral
intron
cellulose
zygote
9-5
Transposable elements litter the genomes of primates, and a few of them are still
capable of moving to new regions of the genome. If a transposable element
jumped into an important gene in one of your cells when you were a baby and
caused a disease, is it likely that your child would also have the disease? Explain.
9-6
What is the most likely explanation of why the overall mutation rates in bacteria
and in humans are roughly similar?
(a)
Cell division needs to be fast.
(b)
Most mutations are silent.
(c)
There is a narrow range of mutation rates that offers an optimal balance
between keeping the genome stable and generating sufficient diversity in a
population.
(d)
It benefits a multicellular organism to have some variability among its
cells.
9-7
For each statement below, indicate whether it is true or false and explain why.
A.
B.
C.
D.
E.
9-8
To meet a challenge or develop a new function, evolution essentially
builds from first principles, designing from scratch, to find the best
possible solution.
Nearly every instance of DNA duplication leads to a new functional gene.
A pseudogene is very similar to a functional gene but cannot be expressed
because of mutations.
Most genes in vertebrates are unique, and only a few genes are members
of multigene families.
Horizontal transfer is very rare and thus has had little influence on the
genomes of bacteria.
Two individuals are represented in each choice in Figure Q9-8; individual 1 is one
of the parents of individual 2. The asterisk seen in each choice indicates the
occurrence of a single mutation during the cell division. Which of the choices in
Figure Q9-8 will lead to a mutation in every cell of the individual in which the
original mutation occurred?
Figure Q9-8
9-9
Two individuals are represented in Figure Q9-9; individual 1 is one of the parents
of individual 2. The asterisk indicates the occurrence of a single mutation.
Figure Q9-9
What is the chance that individual 2 will inherit the mutation in individual 1?
(a)
100%
(b)
50%
(c)
1 in 100,000
(d)
none
9-10
Consider a gene with a particular function. Mutation X and mutation Y each cause
defects in the function of the encoded protein, yet a gene containing both
mutations X and Y encodes a protein that works even better than the original
protein. The odds are exceedingly small that a single mutational event will
generate both mutations X and Y. Explain a simple way that an organism with a
mutant gene containing both mutations X and Y could arise during evolution.
9-11
For each of the following sentences, fill in the blanks with the best word or phrase
in the list below. Not all words or phrases will be used; use each word or phrase
only once.
Most variation between individual humans is in the form of
__________________. __________________ may arise by
recombination within introns and can create proteins with novel
combinations of domains. Scientists and government regulators
must be very careful when introducing herbicide-resistant
transgenic corn plants into the environment, because if resistant
weeds arise from __________________ then the herbicides could
become useless. Families of related genes can arise from a single
ancestral copy by __________________ and subsequent
__________________.
divergence
exon shuffling
gene duplication
horizontal gene transfer
purifying selection
single-nucleotide polymorphisms
synteny
unequal crossing-over
9-12
Figure Q9-12 shows an experiment used to determine the spontaneous mutation
rate in E. coli. If the spontaneous mutation rate in E. coli is 1 mistake in every 109
nucleotides copied, about how many colonies would you expect to see on the
plates lacking histidine if you were to assay 1011 cells from the culture for their
ability to form colonies?
Figure Q9-12
(a)
(b)
(c)
(d)
9-13
1
2
10
100
The spontaneous mutation rate in E. coli was determined by performing assays to
test for the frequency of an AT to GC change. These assays were performed using
E. coli that started out unable to produce histidine (His–) because of an inserted
UGA stop codon that disrupted the region coding for an enzyme required to
produce histidine. When a spontaneous mutation arose that enabled the UGA stop
codon to code for tryptophan, the E. coli cells were then able to produce the
enzyme required for histidine production. Would you expect a change in the
spontaneous mutation rate of 1 mistake every 109 nucleotides copied if reversion
of the stop codon to cysteine (instead of tryptophan) could cause the bacteria to
produce histidine? Explain. (The codon table is shown in Figure Q9-13 to help
you answer this question.)
Figure Q9-13
9-14
Which of the following changes is least likely to arise from a point mutation in a
regulatory region of a gene?
(a)
a mutation that changes the time in an organism’s life during which a
protein is expressed
(b)
a mutation that eliminates the production of a protein in a specific cell
type
(c)
a mutation that changes the subcellular localization of a protein
(d)
a mutation that increases the level of protein production in a cell
9-15
Which of the following statements about gene families is false?
(a)
Because gene duplication can occur when crossover events occur, genes
are always duplicated onto homologous chromosomes.
(b)
Not all duplicated genes will become functional members of gene
families.
(c)
Whole genome duplication can contribute to the formation of gene
families.
(d)
Duplicated genes can diverge in both their regulatory regions and their
coding regions.
9-16
Figure Q9-16 shows the evolutionary history of the globin gene family members.
Figure Q9-16
Given this information, which of the following statements is true?
(a)
The ancestral globin gene arose 500 million years ago.
(b)
The α-globin gene is more closely related to the ε-globin gene than to the
δ-globin gene.
(c)
The nucleotide sequences of the two γ-globins will be most similar
because they are the closest together on the chromosome.
(d)
The fetal β-globins arose from a gene duplication that occurred 200
million years ago, which gave rise to a β-globin expressed in the fetus and
a β-globin expressed in the adult.
9-17
Panels (A) and (B) of Figure Q9-17 show substrates of exon shuffling and the
outcome of exon shuffling after recombination. Horizontal lines and small filled
circles represent chromosomes and centromeres, respectively. Exons are labeled
A, B, C, and D. Homologous recombination or shuffling may take place at short,
repeated homologous DNA sequences in introns; because DNA sequences have a
polarity, the repeated sequences can be considered to have a head and a tail and
thus are drawn as arrows. A large X represents a recombinational crossover. Panel
(A) shows that recombination between two direct repeats located on opposite
sides of the centromere yields one circular product that contains a centromere and
a second product that lacks a centromere and will therefore be lost when the cell
divides. Panel (B) shows that recombination between inverted repeats flanking the
centromere will keep the rearranged chromosome intact. Draw the products of
recombination when the repeated sequences are located on different
chromosomes, as shown in panels (C) and (D). Will these products be faithfully
transmitted during cell division?
Figure Q9-17
9-18
Which of the following would contribute most to successful exon shuffling?
(a)
shorter introns
(b)
a haploid genome
(c)
exons that code for more than one protein domain
(d)
introns that contain regions of similarity to one another
Reconstructing Life’s Family Tree
9-19
Which of the following statements is true?
(a)
The intron structure of most genes is conserved among vertebrates.
(b)
The more nucleotides there are in an organism’s genome, the more genes
there will be in its genome.
(c)
Because the fly Drosophila melanogaster and humans diverged from a
common ancestor so long ago, a gene in the fly will show more similarity
to another gene from the same species than it will to a human gene.
(d)
An organism from the same Order will be more likely to have genomes of
the same size than will a more evolutionarily diverged animal.
9-20
Given the evolutionary relationship between higher primates shown in Figure Q920, which of the following statements is false?
Figure Q9-20
(a)
(b)
(c)
(d)
9-21
The last common ancestor of humans, chimpanzees, gorillas, and
orangutans lived about 14 million years ago.
Chimpanzees are more closely related to gorillas than to humans.
Humans and chimpanzees diverged about 6 million years ago.
Orangutans are the most divergent of the four species shown in Fig. Q920.
In humans and in chimpanzees, 99% of the Alu retrotransposons are in
corresponding positions. Which of the following statements below is the most
likely explanation for this similarity?
(a)
The Alu retrotransposon is not capable of transposition in humans.
(b)
(c)
(d)
9-22
Most of the Alu sequences in the chimpanzee genome underwent
duplication and divergence before humans and chimpanzees diverged.
The Alu retrotransposons are in the most beneficial position in the genome
for primates.
The Alu retrotransposons must also be in the same position in flies.
You are interested in finding out how the budding yeast Saccharomyces
cerevisiae is so good at making bread and have collected five new related species
from the wild. You sequence the genomes of all of these new species and also
consult with a fungal biologist to help you construct the phylogenetic tree shown
in Figure Q9-22. You find that species V, W, and X make pretty good bread
whereas species Y and Z do not, suggesting that the last common ancestor of
species X and S. cerevisiae may have the genes necessary for making good bread.
You compare the gene sequences of species X and S. cerevisiae and find many
identical coding sequences, but you also identify nucleotides that differ between
the two species. Which species would be the best to examine to determine what
the sequence was in the last common ancestor of species X and S. cerevisiae?
Figure Q9-22
(a)
(b)
(c)
(d)
9-23
species V
species W
species Y
species Z
Which of the following statements is false?
(a)
The human genome is more similar to the orangutan genome than it is to
the mouse genome.
(b)
A comparison of genomes shows that 90% of the human genome shares
regions of conserved synteny with the mouse genome.
(c)
(d)
Primates, dogs, mice, and chickens all have about the same number of
genes.
Genes that code for ribosomal RNA share significant similarity in all
eucaryotes but are much more difficult to recognize in archaea.
9-24
The puffer fish, Fugu rubripes, has a genome that is one-tenth the size of
mammalian genomes. Which of the following statements is not a possible reason
for this size difference?
(a)
Intron sequences in Fugu are shorter than those in mammals.
(b)
Fugu lacks the repetitive DNA found in mammals.
(c)
The Fugu genome seems to have lost sequences faster than it has gained
sequences over evolutionary time.
(d)
Fugu has lost many genes that are part of gene families.
9-25
Which of the following regions of the genome is the least likely to be conserved
over evolutionary time?
(a)
the upstream regulatory region of a gene that encodes the region
conferring tissue specificity
(b)
the upstream regulatory region of a gene that binds to RNA polymerase
(c)
the portion of the genome that codes for proteins
(d)
the portion of the genome that codes for RNAs that are not translated into
protein
9-26
The evolutionary relationships between seven different species, G, H, J, K, L, M,
and N are diagrammed in Figure Q9-26.
Figure Q9-26
Given this information, which of the following statements is false?
(a)
These are all highly related species, because the sequence divergence
between the most divergent species is 3%.
(b)
Species M is just as related to species G as it is to species J.
(c)
Species N is more closely related to the last common ancestor of all of
these species than to any of the other species shown in the diagram.
9-28
(d)
Species G and H are as closely related to each other as species J and K are
to each other.
9-27
You are working in a human genetics laboratory that studies causes and
treatments for eye cataracts in newborns. This disease is thought to be
caused by a deficiency in the enzyme galactokinase, but the human gene
that encodes this enzyme has not yet been identified. At a talk by a visiting
scientist, you learn about a strain of baker’s yeast that contains a mutation
called gal1– in its galactokinase gene. Because this gene is needed to
metabolize galactose, the mutant strain cannot grow in galactose medium.
Knowing that all living things evolved from a common ancestor and that
distantly related organisms often have homologous genes that perform
similar functions, you wonder whether the human galactokinase gene can
function in yeast. Because you have an optimistic temperament, you
decide to pursue this line of experimentation. You isolate mRNA gene
transcripts from human cells, use reverse transcriptase to make
complementary DNA (cDNA) copies of the mRNA molecules, and ligate
the cDNAs into circular plasmid DNA molecules that can be stably
propagated in yeast cells. You then transform the pool of plasmids into
gal1– yeast cells so that each cell receives a single plasmid. What will
happen when you spread the plasmid-containing cells on Petri dishes that
contain galactose as a carbon source? How can this approach help you find
the human gene encoding galactokinase?
A.
When a mutation arises, it can have three possible consequences:
beneficial to the individual, selectively neutral, or detrimental. Order these
from most likely to least likely.
The spread of a mutation in subsequent generations will, of course, depend
on its consequences to individuals that inherit it. Order the three
possibilities in part A to indicate which is most likely to spread and
become over-represented in subsequent generations, and which is most
likely to become under-represented or disappear from the population.
B.
9-29
Some types of gene are more highly conserved than others. For each of the
following pairs of gene functions, choose the one that is more likely to be highly
conserved.
A.
genes involved in sexual reproduction / genes involved in sugar
metabolism
B.
DNA replication / developmental pathways
C.
hormone production / lipid synthesis
9-30
Figure Q9-30 shows a hypothetical phylogenetic tree. Use this tree to answer the
following questions.
Figure Q9-30
A.
B.
C.
D.
How many years ago did species M and N diverge from their last common
ancestor?
How much nucleotide divergence is there on average between species M
and N?
Are species M and N more or less closely related to each other than
species P and S are?
In looking for functionally important nucleotide sequences, is it more
informative to compare the genome sequences of species M and N or
those of species M and Q?
9-31
For each statement below, indicate whether it is true or false and explain why.
A.
All highly conserved stretches of DNA in the genome are transcribed into
RNA.
B.
To find functionally important regions of the genome, it is more useful to
compare species whose last common ancestor lived 100 million years ago
rather than 5 million years ago.
C.
Most mutations and genome alterations have neutral consequences.
D.
Proteins required for growth, metabolism, and cell division are more
highly conserved than those involved in development and in response to
the environment.
E.
Introns and transposons tend to slow the evolution of new genes.
9-32
Your friend has sequenced the genome of her favorite experimental organism, a
kind of yeast. She wants to identify the locations of all the genes in this genome.
To aid her search, she collaborates with another researcher, one who has
sequenced the genome of a distantly related yeast species. Luckily, the absence of
introns simplifies the effort. She and her collaborator use a computer program to
align similar stretches of DNA sequence from the two genomes. The program
yields the graphical output shown in Figure Q9-32, where the horizontal lines
represent a portion of the two genomic sequences and vertical lines indicate where
the sequences differ. (No vertical line means that the sequence is identical in the
two yeasts.) Label both the functionally conserved regions and the divergent
(nonconserved) sequences. Are all of the functionally conserved regions likely to
be transcribed into RNA? If not, what might be the function of the nontranscribed
conserved regions?
Figure Q9-32
9-33
The genomes of some vertebrates are much smaller than those of others. For
example, the genome of the puffer fish Fugu is much smaller than the human
genome, and even much smaller than those of other fish, primarily because of the
small size of its introns.
A.
Describe a mechanism that might drive evolution toward small introns or
loss of introns and could therefore account for the evolutionary loss of
introns according to the “introns early” hypothesis.
B.
Describe a mechanism that might drive evolution toward more or larger
introns and could thereby account for the evolutionary appearance of
introns according to the “introns late” hypothesis.
9-34
It is thought that all eucaryotes all have about 300 genes in common. Would you
predict that these genes would be used at different times during the life cycle of
multicellular animals? Explain your answer.
9-35
Which of the following functions do you not expect to find in the set of genes
found in all organisms on Earth?
(a)
DNA replication
(b)
DNA repair
(c)
protein production
(d)
RNA splicing
9-36
Which of the following generalities about genomes is true?
(a)
All vertebrate genomes contain roughly the same number of genes.
(b)
All unicellular organisms contain roughly the same number of genes.
(c)
The larger an organism, the more genes it has.
(d)
The more types of cell an organism has, the more genes it has.
Examining The Human Genome
9-37
The human genome has 3.2 × 109 nucleotide pairs. At its peak, the Human
Genome Project was generating raw nucleotide sequences at a rate of 1000
nucleotides per second. At the rate of 1000 nucleotides per second, how long
would it take to generate 3.2 × 109 nucleotides of sequence?
9-38
The average size of a protein in a human cell is about 430 amino acids, yet the
average gene in the human genome is 27,000 nucleotide pairs long. Explain.
9-39
Which of the following statement about pseudogenes is false?
(a)
Pseudogenes code for microRNAs.
(b)
Pseudogenes share significant nucleotide similarity with functional genes.
(c)
Pseudogenes are no longer expressed in the cell.
(d)
There are estimated to be approximately 20,000 pseudogenes in the human
genome.
9-40
Which of the following statements about the human genome is false?
(a)
More than 40% of the human genome is made up of mobile genetic
elements.
(b)
More of the human genome codes for intron sequences than for exon
sequences.
(c)
About 1.5% of the human genome codes for exons.
(d)
The exons are mainly what is conserved between the genomes of humans
and other mammals.
9-41
The nucleotide sequences between individuals differ by 0.1%, yet the human
genome is made up of about 3 × 109 nucleotide pairs. Which of the following
statements is false?
(a)
In most human cells, the homologous autosomes differ from each other by
0.1%.
(b)
All changes between human individuals are single-nucleotide
polymorphisms.
(c)
Any two individuals (other than identical twins) will generally have more
than 3 million genetic differences in their genomes.
(d)
Much of the variation between human individuals was present 100,000
years ago, when the human population was small.
9-42
Propose a reason to explain why highly repetitive regions of the genome are
particularly susceptible to expansions and contractions in number.
9-43
Which of the following processes is not thought to contribute to diversity in the
genome of human individuals?
(a)
exon shuffling
(b)
single-nucleotide polymorphisms
(c)
CA repeats
(d)
duplication and deletion of large blocks of sequence
9-44
For each statement below, indicate whether it is true or false and explain why.
A.
The increased complexity of humans compared with flies and worms is
largely due to the vastly larger number of genes in humans.
B.
Repeats of the CA dinucleotide are useful for crime investigations and
other forensic applications.
C.
Most single-nucleotide polymorphisms cause no observable functional
differences between individual humans.
D.
There is little conserved synteny between human and mouse genes.
E.
The differences between multicellular organisms are largely explained by
the different kinds of genes carried on their chromosomes.
9-45
The number of distinct protein species found in humans and other organisms can
vastly exceed the number of genes. This is largely due to ______________.
(a)
protein degradation
(b)
alternative splicing
(c)
homologous genes
(d)
mutation
9-46
You are studying a gene that has four exons and can undergo alternative splicing.
Exon 1 has two alternatives, exon 2 has five alternatives, exon 3 has three
alternatives, and exon 4 has four alternatives. If all possible splicing combinations
were used, how many different splice isoforms could be produced for this gene?
(a)
22
(b)
30
(c)
60
(d)
120
9-47
Alternative exons can arise through the duplication and divergence of existing
exons. What type of mutation below would be least tolerated during the evolution
of a new exon?
(a)
a nucleotide change of A to G
(b)
a deletion of three consecutive bases.
(c)
mutation of the first nucleotide in the intron
(d)
a nucleotide change that alters a TT dinucleotide to AA
How We Know: Counting Genes
9-48
Explain how ESTs are identified and how they aid in finding the genes within an
organism’s genome.
9-49
Your friend discovered a new multicellular organism living under the polar ice
caps, and brought it back to the laboratory, where it seems to be growing well.
Your friend is particularly interested in the proteins that allow this organism to
survive in extreme cold. Because he is interested in proteins and because he has
learned that most of the human genome does not code for exons, he is considering
sequencing expressed sequence tags from this organism. What do you think the
pitfalls of this approach might be? Explain.
9-50
The yeast genome was sequenced more than 10 years ago, yet the total number of
genes continues to be refined. The sequencing of closely related yeast species was
important for validating the identity of short (less than 100 nucleotides long) open
reading frames (ORFs) that were otherwise difficult to predict. What is the main
reason that these short ORFs are hard to find?
(a)
The human genome does not have short ORFs.
(b)
(c)
(d)
The short ORFs code for RNAs.
Many short stretches of DNA may, by random chance, not have a stop
codon, making it difficult to distinguish those that code for proteins from
those that do not.
Short ORFs occur mainly in gene-rich regions, making them difficult to
identify by computer programs.
CHAPTER 10
ANALYZING GENES AND GENOMES
 2009 Garland Science Publishing
10-1
Recombinant DNA technologies involve techniques that permit the creation of
custom-made DNA molecules that can be introduced back into living organisms.
These technologies were first developed in the ______.
(a)
1930s
(b)
1950s
(c)
1970s
(d)
1990s
Manipulating and Analyzing DNA Molecules
10-2
Which of the following statements about restriction nucleases is false?
(a)
A reproducible set of DNA fragments will be produced every time a
restriction nuclease digests a known piece of DNA.
(b)
Restriction nucleases recognize specific sequences on single-stranded
DNA.
(c)
Some bacteria use restriction nucleases as protection from foreign DNA.
(d)
Some restriction nucleases cut in a staggered fashion, leaving short singlestranded regions of DNA at the ends of the cut molecule.
10-3
You have purified DNA from your recently deceased goldfish. Which of the
following restriction nucleases would you use if you wanted to end up with DNA
fragments with an average size of 70 kilobase pairs (kb) after complete digestion
of the DNA? The recognition sequence for each enzyme is indicated in the righthand column.
(a)
Sau3AI GATC
(b)
BamHI
GGATCC
(c)
NotI
GCGGCCGC
(d)
XzaI
GAAGGATCCTTC
10-4
You have a piece of circular DNA that can be cut by the restriction nucleases
XhoI and SmaI, as indicated in Figure Q10-4.
Figure Q10-4
If you were to cut this circular piece of DNA with both XhoI and SmaI, how
many fragments of DNA would you end up with?
(a)
1
(b)
2
(c)
3
(d)
4
10-5
You have a piece of circular DNA that can be cut by the restriction nucleases
EcoRI, HindIII, and NotI, as indicated in Figure Q10-5.
Figure Q10-5
Which of the following statements is false?
(a)
One piece of DNA will be obtained when this DNA is cut by NotI.
(b)
A piece of DNA that cannot be cut by EcoRI will be obtained by cutting
this DNA with both NotI and HindIII.
(c)
Two DNA fragments that cannot be cut by HindIII will be obtained when
this DNA is cut by EcoRI and NotI.
(d)
Two DNA fragments of unequal size will be created when this DNA is cut
by both HindIII and EcoRI.
10-6
You have accidentally torn the labels off two tubes, each containing a different
plasmid, and now do not know which plasmid is in which tube. Fortunately, you
have restriction maps for both plasmids, shown in Figure Q10-6. You have the
opportunity to test just one sample from one of your tubes. You have equipment
for agarose-gel electrophoresis, a standard set of DNA size markers, and the
necessary restriction enzymes.
Figure Q10-6
A.
B.
10-7
Outline briefly the experiment you would do to determine which plasmid
is in which tube.
Which restriction enzyme or combination of restriction enzymes would
you use in this experiment?
Assume that defects in a hypothetical gene X have been linked to antisocial
behavior. Two copies of a defective gene X predispose a child to bad behavior
from childhood, whereas a single copy of the gene seems to produce no symptoms
until adulthood. Because early treatment can counteract the effects of the gene, a
program of voluntary genetic testing is being performed with delinquent
prospective parents. Charles S. and Caril Ann F. have been arrested on charges of
robbery and assault, and Caril Ann is pregnant with Charles’s child. You obtain
DNA samples from Charles, Caril Ann, and the fetus. You digest these samples
with NotI and use these samples to perform two Southern blots, which you probe
with two different oligonucleotide probes, A and B, that hybridize to different
parts of the normal gene X, as shown in Figure Q10-7A. Your results are shown
in Figure 10-7B.
Figure Q10-7
A.
B.
C.
10-8
Which of the three individuals have defects in gene X?
Which individuals have a single defective gene and which have two
defective copies of the gene?
Indicate the nature (single-base-pair mutation or deletion) and location of
each individual’s defects on gene X.
Figure Q10-8 shows a restriction map of a piece of DNA containing your favorite
gene. The arrow indicates the position and orientation of the gene in the DNA. In
part (B) of the figure are enlargements showing the portions of the DNA whose
sequences have been used to make oligonucleotide probes A, B, C, and D. Which
of the oligonucleotides can be used to detect the gene in each of the following?
Figure 10-8
A.
B.
10-9
A Southern blot of genomic DNA cut with HindIII.
A Northern blot.
During gel electrophoresis, DNA fragments _______________________.
(a)
travel through a matrix containing a microscopic network of pores
(b)
migrate toward a negatively charged electrode
(c)
can be visualized without stains or labels
(d)
are separated on the basis of their sequence
10-10 A double-stranded DNA molecule can be separated into single strands by heating
it to 90°C because _______________________.
(a)
heat disrupts the hydrogen bonds holding the sugar-phosphate backbone
together
(b)
DNA is negatively charged
(c)
heat disrupts hydrogen bonding between complementary nucleotides
(d)
DNA is positively charged
10-11 You are interested in a single-stranded DNA molecule that contains the following
sequence:
5′- ..... GATTGCAT .... -3′
Which molecule can be used as a probe that will hybridize to your sequence of
interest?
(a)
5′-GATTGCAT-3′
(b)
5′-TACGTTAG-3′
(c)
5′-CTAACGTA-3′
(d)
5′-ATGCAATC-3′
DNA Cloning
10-12 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.
A nuclease hydrolyzes the __________________ bonds in a
nucleic acid. Nucleases that cut DNA only at specific short
sequences are known as __________________. DNA composed of
sequences from different sources is known as
__________________. __________________ can be used to
separate DNA fragments of different sizes. Millions of copies of a
DNA sequence can be made entirely in vitro by the
__________________ technique.
DNA sequencing
endonucleases
exonucleases
gel electrophoresis
hydrogen
nucleic acid hybridization
phosphodiester
polymerase chain reaction
recombinant DNA
restriction nucleases
ribonucleases
10-13 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.
Two fragments of DNA can be joined together by
__________________. Restriction enzymes that cut DNA straight
across the double helix produce fragments of DNA with
__________________. A fragment of DNA is inserted into a
__________________ in order to be cloned in bacteria. A
__________________ library contains a collection of DNA clones
derived from mRNAs. A __________________ library contains a
collection of DNA clones derived from chromosomal DNA.
blunt ends
cDNA
DNA ligase
DNA polymerase
genomic
probe
RNA
staggered ends
vector
10-14 Name three features that a cloning vector for use in bacteria must contain. Explain
your answers.
10-15 Figure Q10-15 shows the cleavage site of several restriction nucleases.
Figure Q10-15
You cut a vector using the PclI restriction nuclease. Which of the following
restriction nucleases will generate a fragment that can be ligated into this cut
vector with the addition of only ligase and ATP?
(a)
HindIII
(b)
NcoI
(c)
MmeI
(d)
NspV
10-16 Figure Q10-16 depicts a strategy by which a DNA fragment produced by cutting
with the EcoRI restriction nuclease can be joined to a DNA fragment produced by
cutting DNA with the HaeIII restriction nuclease.
Figure Q10-16
Note that cutting DNA with EcoRI produces a staggered end, whereas cutting
DNA with HaeIII produces a blunt end. Why must polymerase be added in this
reaction?
(a)
Polymerase will fill in the staggered end to create a blunt end.
(b)
Polymerase is needed to seal nicks in the DNA backbone.
(c)
Polymerase will add nucleotides to the end produced by the HaeIII
restriction nuclease.
(d)
Without polymerase, there will not be enough energy for the reaction to
proceed.
10-17 DNA can be introduced into bacteria by a mechanism called ____________.
(a)
transcription
(b)
ligation
(c)
replication
(d)
transformation
10-18 Which of the following statements about gel-transfer hybridization (or Southern
blotting) is false?
(a)
This technique involves the transfer of DNA molecules from gel onto
nitrocellulose paper or nylon paper.
(b)
In this technique, single-stranded DNA is separated by electrophoresis.
(c)
A labeled DNA probe binds to the DNA by hybridization.
(d)
The DNA that is separated on a gel is not labeled.
10-19 Figure Q10-19 shows the recognition sequences and sites of cleavage for the
restriction enzymes SalI, XhoI, PstI, and SmaI, and also a plasmid with the sites
of cleavage for these enzymes marked.
Figure Q10-19
A.
After which of the five treatments listed below can the plasmid shown in
Figure Q10-19 re-form into a circle simply by treating it with DNA ligase?
Assume that after treatment any small pieces of DNA are removed, and it
is the larger portion of plasmid that will reassemble into a circle.
After digestion with __________.
1.
SalI alone
2.
SalI and XhoI
3.
SalI and PstI
4.
SalI and SmaI
5.
SmaI and PstI
B.
In which of the treatments can the plasmid re-form into a circle by the
addition of DNA ligase after treating the cut DNA with DNA polymerase
in a mixture containing the four deoxyribonucleotides? Again assume that
you are trying to get the larger portion of plasmid to reassemble into a
circle.
10-20 Which of the following statements about genomic DNA libraries is false?
(a)
The larger the size of the fragments used to make the library, the fewer
colonies you will have to examine to find a clone that hybridizes to your
probe.
(b)
The larger the size of the fragments used to make the library, the more
difficult it will be to find your gene of interest once you have identified a
clone that hybridizes to your probe.
(c)
The larger the genome of the organism from which a library is derived, the
larger the fragments inserted into the vector will tend to be.
(d)
The smaller the gene you are seeking, the more likely it is that the gene
will be found on a single clone.
10-21 A DNA library has been constructed by purifying chromosomal DNA from mice,
cutting the DNA with the restriction enzyme NotI, and inserting the fragments
into the NotI site of a plasmid vector. What information cannot be retrieved from
this library?
(a)
gene regulatory sequences
(b)
intron sequences
(c)
sequences of the telomeres (the ends of the chromosomes)
(d)
amino acid sequences of proteins
10-22 You want to design a DNA probe used for hybridization to isolate a clone from a
cDNA library. Which of the following statements about DNA probes is true?
(a)
The shorter the DNA probe used to probe the library, the greater the
number of colonies to which the probe will hybridize.
(b)
A DNA probe that contains sequences that span two exons is better suited
to the purpose than a DNA probe that only contains sequences from one
exon.
(c)
A DNA probe that contains sequences immediately upstream of the DNA
that codes for the first methionine in the open reading frame will usually
not hybridize to clones in a cDNA library.
(d)
Hybridization of a DNA probe to the plasmid of interest will permit the
detection of the clone of interest; labeling of the DNA probe is not
necessary.
10-23 You have the amino acid sequence of a protein and wish to search for the gene
encoding this protein in a DNA library. Using this protein sequence, you deduce a
particular DNA sequence that can encode this protein. Why is it unwise to use
only this DNA sequence you have deduced as the probe for isolating the gene
encoding your protein of interest from the DNA library?
10-24 What is the main reason for using a cDNA library rather than a genomic library to
isolate a human gene from which you wish to make large quantities of the human
protein in bacteria?
10-25 Some clones from cDNA libraries can have defects because of the way in which a
cDNA library is constructed. For each dilemma (A to D) listed below, indicate which of
the outcomes (1 to 4) you might encounter, and explain why. Outcomes may be used
more than once.
10-26 You have an oligonucleotide probe that hybridizes to part of gene A from a
eucaryotic cell. Indicate whether a cDNA library or a genomic DNA library will
be more appropriate for use in the following applications.
A.
You want to study the promoter of a gene A.
B.
Gene A encodes a tRNA and you wish to isolate a piece of DNA
containing the full-length sequence of the tRNA.
C.
You discover that gene A is alternatively spliced and you want to see
which predicted alternative splice products the cell actually produces.
D.
You want to find both gene A and the genes located near gene A on the
chromosome.
E.
You want to express gene A in bacteria to produce lots of protein A.
Note: The following codon table is to be used for Problems Q10-27, Q10-28, Q10-40,
Q10-43, Q10-44, and Q10-46.
10-27 Which of the restriction nucleases listed below can potentially cleave a segment
of cDNA that encodes the peptide KIGDACF?
10-28 Your biochemist friend has isolated a protein he thinks is responsible for making
you feel sleepy. Since he knows you’re taking Cell Biology, he wants you to help
him isolate the gene encoding this protein. Unfortunately, because your friend
could only isolate small amounts of protein, he was only able to obtain three short
stretches of amino acid sequence from the protein:
(a)
(b)
(c)
H-C-W-K-M
R-S-L-L-S
D-A-Q-W-Y
For each of the three peptides above, you design a set of DNA oligonucleotide
probes that can be used to detect the gene in a library. Which of the three sets of
oligonucleotide probes would be preferable for screening a library? Explain.
(Refer to the codon table above Q10-27.)
10-29 Your friend has isolated a protein present in the cheek cells of all straight-A
seniors at your school. She says that this protein helps you remember everything
you read and therefore will help cut down on the number of hours needed to study
for exams. She sequences the protein, which she calls “geniuszyme”, and designs
a probe to isolate the gene that encodes it. To make sure she designed the probe
correctly, she consults with the company that cloned Factor VIII. They have
100% confidence that her probe will work. She also obtains a high-quality liver
cDNA library from the company and uses her probe to try to isolate the gene for
geniuszyme. Unfortunately, she is unable to isolate any clones.
A.
What is the likely explanation for her failure?
B.
Not to be discouraged, your friend has obtained some genomic DNA
isolated from the nuclei of liver cells and has made a genomic library from
that DNA. Do you expect she will succeed in isolating the geniuszyme
gene from this library? Why or why not?
10-30 Insulin is a small protein that regulates blood sugar level, and it is given by
injection to people who suffer from the disease diabetes. Diabetics once used
insulin purified from pig pancreas to control their diabetes. Give two reasons why
the drug companies that produce insulin wanted to clone the human insulin gene
to provide an alternative source of the hormone.
10-31 Which of the following statements about PCR is false?
(a)
PCR uses a DNA polymerase from a thermophilic bacterium.
(b)
PCR is particularly powerful because after each cycle of replication, there
is a linear increase in the amount of DNA available.
(c)
For PCR, every round of replication is preceded by the denaturation of the
doubled-stranded DNA molecules.
(d)
The PCR reaction will generate a pool of double-stranded DNA
molecules, most of which will have DNA from primers at the 5′ ends.
10-32 Why is a heat-stable DNA polymerase from a thermophilic bacterium (the Taq
polymerase) used in the polymerase chain reaction rather than a DNA polymerase
from E. coli or humans?
10-33 Which of the following limits the use of PCR to detect and isolate genes?
(a)
The sequence at the beginning and end of the DNA to be amplified must
be known.
(b)
It also produces large numbers of copies of sequences beyond the 5′ or 3′
end of the desired sequence.
(c)
It cannot be used to amplify cDNAs or mRNAs.
(d)
It will amplify only sequences present in multiple copies in the DNA
sample.
10-34 You want to amplify the DNA between the two stretches of sequence shown in
Figure Q10-34. Of the listed primers, choose the pair that will allow you to
amplify the DNA by PCR.
Figure Q10-34
10-35 Your friend works at the Centers for Disease Control and has discovered a brandnew virus that has recently been introduced into the human population. She has
just developed a new assay that allows her to detect the virus by using PCR
products made from the blood of infected patients. The assay uses primers in the
PCR reaction that hybridize to sequences in the viral genome.
Your friend is distraught because of the result she obtained (see Figure Q10-35)
when she looked at PCR products made using the blood of three patients suffering
from the viral disease, using her own blood, and using a leaf from her petunia
plant.
You advise your friend not to panic, as you believe she is missing an important
control. Which one of the choices listed below is the best control for clarifying the
results of her assay? Explain your answer.
Figure Q10-35
(a)
(b)
a PCR reaction using blood from a patient who is newly infected but does
not yet show symptoms
a PCR reaction using blood from a dog
(c)
(d)
a PCR reaction using blood from an uninfected person
repeating the experiments she has already done with a new tube of
polymerase
Deciphering and Exploiting Genetic Information
10-36 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.
The technique of __________________ hybridization can be used
to detect a specific RNA expression in a particular region of the
brain. Northern blotting detects a specific sequence in
__________________. Southern blotting detects a specific
sequence in __________________. A short, single-stranded DNA
is a(n) __________________. A piece of DNA used to detect a
specific sequence in a nucleic acid by hybridization is known as
a(n) __________________.
DNA
in situ
in vitro
oligonucleotide
polymerase chain reaction
probe
RNA
vector
10-37 In situ hybridization can be used to determine the _________________.
(a)
sequence of a cloned gene
(b)
distribution of proteins in tissues
(c)
size of a gene
(d)
distribution of a given type of mRNA in different tissues
10-38 Why are dideoxyribonucleoside triphosphates used during DNA sequencing?
(a)
They cannot be incorporated into DNA by DNA polymerase.
(b)
They are incorporated into DNA particularly well by DNA polymerases
from thermophilic bacteria.
(c)
Incorporation of a didoxyribonucleoside triphosphate leads to the
termination of replication for that strand.
(d)
Dideoxyribonucleotide triphosphates are more stable than
deoxyribonucleoside triphosphates.
10-39 Which of the following describes a feature found in bacterial expression vectors
but not in cloning vectors?
(a)
origin of replication
(b)
cleavage sites for restriction nucleases
(c)
promoter DNA sequences
(d)
a polyadenylation signal
10-40 You have sequenced a short piece of DNA and produced the gel shown in Figure
Q10-40.
Figure Q10-40
A.
B.
What is the sequence of the DNA, starting from the 5′ end?
If you knew that this sequence is from the middle of a protein-coding
cDNA clone, what amino acid sequence can be deduced from this
sequence? (Refer to the codon table above Q10-27.)
10-41 You have sequenced a fragment of DNA and produced the gel shown in Figure
Q10-41. Near the top of the gel, there is a section where there are bands in all four
lanes (indicated by the arrow). Which of the following mishaps would account for
this phenomenon? Explain your answer.
Figure Q10-41
(a)
(b)
(c)
(d)
You mistakenly added all four dideoxynucleotides to one of the reactions.
You forgot to add deoxynucleotides to the reactions.
Your primer hybridizes to more than one area of the fragment of DNA you
are sequencing.
A restriction nuclease cut a fraction of the DNA you are sequencing.
10-42 You are interested in understanding the gene regulation of a protein called LKP1,
which is normally produced in liver and kidney cells in mice. Interestingly, you
find that LKP1 is not expressed in heart cells. You replace the coding sequence
for LKP1 with the DNA encoding green fluorescent protein (GFP) and examine
the expression of GFP in mice. (GFP is your reporter gene.) You find expression
of GFP in liver and kidney cells but not heart cells; this expression pattern is
similar to how LKP1 is expressed normally. Further experiments demonstrate that
there are three regulatory sequences in the promoter, labeled A, B, and C in
Figure Q10-42, that are important for this expression pattern. You want to
determine the significance of each regulatory sequence, so you create situations
where only a subset of regulatory regions are present upstream of the reporter
gene, as diagrammed in Figure Q10-42.
Figure Q10-42
Given the data, which of the statements below is false?
(a)
Regulatory sequence A switches on LKP1 in the kidney.
(b)
Regulatory sequence B switches on LKP1 in the liver.
(c)
Neither regulatory sequence A nor regulatory sequence B is required for
LKP1 expression in the heart.
(d)
Regulatory sequence C is not necessary for proper expression.
10-43 You are studying a protein, and a small fragment of its sequence is shown below.
You have decided that the glutamine in the protein segment has an important role
in its function. You decide to change this glutamine to a lysine using DNA
technology with the use of site-directed mutagenesis. You have a plasmid that
contains the full-length version of the gene that encodes this protein and wish to
create a new DNA molecule that has a change in only one base and that
substitutes a lysine for a glutamine. Given the partial mRNA sequence that codes
for this stretch of protein below, devise a 21-nucleotide DNA oligonucleotide that
can be used to make this mutation. Be sure to label the 5′ and 3′ ends. (Refer to
the codon table above Q10-27.)
F D P Q G S H
5′-uucgacccgcagggcagccac–3′
10-44 You are studying a protein that contains the peptide sequence RDWKLVI. The
part of the DNA encoding this peptide is included in the sequence shown below.
5′-GGCGTGACTGGAAGCTAGTCATC-3′
3′-CCGCACTGACCTTCGATCAGTAG-5′
This sequence does not contain any HindIII restriction enzyme sites; the target
sequence for the HindIII restriction nuclease is shown in Figure Q10-44.
Figure Q10-44
Your goal is to create a HindIII site on this plasmid without changing the coding
sequence of the protein. Explain how you would do this. (Refer to the codon
table above Q10-27.)
10-45 You are interested in understanding how the brain works, and are using the fruit
fly Drosophila as a model system to study brain development. You perform a
microarray analysis to try to determine genes expressed in the fly brain. For your
microarray experiment, you first prepare cDNA from fly brains and label it with a
red fluorochrome. Then you isolate cDNA from whole flies and label it with a
green fluorochrome. Next you hybridize these cDNA populations to a microarray
containing the Drosophila genes. From this you obtain a list of genes that are
specifically enriched in the brain (those that show up as a red spot on the
microarray).
You are disappointed because your favorite fly gene, tubby, does not appear on
this list, even though you have repeated the microarray experiment 10 times and
did not encounter any technical difficulties. The reason you thought tubby would
appear on this list is that you believe tubby is important for brain development,
because flies mutant in tubby have no brains. Not to be discouraged, you perform
in situ analysis using the tubby DNA as a probe, and see that it is expressed at
high levels in the fly brain of normal flies but not expressed in animals lacking the
tubby gene.
Why do you think tubby did not show up as a gene specifically enriched in the
brain in your microarray experiment?
10-46 You have created a piece of recombinant DNA by placing a cDNA from a gene
you believe is important for the differentiation of liver cells (called LC1) onto an
expression plasmid that contains all the sequences necessary for propagation of
this DNA in bacteria and for the production of the LC1 protein in bacteria. A
picture of this plasmid is shown in Figure Q10-46A, with the segment of the DNA
containing the PK1 gene depicted as a grey rectangle; the promoter sequence is
depicted as a white rectangle. The LC1 protein is phosphorylated on serine 54; the
nucleotide sequence of the portion of the DNA that encodes this region is shown
below. All HindIII and SalI restriction sites have also been mapped on the
plasmid; the recognition sequences for these restriction nucleases are shown in
Figure Q10-46B.
Figure Q10-46
A.
B.
Given the information above, write out the amino acids 52 to 57, encoded
by the nucleotide sequence shown above. Be sure to number the amino
acids appropriately. (Hint: remember, serine is amino acid number 54.)
(Refer to the codon table above Q10-27.)
You want to create a mutant version of the PK1 gene that replaces serine
54 found on this peptide with a glycine. You want to do this by changing
only one nucleotide, and you also want to destroy the HindIII recognition
sequence with this change. Write out a 21-nucleotide DNA primer that can
be used for site directed mutagenesis to accomplish this task. Be sure to (i)
write out the DNA and label the 5′ and 3′ ends, (ii) underline the mutated
HindIII recognition site, and (iii) circle any change made to the original
sequence.
10-47 Which of the following statements about RNA interference (or RNAi) is false?
(a)
RNAi is a natural mechanism used to regulate genes.
(b)
(c)
(d)
During the process of RNAi, hybridization of a small RNA molecule with
the mRNA degrades the mRNA.
Because RNAi depends on the introduction of a double-stranded RNA into
a cell or an organism, it is not a process that can cause heritable changes in
gene expression.
In C. elegans, RNAi can be introduced into the animals by feeding them
with bacteria that produce the inhibitory RNA molecules.
10-48 You have been hired to create a cat that will not cause allergic reactions in catlovers. Your co-workers have cloned the gene encoding a protein found in cat
saliva, expressed the protein in bacteria, and shown that it causes violent allergic
reactions in people. But you soon realize that even if you succeed in making a
knockout cat lacking this gene, anyone who buys one will easily be able to make
more hypoallergenic cats just by breeding them. Which of the following will
ensure that people will always have to buy their hypoallergenic cats from you?
(a)
Inject the modified ES cells into embryos that have a genetic defect to
prevent the mature adult from reproducing.
(b)
Implant the injected embryos into a female cat that is sterile as a result of a
genetic defect.
(c)
Sell only the offspring from the first litter of the female cat implanted with
the injected embryos.
(d)
Surgically remove the sexual organs of all the knockouts before you sell
them.
How We Know: Sequencing the Human Genome
10-49 You have been asked to consult for a biotech company that is seeking to
understand why some fungi can live in very extreme environments, such as the
high temperatures inside naturally occurring hot springs. The company has
isolated two different fungal species, F. cattoriae and W. gravinius, both of which
can grow at temperatures exceeding 95°C. The company has determined the
following things about these fungal species:
By sequencing and examining their genomes, the biotech company hopes to
understand why these species can live in extreme environments. However, the
company only has the resources to sequence one genome, and would like your
input as to which species should be sequenced and whether you believe a shotgun
strategy will work in this case. (Be sure to explain your answer.)
10-50 Figure Q10-50A depicts the restriction map of one segment of the human genome
for four restriction nucleases W, X, Y, and Z. Figure Q10-50B depicts the
restriction maps of four individual BAC clones that contain segments of human
DNA from the region depicted in Figure Q10-50A.
Figure Q10-50
From this information, how would you order these BAC clones, from left to right?
(a)
1, 2, 3, 4
(b)
2, 1, 4, 3
(c)
3, 4, 2, 1
(d)
4, 1, 3, 2
CHAPTER 11
MEMBRANE STRUCTURE
 2009 Garland Science Publishing
The Lipid Bilayer
11-1
Indicate whether the following statements are true or false. If a statement is false,
explain why it is false.
A.
Although cholesterol is a hydrophobic molecule, it has a hydrophilic head
group like all other membrane lipids.
B.
Phosphatidylserine is the most abundant type of phospholipid found in cell
membranes.
C.
Glycolipids lack the glycerol component found in phospholipids.
D.
The highly ordered structure of the lipid bilayer makes its generation and
maintenance energetically unfavorable.
11-2
Which of the following membrane lipids does not contain a fatty acid tail?
(a)
Phosphatidylcholine
(b)
A glycolipid
(c)
Phosphatidylserine
(d)
Cholesterol
11-3
Formation of a lipid bilayer might seem to be energetically unfavorable. However, this
arrangement is actually favored because it allows a higher level of entropy than any other
alternative. What makes bilayer formation energetically favorable?
(a)
Polar head groups form a hydrogen bonding network at the interface with water.
(b)
Water molecules form cage-like structures around hydrophobic molecules.
(c)
Hydrogen bonds form between neighboring polar head groups in the bilayer.
(d)
Fatty acid tails are highly saturated and flexible.
11-4
Which of the following statements is true?
(a)
Phospholipids will spontaneously form liposomes in nonpolar solvents.
(b)
In eucaryotes, all membrane-enclosed organelles are surrounded by one lipid
bilayer.
(c)
Membrane lipids diffuse within the plane of the membrane.
(d)
Membrane lipids frequently flip-flop between one monolayer and the other.
11-5
A bacterium is suddenly expelled from a warm human intestine into the cold world
outside. Which of the following adjustments might the bacterium make to maintain the
same level of membrane fluidity?
(a)
Produce lipids with hydrocarbon tails that are longer and have fewer double
bonds.
(b)
(c)
(d)
11-6
Produce lipids with hydrocarbon tails that are shorter and have more double
bonds.
Decrease the amount of cholesterol in the membrane.
Decrease the amount of glycolipids in the membrane.
Three different membrane components are shown in Figure Q11-6. Using the list below,
identify the three components, and label the chemical groups indicated.
A.
glycerol
B.
sugar
C.
phospholipid
D.
glycolipid
E.
sterol
F.
unsaturated hydrocarbon
G.
saturated hydrocarbon
H.
sterol polar head group
Figure Q11-6
11-7
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.
The specialized functions of different membranes are largely determined
by the __________________ they contain. Membrane lipids are
__________________ molecules, composed of a hydrophilic portion and
a hydrophobic portion. All cell membranes have the same
__________________ structure, with the __________________ of the
phospholipids facing into the interior of the membrane and the
__________________ on the outside. The most common lipids in most
cell membranes are the __________________. The head group of a
glycolipid is composed of __________________.
amphipathic
cholesterol
fatty acid tails
glycolipids
hydrophilic head groups
11-8
hydrophobic
lipid bilayer
lipid monolayer
lipids
phosphatidylcholine
phosphatidylserine
phospholipids
proteins
sterols
sugars
Three phospholipids X, Y, and Z are distributed in the plasma membrane as indicated in
Figure Q11-8. For which of these phospholipids does a flippase probably exist?
Figure Q11-8
(a)
(b)
(c)
(d)
11-9
X only
Z only
X and Y
Y and Z
Where does most new membrane synthesis take place in a eucaryotic cell?
(a)
in the Golgi apparatus
(b)
in the endoplasmic reticulum
(c)
in the plasma membrane
(d)
in the mitochondria
(e)
on ribosomes
11-10 Water molecules readily form hydrogen bonds with other polar molecules, and when they
encounter nonpolar molecules they must form hydrogen-bonding networks with
neighboring water molecules. Which of the following molecules will cause a “cage” of
water to form?
(a)
2-methylpropane
(b)
acetone
(c)
(d)
methanol
urea
11-11 Membranes undergo spontaneous rearrangement if torn. Which of the following would
happen if a cell membrane had a large tear?
11-12 Membrane lipids are capable of many different types of movement. Which of these does
not occur spontaneously in biological membranes?
(a)
switching between lipid layers
(b)
lateral movement
(c)
rotation
(d)
flexing of hydrocarbon chains
11-13 There are two properties of phospholipids that affect how tightly they pack together: the
length of the hydrocarbon chain and the number of double bonds. The degree of packing,
in turn, influences the relative mobility of these molecules in the membrane. Which of the
following would yield the most highly mobile phospholipid (listed as number of carbons
and number of double bonds, respectively)?
(a)
24 carbons with 1 double bond
(b)
15 carbons with 2 double bonds
(c)
20 carbons with 2 double bonds
(d)
16 carbons with no double bonds
11-14 Cholesterol serves several essential functions in mammalian cells. Which of the
following is not influenced by cholesterol?
(a)
membrane permeability
(b)
membrane fluidity
(c)
membrane rigidity
(d)
membrane thickness
11-15 New membrane phospholipids are synthesized by enzymes bound to the _____________
side of the _________________ membrane.
(a)
cytosolic, mitochondrial
(b)
luminal, Golgi
(c)
cytosolic, endoplasmic reticulum
(d)
extracellular, plasma
11-16 Membrane synthesis in the cell requires the regulation of growth for both halves
of the bilayer and the selective retention of certain types of lipids on one side or
the other. Which group of enzymes accomplishes both of these tasks?
(a)
flippases
(b)
phospholipases
(c)
convertases
(d)
glycosylases
11-17 Glycolipids are found on the surface of healthy cells, and contribute to the cell’s defense
against chemical damage and infectious agents.
A.
In which organelle are sugar groups added to membrane lipids?
B.
By what mechanism are glycolipids transported to the plasma membrane and
presented to the extracellular environment?
Draw a diagram to support your answer to part B.
Membrane Proteins
11-18 A group of membrane proteins can be extracted from membranes only by using
detergents. All the proteins in this group have a similar amino acid sequence at their Cterminus: -KKKKKXXC (where K stands for lysine, X stands for any amino acid, and C
stands for cysteine). This sequence is essential for their attachment to the membrane.
What is the most likely way in which the C-terminal sequence attaches these proteins to
the membrane?
(a)
The cysteine residue is covalently attached to a membrane lipid.
(b)
The peptide spans the membrane as an α helix.
(c)
The peptide spans the membrane as part of a β sheet.
(d)
The positively charged lysine residues interact with an acidic integral membrane
protein.
11-19 Although membrane proteins contribute roughly 50% of the total mass of the membrane,
there are about 50 times more lipid molecules than there are protein molecules in cellular
membranes. Explain this apparent discrepancy.
11-20 Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A.
Lipid-linked proteins are classified as peripheral membrane proteins because the
polypeptide chain does not pass through the bilayer.
B.
A protein can be embedded on the cytosolic side of the membrane bilayer by
employing a hydrophobic α helix.
C.
D.
A protein that relies on protein–protein interactions to stabilize its membrane
association is classified as a peripheral membrane protein because it can be
dissociated without the use of detergents.
Membrane proteins that pump ions in and out of the cell are classified as
enzymes.
11-21 A small membrane vesicle containing a transmembrane protein is shown in Figure Q1121. Assume that this membrane vesicle is in the cytoplasm of a cell.
Figure Q11-21
A.
B.
C.
Label the cytosolic and non-cytosolic faces of the membrane vesicle. This
membrane vesicle will undergo fusion with the plasma membrane.
Sketch the plasma membrane after vesicle fusion, indicating the new location of
the vesicle membrane and the transmembrane protein carried by the membrane
vesicle.
On your drawing for B, label the original cytosolic and noncytosolic faces of the
vesicle membrane as it resides in the plasma membrane. Also label the
extracellular space and the cytosol. Indicate the N- and C-terminus of the inserted
transmembrane protein.
11-22 Porin proteins form large, barrel-like channels in the membrane. Which of the following
is not true about these channels?
(a)
They are made primarily of α helices.
(b)
They are made primarily of β sheets.
(c)
They cannot form narrow channels.
(d)
They have alternating hydrophobic and hydrophilic amino acids.
11-23 Unlike soluble, cytosolic proteins, membrane proteins are more difficult to purify. Which
of the following substances is most commonly used to help purify a membrane protein?
(a)
high salt solution
(b)
sucrose
(c)
detergent
(d)
ethanol
11-24 Sodium dodecyl sulfate (SDS) and Triton X-100 are both detergents that can be used to
lyse cells.
A.
B.
If the the goal is to study the activity of membrane proteins after cell lysis, explain
why SDS would not be a good choice.
How does Triton X-100 work in cell lysis, and why is it a better choice of
detergent to help you extract proteins?
11-25 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.
There are several ways that membrane proteins can associate with the cell
membrane. Membrane proteins that extend through the lipid bilayer are
called __________________ proteins and have __________________
regions that are exposed to the interior of the bilayer. On the other hand,
membrane-associated proteins do not span the bilayer and instead
associate with the membrane through an α helix that is
__________________. Other proteins are __________________ attached
to lipid molecules that are inserted in the membrane.
__________________ membrane proteins are linked to the membrane
through noncovalent interactions with other membrane-bound proteins.
amphipathic
cortical
covalently
detergent
hydrophilic
hydrophobic
integral
micelle
noncovalently
peripheral
transmembrane
unfolded
11-26 We know the detailed molecular structure and mechanism of action of the transmembrane
protein bacteriorhodopsin. This protein uses sunlight as the source of energy to pump
______ out of the cell.
(a)
4 ATP
(b)
7 H+
(c)
7 K+
(d)
4 Na+
11-27 Plasma membranes are extremely thin and fragile, requiring an extensive support network
of fibrous proteins. This network is called the ____________.
(a)
cortex
(b)
attachment complex
(c)
cytoskeleton
(d)
spectrin
11-28 Red blood cells have been very useful in the study of membranes and the protein
components that provide structural support. Which of the following proteins is the
principal fibrous protein in the cortex of the red blood cell?
(a)
tubulin
(b)
attachment proteins
(c)
actin
(d)
spectrin
11-29 Anemia, a condition that results in individuals with a low red blood cell count, can be
caused by a number of factors. Why do individuals with defects in the spectrin protein
often have this condition?
11-30 Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A.
When a mouse cell is fused with a human cell, the movement of the respective
membrane proteins is restricted to their original locations at the time of fusion.
B.
Epithelial cell membranes are asymmetric, and proteins from the apical side of the
cell membrane cannot diffuse into the basal side of the membrane.
C.
The longest carbohydrates found on the surfaces of cells are linked to lipid
molecules.
D.
The only role of the carbohydrate layer on the cell surface is to absorb water,
which creates a slimy surface and prevents cells from sticking to each other.
11-31 Consider the apical location of a particular protein expressed in epithelial cells, illustrated
in Figure Q11-31A. Which type of defect described below is the most likely to cause the
redistribution of that protein around the entire cell, shown in Figure Q11-31B?
Figure Q11-31
(a)
(b)
(c)
(d)
a nonfunctional protein glycosylase
the deletion of a junctional protein
the truncation of a protein found in the extracellular matrix
a nonfunctional flippase
11-32 Diversity among the oligosaccharide chains found in the carbohydrate coating of the cell
surface can be achieved in which of the following ways?
(a)
varying the types of sugar monomers used
(b)
varying the types of linkages between sugars
(c)
varying the number of branches in the chain
(d)
all of the above
11-33 Which of the following statements about the carbohydrate coating of the cell surface is
false?
(a)
It is not usually found on the cytosolic side of the membrane.
(b)
It can play a role in cell–cell adhesion.
(c)
The arrangement of the oligosaccharide side chains is highly ordered, much like
the peptide bonds of a polypeptide chain.
(d)
Specific oligosaccharides can be involved in cell–cell recognition.
11-34 Cell membranes are fluid, and thus proteins can diffuse laterally within the lipid bilayer.
However, sometimes the cell needs to localize proteins to a particular membrane domain.
Name three mechanisms that a cell can use to restrict a protein to a particular place in the
cell membrane.
11-35 Both glycoproteins and proteoglycans contribute to the carbohydrate layer on the surface
of the cell. Which of the following is not true of glycoproteins?
(a)
They can be secreted into the extracellular environment.
(b)
They have only one transmembrane domain.
(c)
They have long carbohydrate chains.
(d)
They are recognized by lectins.
11-36 The endothelial cells found closest to the site of an infection express proteins called
lectins. Each lectin binds to a particular ____________ that is presented on the surface of
a target cell.
(a)
oligosaccharide
(b)
aminophospholipid
(c)
polysaccharide
(d)
sphingolipid
11-37 You have isolated two mutants of a normally pear-shaped microorganism that have lost
their distinctive shape and are now round. One of the mutants has a defect in a protein
you call A and the other has a defect in a protein you call B. First, you grind up each type
of mutant cell and normal cells separately and separate the plasma membranes from the
cytoplasm, forming the first cell extract. Then you set aside a portion of each fraction for
later testing. Next, you wash the remaining portion of the membrane fractions with a low
concentration of urea (which will unfold proteins and disrupt their ability to interact with
other proteins) and centrifuge the mixture. The membranes and their constituent proteins
form a pellet, and the proteins liberated from the membranes by the urea wash remain in
the supernatant. When you check each of the fractions for the presence of A or B, you
obtain the results given below.
Which of the following statements are consistent with your results (more than one answer
may apply)?
(a)
Protein A is an integral membrane protein that interacts with B, a peripheral
membrane protein that is part of the cell cortex.
(b)
Protein B is an integral membrane protein that interacts with A, a peripheral
membrane protein that is part of the cell cortex.
(c)
Proteins A and B are both integral membrane proteins.
(d)
The mutation in A affects its ability to interact with B.
How We Know: Measuring Membrane Flow
11-38 We can estimate the relative mobility of a population of molecules along the surface of a
living cell by fluorescently labeling the molecules of interest, bleaching the label in one
small area, and then measuring the speed of signal recovery as molecules migrate back
into the bleached area. What is this method called? What does the abbreviation stand for?
(a)
SDS
(b)
SPT
(c)
GFP
(d)
FRAP
11-39 It is possible to follow the movement of a single molecule or a small group of molecules.
This requires the use of antibodies linked to small particles of gold, which appear as dark
spots when tracked through video microscopy. What is this method called? What does the
abbreviation stand for?
(a)
SDS
(b)
SPT
(c)
GFP
(d)
FRAP
11-40 Data for the mobility of three different proteins (X, Y, and Z) using both fluorescent
recovery after photobleaching (FRAP) are shown in Figure Q11-40A. Separately, singleparticle tracking (SPT) data were collected for these samples, as shown in Figure Q1140B.
Figure Q11-40A
Figure Q11-40B
A.
Assign an SPT profile (A, B, or C) to each of these proteins on the basis of the respective
FRAP profiles.
B.
It is important to remember that in each of these experiments, the results reflect a real,
physical difference in the way in which these proteins are situated in the plasma membrane.
Provide a plausible explanation for the differences observed in proteins X, Y, and Z.
CHAPTER 12
MEMBRANE TRANSPORT
 2009 Garland Science Publishing
Principles of Membrane Transport
12-1
Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A.
CO2 and O2 are water-soluble molecules that diffuse freely across cell
membranes.
B.
The differences in permeability between artificial lipid bilayers and cell
membranes arise from variations in phospholipid content.
C.
Transporters are similar to channels, except that they are larger, allowing folded
proteins as well as smaller organic molecules to pass through them.
D.
Cells expend energy in the form of ATP hydrolysis so as to maintain ion
concentrations that differ from those found outside the cell.
12-2
Although the extracellular environment has a high sodium ion concentration and the
intracellular environment has a high potassium ion concentration, both must be
neutralized by negatively charged molecules. In the extracellular case, what is the
principal anion?
(a)
HCO3–
(b)
Cl–
(c)
PO43–
(d)
OH–
12-3
Circle the molecule in each pair that is more likely to diffuse through the lipid bilayer.
A.
amino acids or
benzene
–
B.
Cl
or
ethanol
C.
glycerol
or
RNA
D.
H2O
or
O2
E.
adenosine
or
ATP
12-4
We can test the relative permeability of a phospholipid bilayer by using a synthetic
membrane that does not contain any protein components. Some uncharged, polar
molecules are found to diffuse freely across these membranes, to varying degrees. Which
of the following has the lowest rate of diffusion across an artificial membrane? Why?
(a)
glucose
(b)
water
(c)
glycerol
(d)
ethanol
12-5
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.
A molecule moves down its concentration gradient by
__________________ transport, but requires __________________
transport to move up its concentration gradient. Transporter proteins and
ion channels function in membrane transport by providing a
__________________ pathway through the membrane for specific polar
solutes or inorganic ions. __________________ are highly selective in the
solutes they transport, binding the solute at a specific site and changing its
conformation so as to transport the solute across the membrane. On the
other hand, __________________ discriminate between solutes mainly on
the basis of size and electrical charge.
active
amino acid
amphipathic
transporter proteins
hydrophilic
hydrophobic
ion channels
noncovalent
passive
Transporters and their Functions
12-6
A hungry yeast cell lands in a vat of grape juice and begins to feast on the sugars there,
producing carbon dioxide and ethanol in the process:
C6H12O6 + 2ADP + 2Pi + H+  2CO2 + 2CH3CH2OH + 2ATP + 2H2O
Unfortunately, the grape juice is contaminated with proteases that attack some of the
transport proteins in the yeast cell membrane, and the yeast cell dies. Which of the
following could account for the yeast cell’s demise?
(a)
toxic buildup of carbon dioxide inside the cell
(b)
toxic buildup of ethanol inside the cell
(c)
diffusion of ATP out of the cell
(d)
inability to import sugar into the cell
12-7
Ion channels are classified as membrane transport proteins. Channels discriminate by size
and charge. In addition to Na+, which one of the following ions would you expect to be
able to freely diffuse through a Na+ channel? Explain your answer.
(a)
Mg2+
(b)
H+
(c)
K+
(d)
Cl–
12-8
Transporters, in contrast to channels, work by ________________.
(a)
specific binding to solutes
(b)
a gating mechanism
(c)
filtering solutes by charge
(d)
12-9
filtering solutes by size
Pumps are transporters that are able to harness energy provided by other components in
the cells to drive the movement of solutes across membranes, against their concentration
gradient. This type of transport is called _____________.
(a)
active transport
(b)
free diffusion
(c)
facilitated diffusion
(d)
passive transport
12-10 Indicate whether the statements below are true or false. If a statement is false, explain
why it is false.
A.
Facilitated diffusion can be described as the favorable movement of one solute
down its concentration gradient being coupled with the unfavorable movement of
a second solute up its concentration gradient.
B.
Transporters undergo transitions between different conformations, depending on
whether the substrate-binding pocket is empty or occupied.
C.
The electrochemical gradient for K+ across the plasma membrane is small.
Therefore, any movement of K+ from the inside to the outside of the cell is driven
solely by its concentration gradient.
D.
The net negative charge on the cytosolic side of the membrane enhances the rate
of glucose import into the cell by a uniporter.
12-11 It is thought that the glucose transporter switches between two conformational states in a
completely random fashion. How is it possible for such a system to move glucose across
the membrane efficiently in a single direction?
12-12 Active transport requires the input of energy into a system so as to move solutes against
their electrochemical and concentration gradients. Which of the following is not one of
the common ways to perform active transport?
(a)
Na+-coupled
(b)
K+-coupled
(c)
ATP-driven
(d)
light-driven
12-13 The Na+-K+ ATPase is also known as the Na+-K+ pump. It is responsible for
maintaining the high extracellular sodium ion concentration and the high
intracellular potassium ion concentration. What happens immediately after the
pump hydrolyzes ATP?
(a)
Na+ is bound.
(b)
ADP is bound.
(c)
The pump is phosphorylated.
(d)
The pump changes conformation.
12-14 If ATP production is blocked in an animal cell, the cell will swell up. Explain this
observation.
12-15 Fill in Table Q12-15. In the “type of transport” column, designate whether the
transporter works by uniport, symport, or antiport mechanisms.
Table Q12-15
12-16 You have prepared lipid vesicles (spherical lipid bilayers) that contain Na+-K+ pumps as
the sole membrane protein. All of the Na+-K+ pumps are oriented in such a way that the
portion of the molecule that normally faces the cytosol is on the inside of the vesicle and
the portion of the molecule that normally faces the extracellular space is on the outside of
the vesicle. Assume that each pump transports one Na+ ion in one direction and one K+
ion in the other direction during each pumping cycle (see Figure Q12-16 for how the
Na+-K+ pump normally functions in the plasma membrane).
Figure 12-16
Predict what would happen in each of the following conditions:
A.
The solutions inside and outside the vesicles contain both Na+ and K+ ions but no
ATP.
B.
The solution outside the vesicles contains both Na+ and K+ ions; the solution
inside contains both Na+ and K+ ions and ATP.
C.
The solution outside contains Na+; the solution inside contains Na+ and ATP.
12-17 The Aeroschmidt weed contains an ATP-driven ion pump in its vacuolar membrane that
pumps potentially toxic heavy metal ions such as Zn2+ and Pb2+ into the vacuole. The
pump protein exists in a phosphorylated and an unphosphorylated form and works in a
similar way to the Na+-K+ pump of animal cells. To study its action, you incorporate the
unphosphorylated form of the protein into phospholipid vesicles containing K+ in their
interiors. (You ensure that all of the protein molecules are in the same orientation in the
lipid bilayer.) When you add Zn2+ and ATP to the solution outside such vesicles, you find
that Zn2+ is pumped into the vesicle lumen. You then expose vesicles containing the
pump protein to the solutes as shown in Table 12-17A.
Table 12-17A
You then determine the amount of phosphorylated and unphosphorylated ATP-driven ion
pump protein in each sample. Your results are summarized in Table 12-17B, where a
minus sign indicates an absence of a type of protein and a plus sign indicates its presence.
Table 12-17B
What would you expect to happen if you treat vesicles as in lane F, but before
determining the phosphorylation state of the protein you wash away the outside buffer
and replace it with a buffer containing only Zn2+?
(a)
Nothing will happen. (No Zn2+ will move into the vesicle; no K+ will move out of
the vesicle; the phosphorylation state of the protein will not change.)
(b)
No Zn2+ will move into the vesicle; no K+ will move out of the vesicle; the protein
will become unphosphorylated.
(c)
A small amount of Zn2+ will move into the vesicle; no K+ will move out of the
vesicle; the phosphorylation state of the protein will not change.
(d)
A small amount of Zn2+ will move into the vesicle; no K+ will move out of the
vesicle; the protein will become unphosphorylated.
12-18 You have generated antibodies that recognize the extracellular domain of the Ca2+ pump.
Adding these antibodies to animal cells blocks the active transport of Ca2+ from the
cytosol into the extracellular environment. What do you expect to observe with respect to
intracellular Ca2+?
(a)
Ca2+ pumps in vesicles membranes keep cystosolic calcium levels low.
(b)
Ca2+ pumps in the ER membrane keep cystosolic calcium levels low.
(c)
Ca2+ pumps in the Golgi apparatus keep cystosolic calcium levels low.
(d)
Ca2+ concentrations in the cytosol increase at a steady rate.
12-19 Cells make use of H+ electrochemical gradients in many ways. Which of the following
proton transporters is used to regulate pH in animal cells?
(a)
light-driven pump
(b)
H+ ATPase
(c)
H+ symporter
(d)
Na+-H+ exchanger
12-20 Which of the following statements is true?
(a)
Amoebae have transporter proteins that actively pump water molecules from the
cytoplasm to the cell exterior.
(b)
Bacteria and animal cells rely on the Na+-K+ pump in the plasma membrane to
prevent lysis resulting from osmotic imbalances.
(c)
The Na+-K+ pump allows animal cells to thrive under conditions of very low ionic
strength.
(d)
The Na+-K+ pump helps to keep both Na+ and Cl– ions out of the cell.
12-21 Ca2+ pumps in the plasma membrane and endoplasmic reticulum are important for
_____________.
(a)
maintaining osmotic balance
(b)
preventing Ca2+ from altering the activity of molecules in the cytosol
(c)
providing enzymes in the endoplasmic reticulum with Ca2+ ions that are necessary
for their catalytic activity
(d)
maintaining a negative membrane potential
12-22 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.
For an uncharged molecule, the direction of passive transport across a
membrane is determined solely by its __________________ gradient. On
the other hand, for a charged molecule, the __________________ must
also be considered. The net driving force for a charged molecule across a
membrane therefore has two components and is referred to as the
__________________ gradient. Active transport allows the movement of
solutes against this gradient. The transporter proteins called
__________________ transporters use the movement of one solute down
its gradient to provide the energy to drive the uphill transport of a second
gradient. When this transporter moves both ions in the same direction
across the membrane, it is considered a(n) __________________; if the
ions move in opposite directions, the transporter is considered a(n)
__________________.
antiport
ATP hydrolysis
concentration
coupled
electrochemical
light-driven
membrane potential
symport
uniport
12-23 The movement of glucose into the cell, against its concentration gradient, can be powered
by the co-transport of Na+ into the cell. Explain this movement with respect to the net
entropy of the system (i.e. thermodynamics).
12-24 You are testing the rate of glucose transport into vesicles using the Na+-glucose pump.
A.
In experiment 1, you employ liposomes that have the pump in the same
orientation as that found in the plasma membrane in epithelial cells. These
liposomes contain glucose but no Na+ ions. You then transfer the liposomes to a
series of tubes with solutions containing the same glucose concentration as that
inside the vesicle and 0, 1, 2, 3, or 10 mM Na+. You measure the initial rates of
glucose transport and plot your results (Figure Q12-24). Why do the initial rates
of glucose transport into the liposome reach a plateau as the concentration of Na+
increases?
B.
In experiment 2, there is one new variable: you have included leaky Na+ channels
in the liposomal membrane. Figure Q12-24 shows your results. Explain the reason
for obtaining such different results in experiment 2 from those in experiment 1.
Figure Q12-24
Ion Channels and the Membrane Potential
12-25 Which of the following best describes the behavior of a gated channel?
(a)
It stays open continuously when stimulated.
(b)
It opens more frequently in response to a given stimulus.
(c)
It opens more widely as the stimulus becomes stronger.
(d)
It remains closed if unstimulated.
12-26 The flow of ions through a gated channel can be studied using a method called “patchclamp recording.”
A.
How is a detached patch-clamp experiment set up and what exactly does it mean
to “clamp” an ion channel?
B.
How is it possible to collect the recordings shown in figures Q12-26A and Q1226B from a single ion channel?
Figure Q12-26
12-27 Indicate whether the statements below are true or false. If a statement is false,
explain why it is false.
A.
Gap junctions are large pores that connect the cytosol to the extracellular space.
B.
Aquaporin channels are found in the plasma membrane, allowing the rapid
passage of water molecules and small ions in and out of cells.
C.
The ion selectivity of a channel completely depends solely on the charge of the
amino acids liningthe pore inside the channel.
D.
Most ion channels are gated, which allow them to open and close in response to a
specific stimulus rather than allowing the constant, unregulated flow of ions.
12-28 The stimulation of auditory nerves depends on the opening and closing of channels in the
auditory hair cells. Which type of gating mechanism do these cells use?
(a)
voltage-gated
(b)
extracellular ligand-gated
(c)
intracellular ligand-gated
(d)
stress-gated
12-29 For each of the following sentences, fill in the blank with the appropriate type of gating
for the ion channel described. You can use the same type of gating mechanism more than
once.
A.
The acetylcholine receptor in skeletal muscle cells is a(n) __________________
ion channel.
B.
__________________ ion channels are found in the hair cells of the mammalian
cochlea.
C.
D.
E.
__________________ ion channels in the mimosa plant propagate the leafclosing response.
__________________ ion channels respond to changes in membrane potential.
Many receptors for neurotransmitters are __________________ ion channels.
12-30 Voltage-gated channels contain charged protein domains, which are sensitive to
changes in membrane potential. By responding to a threshold in the membrane
potential, these voltage sensors trigger the opening of the channels. Which of the
following best describes the behavior of a population of channels exposed to such
a threshold?
(a)
Some channels remain closed and some open completely.
(b)
All channels open completely.
(c)
All channels open partly, to the same degree.
(d)
All channels open partly, each to a different degree.
12-31 K+ leak channels are found in the plasma membrane. These channels open and close in an
unregulated, random fashion. What do they accomplish in a resting cell?
(a)
They set the K+ concentration gradient to zero.
(b)
They set the membrane potential to zero.
(c)
They disrupt the resting membrane potential.
(d)
They keep the electrochemical gradient for K+ at zero.
12-32 The Nernst equation can be used to calculate the membrane potential based on the ratio
of the outer and inner ion concentration. In a resting cell, membrane potential is
calculated taking only K+ ions into account. What is V when Co = 15 mM and Ci =
106 mM?
(a)
438.1 mV
(b)
–52.7 mV
(c)
52.7 mV
(d)
–5.3 mV
12-33 When using the Nernst equation to calculate membrane potential, we are making
several assumptions about conditions in the cell. Which of the following is not a
good assumption?
(a)
The temperature is 37°C.
(b)
The plasma membrane is primarily permeable to Na+.
(c)
At rest, the interior of the cell is more negatively charged than the exterior.
(d)
K+ is the principal positive ion in the cell.
12-34 If Na+ channels are opened in a cell that was previously at rest, how will the resting
membrane potential be affected?
(a)
The membrane potential is not affected by Na+.
(b)
It becomes more negative.
(c)
It becomes more positive.
(d)
It is permanently reset.
Ion Channels and Signaling in Nerve Cells
12-35 Match the numbered lines with the following structures:
A.
nerve terminal
B.
cell body
C.
axon
D.
dendrite
12-36 Indicate whether the statements below are true or false. If a statement is false, explain
why it is false.
A.
Neurotransmitters are small molecules released into the synaptic cleft after the
fusion of synaptic vesicles with the presynaptic membrane.
B.
Action potentials are usually mediated by voltage-gated Ca2+ channels.
C.
Voltage-gated Na+ channels become automatically inactivated shortly after
opening, which ensures that the action potential cannot move backward along the
axon.
D.
Voltage-gated K+ channels also open immediately in response to local
depolarization, reducing the magnitude of the action potential.
12-37 Which of the following is required for the secretion of neurotransmitters in response to an
action potential?
(a)
neurotransmitter receptors
(b)
Na+-K+ pumps
(c)
voltage-gated K+ channels
(d)
voltage-gated Ca2+ channels
12-38 Figure Q12-38 illustrates changes in membrane potential during the formation of an
action potential. What membrane characteristic or measurement used to study action
potentials is indicated by the arrow?
Figure Q12-38
(a)
(b)
(c)
(d)
effect of a depolarizing stimulus
resting membrane potential
threshold potential
action potential
12-39 Figure Q12-39 illustrates changes in membrane potential during the formation of an
action potential. What membrane characteristic or measurement used to study action
potentials is indicated by the arrow?
Figure Q12-39
(a)
(b)
(c)
(d)
effect of a depolarizing stimulus
resting membrane potential
threshold potential
action potential
12-40 Figure Q12-40 illustrates changes in membrane potential during the formation of an
action potential. What membrane characteristic or measurement used to study action
potentials is indicated by the arrow?
Figure Q12-40
(a)
(b)
(c)
(d)
effect of a depolarizing stimulus
resting membrane potential
threshold potential
action potential
12-41 Figure Q12-41 illustrates changes in membrane potential during the formation of an
action potential. What membrane characteristic or measurement used to study action
potentials is indicated by the arrow?
Figure Q12-41
(a)
(b)
(c)
(d)
effect of a depolarizing stimulus
resting membrane potential
threshold potential
action potential
12-42 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.
The action potential is a wave of __________________ that spreads
rapidly along the neuronal plasma membrane. This wave is triggered by a
local change in the membrane potential to a value that is
__________________ negative than the resting membrane potential. The
action potential is propagated by the opening of __________________gated channels. During an action potential, the membrane potential
changes from __________________ to __________________. The action
potential travels along the neuron’s __________________ to the nerve
terminals. Neurons chiefly receive signals at their highly branched
__________________.
anions
axon
synaptic vesicle
cytoskeleton
dendrites
depolarization
hyperpolarization
less
ligand
more
negative
neutral
positive
pressure
voltage
12-43 The stimulation of a motor neuron ultimately results in the release of a neurotransmitter
at the synapse between the neuron and a muscle cell. What type of neurotransmitter is
used at these neuromuscular junctions?
(a)
acetylcholine
(b)
glutamate
(c)
GABA
(d)
glycine
12-44 Both excitatory and inhibitory neurons form junctions with muscles. By what mechanism
do inhibitory neurotransmitters prevent the postsynaptic cell from firing an action
potential?
(a)
by closing Na+ channels
(b)
by preventing the secretion of excitatory neurotransmitters
(c)
by opening K+ channels
(d)
by opening Cl– channels
12-45 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.
Neurons communicate with each other through specialized sites called
__________________. Many neurotransmitter receptors are ligand-gated
ion channels that open transiently in the __________________ cell
membrane in response to neurotransmitters released by the
__________________ cell. Ligand-gated ion channels in nerve cell
membranes convert __________________ signals into
__________________ ones. Neurotransmitter release is stimulated by the
opening of voltage-gated __________________ in the nerve terminal
membrane.
acetylcholine receptor
Ca2+ channels
chemical
postsynaptic
GABA receptor
K+ channels
Na+ channels
presynaptic
synapses
electrical
How We Know: Squid Reveal Secrets of Membrane Excitability
12-46 Studies on the squid giant axon were instrumental in our current understanding of how
action potentials are generated. You decide to do some experiments on the squid giant
axon yourself.
A.
You remove the cytoplasm in an axon and replace it with an artificial cytoplasm
that contains twice the normal concentration of K+ by adding KOAc, where OAc–
is an anion that is impermeable to the membrane. In this way you double the
internal concentration of K+ while maintaining the bulk electrical balance of the
cytoplasmic solution. Will this make the resting potential of the membrane more
or less negative?
B.
You add NaCl to the extracellular fluid and effectively double the amount of
extracellular Na+ cation. How does this affect the action potential?
C.
You replace half of the NaCl in the extracellular fluid with choline chloride.
(Choline is a monovalent cation much larger than Na+. Note that the presence of
choline will not impede the flow of Na+ through its channels.) How will this
affect the action potential?