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B[OL265 Exam 3

The distinct characteristics of different cell tlpes in a multicellular organism result mainly from the

diflerential regulation of the

A)
B)
C)
D),
)

The human genome encodes about 21,000 protein-coding genes. Approximately how many such genes
does the typical differentiated human cell express at any one time?
A) between 5000 and 15,000
B) less than 2100
C) between 18,900 and 21,000-at least 90% of the genes

D)

J.

_.

transcription of genes transcribed by RNA polymerase II.

transcriptionofhousekeepinggenes.
proteins that dtectly bind the TATA box of eukaryotic genes.
replication ofspecific genes.

21,0OG-all of them

Which of the following is not

A) hemoglobin

B)
C)
D)

good example of a housekeeping protein?

ATP synthase

DNA repair enzymes

histones

4.

Which of the following statements about differentiated cells is true?

A) Some of the proteins found in differentiated cells are found in all cells of a multicellular organism.
B) Cells of distinct t)?es express nonoverlapping sets of transcription factors.
C) Once a cell has differentiated, it can no longer change its gene expression.
D) Once a cell has differentiated, it will no longer need to transcribe RNA.

5.

Investigators performed nuclear transplant experiments to determine whether DNA is altered irreversibly
during development. Which of the following statements about these experiments is true?
A) Although nuclear transplantation has been successful in producing embryos in some mammals with
the use of foster mothers, evidence of DNA alterations during differentiation has not been obtained
for plants.
B) Because the donor nucleus is taken from an adult animal, the chromosomes from the nucleus urust
undergo recombination with the DNA in the egg for successful development to occur.
C) The embryo that develops from the nuclear transplant experiment is genetically identical to the
donor of the nucleus.
D) The meiotic spindle of the egg must interact with the chromosomes of the injected nuclei for
successful nuclear transplantation to occur.

Page

Use the following to answer questions 6-9:

You are interested in examining the Ps/gene. It is known that Psf is normally produced when cells are exposed to high levels of both
calcium (Ca*) and magnesium (Mg'*). MetA, MetB, and MetC are important for binding to the promoter of the Ps/gene and are
involved in regulating its transcription. MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C"
site. You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Py'gene. Your results
are summarized in Table Q8-17.

Transcription in the presence of Ca2* andlor Mgz+

Binding sites
A, B, and

present

No Ca2*

or Mgz*

with

Ca2*

with
Mg'*

with

.t'

ca2+

and Mg2*

4 u"d

4oI\'

++

A only
B

only

only

A and B only
A and C only
B

and

only
For this

table:

transcription of Pst
-+ =- no
low level of transcription of Psf, and

++ = high levels of transcription of Psf.

Table Q8-17

6.

Which of the following proteins are likely to act as gene activators?

A) MetB only
B) MetC only
C) Both MetA and MetC
D) MetA only

7.

Which of the following proteins are likely to act as gene repressors?

A) MetB only
B) Both MetA and MetC
C) MetA only
D) MetC only

8.

Which kanscription factors are normally bound to the Ps/promoter in the presence of Mg2* only?
A) MetA, MetB, andMetC

B)
C)
D)
9.

none

MetAonly
MetA and Met B

Which transcription factors are normally bound to the Ps/promoter in the presence of both Mg2* and
Ca2*?

A)
B)
C)
D)

MetA, MetB, andMetC

MetAandMetC
MetAandMetB
MetB andMetC

Page2

Use the following to answer questions l0-13:

You are interested in the regulation of gene Q. Proteins G, H, and J are proteins that are important for regulating gene
e, and bind to

its promoter region in a sequence-specific fashion. Proteins G and H both bind to site "A" but cannot bind to site;.A" ai the same time.
Protein J binds to site "B" on the promoter. The promoter region is diagrammed in Figure Q8-29.

Gt+

m*ftlAaf

gun**

Figure Q8-29
You develop a cell-free transcriptional system to study the effects of proteins G, H, and J on the transcription of gene
e. Using this
system, you can examine the effects of adding these proteins to the transcriptional system in equal amounts and measuring how much
gene Q is produced. When you add these proteins to the system, you get the results shown in Table
Q8-29.

rBflrrlsttr pro**ift

e!$efifn*nt

fi

r,x*mhef

ll

*ddsd I *nHH*
I
laede?
*qf
Ws

?4+*y#
s

ffi
y**

Table Q8-29

10.

Which proteins are likely to act as gene activators?

ll.

Which proteins are likely to act as gene repressors?

t2.

Your colleague looks at your data above and predicts that protein G will bind more strongly to the DNA
at site A, compared to protein H. Which experiment above is critical for this prediction?

A)H
B)J
C) both H and J
D)G
A)J
B)G
C) both H and J
D)H

A)
B)

#6

D)

#5

c)

#2
#3

Page 3

I3.

Which proteins do you predict are bound to the promoter in experiment #8?

A)
B)
C)
D)
t4.

onlyG andH
only J
only H and J
only G and J

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are
far from the promoter?
. by looping out the intervening DNA between their binding site and the promoter
B) by unwinding the DNA between their binding site and the promoter
C) by attracting RNA polymerase and modifying it before it can bind to the promoter
D) by binding to their binding site and sliding to the site of RNA polymerase assembly

A)

15.

The expression of the BRFI gene in mice is normally quite low, but mutations in a gene called.BRF2 lead,
to increased expression of BRFl. You have a hunch that nucleosomes are involved in the regulation of
,BRF1 expression and so you investigate the position of nucleosomes over the TATA box ofBRFl in
normal mice and in mice that lack either the BRF2 protein (BRF2) or part of histone H4 (HHF-) (histone
H4 is encoded by the HHF gene). Table Q8-37 summarizes your results. A normal functional gene is
indicated by a plus sign (+).
Mouse Nucleosome positioning Relative level of BRFI mRNA
BRFZ+ HHF+

specific pattern

BRF2- HHF+

randorn

HHF-

random

BRF2'HHF-

randgm

BRF?+

100

100

Table Q8-37
Which of the following conclusions cannotbe drawn from your data? Explain your answer.
A) The part of histone H4 missing nHHf- mice is not required for the formation of nucleosomes.

B)

The specific pattem of nucleosome positioning over the BXFI upstream region is required for BRFI

C)
D)

BRF2 is requted for the repression of BRFI.

BRF2 is required for the specific pattern of nucleosome positions over the BRFI upstream region.

repression.

16.

Combinatorial control of gene expression

_.
involves groups of transcriptional regulators working together to deiermine the expression of a

A)

gene.

B)

c)
D)

involves only the use ofgene activators used together to regulate genes appropriately.
is seen only when genes are arranged in operons.
involves every gene using a different combination of transcriptional regulators for its proper
expression.

17.

The extent of complementarity of a miRNA with its target mRNA determines

A)
B)

c)
D)

whether the mRNA will be tansported to the nucleus.

whether the miRNA synthesizes a complementary strand.
whether the mRNA will be immediately degraded or whether the rrRNA will fust be transported
elsewhere in the cell before degradation.
whether RISC is degraded.

Page 4

The owners of a local bakery ask for your help in improving a special yeast strain they use to make bread.
They would like you to help them design experiments using RNA interference to turn off genes, to allow
them to test their hlpothesis that certain genes are important for the good flavors found in their bread. Of
the components in the following list, which is the most important to check for in this yeast strain if you'd

like this project to succeed?

A)
B)
C)

the presence of genes in the genome that code for RISC proteins
the presence of single-standed siRNAs within the cell

the presence of foreign double-stranded RNA

the presence of miRNA genes in the genome

D)

You have a circular plasmid that can be cut by the restriction nuclease HindIII, as diagrammed in Figure

Qr0-4.

Figure Q10-4

If you were to cut this circular piece of DNA with HindIII, which of the answers below best predicts what
you would get?
two circular pieces of DNA
two semicircular pieces of DNA
t',vo linqar pieces of DNA
one linearpiece of DNA

A)
B)
C)
D)

You have

piece of circular DNA that can be cut by the restriction nucleases XhoI and SmaI, as indicated

Figure Q10-5

If you were to cut this circular piece of DNA with both XhoI and SmaI, how many fragments of DNA
would you endup with?

A)2
B)4

c)1
D)3

Page 5

21.

You have a piece of circular DNA that can be cut by the reshiction nucleases EcoR[, HindIII, and NotI, as
indicated in Figure Ql0-6.
Notl

EcoRl

Hindlll
Figure Q10-6
Which of the following statements isfalse?
A) A piece of DNA that cannot be cut by EcoRI will be obtained by cutting this DNA with both NotI

B)
C)
D)
22.

and NotI.
Two DNA fragments of unequal size will be created when this DNA is cut by both HindIII and

EcoN.

One piece of DNA

will

be obtained when this

DNA is cut by NotI.

Which of the following statements about gel-transfer hybridization (or Southern blotting) isfalse?
A) A labeled DNA probe binds to the DNA by hybridization.

B)
c)
D)

23.

and HindIII.

Two DNA fragments that cannot be cut by HindIII will be obtained when this DNA is cut by EcoRI

The DNA that is separated on a gel is not labeled.

In this technique, single-stranded DNA is separated by electrophoresis.
This technique involves the transfer of DNA molecules from gel onto nitrocellulose paper or nylon
paper.

DNA ligase is an enzyme used when making recombinant DNA molecules in the lab. In what normal
cellular process is DNA ligase involved?

A)
B)
C)
D)
24,

transcription
transformation

DNA replication
none, it is only found in virally infected cells

Q10-19 shows the cleavage sites of several reskiction nucleases.

5',
3',

otoocrr

3'

5',

3,rEEEh

s,

3',

s'

3'
5'

5'ccAlTGG 3'
3'GGTIACC 5'

ACAT"I, ,,
3' r[crACA 5'
5,

Figure Q10-19
You cut a vector using the PciI restriction nuclease. Which of the following restriction nucleases will
generate a fragment that can be ligated into this cut vector with the additio; of only ligase and
ATp?
A) NspV

B)
C)
D)

HindIII
NcoI
MmeI

Page 6

Figure Q10-20 depicts a strategyby 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.

+ ligase

.ffi

+ deoxyribonucleotides

-+
$tr"

;::gip/;: ;!i#,!;

-T*

+ polymerase

-GAATTI
.wffi$#.&_
*'CfTAA.

.H,H'
,

$_\EtiF-

Figure Q10-20
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) Without polymerase, there will not be enough energy for the reaction to proceed.
B) Polymerase will add nucleotides to the end produced by the HaeIII restriction nuclease.
C) Polymerase will fill in the staggered end to create a blunt end.
D) Polymerase is needed to seal nicks in the DNA backbone.

DNA

A)
B)
C)
D)

can be infoduced into bacteria by a mechanism called

ligation.
replication.
transformation.
transcription.

A plasmid _.

A)
B)
C)
D)

is a single-stranded circular DNA molecule that can undergo horizontal transfer among bacteria.
always becomes part of the bacterial chromosome during transformation.
can confer antibiotic resistance to a bacterium.
is a tool designed in the lab and never found in naturally occurring bacteria.

Which of the following statements about DNA librarie s is true?

A)

Individual bacteria that have taken up most of the library DNA are selected for during the
construction of a DNA library.

B)

c)
D)

The library DNA within the bacteria will only be replicated when it hybridizes to a DNA probe.
By placing the library DNA into bacteria, the bacteria can be used to amplifr the desired DNA
fragments from the DNA library
Production of a DNA library involves the direct insertion of short DNA fragments into bacteria

through transformation.

Which of the following statements about genomic DNA libraries isfalse?

A) The larger the size of the fragments used to make the library, the more difficult it will be to find
your gene ofinterest once you have identified a clone that hybridizes to your probe.
B) 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.
C) The smaller the gene you are seeking, the more likely it is that the gene will be found on a single

D)

clone.
The larger the size of the fragments used to make the library, the fewer colonies you
examine to find a clone that hybridizes to your probe.

PageT

will have to

t30.

Why is an excess of normal deoxyribonucleoside triphosphate molecules (dNTPs) needed during dideoxy
sequencing?

A)
B)
C)

dNTPs are consumed as energy to fuel the sequencing reactions.

When dNTP levels are too low, there will be very few chain-termination events.
The dNTPs can hybridize to the fragment to be sequenced and serve as primers for DNA
polymerase.
potymerase uses the dNTPs to synthesize a DNA molecule complementary to the molecule

D) bN,t

being sequenced.

31.

you create a recombinant DNA molecule that fuses the coding sequence of green fluorescent protein to
the regulatory DNA sequences that control the expression of your favorite genes. Which of the following
pieces of information can you NOIgain by examining the expressiol of this reporter gene?

A)
B)
C)
D)
32.

JJ.

the cell in which the protein encoded by this gene is expressed

when, during an organism's development, this gene is expressed
the tissue where the protein encoded by this gene is expressed
the specific location within the cell of the protein encoded by this gene

In the photosynthetic archaeat Halobacterium halobium, a membrane transport protein called bacteriorhodopsin captures
tom suntigfit and uses it to pump protons out ofthe cell. The resulting proton gradient serves as an energy store that
"r"rgy
can lulter be tapped to generate ATP. Which statement best describes how bacteriorhodopsin operates?
A) The absorption of sunlight triggers a contraction ofthe b barrel that acts as the protein's central channel, squeezing
a proton out of the cell.
B) Th; absorption of sunlight triggers a shift in the conformation of the protein's seven, membrane spanning a
helices, allowing a proton to leave the cell'
C) The absorption of sunlight triggers a restructuring of bacteriorhodopsin's otherwise unstructured core to forrn the
channel through which a proton can exit the cell.
D) The absorption of sunlight triggers the activation of an enzyme that generates ATP.
Insulin is a small protein that regulates blood sugar level and is given to patients who suffer from
diabetes. Many years ago, diabetics were given insulin that had been purified from pig pancreas. Once
recombinant DNA techniques became available, the DNA encoding insulin could be placed into an
expression vector and insulin could be produced in bacteria. Which of the followngis NOT areason why
purifying insulin from bacteria is a better way to produce insulin for diabetics than using insulin purified
from a pig pancreas.
A) Insulin made from a bacterial culture and then purified will be free of any possible contaminating
viruses that pigs (and any other animals) harbor. Since pigs are more closely related to people than
bacteria are, their viruses are more likely to be harmful to people than are viruses that might infect
bacteria.

B)
C)

Insulin can be easily produced in large quantities from cells carrying the cloned DNA sequence.
The pig protein has slight amino acid differences compared to the human protein, so human insulin

D)

produced by bacteria will work better in people.

the creation of transgenic pigs that expressed insulin was very expensive compared to the cost
creating bacteria that expressed insulin.
:,

34.

Which of the following phenomena will be observed if a cell's membrane is pierced?

A)
B)
C)
D)

the membrane collapses

a tear is formed
the membrane expands
the membrane reseals

Page 8

of

The plasma membrane serves many functions, many of which depend on the presence of specialized
membrane proteins. Which of the following roles of the plasma membrane could still occur if the bilayer
were lacking these proteins?

A)
B)
C)
D)

selectivepermeability
import/export of molecules

intercellularcommunication
cellular movement

Which of the following membrane lipids does not contain a fatty acid tail?
A) cholesterol
B) phosphatidylserine
C) phosphatidylcholine

D)

glycolipid

Forrnation of a lipid bilayer is energetically favorable. How does this arrangement result in higher entropy
for the system, and thus make bilayer formation energetically favorable?
A) Water molecules form cagelike structures around hydrophobic molecules.
B) Fatty acid tails are highly saturated and flexible.
C) Polar head groups form a hydrogen-bonding network at the interface with water.
D) Hydrogen bonds fbrm between neighboring polar head groups in the bilayer.

38.

Which of the following statements is true?

A) In eukaryotes, all membrane-enclosed organelles are surrounded by one lipid bilayer.,
B) Membrane lipids frequently flip-flop between one monolayer and the other.

C)
D)

39.

Phospholipids will spontaneously form liposomes in nonpolar solvents.

Membrane lipids difhrse within the plane of the membrane.

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) Decrease the amount of glycolipids in the membrane.
B) Produce lipids with hydrocarbon tails that are longer and have fewer double bonds.
C) Produce lipids with hydrocarbon tails that are shorter and have more double bonds.

D)

Decrease the amount of cholesterol in the membrane.

40.

Some lipases are able to cleave the covalent bonds between the glycerol backbone and the attached fatty
acid. What final products do you expect to accumulate through the action of the enzyme
monoacylglycerol lipase?
A) free phosphate and glycerol
B) glycerol and free fatty acid
C) sterol and glycerol
D) phosphoglycerol and free fatty acid

41.

Which of the following phospholipid precursors is the most hydrophobic?

A) glycerol

B)
C)
D)

phosphate

triacylglycerol
diacylglycerol

Page 9

42.

Three phospholipids X, Y, and Z are dishibuted in the plasma membrane as indicated in Figure Ql1-14.
For which of these phospholipids does a flippase probably exist?

extracellular space

cytosol
Figure Qf l-14

A) Y andZ
B) XandY
C) X only
D) Zonly
43.

New membrane phospholipids are synthesizedby enzymes bound to the

A)
B)
C)
D)
44.

46.

luminal, Golgi
extracellular,plasma

cytosolic,mitochondrial
cytosolic,endoplasmicreticulum

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 en4anes
accomplishes both of these tasks?

A)
B)
C)
D)
45.

side of the

membrane.

convertases
glycosylases
phospholipases
flippases

Membrane curvature is influenced by the differential lipid composition of the two membrane monolayers.
Which factor do you think has the largest impact on the curvature of biological membranes?
A) charge of the lipid head group
B) length of the hydrocarbon tails
C) size of the lipid head group
D) amount of cholesterol

In the photosynthetic archaean Halobacterium halobium, a membrane transport protein called

bacteriorhodopsin captures energy from sunlight and uses it to pump protons out of the cell. The resulting
proton gradient seryes as an energy store that can later be tapped to generate ATP. Which statement best
describes how bacteriorhodopsin operates?
The absorption of sunlight triggers a shift in the conformation of the protein's seven, membrane
spanning a helices, allowing a proton to leave the cell.
The absorption of sunlight triggers the activation of an enzyme that generates ATP.
The absorption of sunlight triggers a contraction of the b barrel that acts as the protein's central
channel, squeezing a proton out ofthe cell.
The absorption of sunlight triggers a restructuring of bacteriorhodopsin's otherwise unstructured
core to form the channel through which a proton can exit the cell.

A)

B)
C)
D)

Page

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47.

Plasma membranes are extremely thin and fragile, requiring an extensive support network of fibrous
proteins. This network is called the
attachment complex.

A)
B)
C)
D)
48.

spectrin
cortx.
cytoskeleton

The lateral movement of transmembrane proteins can be restricted by several different mechanisms.
Which mechanism best describes the process by which focal adhesions are formed to promote cell

motilitf

A)
B)
C)
D)
49.

proteins are tethered to the extracellular matrix

proteins are tethered to the proteins on the surface of another cell
protein movement is limited by the presence of a diffusion barrier
proteins are tethered to the cell cortex

The lateral movement of kansmembrane proteins can be restricted by several different mechanisms.
Which mechanism best describes the process by which an antigen-presenting cell tiggers an adaptive

immune response?
proteins are tethered to the extracellular matrix
proteins are tethered to the proteins on the surface of another cell
protein movement is limited by the presence of a diffirsion barrier
proteins are tethered to the cell cortex

A)
B)
C)
D)
50.

Diversity among the oligosaccharide chains found in the carbohydrate coating of the cell surface can be
achieved in which of the following ways?

A)
B)
C)
D)

varying the types of linkages between sugars

varying the number of branches in the chain
varying the types of sugar monomers used
all of the above

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