Sort the following steps in the order that they normally happen during the process of
repairing double-strand breaks by homologous recombination. Your answer would be a
six-letter string composed of letters A to F only, e.g. DEFABC.
(A)Ligation
(B)DNA synthesis using undamaged DNA as the template
(C)DNA synthesis using original DNA as the template
(D)Release of the invading strand
(E)Strand invasion
(F)Nuclease digestion (resection)
The results of two sets of chromatin immunoprecipitation experiments on two cell types
(1 and 2) are shown in the following simplified graphs for the same genomic region
containing the first two exons of a gene. Antibodies against a transcription regulatory
protein (X) or against a subunit of RNA polymerase II were used in the ChIP-seq
experiments, as indicated. Do you think the protein is a transcriptional activator or
repressor? The results from a parallel RNA-seq experiment are provided in the third
graph. Which profile (a or b) in the graph would you expect to correspond to cell type
1?
A.Activator; profile a
B.Repressor; profile a
C.Activator; profile b
D.Repressor; profile b
According to the model for nuclear transport described in this chapter, what do you
think would happen if you could artificially limit all Ran-GAP activity to the nucleus
and all Ran-GEF activity to the cytosol?
A.Proteins containing an NLS would be actively exported from the nucleus, while
NES-containing proteins would be actively imported.
B.Both import and export of nuclear proteins would be stalled, as they lose their
directionality.
C.Protein import into the nucleus would be reversed, but export would be unaffected.
D.Protein import into the nucleus would be stalled, but export would be unaffected.
E.Nothing would change; this is the normal Ran-GAP and Ran-GEF distribution.
In contrast to growing microtubules, shrinking microtubules …
A.have a GTP cap at their plus end.
B.have strong lateral interactions at their plus ends.
C.have curved protofilaments at their plus ends.
D.cannot be rescued unless microtubule-stabilizing proteins bind and inhibit
depolymerization.
E.All of the above.
Whereas the cholera toxin ADP-ribosylates the ± subunit of stimulatory G protein (Gs),
thereby blocking GTP hydrolysis, pertussis toxin ADP-ribosylates the ± subunit of
inhibitory G protein (Gi) and prevents interaction with the receptor. What is the effect of
these toxins on the concentration of intracellular cAMP?
A.Cholera toxin tends to increase cAMP concentration, whereas pertussis toxin tends to
decrease cAMP concentration.
B.Cholera toxin tends to decrease cAMP concentration, whereas pertussis toxin tends to
increase cAMP concentration.
C.They both tend to increase cAMP concentration.
D.They both tend to decrease cAMP concentration.
Single-molecule detection by fluorescence microscopy is limited by the presence of an
excess of out-of-focus fluorescent molecules. How does a TIRF microscope uniquely
overcome this limitation?
A.By removal of the out-of-focus molecules by selective destruction.
B.By using a deconvolution algorithm that reverses the convolution of signals due to
the out-of-focus molecules.
C.By a confocal set-up that eliminates out-of-focus signals.
D.By exciting only in-focus molecules via an evanescent field.
E.By using an objective lens with extremely high numerical aperture.
Indicate whether each of the following descriptions better matches miRNAs (M) or
siRNAs (S) in animal cells. Your answer would be a four-letter string composed of
letters M and S only, e.g. MMMM.
( )They usually cleave their target RNAs using the slicing activity of the Argonautes.
( )They typically show perfect complementarity with their target RNA.
( )They can bind to the RITS as well as the RISC complex.
( )They seem to be the more ancient form of small noncoding RNAs.
Sanshool is a natural compound found in Sichuan pepper, which is commonly used in
making spicy Asian food, and creates a numbing sensation in the mouth. It is known to
inhibit a subset of potassium leak channels involved in maintaining the resting
membrane potential in sensory neurons. How do you think sanshool affects these
sensory neurons?
A.It elevates the resting potential (to less negative values) and makes it easier to excite
the neuron.
B.It elevates the resting potential and makes it harder to excite the neuron.
C.It lowers the resting potential and makes it easier to excite the neuron.
D.It lowers the resting potential and makes it harder to excite the neuron.
E.It causes hyperpolarization and decreases the spontaneous firing of the neuron.
Consider visual transduction in rod photoreceptors in the vertebrate retina. Which of the
following steps does NOT normally amplify the signal in this pathway?
A.Activation of transducin by active rhodopsin
B.Blockage of Na+ influx by cation-channel closure
C.Cation-channel closure due to cGMP depletion
D.Depletion of cGMP by active cGMP phosphodiesterase
E.All of the above DO involve amplification
In which of the following microscopy techniques are oblique rays of light focused on
the specimen?
A.Bright-field microscopy
B.Dark-field microscopy
C.Phase-contrast microscopy
D.Differential-interference-contrast microscopy
Under iron-starvation conditions in the cell,
A.cytosolic aconitase binds to the 3′ UTR of the mRNA encoding the transferrin
receptor.
B.cytosolic aconitase binds to the 3′ UTR of the mRNA encoding ferritin.
C.cytosolic aconitase blocks translation of the mRNA encoding the transferrin receptor.
D.the mRNA encoding the transferrin receptor is cleaved by an endonuclease.
E.All of the above.
Sort the following events to reflect the normal order in which they occur in
G-protein-coupled receptor signaling leading to transcription of genes with cAMP
response elements. Your answer would be a four-letter string composed of letters A to E
only, e.g. ACBD.
(A)Binding of CREB to PKA
(B)Binding of cAMP to PKA
(C)Dissociation of PKA into catalytic and regulatory subunits
(D)Activation of adenylyl cyclase
In the following schematic diagram of an early Drosophila embryo, which step (A to C)
corresponds to cellularization? Write down A, B, or C as your answer.
A DNA-binding protein binds cooperatively to DNA by fairly weak homodimerization.
The binding of this protein to DNA ___
A.shows a sigmoidal binding curve.
B.occurs in more of an all-or-none manner, compared to a protein that is a constitutive
dimer.
C.occurs despite the fact that the protein molecules are predominantly monomers in
solution.
D.All of the above.
Which one better supports cell proliferation when added to fibroblast cultures: serum or
plasma? This activity is due to the presence of mitogens in this fluid. What is
responsible for making these mitogens?
A.Serum; red blood cells
B.Serum; platelets
C.Plasma; red blood cells
D.Plasma; white blood cells
E.Plasma; platelets
If myosin II heads are attached to a glass slide and actin filaments are allowed to bind to
them, the filaments will glide on the surface …
A.toward their plus end in the presence of ATP.
B.toward their plus end in the presence of GTP.
C.toward their minus end in the presence of ATP.
D.toward their minus end in the presence of GTP.
E.toward their plus end in the presence of ADP.
To study the chromatin remodeling complex SWR1, a researcher has prepared arrays of
nucleosomes on long DNA strands that have been immobilized on magnetic beads.
These nucleosomes are then incubated with an excess of the H2AZ-H2B dimer (which
contains the histone variant H2AZ) in the presence or absence of SWR1 with or without
ATP. She then separates the bead-bound nucleosomes (bound fraction) from the rest of
the mix (unbound fraction) using a magnet, elutes the bound fraction from the beads,
and performs SDS-PAGE on the samples. This is followed by a Western blot using an
antibody specific to the H2AZ protein used in this experiment. The results are shown
below, with the presence (+) or absence (-) of ATP, SWR1, or the H2AZ-H2B dimer in
each incubation reaction indicated at the top of the corresponding lane.
Which of the following statements is confirmed by the Western blot shown?
A.SWR1 deposits H2AZ histones into the nucleosome arrays.
B.SWR1 function is not ATP-dependent.
C.The antibody used in this experiment binds to the SWR1 complex.
D.All of the above.
For the ± subunit of a trimeric G protein, €¦
A.a G-protein-coupled receptor (GPCR) acts as a guanine nucleotide exchange factor
(GEF), whereas a regulator of G protein signaling (RGS) can act as a
GTPase-activating protein (GAP).
B.a GPCR acts as a GAP, whereas an RGS can act as a GEF.
C.both a GPCR and an RGS can act as a GEF.
D.both a GPCR and an RGS can act as a GAP.
Indicate true (T) and false (F) statements below regarding the mitochondrial protein
import system. Your answer would be a four-letter string composed of letters T and F
only, e.g. TTTF.
( )Mitochondrial proteins should fold natively twice: once in the cytosol and once inside
the organelle.
( )²-barrel proteins that are abundant in the mitochondrial outer membrane are imported
from the cytosol independently of the TOM complex.
( )Signal sequences that target precursor proteins to the mitochondrial matrix form an ±-
helix in which positively charged residues cluster near its N-terminus, while uncharged
or hydrophobic residues cluster near the other side.
( )At least two signal sequences are required to direct proteins to the mitochondrial
matrix.
The following schematic drawings show an epithelial sheet. Which example shows a
mutant with planar-cell-polarity defects but no other defects?
Indicate whether each of the following structures has actin organized mostly in a one-
(1), two- (2), or three- (3) dimensional arrangement. Your answer would be a four-digit
number composed of digits 1 to 3 only, e.g. 1333.
( )Stress fibers
( )Invadopodia
( )Lamellipodia
( )Filopodia
Which of the actin-binding proteins (1 to 5) in the following schematic drawing
represents tropomyosin, -actinin, Arp 2/3 complex, CapZ, and myosin, respectively?
Your answer would be a five-digit number composed of digits 1 to 5 only; e.g. 15324.
In the following schematic drawing, a transcribing RNA polymerase is moving toward
the right on the DNA template as indicated. If the polymerase is allowed to rotate freely
while the DNA is kept from doing so, would the enzyme rotate in a right-handed (R) or
left-handed (L) fashion around the template? Write down R or L as your answer.
Complete the DNA sequence below such that the final sequence is identical to that of
the complementary strand. Your answer would be a seven-letter string composed of
letters A, C, T, and G only, e.g. TTCTCAG.
Indicate if each of the following descriptions matches RNA (R) or DNA (D). Your
answer would be a five-letter string composed of letters R and D only, e.g. RDDRR.
( ) It is mainly found as a long, double-stranded molecule.
( ) It contains the sugar ribose.
( ) It normally contains the bases thymine, cytosine, adenine, and guanine.
( ) It can normally adopt distinctive folded shapes.
( ) It can be used as the template for protein synthesis.