Gene duplication can give rise to homologous genes that are part of gene families. For
example, there are six actin genes in the genome of most mammalian species. In
humans, the ACTB gene, which encodes a cytoskeletal actin, is expressed ubiquitously,
while ACTC1 is expressed mainly in cardiac cells. Although bacteria lack the
eukaryotic cytoskeletal organization, the bacterial MreB gene bears recognizable
sequence similarity to mammalian actin genes and codes for a protein that is similar to
actin in structure and function. Which of the following statements is true about these
genes?
A.ACTB is homologous to ACTC1 but not to MreB.
B.ACTB is orthologous to ACTC1 but not to MreB.
C.ACTB is paralogous to ACTC1 but not to MreB.
D.MreB is orthologous to ACTB but not to ACTC1.
E.ACTB is paralogous to both ACTC1 and MreB.
Which of the following normally functions to lower the pH of the cytosol?
A.A Na+-H+ exchanger in the plasma membrane.
B.A Na+-driven Cl–-HCO3
– exchanger in the plasma membrane.
C.A Na+-independent Cl–-HCO3
–exchanger in the plasma membrane.
D.A V-type ATPase in the lysosomal membrane.
E.Both answers A and B above.
A giant aggrecan aggregate can have a molecular mass of 108 daltons or more, and can
be as large as a bacterium. Its structure resembles a brush. What is responsible for
attaching the bristles of the brush to its core?
A.Covalent bonds between aggrecan core protein and keratan or chondroitin sulfate.
B.Noncovalent bonds between aggrecan core protein and keratan or chondroitin sulfate.
C.Covalent bonds between aggrecan core protein and hyaluronan.
D.Noncovalent bonds between aggrecan core protein and hyaluronan.
Persistence length for a cytoskeletal filament is the minimum filament length at which
random thermal fluctuations are likely to cause it to bend. Which of the following
comparisons are true, considering the persistence lengths of (a) an actin filament, (b) a
bundle of cross-linked actin filaments, and (c) a microtubule?
A.(a > b) and (a > c)
B.(a > b) and (a < c)
C.(a < b) and (a > c)
D.(a < b) and (a < c)
E.(a > b) and (b > c)
Proteins of the protein disulfide isomerase (PDI) family share common domains that
harbor an active-site CXXC motif (C = cysteine; X = one of several residues). During
the course of a redox reaction, one of the active-site cysteines in its reduced form can
attack a disulfide bond in a substrate protein (that could itself be another PDI family
member) to form a mixed disulfide between the enzyme and its substrate. This is then
attacked by the other active-site cysteine, releasing the substrate in reduced form. The
reverse of these reactions can occur instead in order to make disulfide bonds in target
proteins. CXXA mutant PDI family proteins-in which one of the active-site cysteines is
mutated to an alanine-can be trapped in the intermediate mixed disulfide state for an
elongated time, facilitating the identification of their substrate proteins. Using these
mutations in each of three interacting PDI family proteins-A, B, and C (one mutation at
a time)-you have discovered that the mutant B interacts with A and C, while mutant A
interacts with C but not with B. Finally, mutant C interacts with neither of the other
two. The following diagram shows the thermodynamically favorable flow of electrons
(plus protons) in the cascade involving these three proteins. Based on your results
above, what proteins correspond to 1, 2, and 3 in the diagram, respectively? Your
answer would be a three-letter string composed of letters A to C only, e.g. CBA.
Three consecutive nucleotides in RNA (such as AUC or GUA) constitute a triplet called
a ___, which can specify an amino acid or a stop signal for translation.
Where are the hypervariable regions located in a typical antibody molecule?
A.Only in the N-terminal region of the light chain
B.Only in the C-terminal region of the light chain
C.Only in the N-terminal region of the heavy chain
D.Only in the C-terminal region of the heavy chain
E.In the N-terminal region of both the light and the heavy chain
Which of the following changes would you expect to increase the phase transition
temperature of a synthetic bilayer composed of phosphatidylserine?
A.Incorporation of phospholipids with longer fatty acid chains.
B.Introduction of double bonds in the fatty acids.
C.Addition of cholesterol.
D.Removal of serine from the head group.
E.None of the above.
What is the function of the 19S cap in the proteasome complex?
A.Recognizing the proteins that will be degraded
B.Unfolding the proteins that will be degraded and threading them into the central 20S
cylinder for digestion
C.Removing the polyubiquitin chain from the proteins that will be degraded
D.Hydrolyzing ATP to make the digestion process highly efficient
E.All of the above
A gene that had been turned off in a liver cell has just been induced to be highly
expressed as the cell responds to a new metabolic load. What observations do you
expect to accompany this change?
A.More than 100 proteins would become associated with the gene for its transcription.
B.The nuclear position of the gene would change to place it in a “transcription factory.”
C.Chromatin modifications associated with the gene would change in favor of higher
expression.
D.All of the above.
In the structure of which of the following proteins are the actin-filament binding sites
furthest apart in space?
A.Spectrin
B.Filamin
C. -Actinin
D.Fimbrin
E.Myosin II
Which of the following events contributes to driving the mammalian cell past the
restriction point of the cell cycle?
A.Phosphorylation of Cdh1-APC/C by G1/S-Cdk
B.Destruction of CKIs that target S-Cdks
C.Phosphorylation of Rb by G1-Cdk, G1/S-Cdk, and S-Cdk
D.Activation of E2F gene expression by active E2F protein
E.All of the above
The specificity of nucleic acid hybridization is remarkable. Even a single mismatch
between a probe and a target sequence can be detected depending on hybridization
conditions. This sensitivity can be employed in applications such as SNP haplotyping.
Consider a probe that is complementary to a 20-nucleotide-long genomic region
including a single polymorphic nucleotide. The probe is perfectly complementary to the
more common allele, but has one mismatch in the case of the minor allele. The
temperature-dependent hybridization of the probe to the single-strand genomic
fragment is schematically presented in the following graph. To detect hybridization, a
fluorescent dye is added to the reaction. The dye fluoresces strongly only when
intercalated between the bases of double-stranded DNA, and is therefore used to
quantify double-strand formation or dissociation. Which “melting curve” (1 or 2) in the
graph do you think corresponds to the more common SNP allele? Which curve shows a
higher melting temperature?
A.1; 1
B.1; 2
C.2; 1
D.2; 2
In the following schematic drawing, a growing axon (in red) is extended to a target
neuron to form three synapses. In its journey, it is guided by a variety of mechanisms.
Sort the following mechanisms to reflect the order in which they guide the navigation
of the growth cone toward the target neuron in this example. Ignore the final
chemoattraction step toward the target neuron itself. Your answer would be a six-letter
string composed of letters A to F only, e.g. FACBDE.
(A)Chemoattraction
(B)Chemorepulsion
(C)Cell surface adhesion
(D)Contact inhibition
(E)Extracellular matrix adhesion
(F)Guidance by pioneer neuron
Indicate whether each of the following histone modifications adds a negative charge to
the histone (A), removes a positive charge from the histone (B), or does neither of these
(C). Your answer would be a four-letter string composed of letters A, B, and C only, e.g.
CABA.
( )H3 lysine 9 acetylation
( )H3 serine 10 phosphorylation
( )H3 lysine 4 trimethylation
( )H3 lysine 9 trimethylation
For each of the following pairs, indicate whether they interact via hydrogen bonds (H)
or ionic bonds (I), or do not favorably interact (N). Your answer would be a four-letter
string composed of letters H, I, and N only, e.g. HNNI.
( )ATP and Mg2+
( )Urea and water
( )Glucose and the enzyme hexokinase (which uses glucose as a substrate)
( )A phospholipid tail and inorganic phosphate
You have grown cultures of the yeast Saccharomyces cerevisiae in a complex medium
alone or supplemented with either glucose or ethanol. In the presence of glucose,
available energy is abundant and the cells can therefore grow by fermenting glucose. In
the presence of ethanol, however, the cells switch to a mostly aerobic respiration to
meet their energy demands. They also shut down many of their anabolic pathways and
activate catabolic pathways to produce more energy to better survive under these
conditions. After the growth phase, you extract total mRNA from the cells, convert
them to cDNA, and label them with a fluorescent molecule. You then hybridize the
cDNAs to a yeast DNA microarray. Part of the results obtained by cluster analysis after
fluorescent measurements is summarized in the following simplified diagram. Here, red
and green indicate increase and decrease, respectively, in expression of a gene
compared to that in the nonsupplemented medium. Which row (1 or 2) do you think
corresponds to the glucose-supplemented medium?
The alternative splicing of a certain transcript can result in the production of two
mRNA isoforms, one predominant in muscle cells and the other in neurons. The gene
contains an exon that is skipped in muscle cells but retained in neurons. You create a
mutant version of the gene in which the 3′ splice site near this exon is deleted. However,
when you introduce this into a culture of neural cells, an even longer pre-mRNA is
produced, consistent with the activation of a secondary splice site located near the
deleted one. Is the secondary splice site within the exon (E) or its neighboring intron
(I)? Write down E or I as your answer.
Consider the two feed-forward loops below containing three transcription regulators A,
B, and C, where A receives the input signal and C generates the output. In the so-called
coherent loop (left), A activates C both directly and indirectly, whereas in an incoherent
loop (right), A activates C via one route and inactivates it via the other. Answer the
following question(s) based on these network motifs.
Would you expect a coherent (C) or an incoherent (I) loop to generate the following
response pattern? In this example, A is stimulated by the input, and the transcription of
C is measured as the output. Write down C or I as your answer.
Fill in the blank in the following paragraph.
“Cytosolic Ca2+ can be sensed by …, a small, conserved, dumbbell-shaped protein with
four Ca2+-binding sites. Upon Ca2+ binding, it binds and activates dozens of proteins by
changing its conformation in different ways.”
The requirement for accumulation of multiple mutations in cancer progression is
manifested in the normalized percentage of new cases of cancer diagnosed in different
age groups. Which of the curves A to E in the following graph better represents the
incidence of human cancers as a function of age?
A replication fork is shown schematically below. The strand labeled A is called the ___
strand.
The structural formulas for the 20 naturally occurring amino acid residues are shown in
the panel below. Answer the following question(s) with the help of this panel.
What is the amino acid sequence of the peptide depicted below? Write down the
sequence from the N- to the C-terminus, and use only the one-letter abbreviations, e.g.
AGCNT.
Which cell behavior depicted below is involved in the tube formation that underlies the
development of lungs and trachea?
Expression of the Even-skipped (Eve) gene in early Drosophila embryos is under the
control of several transcription regulators. In one example, one of the Eve stripes is
positioned near the anterior region of the embryo, and its regulatory module contains
binding sites for Bicoid and Hunchback (activators) as well as Giant and Kr¼ppel
(inhibitors) such that the gene is expressed only in the region where concentrations of
the two activators are high and the concentrations of the two inhibitors are low. A
reporter gene can be placed under the control of this module, and it can be shown to
form a stripe in the same place in the embryo as the corresponding stripe of Eve.
Answer the following question(s) based on these findings.
In the following schematic diagrams of an early Drosophila embryo, in which region
would you expect to find the reporter protein put under the control of the regulatory
module mentioned above?