Consider a cis-regulatory enhancer sequence in the Escherichia coli chromosome that is
located thousands of nucleotide pairs upstream of the gene that it regulates. If the
regulatory sequence is mutated to become nonfunctional, the introduction of the
wild-type enhancer on a plasmid fails to regulate the gene. This implies that ___
A.the regulatory sequence encodes a regulatory protein that binds near the promoter of
the target gene and controls RNA polymerase binding.
B.the regulation of the target gene involves looping out of the intervening DNA, and the
promoter of the cis-regulatory sequence must be on the same chromosome.
C.the regulatory sequence can bind directly to the RNA polymerase.
D.the regulatory sequence cannot bind to a protein.
Imagine a protein that can be independently phosphorylated on any of its 10 tyrosine
residues and acetylated on either of its 2 lysine residues. In principle, how many
different combinations of these modifications are possible for this protein?
A.210
B.220
C.1010
D.1220
E.212
A cell expresses a transmembrane protein that is cleaved at the plasma membrane to
release an extracellular fragment. The fragment binds to receptor proteins on nearby
cells and activates signaling pathways resulting in altered gene expression patterns in
the cells. What form of intercellular signaling does this represent?
A.Contact-dependent signaling
B.Paracrine signaling
C.Synaptic signaling
D.Endocrine signaling
E.Autocrine signaling
Which of the following proteins activates the mitochondrial pathway of apoptosis?
A.The tumor suppressor protein p53, when activated in response to extensive DNA
damage.
B.The BH3-only protein Bid, when cleaved by the initiator caspase-8 (from the
extrinsic pathway).
C.The anti-IAP protein Omi, when activated by dephosphorylation.
D.The BH3-only protein Bad, when activated by dephosphorylation.
E. All of the above.
Which of the following methods provides the most sensitive and accurate way of
measuring and comparing mRNA levels of a set of genes in two different tissues. The
genes are expressed at relatively low levels in these tissues, and do not necessarily code
for protein.
A.RNA-seq
B.RT-PCR
C.DNA microarray analysis
D.ChIP-seq
E.Ribosome profiling
Assuming that the only function of Short gastrulation (Sog) in fruit flies is to regulate
Decapentaplegic (Dpp), which of the following genetic interactions would you NOT
expect to observe?
A.Mutant embryos lacking both Sog and Dpp phenotypically resemble those lacking
only Dpp.
B.Partial loss of Sog suppresses the phenotype of partial loss of Dpp.
C.Gain of Dpp suppresses the phenotype of partial loss of Sog.
D.Gain of Sog suppresses the phenotype of gain of Dpp.
Indicate true (T) and false (F) statements below regarding the nucleus and nuclear
protein transport. Your answer would be a four-letter string composed of letters T and F
only, e.g. TTTF.
( )The inner and outer nuclear membranes are continuous with each other, yet maintain
distinct protein compositions.
( )The outer nuclear membrane is studded with ribosomes engaged in protein synthesis.
( )The endoplasmic reticulum lumen is continuous with the nuclear interior.
( )Ribosomal proteins pass through the nuclear pore complexes twice; they are imported
into the nucleus after synthesis, and are exported from the nucleus after assembly with
ribosomal RNA.
Indicate whether each of the following descriptions better applies to equilibrium
sedimentation (E) or velocity sedimentation (V). Your answer would be a four-letter
string composed of letters E and V only, e.g. EEEE.
( )It separates subcellular components based on their buoyant density.
( )It can conveniently separate 15N-containing and 14N-containing DNA.
( )It uses a shallow sucrose gradient to stabilize the sedimentation bands against
convection.
( )In this method, subcellular components may either move up or down to form discrete
bands.
Toxoplasma gondii is an intracellular eukaryotic parasite that can cause serious human
infections. Which of the following is NOT true regarding this parasite?
A.It lyses its host cell to leave.
B.The energy for its invasion into the host cell comes from actin polymerization in the
host cell.
C.Once inside the cell, it is surrounded by a host-cell membrane that is deprived of
many host transmembrane proteins.
D.Once inside the cell, it absorbs nutrients and small metabolites from the host cytosol.
E.Its invasion mechanism is similar to that of malaria parasites.
An animal cell has been wounded and has a small rupture in its plasma membrane.
Which of the following is more likely to happen next?
A.The cell rapidly cleaves by cytokinesis.
B.The rate of receptor-mediated endocytosis is increased.
C.The rate of exocytosis is increased.
D.The rate of pinocytosis is increased.
E.All of the above.
Collagens are extremely rich in …
A.alanine and valine.
B.glycine and proline.
C.lysine and arginine.
D.serine and threonine.
E.tyrosine and phenylalanine.
Once expressed in a neuron in the mouse brain and subjected to a flash of light, how
does channelrhodopsin affect the membrane potential?
A.It causes neurotransmitter release, leading to an action potential in the postsynaptic
neuron.
B.It increases the membrane permeability to cations and makes the membrane potential
more negative.
C.It depolarizes the membrane, leading to the opening of voltage-gated Na+ channels.
D.It hyperpolarizes the membrane, leading to the inactivation of voltage-gated K+
channels.
E.It changes the membrane potential such that voltage-gated K+ channels but not
voltage-gated Na+ channels are activated.
Which of the following is directed by transcription activators in eukaryotic cells in
order to provide a more accessible DNA for the transcription machinery?
A.Nucleosome remodeling
B.Histone removal
C.Histone replacement
D.Histone modifications
E.All of the above
This large glycoprotein of the extracellular matrix is associated with elastin fibers and is
essential for their integrity. Its deposition in the developing connective tissues often
precedes the appearance of elastin. It is part of microfibrils that cover the elastic fibers.
This protein is …
A.collagen.
B.fibronectin.
C.fibrillin.
D.filamin.
E.laminin.
The wild-type nematode Caenorhabditis elegans has a bent body with the shape of a
wave. In the presence of increasing concentrations of ethanol, however, the body bend
is progressively diminished. Loss-of-function mutations in SLO-1, a gene that codes for
an ion channel, confer ethanol resistance and allow the worm to maintain its body bend
up to higher ethanol concentrations. The channel function is defined based on the ability
of the channel to conduct ions across the membrane. According to these observations,
would you expect the channel to open or close in the presence of ethanol in wild-type
worms? Would a gain-of-function mutation in SLO-1 tend to increase or decrease body
bend?
A.Open; increase
B.Open; decrease
C.Close; increase
D.Close; decrease
Activated STATs can induce the expression of SOCS proteins, which in turn inhibit the
JAK-dependent phosphorylation of the STATs. Under sustained serum stimulation of
mouse fibroblast cells, a number of oscillations can be observed as a consequence of
this delayed negative feedback loop, as shown in the following simplified graph.
According to this graph, approximately how long is the delay in the feedback response,
and what process is mainly responsible for it?
A.1 hour; transcription
B.2 hours; transcription
C.1 hour; mRNA export
D.1 hour; mRNA translation
E.2 hours; mRNA translation
A polyubiquitin chain has been attached to a protein. The ubiquitin molecules are linked
together via isopeptide bonds between Lys48 of one molecule and the carboxyl end of
the next one. This protein is expected to ___
A.be a part of chromatin.
B.undergo proteasomal degradation.
C.be involved in DNA repair.
D.be targeted to endocytic vesicles.
E.None of the above.
A membrane potential is plotted over time in the following graph. The Nernst
equilibrium potentials for four ions (A to D) that affect the membrane potential in this
system are indicated in the graph. What happened in the time period indicated by a
question mark?
A.Channels conducting ion A opened.
B.Channels conducting ion B opened.
C.Channels conducting ion C opened.
D.Channels conducting ion D opened.
E.Channels conducting ion A and C opened.
Indicate whether each of the following descriptions matches Cdc42 (C), Rac (R), or
Rho (H) from the Rho family of monomeric GTPases. Your answer would be a
three-letter string composed of letters C, R, and H only, e.g. HRR.
( )It activates formin.
( )It inhibits myosin II activity.
( )When constitutively active, it induces the formation of many prominent stress fibers.
Indicate true (T) and false (F) statements below regarding N-linked glycosylation of
proteins. Your answer would be a four-letter string composed of letters T and F only,
e.g. TTTF.
( )N-linked glycosylation can be carried out co-translationally, possibly at multiple
asparagine residues on the same protein molecule.
( )N-linked glycosylation is a gradual process, with step-by-step addition and trimming
events that commence with the addition of N-acetylglucosamine to an asparagine side
chain.
( )Most proteins synthesized in the rough ER are N-glycosylated, and some of them
require this modification for their correct folding.
( )Once a protein is properly folded in the ER, its attached oligosaccharides are quickly
removed by an N-glycanase, although it may be glycosylated again later.
Indicate whether each of the following membrane proteins releases its protein ligand
(R), remains bound to its protein ligand (B), or is degraded in the lysosome along with
its protein ligand (D) following receptor-mediated endocytosis. Your answer would be a
three-letter string composed of letters R, B, and D only, e.g. RBD.
( )LDL receptor
( )Transferrin receptor
( )EGF receptor
Indicate whether each of the following descriptions better matches bone (B) or cartilage
(C). Your answer would be a four-letter string composed of letters B and C only, e.g.
CCCC.
( )Its extracellular matrix is mainly composed of type I collagen and calcium crystals.
( )Its extracellular matrix is made by osteoblasts.
( )It grows by expansion (as opposed to surface apposition).
( )Its cells are connected via canaliculi and form gap junctions.
Indicate true (T) and false (F) statements below regarding cancer. Your answer would
be a four-letter string composed of letters T and F only, e.g. TFFF.
( )Cancer can be induced by infectious agents such as viruses.
( )The earlier a cancer is diagnosed, the better the chances are for a cure.
( )Most cancers originate from a single aberrant cell.
( )A single mutation is NOT enough to turn a normal cell into a cancer cell.
Imagine a human protein containing 33 repeats of a simple domain arranged in tandem.
In contrast, a homolog found in bacteria contains only one domain. What is the
minimum number of duplication events that can account for the evolution of this
protein since our divergence from bacteria? Write down the number as your answer, e.g.
200.
Indicate which feature (1 to 4) in the schematic drawing below of a chromatin fiber
corresponds to each of the following. Your answer would be a four-digit number
composed of digits 1 to 4 only, e.g. 2431
( )Nucleosome core particle
( )Linker DNA
( )Histone octamer
( )Non-histone protein