Which of the following is correct regarding aequorin?
A.It is a small molecule used to detect calcium ions in vivo.
B.It is a fluorescent dye.
C.It emits blue light in the presence of calcium ions.
D.It can be used in animal cells but not plant cells.
E.All of the above.
In the following schematic drawings showing four different network motifs in gene
transcription circuits, indicate whether each of the motifs 1 to 4 corresponds to a
feed-forward loop (E), flip-flop device (F), negative feedback loop (N), or positive
feedback loop (P). Your answer would be a four-letter string composed of letters E, F,
N, or P only, e.g. PNEF.
Consider a signaling protein that is only made up of one SH2 domain and two SH3
domains. This protein is most likely …
A.a monomeric G protein.
B.a guanine nucleotide exchange factor.
C.a kinase associated with receptor tyrosine kinase signaling.
D.an adaptor protein.
E.a negative regulator of receptor tyrosine kinase signaling.
The copy number of some human genes, such as the salivary amylase gene AMY1,
varies greatly between different individuals. The salivary amylase breaks down some of
the dietary starch into smaller sugars. In the case of AMY1, a positive correlation has
been observed between the copy number and the amount of amylase in the saliva. Gene
copy number per diploid genome can be estimated by performing a quantitative
polymerase chain reaction (PCR) using primers specific to the gene of interest. You
have performed such PCR experiments on samples from two human populations that
have traditional diets with low and high starch levels, respectively, and have plotted the
data in the histogram below. Which population (A or B) in the histogram is likely to be
the one with traditionally higher dietary starch? Write down A or B as your answer.
Which of the following is NOT a common second messenger in cell signaling?
A.Ca2+
B.Cyclic adenosine monophosphate
C.Diacylglycerol
D.Tyrosine
E.Inositol trisphosphate
Which of the following cell types is NOT phagocytic?
A.Macrophage
B.Monocyte
C.Neutrophil
D.Lymphocyte
E.Dendritic cell
In which phases of the eukaryotic cell cycle does homologous recombination often
occur to repair DNA damage?
A.G1 and S phases
B.S and G2 phases
C.G2 and M phases
D.M and G1 phases
E.G1 and G2 phases
Which microscopy set-up uses a longer wavelength of light than usually excites a
particular fluorophore? Which one allows researchers to peek deeper into biological
samples?
A.Single-photon; single-photon
B.Single-photon; two-photon
C.Two photon; single photon
D.Two-photon; two-photon
The centromeric regions in the fission yeast Schizosaccharomyces pombe are wrapped
by nucleosomes containing the CENP-A histone H3 variant, and are flanked by clusters
of tRNA genes that separate them from the surrounding pericentric heterochromatin. If
the tRNA clusters are removed from this region, the HP1-bound heterochromatin
spreads further to cover the centromeric regions. The tRNA genes are transcribed by
strong RNA polymerase III promoters, which can associate with transcription factors
and recruit chromatin-modifying enzymes.
Based on these observations, indicate which blanks (A to E) in the paragraph below
correspond to each of the following phrases. Your answer would be a five-letter string
composed of letters A to E only, e.g. BCDEA.
“The ___(A) are not sufficient to prevent heterochromatin expansion to the centromeric
regions. Instead, the ___(B) are acting as ___(C) in S. pombe, similar to the role of the
___(D) in the -globin locus in chickens and humans. Likely candidates for the
histone-modifying enzymes recruited by the RNA polymerase III complexes are
___(E).”
( )HS4 element
( )chromatin boundaries
( )histone acetyl transferases
( )tRNA genes
( )CENP-A-containing histones
Indicate true (T) and false (F) statements below regarding the initiation of replication in
human cells. Your answer would be a four-letter string composed of letters T and F
only, e.g. TFFF.
( )Tens of thousands of replication origins are used each time a cell in our body
replicates its DNA.
( )Different cells in our body use different sets of replication origins.
( )Both replication forks in a replication bubble are normally active in replication.
( )Gene expression and chromatin structure can affect the choice of the origins to use as
well as the order in which they are activated.
You know that a particular sequence at the C-terminus of the lectin ERGIC53 enhances
its exit from the endoplasmic reticulum (ER). You create two mutant versions of the
protein, one without the suspected sequence (1) and one in which the sequence is
replaced with an ER retention signal (2). You transfect a fibroblast cell line with a
plasmid that encodes either wild-type ERGIC53 (0) or one of the engineered versions of
it (1 or 2). After inducing the expression of the proteins, you lyse the cells and either
treat the lysate with endoglycosidase H (Endo H) or leave the lysate untreated, as
indicated below. You then separate the proteins by SDS-PAGE and perform a Western
blot to detect the bands corresponding to ERGIC53. Your results are represented in the
following drawing. Which lanes (A to C) do you expect to correspond to each of the
proteins 0, 1, and 2, respectively? Your answer would be a three-letter string composed
of letters A to C only, e.g. CAB.
Indicate true (T) and false (F) statements below regarding RNA editing. Your answer
would be a four-letter string composed of letters T and F only, e.g. TTTF.
( )RNA editing in animal cells mainly takes place through adenine or cytosine
deamination.
( )RNA editing can change the pattern of pre-mRNA splicing.
( )RNA editing in coding regions can result in changes in the protein sequence.
( )Retroviruses such as HIV encode RNA-editing components to confront the host
defense mechanisms.
Indicate true (T) and false (F) statements below regarding the properties of cancer cells.
Your answer would be a four-letter string composed of letters T and F only, e.g. TFFF.
( )Cancer cells invade and colonize territories that normally belong to other cells.
( )Unlike in normal tissues, cell death is extremely rare in tumors.
( )Cancer cells grow and proliferate in defiance of normal restraints.
( )Malignant tumors are composed of cells that grow and proliferate, but still have not
acquired invasiveness.
In which of the following schematic drawings of signaling pathways does the activation
of the receptor lead to gene expression? Activating and inhibitory steps are indicated
with (+) and (€), respectively.
Indicate whether each of the following descriptions applies to visual signal transduction
(V), olfactory signal transduction (O), or both (B). Your answer would be a four-letter
string composed of letters V, O, and B only, e.g. VOVV.
( )It involves cGMP as a second messenger.
( )A rise in cyclic mononucleotide concentration follows the arrival of the signal.
( )The signal is received by a G-protein-coupled receptor.
( )An incoming signal leads to membrane hyperpolarization.
In the following graphs, the cellular response, as measured in real time by the
concentration of a certain active effector protein, is plotted over time for five cell types
(A to E) that are treated with three different concentrations of a signal molecule. During
the time period indicated by the horizontal gray bar, the signal molecule is present in
the culture media at a concentration of 1 nM (dotted curve), 5 nM (gray curve), or 25
nM (solid curve). Answer the following question(s) based on these graphs.
Which of the cell types A to E shows a response with the highest persistence?
Indicate whether each of the following descriptions better applies to a Wee1 protein (W)
or a Cdc25 protein (C). Your answer would be a four-letter string composed of letters W
and C only, e.g. WWCW.
( )It is a protein kinase.
( )It activates M-Cdk complexes.
( )It is activated by M-Cdk complexes.
( )Its loss in fission yeast results in small cell size.
Imagine a morphogen gradient established from left to right in a field of cells in a
developing tissue, as shown in the following schematic diagram. Below a first threshold
of morphogen concentration, cells do not respond to the morphogen and express gene
“red” by default. Cells exposed to morphogen concentrations above this threshold
respond by expressing gene “white” instead, while those exposed to even higher
concentrations, above a second threshold, express gene “blue.” As shown, the initial
pattern resembles a French flag with equally wide blue, white, and red expression
domains. With no other change, if the diffusion rate of the morphogen is increased (by a
modification that decreases its affinity for heparan sulfate proteoglycans, for example),
the gradient profile changes from the gray curve to the black curve, as indicated. Under
this new condition, indicate whether each of the following would be expected to
increase (I), decrease (D), or remain unchanged (U) in its range. Your answer would be
a three-letter string composed of letters I, D, and U only, e.g. UUI.
( )Blue expression domain
( )White expression domain
( )Red expression domain
Beckwith-Wiedemann syndrome in humans is characterized by “overgrowth” in
childhood, sometimes leading to unusually large parts of the body. An imprinted gene
cluster on chromosome 11 is associated with this disease. The cluster contains several
genes including Igf2 and H19. Igf2 encodes an insulin-like growth factor that is
maternally imprinted, i.e. the maternal copy is not expressed. However, the DNA
methylation pattern of this locus is not different between the two homologous
chromosomes. On the other hand, H19 is also imprinted and its methylation pattern
does differ between the two parental chromosomes. H19 is transcribed into a noncoding
RNA that appears to silence the transcription of the Igf2 gene in cis. Would you expect
the H19 locus to be hypermethylated in the maternally inherited chromosome (M) or
paternally inherited chromosome (P)? Write down M or P as your answer.
The schematic graph below represents the nullclines (solid curves) and a few selected
trajectories (dotted curves) for a system composed of two proteins (X and Y) with a
complex regulatory behavior. According to the graph, indicate whether each of the
following statements is (Y) or is not (N) acceptable. Your answer would be a four-letter
string composed of letters Y and N only, e.g. YYYY.
( )The system is bistable.
( )There are three steady states in the system.
( )The system contains positive feedback.
( )The system contains delayed negative feedback.