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In the following schematic graph of a hypothetical set of RNA-seq data, the number of
reads is plotted for a region of chromosome containing two genes, from samples
obtained from two different tissues. Which gene (X or Y) do you think is more likely a
"housekeeping" gene? Which region (1 or 2) within gene Y most likely corresponds to
an exon?
A.Gene X; region 1
B.Gene X; region 2
C.Both genes; region 1
D.Gene Y; region 1
E.Gene Y; region 2
To discover genes that have undergone accelerated evolution in the human lineage, you
compared the amino acid sequences of dozens of proteins from orthologous
protein-coding genes in humans, chimpanzees, and mice. For each gene, you build an
unrooted phylogenetic tree in which the branch lengths (a, b, or c) correspond to the
number of amino acid substitutions in that branch, as depicted below. Primates and
rodents diverged ~90 million years ago, and humans and chimpanzees diverged ~5.5
million years ago. For each individual gene shared by the three species, you therefore
define the "normalized substitution rate" parameters h and k as h = (a/5.5)/[c/([2 x 90] -
5.5)], and k=(b/5.5)/[c/([2 x 90] - 5.5)]. Based on these definitions, which genes are
more likely to be responsible for "uniquely human" traits?
A.Genes with very high h and k values
B.Genes with very low h and k values
C.Genes with very high h values but not very high k values
D.Genes with very high k values but not very high h values
Imagine a gene encoding a pre-mRNA with twelve exons, ten of which can be
alternatively spliced in vivo. Assuming that alternative splicing for this RNA only
occurs through exon skipping, how many different proteins can possibly be made from
this pre-mRNA as a result of alternative splicing?
A.About 10
B.About 20
C.About 100
D.About 200
E.About 1000
The bond energies associated with noncovalent attractions in the cell are too weak to
resist disruption by thermal motion. However, cellular macromolecules can interact
specifically AND strongly with each other (or fold by themselves) merely via such
interactions. How is this possible?
A.The bond energies increase radically when two interacting molecules approach each
other.
B.The interacting molecules also fortify their binding via covalent bonds to keep them
from dissociation.
C.Many weak bonds together in a complementary geometry can afford a strong binding.
D.The cell lowers its internal temperature to reduce thermal motion of molecules and
enhance the weak attractions.
Which of the following elements is not normally found in cells?
A.Copper
B.Iron
C.Silver
D.Cobalt
E.Zinc
Loss of the gene encoding shugoshin in many multicellular organisms leads to sterility,
suggesting defects in meiosis. What would you expect to occur in meiotic cells lacking
shugoshin?
A.The homologs fail to separate in anaphase I.
B.The sister chromatids fail to separate in anaphase II.
C.All chromatids separate prematurely in anaphase I.
D.Removal of cohesion between homolog arms fails in prophase I.
E.Removal of cohesion between sister chromatids fails in prophase II.
TSH is a pituitary hormone that stimulates the production of thyroid hormone by the
thyroid gland. This production can be blocked by sodium perchlorate (SP), which
inhibits the cellular import of iodine necessary for thyroid hormone synthesis. What
would be the effect of TSH or SP exposure, respectively, on the timing of
metamorphosis in frog larvae?
A.Premature metamorphosis; premature metamorphosis
B.Premature metamorphosis; delayed metamorphosis
C.Delayed metamorphosis; premature metamorphosis
D.Delayed metamorphosis; delayed metamorphosis
Consider two N-linked oligosaccharide chains on the same protein. The first chain
contains three mannose residues and three negatively charged sialic acid residues, as
well as other residues. The second chain contains only two N-acetylglucosamine and
eight mannose residues. Which chain seems to have been added to the protein such that
it is NOT fully accessible to the processing enzymes in the Golgi apparatus? Which
chain is Endo H-sensitive?
A.Chain one; chain one
B.Chain one; chain two
C.Chain two; chain one
D.Chain two; chain two
In many animals, siRNAs can only function within the cell in which the siRNA is
introduced. In contrast, the worm Caenorhabditis elegans can be fed with bacteria that
synthesize double-stranded RNAs, and the RNAi spreads throughout the animal. A
genetic screen to identify genes involved in systemic RNAi led to the discovery of
Sid-1, a transmembrane protein expressed in most tissues in the adult worm.
Loss-of-function mutations in the gene encoding Sid-1 restrict the RNAi activity to the
cells surrounding the digestive tract after siRNA feeding. Ectopic expression of Sid-1 in
Drosophila melanogaster cells that normally lack systemic RNAi and are unable to take
up siRNAs from the medium, enables these cells to passively take up siRNA . These
findings suggest that ___
A.Sid-1 is necessary and sufficient for systemic RNAi and siRNA uptake, respectively.
B.Sid-1 is necessary but not sufficient for systemic RNAi and siRNA uptake,
respectively.
C.Sid-1 is not necessary but is sufficient for systemic RNAi and siRNA uptake,
respectively.
D.Sid-1 is not necessary and not sufficient for systemic RNAi and siRNA uptake,
respectively.
Sort the following events to show the sequence in the mechanochemical cycle of
myosin II, following ATP binding by the head domain. Your answer would be a
four-digit number composed of digits 1 to 4 only, e.g. 1342.
(A)Myosin head binds tightly to actin.
(B)Power stroke is triggered.
(C)Cocking occurs and the head is displaced along the actin filament.
(D)The binding affinity of myosin for actin is reduced.
All cells in a multicellular organism have normally developed from a single cell and
share the same genome, but can nevertheless be wildly different in their shape and
function. What in the eukaryotic genome is responsible for this cell-type diversity?
A.The genes that encode transcription regulatory proteins
B.The regulatory sequences that control the expression of genes
C.The genes that code for molecules involved in receiving cellular signals
D.The genes that code for molecules involved in sending cellular signals to other cells
E.All of the above
Mutations in two important cancer-critical genes, encoding p53 and Rb, respectively,
are commonly found in cancers. What type of mutations are these expected to be?
A.Loss-of-function mutations in both genes
B.Loss-of-function mutation in p53 and gain-of-function mutation in Rb
C.Gain-of-function mutation in p53 and loss-of-function mutation in Rb
D.Gain-of-function mutations in both genes
The time courses of seeded actin polymerization under two different conditions are
compared in the following graph. If the overall kon for polymerization is known to be
the same under both of these conditions, which curve-(1) or (2)-corresponds to the
condition with a higher koff rate constant? Which one corresponds to a higher Cc for
polymerization?
A.Curve (1); curve (1)
B.Curve (1); curve (2)
C.Curve (2); curve (1)
D.Curve (2); curve (2)
E.Curve (2); both curves have the same Cc.
Dynamitin is a subunit of the dynactin complex. Its overexpression leads to the
disassembly of the complex, and it is therefore considered a dynactin inhibitor. Which
of the following processes would happen if dynamitin is overexpressed in a cell?
A.The motile cilia (if any) would stop beating because the axonemal dyneins could not
attach to their neighboring microtubules.
B.The Golgi apparatus would fragment and become dispersed because the cytoplasmic
dyneins could not associate with the Golgi membranes.
C.The endoplasmic reticulum would collapse because it could not recruit enough
kinesins.
D.The nuclear envelope would disintegrate because the nuclear lamins could not
interact with the cytoplasmic cytoskeleton.
E.The cortex would lose its integrity because the Arp 2/3 complex would also be
inhibited.
A hydrophobic molecule is typically ___
A.able to form hydrogen bonds with itself but not with water.
B.able to form hydrogen bonds with water.
C.charged.
D.hard to dissolve in a solvent.
E.incapable of interacting favorably with water.
The qualitative graph below shows the molecular changes accompanying vernalization
in the flowering plant Arabidopsis thaliana. Indicate which curve (A to D) in the graph
better represents the temporal changes in each of the following variables. Your answer
would be a four-letter string composed of letters A to D only, with each letter used once,
e.g. BACD.
( )
( )
( )
( )
The simplified drawing below depicts early stages of animal development. Indicate
which letter (A to E) in the drawing corresponds to each of the following terms. Your
answer would be a five-letter string composed of letters A to E only, e.g. ECDBA.
( )Blastula
( )Ectoderm
( )Endoderm
( )Mesoderm
( )Gastrula
In the fission yeast Schizosaccharomyces pombe, the proteins Cut1 and Cut2 form a
complex that is catalytically inactive. At the onset of anaphase, Cut2 is
polyubiquitylated by a large E3 complex containing Cut4, Cut9, Cut23, and other
proteins, and is subsequently destroyed. Cut1 then cleaves Rad21, a non-SMC
component of a complex that also contains two SMC proteins, thus allowing
sister-chromatid separation. Mutations in the cut genes lead to the cut phenotype, in
which the cell attempts cytokinesis without chromosome segregation. Indicate which of
the following proteins or protein complexes corresponds to or contains the product of
the genes cut1 (A), cut2 (B), cut4 (C), and rad21 (D). Your answer would be a
four-letter string composed of letters A to D only, e.g. DCAB.
( )Securin
( )Cohesin
( )Anaphase-promoting complex
( )Separase
Some viruses encode a protease that cleaves the translation initiation factor eIF4G,
rendering it unable to bind to eIF4E. What is the consequence of this cleavage?
A.It shuts down most of the cellular translation machinery, which causes the release of
virus particles.
B.It favors viral protein synthesis because IRES-dependent translation initiation is
inhibited.
C.It shuts down most host-cell protein synthesis and diverts the translation machinery to
IRES-dependent initiation, thus favoring viral protein synthesis.
D.It favors viral protein synthesis by shutting down translation from uORFs.
E.It shuts down IRES-dependent translation, forcing the virus into latency.
Considering the role of Notch and Wnt signaling pathways in epithelial cell
differentiation in the mammalian intestine, indicate whether each of the following
changes in "minigut" organoids in culture is expected to lead to a higher (H) or lower
(L) number of stem cells. Your answer would be a two-letter string composed of letters
H and L only, e.g. HH.
( )RNA interference knockdown of Hes1, an essential downstream effector of the Notch
signaling pathway
( )Deletion of the gene encoding Apc, a gene that is mutated in many colorectal cancers
Indicate true (T) and false (F) statements below regarding peroxisomal proteins. Your
answer would be a four-letter string composed of letters T and F only, e.g. TTTF.
( )All peroxisomal proteins are encoded in the nucleus.
( )Some peroxisomal proteins are synthesized by ribosomes attached to the rough
endoplasmic reticulum.
( )All peroxisomal proteins reach the organelle after their synthesis is completed.
( )Peroxisomal proteins have to be unfolded before import.
As each cell in our body prepares for mitosis, its chromosomes start to look different.
What are the changes in chromosome appearance that accompany the entry into M
phase? Indicate true (T) and false (F) descriptions below. Your answer would be a
five-letter string composed of letters T and F only, e.g. TTFFT.
( )The chromosomes become readily visible by the naked eye.
( )The chromosomes coil up further to become about 10 times shorter.
( )Each chromosome is condensed and then replicated to form two sister chromatids.
( )The typical diameter of a mitotic chromosome arm is about 70 nm.
( )The two sister chromatids are disentangled from each other by the time chromosome
condensation is complete.
In each of the following examples of contact signaling between adjacent cells in the
mammalian gut epithelia, indicate whether the signaling is mainly mediated by Delta
(D) or Ephrin (E) signals. Your answer would be a three-letter string composed of
letters D and E only, e.g. EDE.
( )Separation of crypt cell types from villus cell types
( )Regulation of stem-cell differentiation by Paneth cells
( )Differentiation of transit amplifying cells into either secretory cells or absorptive cells
Indicate true (T) and false (F) statements below regarding developmental timing in
animals. Your answer would be a four-letter string composed of letters T and F only,
e.g. TTTT.
( )Cell-division cycles generally serve as an intracellular timer that controls the timing
of cellular differentiation.
( )Developmental transitions are often regulated by microRNAs.
( )Intracellular developmental programs are often followed even if the cells are taken
from the developing embryo and maintained in culture.
( )Timing of developmental transitions can be coordinated by cell-cell interactions as
well as globally by hormones.
Indicate true (T) and false (F) statements below regarding meiosis in eukaryotic cells.
Your answer would be a four-letter string composed of letters T and F only, e.g. TFFF.
( )Bivalents form before prophase I.
( )Crossing-over begins before the synaptonemal complex assembly.
( )Chiasmata can first be seen under the microscope after the disassembly of the
synaptonemal complexes.
( )All recombination events lead to crossovers.
Fill in the blank: "The ... is a large structure formed at the centromeric region of each
eukaryotic chromosome. It captures spindle microtubules in mitosis, and therefore
serves to attach the chromosomes to the spindle poles."
Each cycle of PCR doubles the amount of DNA synthesized in the previous cycle. A
pair of primers is used to direct the specific synthesis of a desired DNA segment. The
following diagram shows the products of PCR amplification after three cycles. The
DNA strands of the desired segment are indicated in yellow boxes in the diagram. As
shown, at the end of the third cycle, 8 out of 16 strands have the desired length and are
boxed. After four more cycles (i.e. at the end of the seventh cycle), how many strands
of DNA are expected to be synthesized? How many of them have the desired length?
Write down the two numbers and separate them with a comma, e.g. 16,8.
Indicate whether each of the following descriptions better applies to a cancer cell (C) or
a normal adult cell (N). Your answer would be a four-letter string composed of letters C
and N only, e.g. CCNC.
( )Higher lactate production
( )Higher oxidative phosphorylation
( )Contact inhibition
( )Anchorage independence
