To enter the host cell, intracellular bacterial pathogens can induce phagocytosis in cells
that are normally nonphagocytic. This is done by two major mechanisms depicted in the
following schematic diagrams (A and B). Indicate whether each of the following
descriptions better applies to mechanism A or B. Your answer would be a four-letter
string composed of letters A and B only, e.g. ABAA.
( )It is called the zipper mechanism.
( )It depends on invasin proteins on the surface of the bacterium that bind to their receptors
on the surface of the host cell.
( )It depends on the injection of effector proteins into the host cell by a bacterial secretion
system.
( )It resembles the process of macropinocytosis.
You have synchronized a culture of HeLa cells so that the cells are all at the same stage
in the cell cycle. You then treat the cells with serum containing nutrients and growth
factors in the presence or absence of the drug rapamycin. The distribution of cell sizes
in the two cell populations is shown below. Based on these results, do you think
rapamycin is an activator or inhibitor of the TOR complex? Is the S6 kinase expected to
be up-regulated or down-regulated in the presence of rapamycin?
A
A.Activator; up-regulated
B.Activator; down-regulated
C.Inhibitor; up-regulated
D.Inhibitor; down-regulated
Which of the following statements is true regarding reactions involving oxidation and
reduction?
A.The carbon atom is more oxidized in formaldehyde (CH2O) than in methanol
(CH3OH).
B.Oxidation of food in all organisms requires oxygen.
C.A molecule is oxidized if it gains an electron (plus a proton) in a reaction.
D.A dehydrogenation reaction is a reduction.
E.In an organic molecule, the number of C-H bonds increases as a result of oxidation.
The following schematic graph shows the result of two quantitative RT-PCR
experiments. Total mRNA from two tissue samples (1 and 2) was isolated and subjected
to RT-PCR using primers designed to amplify a tissue-specific gene. Added to the
reaction was a fluorescent dye that fluoresces only when bound to double-stranded
DNA. According to the graph, which tissue has a higher level of this mRNA? By how
much?
A.About 2-fold higher in tissue 1
B.About 1000-fold higher in tissue 1
C.About 2-fold higher in tissue 2
D.About 1000-fold higher in tissue 2
Rough microsomes can be subjected to a ‘salt extraction” procedure in which a high salt
concentration is used to remove membrane-associated ribosomes and peripheral
proteins. Such salt-extracted microsomes are known to be translocation-incompetent,
meaning that when present co-translationally in vitro, they fail to protect translated
proteins from protease digestion. However, adding back an 11S particle (S is the
sedimentation coefficient) purified from the salt-wash fraction is sufficient to restore the
protein-translocation activity of the salt-extracted microsomes. Which of the following
do you think is true regarding the 11S particle?
A.It is composed of 21 proteins.
B.It is a digestion product of ER-associated ribosomes.
C.It is normally assembled in the nucleus and exported to the cytoplasm by exportins.
D.It is an ER integral membrane protein that can interact with the translocon.
E.It requires high salt concentration for its function in vivo.
Electron microscopy samples are often chemically fixed before dehydration,
resin-embedding, and sectioning. But they can also be “fixed” by rapid freezing, in a
way that precludes ice-crystal formation, to ensure minimal damage to the original cell
structures. How can this be done?
A.High-pressure cooling
B.Plunging into liquid nitrogen
C.Spraying with a jet of liquid propane
D.Contact with a copper block cooled by liquid helium
E.All of the above
For each of the following genes involved in regulation of cell growth through the
mTOR pathway, indicate whether the gene is activated (A) or inactivated (I) in cancer
cells compared to normal healthy cells. Your answer would be a four-letter string
composed of letters A and I only, e.g. AAAA.
( )mTOR
( )Akt
( )PTEN
( )PI3K
Which of the following processes takes place in the nucleoli within the eukaryotic
nucleus?
A.Ribosome assembly
B.rRNA gene transcription
C.Telomerase assembly
D.tRNA processing
E.All of the above
Two ligands, A and B, bind to two different conformations of the enzyme X. The ligand
A is the enzyme’s substrate, whereas ligand B binds to a remote allosteric site. Which of
the following is a consequence of this arrangement?
A.Binding of A to X does not affect the affinity of X for binding to B.
B.Binding of B to X does not affect the rate of reaction catalyzed by X.
C.Binding of A to X increases the affinity of X for B.
D.Binding of B to X decreases the affinity of X for A.
E.Binding of B to X has a large effect on the binding of A to X, but binding of A to X
has a small effect on X-B binding.
In the following representation of a single-stranded RNA molecule, the nucleotide
residues are drawn as gray circles, while base-pairing interactions between them are
indicated by dashed lines. The structure of this RNA molecule has___
A.one hairpin loop and one pseudoknot.
B.one pseudoknot only.
C.three hairpin loops and a four-stem junction.
D.two hairpin loops and a three-nucleotide bulge.
E.three hairpin loops.
In the following schematic graph, the fraction of promoters (px) bound to the regulatory
protein A is plotted at various concentrations of A. Which of the following quantities
represents X in the graph?
A.[Total px]
B.[px]
C.kon / koff
D.koff / kon
E.kon[px] / koff
A simple protein interaction map is shown below for human cytochrome c (Cyt), a
heme-containing protein that is normally found inside the mitochondria and is
associated with the electron-transport chain (ETC) of the inner mitochondrial
membrane. Under special emergency conditions, this protein can also moonlight as a
signal transducer for the onset of a pathway leading to programmed cell death (PCD).
As shown in the map, it also interacts with a group of phosphoprotein phosphatases
(PPP) involved in cell signaling pathways. Assuming that the functions of the proteins
labeled as X, Y, and Z are unknown, which of the following points can be reasonably
argued from this interaction map?
A.The protein labeled X probably functions in PCD as well as in the ETC, because it
interacts with cytochrome c, which is known to be closely involved in PCD, and it also
interacts with several proteins from the ETC group.
B.The protein labeled Y probably has a role in PCD, especially if its orthologs in other
organisms have such a role and show a similar pattern of interactions.
C.If the proteins in the PCD group are known to form a large complex, then the protein
labeled Z is likely to be the scaffold protein for that complex.
D.The protein labeled Y probably has a phosphatase function, because it interacts with
the proteins of the PPP group.
E.The protein labeled Z is probably not an essential protein because it only interacts
with one other protein in this map.
The human estrogen receptor is a symmetrical dimeric nuclear protein that can regulate
gene expression by binding to a DNA sequence called an estrogen response element
(ERE) near the promoter of its target genes. Each subunit of the receptor binds to about
six base pairs of DNA. Which of the following sequences is a likely candidate for the
ERE? The sequences are written in the 5′-to-3′ direction. The letter N represents any of
the four DNA bases.
A.AGGTCANNNTGACCT
B.AGGTCANNNAGGTCA
C.AGGTCANNNACTGGA
D.AGGTCANNNATATAT
E.AGGCCTNNNTCATGA
Insulin is a secretory protein made by the cells in the pancreas. This protein ___
A.is released by the cells in response to increased intracellular Ca2+ concentration.
B.is first synthesized as preproinsulin.
C.is stored as aggregates inside secretory vesicles in the cells.
D.undergoes proteolytic cleavage before secretion.
E.All of the above.
In a cross section of a vertebrate axon, longitudinally organized cytoskeletal proteins
can be seen as dots, as shown in the schematic drawing below. What type of filaments
do these dots represent?
A.Microtubules and microfilaments
B.Microtubules and vimentins
C.Microtubules and neurofilaments
D.Microtubules and keratins
E.Microtubules and septins
What is the advantage of using quantum dots as an alternative to organic fluorochromes
such as Cy3 and Alexa dyes?
A.They are brighter.
B.Their emission spectra can be precisely fine-tuned.
C.They have a longer lifetime and bleach more slowly.
D.All of the above.
In interactions between proteins, each hydrogen bond contributes to the free energy of
binding by about -4 kJ/mole. If two proteins bind to each other through nine hydrogen
bonds, six of which are eliminated when one of these proteins is mutated, how much
would you expect the equilibrium constant for their binding to change as a result of the
mutation? ( G° = -5.9 x log Keq)
A.Increase sixfold
B.Decrease fourfold
C.Decrease by six orders of magnitude
D.Increase 1 million-fold
E.Decrease by four orders of magnitude
Consider a transcription regulatory protein that has both a nuclear localization and a
nuclear export signal and is normally found both in the nucleus and in the cytosol at
comparable concentrations. This protein has a high-affinity binding partner in the
nucleus. Upon activation of a certain signaling pathway, the binding protein is
ubiquitylated and degraded. As a result of this, ___
A.the transcription regulatory protein accumulates in the nucleus.
B.the transcription regulatory protein accumulates in the cytosol.
C.the distribution of the transcription regulatory protein does not change, but the
expression of its target genes may be altered.
D.the distribution of the transcription regulatory protein does not change, and the
expression of its target genes is not necessarily changed as a result of the degradation
event.
T cell receptors that do not interact at all with self-peptide-MHC complexes during T
cell development in the thymus normally undergo …
A.positive selection.
B.negative selection.
C.receptor editing.
D.clonal suppression.
E.”death by neglect.”
Indicate true (T) and false (F) statements below regarding the interaction of cells with
the extracellular matrix using matrix receptors. Your answer would be a four-letter
string composed of letters T and F only, e.g. TFTT.
( )Integrins are the only known matrix receptors in animal cells.
( )Integrins can transmit signals in both directions across the membrane; that is, both
outside-in and inside-out.
( )Tension can increase the binding affinity of an integrin for its intracellular and
extracellular ligands.
( )Integrins can convert molecular signals into mechanical ones.
If a certain isoform of myosin II is depleted from a cell, stress fibers are lost and focal
adhesions disappear. If these cells are placed on a surface coated with an array of
flexible pillars to measure traction forces, would you expect the traction to increase (I)
or decrease (D) in these cells compared to wild-type cells? Write down I or D as your
answer.
The pathogen Listeria monocytogenes can hijack the actin cytoskeleton in human cells
and spread inside the host. Indicate true (T) and false (F) statements below about this
phenomenon. Your answer would be a four-letter string composed of letters T and F
only; e.g. TTFF.
( )The movement can be reconstituted in vitro by placing the bacteria in a mixture of
actin, formin, gelsolin, and capping protein.
( )Cofilin counteracts the movement by depolymerizing actin filaments.
( )The actin filaments grow with their minus ends pointed toward the bacterium.
( )The movement depends on myosin activity to transport the bacteria on the actin
filaments.
Fill in the blank in the following paragraph. DO NOT use abbreviations.
“A significant fraction of total membrane area in a eukaryotic cell encloses the lumen of
the ___, which forms an extended netlike labyrinth of tubules and sacs. Secretory
proteins are normally synthesized by ribosomes bound to a special type of this
compartment.”
You are viewing a sample of pond water under the microscope. The sample contains a
variety of microorganisms, some moving faster than others. You spot a Paramecium that
is being followed by a Didinium almost as large as itself; the Paramecium initially
swims away and tries to escape, but Didinium, which moves in faster bursts, finally
stops it and attaches firmly onto the side of the Paramecium and proceeds to eat it.
What type of endocytosis will ensue? Write down the name of the process as your
answer. Do not use abbreviations.
Cadherin molecules at the cell surface are often clustered side-to-side to create a
molecular Velcro that attaches the cell to another cell or to the extracellular matrix. In
the following simplified drawings, two cells are initially attached via such a Velcro.
When one of the cells moves in either of three different ways (A to C), it is faced with a
mechanical resistance from the cadherin interactions. The resistance against which type
of movement do you think is the weakest? Write down A, B, or C as your answer.