Which of the following actin-binding proteins cannot bind to the same actin filament
simultaneously?
A.Gelsolin and tropomodulin
B.Tropomyosin and tropomodulin
C.Profilin and tropomodulin
D.Cofilin and CapZ
E.Formin and CapZ
This protein folds into a doughnut shape that can encircle DNA. It can load on the DNA
only when the DNA is broken in both strands, so that the DNA can thread through the
hole in the protein. Which of the following proteins do you think matches this
description?
A.PCNA, the sliding clamp for DNA polymerases at the replication forks
B.Ku, the protein that recognizes DNA ends and can initiate nonhomologous end
joining
C.MCM, the helicase critical for the initiation and elongation of replication
D.Topoisomerase II, which can create or relax superhelical tension in DNA
E.RecA/Rad51, which carries out strand invasion in homologous recombination
If this protein is unable to hydrolyze its bound GTP, invaginated clathrin-coated pits
accumulate but fail to pinch off from the plasma membrane. In neurons, long vesicle
necks collared by the protein are observed and presynaptic endocytosis is blocked. This
protein ___
A.contains a PI(4,5)P2 binding domain and a GTPase domain.
B.recruits other proteins to the neck of the vesicle.
C.may change the membrane lipid composition by recruiting lipid-modifying enzymes.
D.may directly distort the membrane using the energy from GTP hydrolysis.
E.All of the above.
Indicate true (T) and false (F) statements below regarding mRNA splicing in human
cells. Your answer would be a four-letter string composed of letters T and F only, e.g.
TFFF.
( )Introns must be removed in the order in which they occur along the pre-mRNA.
( )Nucleosomes tend to be positioned over exons (on average, about one nucleosome
per exon).
( )Exon size tends to be much more variable than intron size.
( )The exon junction complexes mark the sites on the mRNA where splicing has not
been successful.
The p53 gene is an important tumor suppressor gene in our genome. It codes for a
transcription regulatory protein that can assemble into tetramers. A number of mutations
in p53 render the protein inactive. These mutant protein molecules form mixed
tetramers with wild-type p53 proteins and, in this case, the tetramer is inactive. The
mutations can therefore be categorized as ___
A.null.
B.gain-of-function.
C.recessive lethal.
D.dominant-negative.
E.suppressor.
From left to right, indicate if each of the following schematic drawings represents the
typical overall organization of actin filaments (A), microtubules (M), or intermediate
filaments (I) in an animal cell. Your answer would be a three-letter string composed of
letters A, M, and I only; e.g. AMI.
In sequence alignments such as those generated by a BLAST search, the significance of
the alignment can be presented as an E-value, which specifies how likely it is for a
match this good to be found in a database of a given size by chance. You have scanned
a large sequence database with a sequence query, hoping to find a significant match.
Which one would you look at: (A) a match with an E-value of 1, or (B) one with an
E-value of 0.001? Write down A or B as your answer.
In antigen presentation to helper T cells (TH cells), both the TCR and co-receptor
proteins…
A.are expressed on the dendritic cell.
B.bind to the class II MHC protein.
C.bind to the presented peptide antigen.
D.All of the above.
Imagine the reaction A –> B with a negative G value under experimental conditions.
Which of the following statements is true about this reaction?
A.The reaction is energetically unfavorable.
B.The reaction proceeds spontaneously and rapidly under these conditions.
C.Increasing the concentration of B molecules would increase the G value (toward
more positive values).
D.The reaction would result in a net decrease in the entropy (disorder) of the universe.
E.The reaction cannot proceed unless it is coupled to another reaction with a positive
value of G.
What is the effect of using scaffold proteins on precision and amplification capacity in
cell signaling?
A.Both precision and amplification are improved.
B.Precision is improved, but amplification is limited.
C.Precision is compromised, but amplification is improved.
D.Both precision and amplification are limited.
A viral version of the Src kinase called v-Src is found in some retroviruses. Unlike the
cellular Src, the v-Src kinase is constitutively active, and can drive the cell into
uncontrolled growth and tumor formation. Which of the following molecular
differences between the two versions of Src is more likely to be responsible for this?
A.v-Src lacks the active-site tyrosine residue.
B.v-Src lacks a lobe of the kinase domain.
C.v-Src has multiple inhibitory tyrosine phosphorylation sites in the kinase domain.
D.v-Src lacks the C-terminal tail that can bind to Src’s SH2 domain.
E.v-Src has a longer C-terminal tail.
Indicate whether each of the following descriptions better applies to Illumina
sequencing (I), Ion Torrent sequencing (T), or both sequencing technologies (B).
Your answer would be a four-letter string composed of letters B, I, and T only, e.g.
IBBB.
( )It uses fluorescently labeled nucleotides.
( )It uses PCR-generated copies of DNA.
( )It is a second-generation sequencing technology and employs a cyclic
wash-and-measure paradigm.
( )It relies on the fidelity of DNA polymerase for its accuracy.
Which stage is usually the longest in meiosis?
A.Prophase I
B.Prometaphase I
C.Telophase I
D.Prophase II
E.Prometaphase II
Adaptor proteins select cargo proteins that will be incorporated into clathrin-coated
vesicles. An adaptor protein such as AP2 ___
A.can induce membrane curvature even before clathrin molecules bind.
B.acts as a coincidence detector, assembling only when a number of requirements are
met.
C.binds to phosphoinositides in the cytosolic leaflet of the membrane.
D.alternates between a locked cytosolic form and an unlocked membrane-bound form.
E.All of the above.
In Drosophila melanogaster, loss-of-function mutations in either Pink1 or Parkin show
similar phenotypes including impaired ability to fly, male sterility, and degeneration of
dopaminergic neurons. Transgenic overexpression of Parkin in mutants lacking Pink1
significantly ameliorates the loss-of-function phenotype, but overexpression of Pink1
cannot rescue the Parkin loss-of-function phenotype. According to these findings,
which protein is more likely to act upstream of the other one? Assuming that the Parkin
loss-of-function phenotype is merely due to defects in autophagy, would you expect
Parkin overexpression to also rescue an ATG9 loss-of-function phenotype?
A.Parkin acts upstream of Pink1; yes
B.Parkin acts upstream of Pink1; no
C.Pink1 acts upstream of Parkin; yes
D.Pink1 acts upstream of Parkin; no
Which of the following is a major consequence of activation of phospholipase C-
(PLC ) by the Gq trimeric GTPase?
A.Elevation of intracellular cAMP levels, leading to the activation of protein kinase A
B.Elevation of PIP3 levels in the plasma membrane, leading to the activation of protein
kinase B
C.Elevation of intracellular Ca2+ levels, leading to the activation of protein kinase C
D.Elevation of IP3 in the plasma membrane, leading to the activation of protein kinase
D
E.Elevation of intracellular cGMP levels, leading to the activation of protein kinase G
In intestinal epithelial cells, the different plasma membrane domains are separated from
each other by special barriers. Indicate true (T) and false (F) statements below
regarding this separation. Your answer would be a four-letter string composed of letters
T and F only, e.g. FFFF.
( )These barriers are set up by nanoscale lipid raft domains.
( )Proteins normally cannot pass through these barriers, whereas any membrane lipid
can do so freely.
( )The asymmetric distribution of membrane proteins resulting from these barriers is
functionally important.
( )These barriers are a result of proteins of the apical surface forming a large aggregate
together that excludes proteins of the other domains.
Which of the following schematic drawings better depicts the regulatory network that
maintains Engrailed (en), Hedgehog (hh), and Wingless (wg) expression following
cellularization in a developing Drosophila embryo?
Indicate whether each of the following occurs on the cytosolic side of the ER
membrane (C), on the lumenal side of the ER membrane (L), or in the Golgi apparatus
(G). Your answer would be a five-letter string composed of letters C, L, and G only, e.g.
GGGLC.
( )Assembly of GlcNAc oligosaccharides on dolichol phosphate
( )Synthesis of phosphatidylcholine
( )Synthesis of sphingomyelin
( )Ubiquitylation of misfolded ER protein
( )Synthesis of phosphatidic acid
Consider the movement in the host cell of two intracellular pathogens, the herpes
simplex virus (H) and the bacterium Listeria monocytogenes (L). Indicate whether each
of the following descriptions better applies to the virus (H) or the bacterium (L). Your
answer would be a four-letter string composed of letters L and H only, e.g. HLLL.
( )It moves by a “pushing” mechanism (as opposed to a “pulling” mechanism).
( )It can collide with the plasma membrane and create long, thin protrusions from the
cell that can then be engulfed by a neighboring cell.
( )Its movement is powered by ATP hydrolysis by kinesin and dynein motors.
( )Its movement relies on dynamic cytoskeletal filaments.
Indicate true (T) and false (F) statements below regarding cellular signaling mediated
by nitric oxide (NO). Your answer would be a four-letter string composed of letters T
and F only, e.g. TTTF.
( )Once produced, NO can diffuse to neighboring cells.
( )NO has known roles in cGMP-independent as well as cGMP-dependent signaling.
( )NO normally decreases cGMP concentration by activating cGMP phosphodiesterase.
( )The drug Viagra counteracts the effects of NO on penile blood vessels.
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.
( )Cancers become less and less heterogeneous as they progress.
( )Knocking out Ras or Myc genes individually leads to a higher incidence of cancers in
mice, and knocking out both genes simultaneously has an even stronger phenotype.
( )Wnt signaling is important in colon epithelial cells and, correspondingly, mutations in
genes in the Wnt pathway are present in most colorectal cancers.
( )Genome destabilization in a subset of colorectal cancers that have defects in DNA
mismatch repair takes the form of chromosome breaks, translocations, and deletions.
Indicate whether each of the following cancers can be best classified as a carcinoma
(C), sarcoma (S), or neither of the two (N). Your answer would be a four-letter string
composed of letters C, S, and N only, e.g. SSNC.
( )Breast cancer
( ) Lung cancer
( ) Colorectal cancer
( )Myeloma
You have isolated epithelial cells from mouse mammary glands and have grown them in
a three-dimensional gelatinous matrix in the presence or absence of a specific inhibitor
that targets a transmembrane metalloprotease. The protease is capable of cleaving
cadherin near the base of its extracellular domain to release an N-terminal fragment
containing the extracellular cadherin domains. The distribution of the cells in the
matrix, as seen under a light microscope, one day after the transplantation of the
isolated tissue is presented in the following schematic drawings. Which condition (1 or
2) do you think corresponds to the presence of the protease inhibitor? Write down 1 or 2
as your answer.
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.
Which amino acid residues shown above have acidic side chains? Write down the
one-letter abbreviations for them, in alphabetical order, e.g. ACGNV.