Which of the following is NOT true regarding vertebrate segmentation?
A.The presomitic mesoderm retreats tailward as new somites are generated.
B.The period of gene-expression oscillations in the presomitic mesoderm determines
the size of each somite.
C.If feedback delays in the gene-expression oscillations are increased, somite size will
consequently increase as well.
D.Notch-mediated lateral inhibition ensures that the segmentation clock is different in
neighboring cells in the presomitic mesoderm.
Considering the following hydropathy plot for a multipass transmembrane protein in the
plasma membrane, are the protein termini expected to be located inside (I) or outside
(O) of the cell? Which of the regions indicated as 2 and 3 in the plot is expected to have
more positively charged residues? The position of positively charged residues near the
first transmembrane helix is indicated by an asterisk on the plot.
A.I; 2
B.I; 3
C.O; 2
D.O; 3
The nuclear DNA polymerases in human cells ___
A.polymerize about 1000 nucleotides per second during DNA replication in vivo.
B.are incapable of 3′-to-5′ exonuclease activity.
C.are capable of 3′-to-5′ DNA polymerase activity.
D.have a single active site that is used for both polymerization and editing.
E.are unable to initiate polymerization de novo (i.e. in the absence of a primer).
Steps 6 and 7 of glycolysis are catalyzed by the enzymes glyceraldehyde 3-phosphate
dehydrogenase and phosphoglycerate kinase, respectively. Together, they …
A.result in the oxidation of an aldehyde to a carboxylic acid.
B.produce both ATP and NADH.
C.couple the oxidation of a C-H bond to the activation of carrier molecules.
D.catalyze the only glycolytic reactions that create a high-energy phosphate linkage
directly from inorganic phosphate.
E.All of the above.
Modifications of membrane traffic in host cells by three bacterial pathogens are shown
in the following schematic drawing. Indicate whether each of the following bacteria is
represented by A, B, or C in the drawing. Your answer would be a three-letter string
composed of letters A to C only, e.g. BCA.
( )It is a common cause of food poisoning in humans.
( )It causes the life-threatening lung infection tuberculosis.
( )It is the cause of a type of pneumonia known as Legionnaire’s disease.
What is the main source of the free energy for the mechanical work performed by DNA
helicases during DNA replication in our cells?
A.The hydrogen-bonding energy in the DNA double helix
B.Thermal energy in the nucleus
C.ATP hydrolysis by the helicase
D.The energy of SSB binding to single-stranded DNA
E.ATP hydrolysis by DNA topoisomerases
Which of the following events occurs in mitotic metaphase?
A.Nuclear envelope breakdown
B.Nuclear envelope reassembly
C.Chromosome attachment to spindle microtubules for the first time
D.Chromosome alignment at the spindle equator
E.Mitotic spindle assembly
Both Vibrio cholerae and Bacillus anthracis …
A.secrete a lethal factor and an edema factor.
B.secrete toxins that enter the cell in endosomes and eventually enter the cytosol after
reaching the endoplasmic reticulum.
C.raise cyclic AMP levels in the cytosol of their target cells.
D.secrete toxins that have enzymatic adenylyl cyclase activity.
E.All of the above.
Which of the following is NOT true regarding the tree of life?
A.Most bacteria and archaea have 1000 to 6000 genes in their genomes.
B.Eukaryotes are more similar to archaea than to bacteria with respect to the proteins
that act on their DNA.
C.Most bacteria and archaea have genome sizes between one and ten million nucleotide
pairs, whereas eukaryotic genomes can be millions of times larger.
D.Archaeal species were thought to belong to the eukaryotic world before sequence
analysis placed them in a separate domain of life.
E.Photosynthetic bacteria are thought to be the ancestors of the eukaryotic chloroplasts.
In terms of cellular lifestyle, different kingdoms of life can be likened to hunters,
farmers, and scavengers. Which of the following is true in this scheme?
A.The ancestral eukaryotic cell was a farmer, but it turned into a hunter once it acquired
mitochondria.
B.Plant cells are considered scavengers, because their cell wall does not allow them to
move.
C.Most protozoa are hunters, whereas animal cells are farmers.
D.The ancestral eukaryotic cell was a hunter, but upon acquiring chloroplasts it made
the transition into farming.
E.Fungi are scavengers without mitochondria.
Indicate whether each of the following descriptions better applies to patterning by
lateral inhibition (L), reaction-diffusion systems (R), or sequential induction (S). Your
answer would be a four-letter string composed of letters L, R, and S only, e.g. SSRR.
( )It does NOT generate asymmetrical patterns from an initial noisy field.
( )It is based on short-range activation and long-range inhibition.
( )It can readily generate complex patterns resembling the spots of a leopard or stripes
of a zebra.
( )It is commonly mediated by Notch signaling.
Consider two solution chambers of equal volume divided by a dialysis membrane that is
impermeable to antibody molecules but permeable to small antigens. Starting with an
antigen concentration of 4.8 nM in both chambers, you add its specific IgG antibody to
one of the chambers at 1 nM concentration. You then measure the concentration of the
antigen in the other chamber after equilibrium is reached, which turns out to be about 4
nM. What is the association constant (Ka) for the binding of the antigen to each
antigen-binding site of IgG? Assume independent antigen-binding sites in each
antibody molecule. Write down your answer in liters per mole, in scientific notation
with one decimal place, e.g. 5.0 x 102 liters/mole).
Indicate true (T) and false (F) statements below regarding cadherins. Your answer
would be a four-letter string composed of letters T and F only, e.g. TFTT.
( )Cadherins are present in all multicellular organisms.
( )Adhesion by cadherins is dependent on Ca2+ ions.
( )In contrast to nonclassical cadherins, classical cadherins are more closely related in
sequence.
( )E, N, and P cadherins are mainly found in desmosomes.
Indicate true (T) and false (F) statements below regarding fibronectin in the
extracellular matrix. Your answer would be a four-letter string composed of letters T
and F only, e.g. TFTT.
( )Fibronectin carries asparagine-linked oligosaccharides.
( )Fibronectin often forms homodimers by cross-linking through covalent attachment of
lysine residues.
( )Fibronectin binds to integrins, collagens, and glycosaminoglycans through its type III
repeats.
( )Fibronectin molecules can assemble into fibrils only in the vicinity of cells.
Some protein domains are found in many different proteins and have been especially
mobile during evolution. A domain of this kind is called a “protein ___”
CFSE (carboxyfluorescein succinimidyl ester) is a cell-tracing molecule that, once
inside a cell, is modified to yield a highly fluorescent molecule that is retained within
the cell. Due to its stability, it can be used to trace cells and follow their divisions: each
division dilutes the fluorescent dye twofold. You label T cells from a healthy mouse
with CFSE and inject them into either a wild-type strain of mouse or a strain with T cell
deficiency, both of which are immunologically compatible with the donor mouse. You
later collect and analyze peripheral T cells from the recipient mice and draw the
following histograms according to the fluorescent intensity per cell. Based on these
results, do you think the total number of T cells in the mouse body is (1) controlled by
intracellular programs (as in the thymus, for example) or is (2) regulated as a whole (as
in the spleen)? Write down 1 or 2 as your answer.
Indicate whether each of the following conditions favors a larger (L) or smaller (S)
tissue or body size. Your answer would be a four-letter string composed of letters L and
S only, e.g. SSSS.
( )Hippo overexpression
( )Insulin-like growth factor overexpression
( )Myostatin deletion
( )Growth hormone deficiency
Reference: FACS Data Analysis
You have been studying the effect of loss-of-function mutations in the Cdk inhibitor
protein (CKI) p21. You add the drug fucoxanthin to cell cultures harboring either
wild-type or mutant versions of the p21 gene. Fucoxanthin is known to induce
cell-cycle arrest in G1. After a day, you add the thymidine analog BrdU to the culture
media, collect the cells after an hour, treat them with anti-BrdU antibody and the
fluorescent DNA stain DAPI, and finally subject them to fluorescence-activated cell
sorting (FACS). The FACS data can be viewed as a two-dimensional dot plot composed
of thousands of dots, in which each cell is represented by one dot at coordinates that
correspond to the intensities of the DAPI fluorescence signal (X axis) and BrdU
fluorescence signal (Y axis) for that cell. Answer the following question(s) according to
the simplified dot plot below, generated from your experiment.
Which one of the FACS plots (a or b) would you expect to correspond to the
loss-of-function p21 mutants? Write down a or b as your answer.
In the following graph, the magnitude of concentration difference across the nuclear
pore complexes (NPCs) is plotted for four molecules (A to D) as a function of time,
starting from an arbitrarily chosen initial concentration difference. Indicate which curve
corresponds to each of the following molecules. Your answer would be a four-letter
string composed of letters A to D only, e.g. ABCD.
( )A large protein that is being actively transported across the NPC
( )A small water-soluble molecule
( )A small protein composed of a few dozen residues
( )A large protein that is NOT actively transported into or out of the nucleus
You performed a co-immunoprecipitation experiment to identify cellular proteins
associated with protein X. For the experiment, you used antibodies against protein X
that were immobilized on beads. You incubated these beads with cell lysates from either
wild-type cells or cells lacking the gene encoding protein Y. After washing and eluting
the bound protein off the beads, you separated each bound and unbound fraction by
SDS-PAGE. Finally, you performed immunoblotting using antibodies against either
protein Y or protein Z. The results of the Western blots are presented in the following
schematic drawings. According to these results, do you think protein Y enhances (E) or
inhibits (I) binding of protein X to protein Z? Write down E or I as your answer.