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Cofilin binds preferentially to ADP-containing actin filaments rather than to
ATP-containing filaments. Consequently, this protein ...
A.competes with profilin for actin binding.
B.binds to older actin filaments.
C.binds to the plus end of actin filaments.
D.stabilizes actin filaments.
E.All of the above.
The proteins of the ERM family such as moesin ...
A.bind to and organize the cortical actin cytoskeleton.
B.interact with transmembrane proteins.
C.affect cortical stiffness and cell shape.
D.affect the localization and activity of cell signaling molecules.
E.All of the above.
In purifying proteins by column chromatography, elution can be performed in different
ways, depending on the type of matrix. For example, bound proteins can be eluted by
gradually increasing or decreasing salt concentration in the solution applied to the
column. For which of the following matrices do you think increasing and decreasing
salt concentration, respectively, are used for elution?
A.Ion-exchange; hydrophobic
B.Affinity; ion-exchange
C.Hydrophobic; affinity
D.Hydrophobic; ion-exchange
E.Ion-exchange; gel-filtration
Stem cells ...
A.always divide asymmetrically to give rise to two different daughter cells.
B.are terminally differentiated.
C.can divide for the entire lifetime of the organism.
D.divide at a relatively fast rate.
E.All of the above.
Which of the following does NOT typically involve horizontal gene transfer?
A.Sexual reproduction in humans
B.Bacteriophage infection of bacteria
C.The evolutionary history of the eukaryotic cell
D.The accidental duplication of a small region of a bacterial chromosome followed by
cell division
E.Introduction of plasmids into bacteria in a laboratory
Polytene chromosomes are useful for studying chromatin because they ___
A.are smaller than regular chromosomes and easier to manipulate.
B.lack heterochromatin.
C.have distinct visible banding patterns.
D.can make polyploid cells.
E.All of the above.
Which of the following is NOT true regarding the members of a protein family in
general?
A.They have similar three-dimensional conformations.
B.They share an ancestry; i.e. they are homologs.
C.They can functionally replace each other.
D.Their gene sequence is less well conserved than their structure.
E.Over evolutionary time scales, the family has expanded mainly through gene
duplication events.
Keratins are intermediate filaments that ...
A.are localized inside the nucleus.
B.are composed of 50% type I and 50% type II keratin proteins.
C.are bundled in the epidermis to make cells more flexible.
D.anchor the intermediate filament network at the adherens junctions.
E.All of the above.
Which of the following features is common between the replication origins in
Escherichia coli and Saccharomyces cerevisiae?
A.They both normally exist in one copy per genome.
B.Both are specified by DNA sequences of tens of thousands of nucleotide pairs.
C.Both contain sequences that attract initiator proteins, as well as stretches of DNA rich
in A-T base pairs.
D.Both contain GATC repeats that are methylated to prevent the inappropriate "firing"
of the origin.
E.All of the above.
Which of the following is the reason why an aquaporin does not pass ions (such as Na+)
through?
A.The Na+ ions are too small to pass through the pore rapidly enough.
B.The Na+ ions are too large to pass through the narrow pore.
C.The Na+ ions do not favorably interact with the wall of the pore and therefore cannot
be dehydrated.
D.Two Asn residues in the channel prevent the passage of Na+ ions.
E.A Na+ ion must become fully hydrated to pass through.
The phosphofructokinase (PFK) enzyme is one of the key players in the glycolytic
pathway in which glucose eventually breaks down into pyruvate, some ATP is
generated, and some NAD+ is reduced. PFK catalyzes the committed step in the
pathway and is under extensive regulation. Which of the following compounds would
you expect to activate PFK?
A.ADP
B.NADH
C.Pyruvate
D.ATP
E.All of the above
Ethylene receptors in plant cells ...
A.are located primarily at the plasma membrane.
B.are single-pass transmembrane proteins.
C.interact with CTR1, which is closely related to the monomeric G protein Ras.
D.have a copper-containing ethylene-binding domain.
E.All of the above.
The permeability of a protein-free lipid bilayer to various molecules depends on their
properties. Sort the following in order of low to high permeability from left to right.
Your answer would be a six-digit number composed of digits 1 to 6, e.g. 123456.
(A)O2
(B)ATP
(C)RNA oligonucleotide
(D)Na+
(E)Glucose
(F)Urea
How is tandem affinity purification distinct from other purification schemes such as
simple affinity or ion-exchange chromatography?
A.In its use of antibodies
B.In its use of proteases
C.In its use of glutathione S-transferase
D.In its use of viral peptides
E.In its use of limited washing steps
Indicate whether each of the following descriptions better applies to an adaptive (A) or
innate (I) immune response. Your answer would be a four-letter string composed of
letters A and I only, e.g. AAAA.
( )It is found in invertebrate and vertebrate animals as well as in plants.
( )It has a long-lasting memory.
( )It is highly specific to the particular invading pathogen.
( )It employs natural killer (NK) cells to induce apoptosis in infected host cells.
The globin gene family in mammals, birds, and reptiles is organized into - and
-globin gene clusters that are located on two different chromosomes. In most fish and
amphibians, however, the globin genes are close to each other on one chromosome. At
which point (A to E) in the following simplified phylogenetic tree is a chromosomal
translocation likely to have happened that placed the ±- and -globin genes on two
separate chromosomes?
The Src kinase can be regulated by at least two mechanisms. Kinases of the CSK family
inactivate Src by phosphorylating a C-terminal tyrosine residue. On the other hand,
binding of activating ligands (including some activated receptor tyrosine kinases, or
RTKs) results in autophosphorylation at a tyrosine residue near the active site,
stimulating Src activity. Full activation of Src therefore requires both dephosphorylation
at the inhibitory tyrosine and binding to an RTK. Which of the following logic gates (A
to E) correctly models the activation of Src kinase (output) as a function of the activity
of the upstream regulators (inputs)?
Platelets that express a constitutively active Rap1 are able to activate integrins even in
the absence of thrombin stimulation. In contrast, cells expressing a binding-deficient
version of talin are unable to perform integrin activation. In platelets expressing both of
these mutant proteins, what would you expect to observe: the Rap1 gain-of-function
phenotype (R) or the talin loss-of-function phenotype (T), as described above? Write
down R or T as your answer.
Atomic Force Microscopy
Atomic force microscopy (AFM) is used in an experiment to unfold a multidomain
protein by applying mechanical force. The protein contains several copies of an
immunoglobulin domain that are unfolded one by one as the two ends of the molecule
(one attached to a cover slip, and the other to the AFM tip) are being pulled apart,
resulting in the 'sawtooth" force-extension curves shown below. The same experiment is
done twice, once in the presence and once in the absence of a chaperone protein that
stabilizes the immunoglobulin domains. Answer the following questions based on this
graph.
According to the force-extension graph, which curve (1 or 2) would you expect to
correspond to the reaction in the presence of the chaperone protein? Write down 1 or 2
as your answer.
Fill in the blank in the following paragraph regarding chromatin organization. Do not
use abbreviations.
"Our ~6.4-giganucleotide nuclear DNA is organized into 46 chromosomes, each
occupying a territory inside the interphase nucleus. In each chromosome, the chromatin
is thought to be composed of €open' and €closed' chromatin compartments. At the
meganucleotide scale, each compartment is organized into knot-free arrangements
called ___ that allow tight packing and simultaneously avoid entanglement."
Imagine a bistable system composed of two repressor proteins X and Y, each of which
binds to the cis-regulatory sequences of the gene encoding the other protein, i.e. X
represses the expression of Y, and Y represses the expression of X. A researcher
engineers the genes such that they encode protein X fused to green fluorescent protein
(GFP) and protein Y fused to red fluorescent protein (RFP). Cells containing the fusion
constructs are then grown and sorted by fluorescence-activated cell sorting (FACS)
based on their GFP and RFP signals. The results are presented in the following dot plot.
Each cell is represented by a dot whose coordinates correspond to GFP and RFP
fluorescence in the cell. According to these results, which protein (X or Y) do you think
binds to its target DNA sequence with a higher degree of cooperativity? Write down X
or Y as your answer.
Robo3.1 is an alternative splice form of Robo3 that blocks the reception of Slit signals
by the Robo1 and Robo2 receptors. Considering the guidance of commissural neurons
crossing the ventral midline in the embryonic spinal cord of a vertebrate, would you
expect Robo3.1 activity to increase (I) or decrease (D) as the growth cone crosses the
midline? Write down I or D as your answer.
Indicate whether each of the following descriptions refers to protein import into
mitochondria (M), chloroplasts (C), or both (B). Your answer would be a five-letter
string composed of letters M, C, and B only, e.g. BBBMC.
( )ATP and GTP hydrolysis drive translocation into the organelle.
( )The organelle has an extra compartment that requires extra signal sequences for
protein targeting.
( )Transport through the double membrane is driven in part by an H+ gradient across the
inner membrane.
( )Imported precursor proteins have amphiphilic N-terminal signal sequences that are
usually removed after use.
( )Hsp70 family chaperones inside the organelle assist in protein translocation during
import.
Fill in the blank in the following paragraph. Do NOT use abbreviations.
"In human cells, the predominant pathway to repair double-strand breaks is ___, in
which the broken ends are simply rejoined with the concomitant loss of a few
nucleotides. This leaves scars at the breakage sites. This pathway can potentially create
chromosome translocations."
The citric acid cycle is summarized in the following figure. Answer the following
question(s) about this cycle.
In the citric acid cycle shown above, which steps produce either NADH or FADH2?
List all such steps by their number, from the smallest number to the largest. Your
answer would be a number composed of digits 1 to 8 only, e.g. 258.
