Download Name_____________________________________ Which is the

Name_____________________________________
1. Which is the most abundant in a cell?
a. Protein
b. Carbohydrate
c. Water
d. Lipid
2. What make the hydrophilic molecules soluble in water?
a. van der Waals interaction
b. hydrogen bond
c. ionic bond
d. both b and c
3. The following is a eukaryote:
a. E. coli
b. Bacillus
c. Cyanobacteria
d. Yeast
4. List two ways that mitochondria differ from other organelles (2 points):
a.
b.
5. Eucaryote means true nucleus. Using the hypothetical model for the evolution of
eucaryotic cells we discussed in class, explain how a eucaryote is derived. Molecule
A can diffuse freely into the nucleus of the cell, how many lipid bilayers it has to go
through? State the locations of those lipid bilayers (4 points).
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6. Identify the four organelles (pointed by arrows) below (2 points)
7. What determines the final 3-D folding structure of protein?
a. the minimum free energy
b. peptide sequence
c. ribosome
d. Golgi
8. The -helix is an example of what kind of structure:
a. Primary
b. Secondary
c. Tertiary
d. Quaternary
9. To activate NFAT (nuclear factor of activated T cell), three phosphates have to be
removed from the molecule. Fill in the rest of diagram below with enzymes and
molecules involved in the activation. (3 points)
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10. Explain how the plasma membrane avoids the catastrophe of undergoing a phase
transition from a dancing lipid bilayer to a crystallized, rigid structure (2 points).
11. What does the FRAP experiment measure?
a. The speed at which fluorescence molecules is bleached
b. The lateral diffusion of lipid molecules
c. The fusion between two cells
d. The lateral diffusion of membrane proteins
12. In the fluid-mosaic model, what is true about the membrane proteins?
a. They form a coating on the lipid molecules.
b. They are inserted into the lipid bilayer.
c. They are shuttled back and forth between the membrane and the nucleus.
d. They are always linked to F-actin.
13. Explain how phospholipids assemble into a self-sealed bilayer. What make the selfsealed bilayer different from a lipid micelle? (4 points)
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14. Identify cytoskeleton filaments shown in the following pictures (3 points):
_______________
_______________
______________
15. Which is true about the treadmilling phenomenon?
a. The length of actin filament is static.
b. The length of actin filament is constant.
c. C+critical = C-critical
d. None of the above
16. Dynamic instability causes microtubules either to grow or to shrink rapidly. Consider
an individual microtubule that is in a shrinking phase (3 points).
A) What must happen at the end of microtubule in order for it to stop shrinking and to
start growing?
B) What would happen if only GDP, but not GTP, were present in the solution?
C) What would happen if the solution contains GTP that cannot be hydrolyzed?
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17. Which of the following changes takes place when a skeletal muscle contracts?
a) Z discs move further apart.
b) Actin filaments contract.
c) Myosin filaments contract.
d) Sarcomeres become shorter.
18. How do motor proteins move along cytoskeleton?
a) ATP hydrolysis of the head domain generates force to move motor proteins forward
b) By thermal vibration
c) ATP hydrolysis of the tail domain generates force to move motor proteins forward
d) Adhesion proteins bind motor proteins to cytoskeletal filaments
18. Circle the correct options in the following sentences (0.5 point per answer):
Extracellular signals can induce the direction of cell motility. In a (chemotaxis/
haptotaxis/ mechanotaxis) experiment, a soluble growth factor is given to a
fibroblast cell. After the cell surface receptors bind to growth factor, (GTP/ ATP/
GDP) is added to Rac, a molecular switch that regulates lamellipodial extension. The
protrusion of lamellipodium is supported by (microtubule/ intermediate filament/
actin) polymerization. After focal adhesion is formed beneath the lamellipodium,
(attachment/ protrusion/contraction) at the cell rear completes the coordinated
steps as the cell moves forward.
19. List two examples of proteins found in ECM (2 points)
a)
b)
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20. What is the potential significance of an RGD sequence in a fibronectin protein?
a. It binds growth factors.
b. It binds integrins, promoting cell attachments
c. It binds cytoskeleton.
d. It promotes crossliking of elastic fibers
21. The major GAGs component in cartilage is aggrecan. If there is a mutation that
decreases the sulfation of GAGs, what will be the most probable consequence?
a. Interaction of aggrecan with link protein would be inhibited
b. The ability of aggrecan to bind water would be reduced
c. Aggrecan with mutation will occupy larger volume than normal aggrecan
d. Aggrecan will no longer bind fibronectin
22. Which is NOT true about collagen?
a. It is the major protein in connective tissue and bone.
b. It is rich in glycine.
c. Each alpha chain is crosslinked together to form an extensible network.
d. It has a triple-stranded helical structure.
23. If the amount of extracellular Ca++ decreases rapidly, which one of the following
adhesion molecules can maintain its physiological function?
a. Ig superfamily
b. Cadherin
c. Selectin
d. Integrin
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24. Fill in the blank (1 point for each answer)
A cell in suspension uses its surface receptors, which are known as ______________, to
bind adhesion motifs on the underlying ECM. This binding leads to clustering of such
surface receptors to form a specific type of anchoring junction called
____________________. Adhesion proteins at this anchoring junction link integrins to
_____________________, which polymerize and bundle into stress fibers to
mechanically support cell spreading. In addition, many downstream signaling pathways
propagate from the anchoring junction to _________________ (hint: organelle), which
regulates cell proliferation, migration and survival.
25. Which is true about fibronectin?
a. It exists only in soluble form.
b. It mediates cell attachment, migration and proliferation.
c. It contains only one protein domain.
d. It interacts with cells, but not with other extracellular matrix molecules.
26. Small soluble molecules can diffuse across the two adjacent epithelial cells through:
a. Tight junction
b. Desmosome
c. Focal adhesion
d. Gap junction
27. Which one of these statements about cell-cell junction proteins is true?
a. Gap junctions mediate cytoskeletal links between cell-cell junctions and integrins.
b. Tight junctions permit delivery of small molecules between adjacent cells.
c. Adherens junctions facilitate nuclear signaling by activating oncogenes.
d. Desmosomes mediate mechanical forces between cells through intermediate
filaments.
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28. On the extracellular domain, selectin binds ____________?
a. oligosaccharide
b. fibronectin
c. collagen
d. laminin
29. Which of the following is the key feature of GAGs?
a. Are extremely hydrophobic
b. Have a net negative charge
c. Occupy a small volume compared to protein
d. Are branched polysaccharide chains
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30. Suppose you had a method of cutting DNA at specific sequences of nucleotides.
How many nucleotides long (on average) would such a sequence have to be in order
to make just one cut in a bacterial genome of 3 x 106 nucleotide pairs? (2 points)
(Given, log3 = 0.477; log4 = 0.602; log6 = 0.778)
31. The two strands of DNA double helix can be separated by heating. If you raise the
temperature of a solution containing the following three DNA molecules, in what
order do you suppose they would “melt” (i.e. the two strands come apart)? (2
points)
A. 5’-GCGGGCCAGCCCGAGTGGGTAGCCCAGG-3’
3’-CGCCCGGTCGGGCTCACCCATCGGGTCC-3’
B. 5’-ATTATAAAATATTTAGATACTATATTTACAA-3’
3’-TAATATTTTATAAATCTATGATATAAATGTT-5’
C. 5’-AGAGCTAGATCGAT-3’
3’-TCTCGATCTAGCTA-5’
Melt first _____, _____, _____ Melt last
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32. In the diagram below, which represents half of a replication fork, show the leading
strand, its direction of synthesis. Also, show okazaki fragments and their direction of
synthesis. Remember to identify the 5’ and 3’ ends. (5 points)
= deoxynucleotide
33. Imagine that you want to replicate a DNA molecule in a test tube. You are given the
DNA molecule, DNA polymerase, the four deoxynucleoside tri-phosphates (dATP,
dTTP, dGTP, dCTP), a favorable environment for the enzyme to function (i.e. an
appropriate buffer solution) and an imaginary set of DNA primers (5 nucleotides
long, each). Schematically draw out where your primers would bind to the DNA
template below so that the entire template molecule could be replicated. Don’t
forget to label their 5’ and 3’ ends. (2 points)
= deoxynucleotide
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34. List three differences between replication and transcription (3 points)
Items
Replication
Transcription
1.
2.
3.
35. Among replication, transcription and translation, which process is the most
accurate?
Most accurate = _____________________ (1 point)
Explain a mechanism for this high accuracy. (1 point)
36. Circle the TRUE statement:
a. DNA is made in the nucleosome
b. RNA is made at the plasma membrane
c. RNA is made in the nucleus and enters the cytoplasm through a nuclear pore
d. In a healthy cell, RNA is made in the cytoplasm and enters the nucleus
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37. Circle the correct options in the following sentences (2 points):
Processing of pre-mRNA takes place in the ( ribosome / mitochondria / nucleus ).
During processing, a long piece of pre-mRNA containing both ( exons and a poly-U
tail / exons and introns / histones and introns ) is cut and spliced, resulting in mRNA
that contains the coding regions of the gene. Processing or splicing is mediated by (
ribosomes / nucleosomes / spliceosomes ), which are made of ( snRNAs only /
tRNAs and proteins / snRNAs and proteins ).
38. The Lacheinmal protein in a hypothetical protein that causes people to smile more
often. It is inactive in many chronically unhappy people. The mRNA isolated from a
number of different unhappy persons in the same family was found to lack an
internal stretch of 173 nucleotides that is present in the Lacheinmal mRNA in a
control group of happy people. The DNA sequences of the Lacheinmal genes from
the happy and unhappy families were determined and compared. They differed by a
single nucleotide substitution, which lay in an intron. What can you say about the
molecular basis of unhappiness in the family? (3 point)
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Name_____________________________________
39. Which of the following statements is TRUE regarding the translation process?
a. A ribosomal RNA within the large subunit of ribosome is responsible for
catalyzing the peptidyltransferase reaction
b. Translation termination is brought about by binding of the release factor at the P
site of the small ribosomal subunit
c. Ribosomes will scan a mRNA for the promoter to initiate translation at the
nearest AUG codon
d. Only a single ribosome can translate a eukaryotic mRNA molecule at a time
40. A mutation in DNA generates a UGA stop codon in the middle of the RNA coding for
a particular protein. A second mutation in the cell leads to a single nucleotide
change in a tRNA that allows the correct translation of the protein; that is the second
mutation “suppresses” the defect caused by the first. The altered tRNA translates
the UGA as tryptophan (Trp). What nucleotide change has probably occurred in the
mutant tRNA molecule? The genetic codes are given below. (3 point)
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41. Which statement is TRUE regarding protein folding?
a. Protein starts to fold after its synthesis is complete and when it folds, most of its
hydrophobic residues are buried inside
b. Protein folds rapidly into the ‘molten globule,’ after which it slowly adjusts the
side chains to appropriate tertiary structure
c. Molecular chaperones recognize hydrophobic patches of the unfolded protein,
and hydrolyze GTPs as they bind and release the target protein
d. Hsp60 and Hsp70 interact as a single large chaperonin complex, which provide a
suitable environment for the target protein to fold appropriately
42. Which statement is FALSE regarding the proteasome pathway?
a. Proteasome is a large complex of ATP-dependent proteases, which unfold and
digest target proteins with high processivity
b. Ubiquitin is a short polypeptide chain which is attached to unfolded proteins and
targets them for folding
c. A ubiquitin ligase interacts specifically with a set of target proteins; therefore, a
cell requires a large number of different ubiquitin ligases in order to orchestrate
its protein degradation in various cellular processes
d. Misfolded proteins could be deleterious to the cell; if unable to fold into an
appropriate structure, they will be sent to the proteasome for degradation
43. Interaction between proteins and DNA mostly occur through which protein
structure?
a. Double helix
b. Beta-sheet
c. Alpha-helix
d. Disulfide bridge
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Name_____________________________________
44. Which statement is FALSE regarding the regulation of gene expression?
a. Gene regulatory proteins often recognize and bind to a short stretch of DNA
sequence
b. Gene regulatory protein is complete in its function and often acts by itself to
regulate gene expression
c. A need for dimerization may occur when a gene regulatory protein by itself does
not have enough binding affinity with the target DNA sequence
d. In eukaryotes, chromatin remodeling complexes and histone acetyl transferases
may be required for a gene activator to gain access to its target gene.
45. Given that CAP is a positive regulator and I is a repressor and without a gene
transcription factor there is no transcription from E. coli lac operon. Indicate
whether RNA polymerase can initiate transcription from the lacZ gene for each of
the following DNA-protein configuration. (2 points)
lacZ transcription (ON/OFF)
______________
______________
______________
______________
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46. Describe the synergistic effects of transcription factors on gene expression (2
points)
47. The enzymes for arginine biosynthesis are located at several positions around the
genome of E. coli, and they are regulated coordinatedly by a transcription regulator
encoded by the ArgR gene. The activity of ArgR protein is modulated by arginine.
Upon binding arginine, ArgR protein alters its conformation, dramatically changing
its conformation for the DNA sequence in the promoters of the genes for arginine
biosynthetic enzymes. Given that ArgR is a repressor protein, would you expect that
ArgR would bind more tightly or less tightly to the DNA sequences when arginine is
abundant? (1 points)
If ArgR functions instead as an activator protein, would you expect the binding of
arginine to increase or to decrease its affinity for its regulatory DNA sequences, upon
binding with arginine. (1 points)
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48. Imagine two situations. In cell I, a transient signal induces the synthesis of protein
A, which is a gene regulator that turns on many genes including its own. In cell II, a
transient signal induces the synthesis of protein R, which is a gene repressor that
turns off many genes including its own. In which, if either, of these situations will
the descendants of the original cell “remember” that the progenitor cell had
experienced the transient signal? Explain your answer. (2 points)
49. Which of the followings is not a cell cycle checkpoint?
a. Chromatin condensation checkpoint
b. G1 DNA damage checkpoint
c. G2 DNA damage checkpoint
d. Spindle attachment checkpoint
50. Which of the following statements is FALSE?
a. Activities of a Cyclin-Cdk complex can be modulated and controlled through
phosphorylation and dephosphorylation of Cdk
b. The activity of Cdk rises and falls with the level of its Cyclin partner
c. M-Cdk will be activated upon DNA damage
d. S-Cdk activation cannot be achieved upon DNA damage
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51. Which Cyclin-Cdk complex is most likely to have the activity profile as shown in the
diagram? (2 points)
_____-Cdk
_____-Cdk
52. Which is the correct order of events during the cell cycle?
a. DNA synthesis, nuclear division, mitosis
b. Cell growth, DNA synthesis, mitosis, cytokinesis (cell division)
c. G1, M, G2, S
d. G1, S, DNA damage checkpoint, nuclear division, spindle attachment checkpoint
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53. When a G1-phase mammalian cell is fused with a G2-phase mammalian cell, which
of the following statements is most likely to happen?
a. G1-phase nucleus immediately enters S phase; G2-phase nucleus replicates its
DNA
b. G1-phase nucleus enters S phase according to its own timetable; G2-phase
nucleus stays in G2 until the other nucleus finishes DNA replication
c. G1-phase nucleus stays in G1 phase; G2-phase nucleus undergoes mitosis
d. G1-phase nucleus stays in G1 phase; G2-phase nucleus stays in G2 phase
54. The shortest eukaryotic cell cycles of all – shorter even than those of many bacteria
– occur in many early embryos. These so-called cleavage divisions take place
without any significant increase in the weight of the embryo. Which phase of the
cell cycle would be most reduced? (2 points)
55. One of the functions of M-Cdk is to cause a precipitous drop in M-cyclin
concentration halfway through M phase. Describe consequences of this sudden
decrease and suggest possible mechanisms by which it might occur. (4 points)
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