Structural Biology Exam Solutions
Course Introduction
Structural Biology explores the architecture and dynamics of biological macromolecules, such as proteins, nucleic acids, and their complexes. This course delves into the principles that govern molecular structure, the techniques used for structure determination including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy and how these structures relate to biological function. Students will examine how understanding macromolecular structures advances knowledge in areas such as enzymatic mechanisms, signal transduction, and drug design, with an emphasis on interpreting and analyzing experimental data and integrating structural information into broader biological contexts.
Recommended Textbook
Molecular Biology of the Cell 6th Edition by Bruce Alberts
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Chapter 1: Cells and Genomes
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Sample Questions
Q1) Imagine two spherical cells, one of which is 5000 times larger in volume than the other. The smaller is a prokaryote, and the larger cell is a eukaryote with 20% of its volume confined in a spherical nucleus. If the diameter of the prokaryotic cell is 0.7 micrometers, what is the diameter of the nucleus in the eukaryotic cell in micrometers? Write down your answer as a number only.
Answer: 7
Q2) Didinium nasutum is a single-celled eukaryote that can hunt and feed on other living cells. It has an elaborate anatomy with beating cilia, a "mouth opening," an "anal aperture," and a set of contractile bundles; it can also shoot "darts" to paralyze its prey. What group of living cells does D. nasutum represent?
A) Protozoa
B) Yeasts
C) Algae
D) Animals
E) It can belong to any of the above
Answer: A
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Chapter 2: Cell Chemistry and Bioenergetics
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Q1) Which of the following is true regarding a fatty acid molecule in water?
A) It is positively charged at physiological pH, but can become neutral when the pH is high enough.
B) It is positively charged at physiological pH, but can become neutral when the pH is low enough.
C) It is negatively charged at physiological pH, but can become neutral when the pH is high enough.
D) It is negatively charged at physiological pH, but can become neutral when the pH is low enough.
E) It is not charged at physiological pH.
Answer: D
Q2) Which of the following represents an "activated" carrier molecule?
A) AMP
B) NADH
C) NAD
D) NADP
E) CoA
Answer: B
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Chapter 3: Proteins
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Sample Questions
Q1) An enzyme acts on a tyrosine residue in a target protein to create a binding site for the SH2 domain. This enzyme is most specifically
A) an isomerase.
B) a nuclease.
C) a phosphatase.
D) a kinase.
E) a synthase.
Answer: D
Q2) Enzymes can catalyze cellular reactions through various mechanisms. Which of the following statements is NOT true regarding enzymes?
A) They can provide the chemical groups necessary for simultaneous acid and base catalysis.
B) They have a higher affinity for the transition state of the substrate than for its stable form.
C) They can form covalent bonds with the substrate during catalysis.
D) They can strain a substrate to force it toward a specific transition state.
E) They accelerate a cellular reaction by destabilizing the transition state.
Answer: E
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Chapter 4: DNA, Chromosomes, and Genomes
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Sample Questions
Q1) 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.
Q2) If species A in the distance matrix represents human, indicate which of the other species (B to D) represents chimpanzee, gorilla, and orangutan, respectively. Your answer would be a three-letter string composed of letters B, C, and D only, e.g. DCB.
Q3) The genetic information carried by a cell is passed on, generation after generation, with astonishing fidelity. However, genomes are still altered over evolutionary time scales, and even their overall size can change significantly. Which of the following genome-altering events has increased the size of the mammalian genome the most?
A) Transposition
B) Point mutation
C) Chromosomal deletion
D) Chromosomal inversion
E) Chromosomal translocation
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Chapter 5: DNA Replication, Repair, and Recombination
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Q1) In meiosis, a crossover in one position is thought to inhibit crossing-over in the neighboring regions. This regulatory mechanism
A) results in a very uneven distribution of crossover points along each chromosome.
B) ensures that even small chromosomes undergo at least one crossover.
C) controls how the Holliday junctions are resolved.
D) All of the above.
Q2) If this protein complex does not function normally, the ends of the eukaryotic chromosomes would activate the cell's DNA damage response, causing chromosomal fusions and other genomic anomalies. What is this protein complex called?
A) Telomerase
B) T-loop
C) ORC
D) Shelterin
E) RecA
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Chapter 6: How Cells Read the Genome: From DNA to Protein
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Sample Questions
Q1) Sort the following events in the order that they occur during transcription initiation in Escherichia coli. Your answer would be a four-letter string composed of letters A to D only; e.g. DCAB.
(A) Abortive initiation trials
(B) ? Factor release from the RNA polymerase holoenzyme (C) Binding of the holoenzyme to the promoter in the "closed" complex (D) Formation of the transcription bubble
Q2) What is the function of the 19S cap in the proteasome complex?
A) Recognizing the proteins that will be degraded
B) Unfolding the proteins that will be degraded and threading them into the central 20S cylinder for digestion
C) Removing the polyubiquitin chain from the proteins that will be degraded
D) Hydrolyzing ATP to make the digestion process highly efficient
E) All of the above
Q3) Fill in the blank. These RNA molecules can catalyze a wide variety of biochemical reactions, including peptide bond formation and RNA splicing. They can be found in nature or selected in vitro for a desired function. Such a molecule is called a(n) ...
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Chapter 7: Control of Gene Expression
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Sample Questions
Q1) You have engineered the X chromosomes in female mice such that one X chromosome expresses green fluorescent protein when active, while the other expresses red fluorescent protein. You have used these mice to study cancer in females. You know that each tumor is a clonal cellular proliferation, meaning all of its proliferating cells are descendants of a single original cancer-causing cell. It follows that, unless X-chromosome inactivation is perturbed in tumors,
A) all tumor cells in one mouse should express the same fluorescent protein (either red or green), but tumor cells from different mice can show either red or green fluorescence. B) the cells in any tumor should all express the same fluorescent protein (either red or green), but independently derived tumors in the same mouse can show either green or red fluorescence.
C) different cells within each tumor can express different fluorescent proteins, and the tumors would therefore show yellow fluorescence, but each cell shows either red or green fluorescence.
D) each cell can express both fluorescent proteins and would therefore emit yellow fluorescence, and the tumors would glow in yellow as well.
E) different tumors would show red, yellow, or green fluorescence.
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Chapter 8: Analyzing Cells, Molecules, and Systems
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Sample Questions
Q1) Bacterial artificial chromosomes (BACs)
A) are derived from the E. coli chromosome.
B) are present in high copy numbers per cell.
C) can maintain DNA sequences of hundreds of thousands of nucleotide pairs.
D) are generally not stable.
E) All of the above.
Q2) What are the advantages of monoclonal antibodies over antisera?
A) They can be produced in higher quantities.
B) They can be produced with higher purity.
C) They have a more uniform specificity.
D) They can be made against molecules that constitute only a minor component of a complex mixture.
E) All of the above.
Q3) Sort the following steps in the common procedure to create transgenic plants. Your answer would be a four-letter string composed of letters A to D, e.g. DABC.
(A) Callus growth
(B) Agrobacterium infection
(C) Shoot/root induction
(D) Removal of leaf tissue from a plant
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Chapter 9: Visualizing Cells
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Sample Questions
Q1) Consider an engineered chimeric protein made from fusion of three proteins: a blue fluorescent protein (BFP), a calmodulin-binding peptide, and a green fluorescent protein (GFP). Calmodulin is an abundant calcium-binding protein in eukaryotes. Once bound to calcium ions, it can recognize the calmodulin-binding peptide in the fusion protein, change conformation, wrap around the peptide, and bring the BFP and GFP components in close proximity. This results in fluorescence resonance energy transfer (FRET) between BFP and GFP. Accordingly, the fusion protein
A) is a luminescent ion-sensitive indicator that red-shifts its emission wavelength in the presence of calcium.
B) is a luminescent ion-sensitive indicator that increases its emission in the presence of calcium.
C) is a genetically encoded calcium indicator that red-shifts its emission wavelength in the presence of calcium.
D) is a genetically encoded calcium indicator that increases its emission in the presence of calcium.
Q2) 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.
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Chapter 10: Membrane Structure
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Q1) What do all -barrel transmembrane proteins have in common?
A) The number of strands.
B) The diameter of the barrel.
C) The number of negative peaks in their hydropathy plots.
D) The general function, i.e. membrane transport.
E) The structural rigidity compared to -helical transmembrane proteins.
Q2) Which of the following is correct regarding the composition of various biological membranes?
A) Bacterial plasma membranes are often composed of one main type of phospholipid and lack cholesterol.
B) Cholesterol in the eukaryotic plasma membrane induces phase transition to the gel state.
C) Inositol phospholipids are the most abundant lipids in the endoplasmic reticulum membrane.
D) The mitochondrial and bacterial membranes are rich in glycolipids.
E) Yeast cells synthesize more fatty acids with cis?-double bonds when the temperature in the environment rises.
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Chapter 11: Membrane Transport of Small Molecules and the Electrical Properties of Membranes
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Sample Questions
Q1) Dopamine is a neurotransmitter involved in the reward pathways in the brain, and its decreased activity has been associated with diseases such as Parkinson's disease and attention-deficit/hyperactivity disorder (ADHD). Which of the following drugs is NOT a likely candidate to treat these diseases?
A) Methylphenidate, a dopamine reuptake inhibitor
B) Amphetamine, a dopamine-releasing agent that triggers the release of dopamine into the synaptic cleft
C) Carbidopa, which enhances the availability of the dopamine synthesis precursors in the brain
D) Forskolin, a sensitizer of dopamine receptors
E) Chlorpromazine, a dopamine antagonist that binds to and inhibits dopamine receptors
Q2) The inactivation rate of voltage-gated Na and K channels can regulate the firing frequency of neurons. Which of the following combinations results in the highest firing frequency?
A) Rapid inactivation of both Na and K channels
B) Rapid inactivation of Na channels, slow inactivation of K channels
C) Slow inactivation of Na channels, rapid inactivation of K channels
D) Slow inactivation of both Na and K channels
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Chapter 12: Intracellular Compartments and Protein Sorting
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Sample Questions
Q1) Fill in the blank in the following paragraph regarding the recognition of tail-anchored proteins by their targeting machinery. DO NOT use abbreviations.
"When the hydrophobic transmembrane ? helix at the C-terminus of an ER tail-anchored protein emerges from the ribosome, the tail-anchored-binding domain (TABD) of the Get3 ATPase binds to it. The job of TABD in Get3 is similar to that of the flexible hydrophobic domain in the SRP54 protein of the signal-recognition particle, in that it also has to recognize a degenerate set of hydrophobic ?- helices. Therefore, it is not surprising that, just like the corresponding domain in SRP54, the binding site in Get3 is rich in ... residues."
Q2) The signal-recognition particle (SRP) ...
A) is a heterodimeric protein.
B) transiently inhibits translation and polypeptide elongation by binding to and inhibiting the elongation factors.
C) accompanies the nascent polypeptide all the way into the ER lumen.
D) binds GTP.
E) is permanently attached to the cytosolic face of the ER membrane, thus bringing the ribosomes into close proximity of the translocon.
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Chapter 13: Intracellular Membrane Traffic
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Q1) Lysosomes are the principal site of cellular digestion. They
A) normally maintain a pH of about 2.0 to 2.5.
B) contain F-type ATPases that pump protons into the organelles.
C) contain heavily glycosylated membrane proteins.
D) are homogeneous in size and shape.
E) All of the above.
Q2) Indicate true (T) and false (F) statements below regarding receptor-mediated endocytosis of LDL particles. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF.
( ) LDL receptors are normally degraded in the lysosome along with their LDL ligands.
( ) LDL receptors that do not bind to extracellular LDL cannot be internalized in clathrin-coated vesicles.
( ) A mutation that impairs the attachment of an LDL receptor to a clathrin-coated pit would cause depletion of blood LDL levels.
( ) LDL receptors at the plasma membrane are usually concentrated in clathrin-coated pits.
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Chapter 14: Energy Conversion: Mitochondria and Chloroplasts
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Q1) Which of the following is true regarding light-harvesting complexes in plant chloroplasts?
A) They contain chlorophyll and other pigments.
B) They are found in both photosystem I and photosystem II.
C) They can protect the cell by preventing the generation of reactive oxygen species.
D) They cannot carry out charge separation.
E) All of the above.
Q2) You have isolated mitochondria from a liver tissue sample, suspended them in a hypotonic buffer that causes them to swell and burst their outer membrane, and then added sucrose to a final concentration of about 25%. You then layer the suspension on a density gradient, ultracentrifuge, collect the different fractions, and analyze their protein content. Which of the following proteins would you expect to be highly enriched in the lower density and higher density fractions, respectively?
A) Cytochrome oxidase; porin
B) Cytochrome oxidase; ATP synthase
C) ATP synthase; cytochrome oxidase
D) Porin; ATP synthase
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Chapter 15: Cell Signaling
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Q1) Indicate true (T) and false (F) statements below regarding the mTOR complexes. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF.
( ) mTOR in complex 1 contains the protein raptor, is sensitive to rapamycin, and stimulates cell growth.
( ) Akt activation is stimulated by mTOR in complex 2, which contains the protein rictor.
( ) Akt activates mTOR in complex 2 by activating a Rheb-GAP called Tsc2.
( ) mTOR in complex 1 is activated in the presence of growth factors.
Q2) Which of the following is NOT part of a negative feedback mechanism in adaptation to light in retinal rod cells?
A) Phosphorylation of G-protein-coupled receptor
B) Binding of arrestin to G protein
C) Stimulation of guanylyl cyclase by decreased Ca² levels
D) Binding of regulator of G protein signaling to transducin
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Chapter 16: The Cytoskeleton
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Q1) 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
Q2) Indicate if each of the following descriptions matches actin filaments (A), microtubules (M), or intermediate filaments (I). Your answer would be a four-letter string composed of letters A, M, and I only; e.g. AAMM.
( ) They form hollow structures with multiple lateral interactions.
( ) They form strong structures that are more resilient than the other two cytoskeletal filaments.
( ) Their subunits bind GTP and hydrolyze it.
( ) They form coiled-coil interactions between the subunits.
Q3) Fill in the blank: Each microtubule is typically made of thirteen parallel . that associate laterally to form a hollow tube.
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Chapter 17: The Cell Cycle
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Q1) Which of the following is more directly driven by active M-Cdk?
A) Centrosome maturation
B) Centrosome duplication
C) Nuclear envelope reassembly
D) Inactivation of APC/C
E) Cell cleavage
Q2) Indicate true (T) and false (F) statements below regarding meiosis in eukaryotic cells. Your answer would be a four-letter string composed of letters T and F only, e.g. TFFF.
( ) Bivalents form before prophase I.
( ) Crossing-over begins before the synaptonemal complex assembly.
( ) Chiasmata can first be seen under the microscope after the disassembly of the synaptonemal complexes.
( ) All recombination events lead to crossovers.
Q3) Which stage is usually the longest in meiosis?
A) Prophase I
B) Prometaphase I
C) Telophase I
D) Prophase II
E) Prometaphase II
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Chapter 18: Cell Death
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Q1) Which of the following proteins activates the mitochondrial pathway of apoptosis?
A) The tumor suppressor protein p53, when activated in response to extensive DNA damage.
B) The BH3-only protein Bid, when cleaved by the initiator caspase-8 (from the extrinsic pathway).
C) The anti-IAP protein Omi, when activated by dephosphorylation.
D) The BH3-only protein Bad, when activated by dephosphorylation.
E) All of the above.
Q2) Apoptotic cells are efficiently phagocytosed by neighboring cells or macrophages. Which of the following DOES NOT normally happen in this process?
A) The apoptotic cell releases some of its cytoplasmic content to induce a local inflammatory response.
B) The apoptotic cell exposes phosphatidylserine at its surface, which interacts with receptor proteins on the surface of phagocytes via "bridging" proteins.
C) The apoptotic cell loses or inactivates "don't eat me" signals.
D) The apoptotic cell rounds up and detaches from its neighbors, which facilitates phagocytosis.
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Chapter 19: Cell Junctions and the Extracellular Matrix
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Q1) Which of the following is NOT an anchoring junction?
A) Adherens junction
B) Desmosome
C) Actin-linked cell-matrix junction
D) Hemidesmosome
E) Tight junction
Q2) A cell's response is not the same when placed on a rigid compared to a soft matrix. Indicate whether each of the following is expected to occur in a cell that is placed on a rigid matrix (R) or a soft matrix (S). Your answer would be a three-letter string composed of letters R and S only, e.g. RSR.
( ) More tension is generated in cell-matrix contacts.
( ) More vinculin proteins would bind to the C-terminal tail of talin.
( ) More actin filaments are recruited to the site of cell-matrix adhesion.
Q3) Consider two cells attached to each other via adherens junctions. The forces generated by the actin cytoskeleton in one cell
A) are dependent on myosin activity.
B) are normally balanced by similar forces in the neighboring cell.
C) can strengthen the adherens junction by unfolding catenin proteins.
D) All of the above.
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Chapter 20: Cancer
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Q1) Which of the following proteins is NOT encoded by a proto-oncogene?
A) Src
B) Ras
C) EGF receptor
D) Myc
E) E-cadherin
Q2) Suppose you are studying tumor heterogeneity in a certain type of melanoma. You have used fluorescence-activated cell sorting (FACS) to specifically isolate those melanoma tumor cells that either do (first category) or do not (second category) express a specific marker present in normal stem cells in the tissue of origin (i.e. the melanocyte stem cells). You implant the same number of cells from each of these categories into severely immunodeficient mice and compare the tumor-formation efficiencies after several weeks, which turn out to be significantly higher for the first category. You then analyze the new tumors using FACS, and find out that the majority of the cells in the tumors that originated from the first category of cells harbor the stem-cell marker, whereas the majority of the cells in the tumors that originated from the second cell category lack the marker, just like their respective founder cells. Do these observations support the existence of cancer stem cells? Write down Yes or No as your answer.
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Chapter 21: Development of Multicellular Organisms
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Q1) During branching morphogenesis in lung development,
A) FGF10 is secreted by epithelial cells at the tip of the growing epithelial tubes.
B) FGF10 inhibits Shh production by the epithelial cells at the tip of the growing epithelial tubes.
C) Shh inhibits FGF10 production by the epithelial cells at the tip of the growing epithelial tubes.
D) Shh is produced by epithelial cells at the tip of the growing epithelial tubes.
E) None of the above.
Q2) Sort the following primary axes in the order that they are established during the development of Xenopus laevis. Your answer would be a three-letter string composed of letters A to C only, e.g. ACB.
(A) A-P
(B) D-V
(C) A-V
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Chapter 22: Stem Cells and Tissue Renewal
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Q1) In each of the following examples of contact signaling between adjacent cells in the mammalian gut epithelia, indicate whether the signaling is mainly mediated by Delta (D) or Ephrin (E) signals. Your answer would be a three-letter string composed of letters D and E only, e.g. EDE.
( ) Separation of crypt cell types from villus cell types
( ) Regulation of stem-cell differentiation by Paneth cells
( ) Differentiation of transit amplifying cells into either secretory cells or absorptive cells
Q2) An increasing number of lymphomas are being treated with "stem-cell transplantation" therapy that is composed of the following overall steps. Sort these steps into the correct order. Your answer would be a three-letter string composed of letters A to C only, e.g. BAC.
(A) Injection of cells into the blood
(B) Harvesting and isolating selected cells from the patient's bone marrow
(C) Heavy x-ray irradiation of the patient
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Chapter 23: Pathogens and Infection
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Q1) 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.
Q2) Indicate true (T) and false (F) statements below regarding bacterial, viral, and eukaryotic pathogens. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTT.
( ) Compared to bacteria and viruses, eukaryotic parasites have simpler life cycles.
( ) Most important pathogenic fungi show dimorphism, growing as either yeast or mold.
( ) Protozoan parasites often require more than one host to complete their life cycle.
( ) Plasmodium falciparum can invade human liver and red blood cells, as well as cells lining the gut in female Anopheles mosquitoes.
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Chapter 24: The Innate and Adaptive Immune Systems
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Q1) Mammals produce five major classes of immunoglobulins. Indicate whether each of the following descriptions better applies to the immunoglobulin A, D, E, G, or M class. Your answer would be a five-letter string composed of letters A, D, E, G, and M only, e.g. GMADE.
( ) It binds to cells that secrete histamine.
( ) It is the major antibody in secretions such as saliva.
( ) It is the major antibody circulating in the blood.
( ) It is found on the surface of naïve B cells along with IgM.
( ) It forms wheel-like pentamers involved in the primary immune response.
Q2) Indicate whether each of the following cell-surface proteins is expressed mainly by B cells (B), dendritic cells (D), or T cells (T). Your answer would be a four-letter string composed of letters B, D, and T only, e.g. DBBB.
( ) Co-stimulatory protein B7, which is recognized by CD28
( ) Invariant CD3 complex
( ) Inhibitory CTLA4 protein
( ) CD40 receptor, which recognizes the co-stimulatory protein CD40 ligand on a helper T cell
Q3) How many hypervariable loops are there in a bivalent IgG antibody? Write down your answer in digits, e.g. 5.
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