Bio Practice Questions & answers
The figure below shows how transport vesicles recognize and fuse with a specific target membrane. Identify components labeled A-D. Hint: a word list is included below the figure. Describe how the events in steps 1-3 allow a transport vesicle to recognize and fuse with a specific target membrane. BONUS: What is missing in this diagram? What role does it play in this process?
A = Rab-GTP, B = v-SNARE, C = tethering protein, D = t-SNARE The sequence of events that allow a transport vesicle to recognize and fuse with a specific target membrane is as follows: Step 1 (tethering): A tethering protein on the target membrane recognizes and binds to a specific Rab protein on the surface of the transport vesicle. The specific interaction between a tethering protein and Rab protein allows a particular vesicle and target membrane to initially recognize each other. Step 2 (docking): A v-SNARE on the vesicle binds to a complementary t-SNARE on the target membrane. Like the tethering protein and Rab protein in the previous step, the v-SNARE and t-SNARE are specific for each other, further ensuring that transport vesicles dock at the appropriate target molecule. Step 3 (fusion): t-SNAREs and v-SNAREs catalyze the fusion of the two membranes. When triggered, the SNAREs wind together, squeezing out water molecules between the two membranes, allowing the lipids to flow into a continuous bilayer. BONUS: The figure in the question did not show Rab GTPase-Activating Protein (Rab GAP) on the target membrane. The figure from lecture which includes Rab GAP is shown below. Rab GAP stimulates Rab to hydrolyze its bound to GTP to GDP, causing the tethering protein and Rab to release. Rab-GDP is soluble and moves off the membrane into the cytoplasm.
Explain how the Ran-GTPase cycle drives nuclear import. Identify A, B, C, and D in the figure below. Describe the process by making a list of sequential steps.
A = nuclear import receptor; B = nuclear pore; C = Ran-GTP; D = Ran-GDP 1. In the cytoplasm, a nuclear import receptor binds to a prospective nuclear protein with a nuclear localization signal (cargo). 2. The nuclear import protein guides its cargo (the prospective nuclear protein) through the nuclear pore by making specific interactions with proteins in the pore. 3. Once inside the nucleus, Ran-GTP binding displaces the cargo, releasing the nuclear protein into the nucleus. 4. The nuclear import receptor bound to Ran-GTP leaves the nucleus. 5. In the cytosol, Ran hydrolyzes its bound GTP to GDP and Ran-GDP dissociates from the nuclear import receptor. 6. The nuclear import receptor can then bind another prospective nuclear protein.
Identify the components of the Golgi apparatus in the figure below.
A cis Golgi network B cis cisterna C medial cisterna D trans cisterna E trans Golgi network
Where are the majority of chloroplast proteins translated? A. in the cytosol B. in the mitochondria C. in the chloroplast D. on the endoplasmic reticulum
A. is correct. The majority of proteins in the chloroplast are translated in the cytosol and the sorting signals on the protein direct them to the chloroplast.
A large protein that passes through the nuclear pore must have an appropriate ___________. A. signal sequence, which typically contains the positively charged amino acids lysine and arginine. B. signal sequence, which typically contains the hydrophobic amino acids leucine and isoleucine. C. sequence to interact with the nuclear fibrils. D. Ran-interacting protein domain.
A. is correct. The nuclear signal sequence, which typically contains several positively charged lysines or arginines, is recognized by the nuclear import receptors. The nuclear import receptor interacts with the fibrils of the nuclear pore and Ran, which hydrolyses GTP.
Explain how cells control where Ran is active by using the dropdown menus to complete the following statements. Ran-GAP (GTPase-activating protein) is found exclusively ___________ and _________________ . Ran-GEF (guanine nucleotide exchange factor) is found____________ and _________________.
Answer 1: : exclusively in the cytosol Answer 2triggers GTP hydrolysis Answer 3exclusively in the nucleus Answer 4:causes Ran-GDP to release GDP and take up GTP
What is the role of the nuclear signal sequence in a prospective nuclear protein? A. It is bound by a cytoplasmic protein that guides the prospective nuclear protein through a nuclear pore. B. It enables the protein to enter the perinuclear space (space between the two nuclear membranes). C. It aids in protein unfolding so that the protein can thread through nuclear pores. D. It prevents the protein from diffusing out of the nucleus through nuclear pores.
Answer: A. is correct. The nuclear signal sequence on a prospective nuclear protein allows it to bind to a nuclear import receptor, a protein found in the cytosol. B. is incorrect. Prospective nuclear proteins pass through both nuclear membranes. C. is incorrect. Proteins are not unfolded as they enter the nucleus. D. is incorrect. Proteins do not diffuse through the nuclear pores and are actively transported in and out of the nucleus.
How would a drug that blocks the ability of Ran to exchange GDP for GTP affect nuclear transport? A. Nuclear transport receptors would be unable to bind cargo. B. Nuclear transport receptors would be unable to enter the nucleus. C. Nuclear transport receptors would be unable to release their cargo in the nucleus. D. Nuclear transport receptors would interact irreversibly with the nuclear pore fibrils.
Answer: C When Ran-GTP binds to the nuclear transport receptor, cargo is released. If Ran could not exchange its GDP for GTP, this would not happen. Ran-GTP is not needed for cargo binding, for nuclear entry, or for interactions with the nuclear pore fibrils during nuclear import.
Signal sequences that direct proteins to the correct compartment are ________. A. added to proteins through post-translational modification. B. added to a protein by a protein translocator. C. encoded in the amino acid sequence and sufficient for targeting a protein to its correct destination. D. always removed once a protein is at the correct destination.
Answer: C. encoded in the amino acid sequence and sufficient for targeting a protein to its correct destination. C. is correct. Signal sequences are found within the amino acid sequence of proteins and are both necessary and sufficient for sorting. A. is incorrect. See above. B. is incorrect. A protein translocator resides in the membrane and helps transport soluble proteins across the membrane, but does not add signal sequences to proteins. C. is incorrect. Signal sequences are sometimes removed when the protein is at the correct destination, but not all are removed. For example, nuclear import signals are not removed once a protein is inside the nucleus.
Proteins that are fully translated in the cytosol and lack a sorting signal will end up in the ______. A. cytosol B. mitochondria C. chloroplast D. Golgi apparatus
Answer: Cytosol
With the exception of proteins encoded by mitochondrial and chloroplast DNA, the synthesis of all proteins begins in the __________ . A. nucleus B. cytosol C. ER D. Golgi apparatus E. more than one of the above
Answer: Cytosol Explanation: (see image)
Use the dropdown menus to complete the following statements. Transport vesicles traveling from the Golgi apparatus to the plasma membrane move toward the_________ of microtubules and contain ________. Transport vesicles traveling from the endoplasmic reticulum to the Golgi apparatus move toward the [ Select ] of microtubules and contain [ Select ] .
Answers: 1) plus ends 2) kinesin 3) minus ends 4) dynein
An individual transport vesicle __________ . A. contains only one type of protein in its lumen. B. will fuse with only one type of membrane. C. is endocytic if it is traveling toward the plasma membrane. D. is enclosed by a membrane with the same lipid and protein composition as the membrane of the donor organelle.
B is correct. An individual transport vesicle only fuses with one type of membrane. A is incorrect because an individual vesicle may contain more than one type of protein in its lumen, all of which will contain the same sorting signal (or will lack specific sorting signals). C is incorrect because endocytic vesicles generally move away from the plasma membrane. D is incorrect because the vesicle membrane will not necessarily contain the same lipid and protein composition as the donor organelle because the vesicle is formed from a selected subsection of the organelle membrane from which it budded.
Which of the following is NOT a function of clathrin on a coated vesicle? A. help shape membrane into a bud that will form vesicle. B. select specific cargo molecules for transport C. capture cargo molecules for transport D. all of the above are functions of the protein coat on a coated vesicle.
B. Clathrin, a coat protein, does not play a role in selecting specific cargo molecules for vesicular transport. Adaptors select cargo molecules for transport by capturing the particular cargo receptors that bind specific cargo molecules.
The figure below shows the organization of a protein that normally resides in the plasma membrane. The boxes labeled 1 and 2 represent membrane-spanning sequences and the arrow represents a site of action of signal peptidase. Given this diagram, which of the following statements must be TRUE? A. The N-terminus of the protein is cytoplasmic B. The C-terminus of the protein is cytoplasmic. C. The mature version of this protein will span the membrane twice, with both the N- and C-terminus in the cytoplasm.
B. The protein will span the membrane once, with membrane-spanning segment 2 in the membrane and the C-terminus facing the cytoplasm.
Which of the following statements about transport into mitochondria and chloroplasts is FALSE? A. The signal sequence on proteins destined for these organelles is recognized by a receptor protein in the outer membrane of these organelles. B. After a protein completely moves through the protein translocator in the outer membrane of these organelles, the entire protein diffuses in the lumen (space between the inner and outer membrane) until it encounters a protein translocator in the inner membrane. C. Proteins that are transported into these organelles are unfolded as they are being transported. D. Signal peptidase will remove the signal sequence once the protein has been imported into these organelles.
B. is the FALSE statement. Once a protein is bound to the import receptor, the protein—in a complex that includes the protein translocator—will diffuse along the outer membrane until it reaches a specialized site where the inner and outer membranes contact each other, and will then be translocated simultaneously across the inner and outer membranes.
You are working in a biotech company that has discovered a small-molecule drug called H5434. H5434 binds to LDL receptors when they are bound to cholesterol. H5434 binding does not alter the conformation of the LDL receptor's intracellular domain. Interestingly, in vitro experiments demonstrate that addition of H5434 increases the affinity of LDL for cholesterol and prevents cholesterol from dissociating from the LDL receptor even in acidic conditions. Which of the following is a reasonable prediction of what may happen when you add H5434 to cells? A. Cytosolic cholesterol levels will remain unchanged relative to normal cells. B. Cytosolic cholesterol levels will decrease relative to normal cells. C. The LDL receptor will remain on the plasma membrane. D. The uncoating of vesicles will not occur.
B. is the correct answer. Normally, cholesterol dissociates from the LDL receptor in the acidic environment of the endosomes and is released into the cytosol. If the drug prevents cholesterol from dissociating from the LDL receptor in acidic conditions, cholesterol may not become released into the cytosol, and thus cytosolic cholesterol levels are likely to decrease relative to those in normal cells. There is no reason to believe that the LDL receptor will remain on the plasma membrane, because the cytosolic region of the receptor is not directly altered by the drug. Vesicle uncoating is also unlikely to be altered, because this occurs after vesicles are pinched off from the membrane.
Which of the following reflects the correct sequence of locations through which a protein destined for the plasma membrane travels? A. lysosome -> endosome -> plasma membrane B. ER -> lysosome -> plasma membrane C. ER -> Golgi -> plasma membrane D. Golgi -> lysosome -> plasma membrane E. More than one of the above
C is correct
Which of the following statements about the unfolded protein response (UPR) is FALSE? A. Activation of the UPR results in the production of more ER membrane. B. Activation of the UPR results in the production of more chaperone proteins. C. Activation of the UPR occurs when receptors in the cytoplasm sense misfolded proteins. D. Activation of the UPR results in the cytoplasmic activation of gene regulatory proteins.
C. is FALSE. The receptors for the unfolded proteins are on the ER membrane, and they sense the misfolded proteins using their luminal domains. A., B., and D. are TRUE. UPR leads to the activation of chaperone genes and other genes that increase the protein-folding capacity of the ER.
Which of the following statements is TRUE? A. The signal sequences on mitochondrial proteins are usually at the C-terminus. B. Most mitochondrial proteins are not imported from the cytosol but are synthesized inside the mitochondria. C. Chaperone proteins in the mitochondria facilitate the movement of proteins across the outer and inner mitochondrial membranes.
C. is correct. A. is incorrect. The signal sequences on a protein destined for the mitochondria are on its N-terminus. B. is incorrect. Most mitochondrial proteins are encoded by genes in the nucleus and imported into the mitochondria after synthesis in the cytosol. D. is incorrect. Mitochondrial proteins are unfolded as they enter the mitochondria through protein translocators.
Which of the following statements about nuclear transport is TRUE? A. Ran-GTP binds to nuclear import receptors in the cytosol, allowing the receptors to transport proteins into the nucleus. B. Nuclear import receptors bind to proteins in the cytosol and bring the proteins to the nuclear pores, where the proteins are released from the receptors into the pores for transit into the nucleus. C. Nuclear pores contain proteins with disordered segments that fill the channel and allow small water-soluble molecules to pass through in a non-selective fashion. D. Nuclear pores are made up of many copies of a single protein.
C. is correct. Many of the proteins that line the nuclear pore have largely disordered segments and allow small molecules and very small proteins to pass through. Larger proteins are too big to pass through alone and require nuclear import receptors. A. is incorrect. Ran-GTP binds to nuclear import receptors in the nucleus, causing the nuclear import receptor to release its cargo protein. B. is incorrect. Nuclear import receptors bind to proteins in the cytosol and transit with them across the nuclear pore into the nucleus. D. is incorrect. Nuclear pores are made up of many copies of multiple proteins (approximately 30 different proteins).
Question 12 Outline the process of co-translational translocation using the figure below as a template. Your explanation should include the cellular location where this occurs and identify the following components in the figure below: lipid bilayer, cytosol, organelle lumen, ribosomes, mRNA, ER signal sequence, signal-recognition particle (SRP), SRP receptor, protein translocator.
Co-translational translocation describes the process by which proteins with an ER signal sequence are translocated across the ER membrane while being by translated by ribosomes on the ER membrane. 1. A ribosome begins translation of a protein with an ER signal sequence in the cytosol. The green blobs represent the ribosomal subunits, the horizontal blue line represents the mRNA, and the green line represents the growing polypeptide chain with an ER signal sequence (the red portion at the end). 2. A signal recognition particle (SRP) in the cytosol binds the exposed ER signal sequence and the ribosome, slowing protein synthesis by the ribosome. The brown blob is the SRP. 3. The SRP-ribosome complex binds to an SRP receptor in the ER membrane. The SRP receptor is the dark blue semi-circular unit sticking out of the gray membrane (ER membrane). 4. The SRP is released into the cytosol for reuse and the ribosome passes from the SRP receptor to a protein translocator. The light blue cylinder in the ER membrane is the protein translocator. 5. Protein synthesis resumes and the protein translocator transfers the growing polypeptide across the ER membrane into the lumen of the ER (area below ER membrane).
The figure below shows the organization of a protein that resides on the ER membrane. The N- and C-termini of the protein are labeled. Boxes 1, 2, and 3 represent membrane-spanning sequences. Non-membrane-spanning regions of the protein are labeled "X," "Y," and "Z." Once this protein is fully translocated, where will region Y be? A. in the cytosol B. in the ER lumen C. inserted into the ER membrane. D. degraded by signal peptidase
Correct Answer is A
Which of the following statements about vesicular membrane fusion is FALSE? A. Rabs and v-SNARES on the transport vesicle are specific for tethering proteins and t-SNARES on the target membrane, respectively. B. The hydrophilic surfaces of membranes have water molecules associated with them that must be displaced before vesicle fusion can occur. C. The GTP hydrolysis of the Rab proteins provides the energy for membrane fusion. D. The interactions of the v-SNAREs and the t-SNAREs pull the vesicle membrane and the target organelle membrane together so that their lipids can intermix.
Correct Answer is C Rab proteins are important for docking but are not involved in the catalysis of membrane fusion.
The figure below shows the orientation of the Krt1 protein on the membrane of a Golgi-derived vesicle that will fuse with the plasma membrane. Which of the following statements is TRUE? A. When this vesicle fuses with the plasma membrane, the entire Krt1 protein will be secreted into the extracellular space. B. When this vesicle fuses with the plasma membrane, the C-terminus of Krt1 will be inserted into the plasma membrane. C. When this vesicle fuses with the plasma membrane, the N-terminus of Krt1 will be in the extracellular space. D. When this vesicle fuses with the plasma membrane, the N-terminus of Krt1 will be cytoplasmic.
Correct Answer: C. When this vesicle fuses with the plasma membrane, the N-terminus of Krt1 will be in the extracellular space. The orientation of Krt1 as the vesicle fuses with the plasma membrane is shown in the figure below. The darker-colored lines in the membrane represent the membranes contributed by the vesicle during fusion.
Which of the following is NOT a process that delivers material to the lysosome? A. pinocytosis B. phagocytosis C. autophagy D. all of the above deliver material to the lysosome.
Correct answer is D
TRUE or FALSE: Proteins destined for the endoplasmic reticulum may not have an N-terminal signal sequence. A)True B)False
Correct answer: True Proteins destined for the ER may have an internal signal sequence instead of an N-terminal signal sequence.
You are interested in Fuzzy, a soluble protein that functions within the ER lumen. Given that information, which of the following statements must be TRUE? A. Fuzzy has a C-terminal signal sequence that binds to SRP B. Only one ribosome can be bound to the mRNA encoding Fuzzy during translation. C. Fuzzy must contain a hydrophobic stop-transfer sequence. D. Once the signal sequence from Fuzzy has been cleaved, the signal peptide will be ejected into the ER membrane and degraded.
D. is correct. ER signal sequences are removed from ER luminal proteins once they are translocated into the cytosol. A. is incorrect. ER signal sequences are at the N-terminus or internal and not the C-terminus. ER signal sequences bind to signal recognition particles (SRPs). B. is incorrect. More than one ribosome can bind to an mRNA molecule. C. is incorrect. Hydrophobic stop-transfer sequences are found on membrane-inserted proteins and not on soluble proteins.
Proteins that are fully translated in the cytosol do not end up in ___________. A. the cytosol B. the mitochondria C. the interior of the nucleus D. transport vesicles
D. is correct. Proteins destined for transport vesicles will be translated on ribosomes associated with the endoplasmic reticulum.
N-linked oligosaccharides on secreted glycoproteins are attached to _________. A. nitrogen atoms in the polypeptide backbone. B. the serine or threonine in the sequence Asn-X-Ser/Thr. C. the N-terminus of the protein. D. the asparagine in the sequence Asn-X-Ser/Thr.
D. is correct. Remember: N-linked glycosylation is called "N-linked" because the sugar is attached to the nitrogen on the asparagine side chain. It is not referring to the N-terminus.
Briefly, in your own words, explain what it is meant by the statement "signal sequences are necessary and sufficient to direct a protein to its destination." Describe how this could be demonstrated experimentally.
Signal sequences are necessary to direct a protein to its destination because without a signal sequence, the protein will not go to its appropriate destination. This could be demonstrated experimentally by removing the signal sequence from an ER protein. The ER protein without its signal sequence would remain in the cytoplasm (the default location for proteins without a signal sequence), demonstrating that a signal sequence is required to target a protein to its correct destination. Signal sequences are sufficient to direct a protein to its destination because altering the signal sequence will change the destination of the protein. This could be demonstrated experimentally by adding an ER signal sequence to a cytoplasmic protein. The cytoplasmic protein with the ER signal sequence would be found in the ER, demonstrating that the signal sequence is sufficient to target a protein to a particular destination.
Briefly describe the mechanism by which an internal stop-transfer sequence in a protein causes the protein to become embedded in the lipid bilayer as a transmembrane protein with a single membrane-spanning region. Assume that the protein has an N-terminal signal sequence and just one internal hydrophobic stop-transfer sequence. Optional follow-up question: you have a single-pass transmembrane protein with one internal start transfer sequence and no stop-transfer sequence. On which side of ER membrane would the N-terminus and C-terminus be located?
The N-terminal signal sequence initiates translocation and the protein chain starts to thread through the translocation channel. When the stop-transfer sequence enters the translocation channel, the channel discharges both the signal sequence and the stop-transfer sequence sideways into the lipid bilayer. The signal sequence is then cleaved, so that the protein remains held in the membrane by the hydrophobic stop-transfer sequence. Optional follow-up answer: the N-terminus would be in the ER lumen and the C-terminus in the cytosol. The internal start-transfer sequence would result in the translocation of the following portion of the polypeptide into the ER lumen, leaving the N-terminus in the cytosol. Because there is no stop-transfer sequence, the remainder of the protein would be translocated across the ER membrane and as a result, the C-terminus would be found in the ER lumen. Remember: signal peptidase only recognizes and cleaves N-terminal signal sequences.
The figure below depicts the vesicle budding from the ER. Identify the ER lumen and cytosolic side of the membrane and identify A-E. Hint: a word list is included below the figure. Describe the sequence of events (stages 1-4) that ultimately lead to the creation of a transport vesicle containing specific cargo
The cytosolic side of the plasma membrane is the white area and the extracellular space is the gray area. A = cargo receptor; B = adaptors; C = coat proteins; D = coated vesicle; E = naked transport vesicle Important events and processes driving the progression through the stages are as follows: Stage 1: Cargo receptors recognize and bind specific cargo molecules using "sorting signals." Adaptors capture specific cargo receptors and their associated cargo molecules by binding to "sorting signals" on the cytosolic tails of the transmembrane cargo receptor. Stage 2: Coat proteins bind adaptors to shape membrane into a vesicle. Stage 3: Vesicle pinches off the membrane. Stage 4: The vesicle uncoats and is ready to fuse with target membrane
Outline the process of protein translocation into the mitochondria using the figure below as a template. Your response should: Identify and include the following components: cytosol, mitochondrial outer membrane, mitochondrial inner membrane, mitochondrial matrix, precursor protein, mitochondrial signal sequence, import receptor protein, protein translocators, mature mitochondrial protein. Describe the function of chaperone proteins and signal peptidase (not illustrated in the figure). Note when the protein is folded or unfolded. Important follow-up question: a similar process occurs in which organelle?
The inner and outer mitochondrial membranes are shown as grey lines in the figure and the mitochondrial matrix is the light gray shaded region inside the inner membrane. The cytosol is the white unshaded area surrounding the mitochondria. A folded mitochondrial precursor protein is shown as a green squiggly line with a red portion representing a signal sequence. 1. The signal sequence on the folded mitochondrial precursor protein in the cytosol binds to an import receptor protein (lime green lollipop structure) on the outer mitochondrial membrane. 2. The import receptor protein is associated with a protein translocator (yellow oval with a slot) on the outer mitochondrial membrane, which transports the signal sequence across the outer mitochondrial membrane into the inner membrane space. 3. The complex of the precursor protein, import receptor, and translocator diffuse laterally in the outer membrane until the signal sequence is recognized by a translocator in the inner mitochondrial membrane (orange oval with a slot and protrusion). 4. The two translocators transport the protein across both mitochondrial membranes into the mitochondrial matrix, unfolding the protein in the process. 5. Chaperone proteins in the mitochondrial matrix (not shown in the figure), facilitate protein translocation into the mitochondrial matrix and prevent the protein from backslidingout of the mitochondria. 7. Signal peptidase (not shown in the figure) inside the mitochondrial matrix cleaves the signal sequence and the protein folds into its mature form. Important follow-up answer: a similar process occurs in chloroplasts.
If a lysosome breaks, what protects the rest of the cell from lysosomal enzymes?
The lysosomal enzymes are all acid hydrolases, which have optimal activity at the low pH (about 5.0) found in the interior of lysosomes. If a lysosome were to break, the acid hydrolases would find themselves at pH 7.2, the pH of the cytosol, and would therefore do little damage to cellular constituents.
After isolating the rough endoplasmic reticulum from the rest of the cytoplasm, you purify the RNAs attached to it. Which of the following proteins do you expect the RNA from the rough endoplasmic reticulum to encode? A. soluble secreted proteins B. ER membrane proteins C. plasma membrane proteins D. all of the above
The rough ER consists of ER membranes and polyribosomes that are in the process of translating and translocating proteins into the ER membrane and lumen. Thus, all proteins that end up in the lysosome, Golgi apparatus, or plasma membrane or that are secreted will be encoded by the RNAs associated with the rough ER.
In a cell capable of regulated secretion, what are the three main classes of proteins that must be separated before they leave the trans Golgi network?
The three main classes of protein that must be sorted before they leave the trans Golgi network in a cell capable of regulated secretion are (1) those destined for lysosomes, (2) those destined for secretory vesicles, and (3) those destined for immediate delivery to the cell surface.
