Chapter 15 Cell Biology

Match the components involved with ER transport with the appropriate cellular location. Locations can be used more than once, or not at all. 1. Signal-recognition particle 2. Protein translocator 3. mRNA 4. SRP receptor 5. Active site of signal peptidase A. Cytosol B. ER lumen C. ER Membrane

1. A 2. C 3. A 4. C 5. B

A large protein that passes through the nuclear pore must have an appropriate _________. (a) sorting sequence, which typically contains the positively charged amino acids lysine and arginine. (b) sorting 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

Figure Q15-31: Once this protein is fully translocated, where will region Y be? (a) in the cytoplasm (b) in the ER lumen (c) inserted into the ER membrane (d) degraded by signal peptidase

A

Proteins that are fully translated in the cytosol and lack a sorting signal will end up in ____. (a) the cytosol. (b) the mitochondria. (c) the interior of the nucleus. (d) the nuclear membrane.

A

What is the role of the nuclear localization sequence in a nuclear protein? (a) It is bound by cytoplasmic proteins that direct the nuclear protein to the nuclear pore. (b) It is a hydrophobic sequence that enables the protein to enter the 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.

A

Which of the following statements about membrane-enclosed organelles is true? (a) In a typical cell, the area of the endoplasmic reticulum membrane far exceeds the area of plasma membrane. (b) The nucleus is the only organelle that is surrounded by a double membrane. (c) Other than the nucleus, most organelles are small and thus, in a typical cell, only about 10% of a cell's volume is occupied by membrane-enclosed organelles; the other 90% of the cell volume is the cytosol. (d) The nucleus is the only organelle that contains DNA.

A

Which of the following statements about peroxisomes is false? (a) Most peroxisomal proteins are synthesized in the ER. (b) Peroxisomes synthesize phospholipids for the myelin sheath. (c) Peroxisomes produce hydrogen peroxide. (d) Vesicles that bud from the ER can mature into peroxisomes.

A

Which of the following statements about phagocytic cells in animals is false? (a) Phagocytic cells are important in the gut to take up large particles of food. (b) Phagocytic cells scavenge dead and damaged cells and cell debris. (c) Phagocytic cells can engulf invading microorganisms and deliver them to their lysosomes for destruction. (d) Phagocytic cells extend pseudopods that surround the material to be ingested.

A

Which of the following statements about secretion is true? (a) The membrane of a secretory vesicle will fuse with the plasma membrane when it discharges its contents to the cell's exterior. (b) Vesicles for regulated exocytosis will not bud off the trans Golgi network until the appropriate signal has been received by the cell. (c) The signal sequences of proteins destined for constitutive exocytosis ensure their packaging into the correct vesicles. (d) Proteins destined for constitutive exocytosis aggregate as a result of the acidic pH of the trans Golgi network.

A

Which of the following statements about vesicle budding from the Golgi is false? (a) Clathrin molecules are important for binding to and selecting cargoes for transport. (b) Adaptins interact with clathrin. (c) Once vesicle budding occurs, clathrin molecules are released from the vesicle. (d) Clathrin molecules act at the cytosolic surface of the Golgi membrane.

A

Figure Q15-35: Indicate on your drawing the extracellular space, the cytosolic face, and the plasma membrane, as well as the N- and C-terminus of the protein. A. deleting the first signal sequence B. changing the hydrophobic amino acids in the first, cleaved sequence to charged amino acids C. changing the hydrophobic residues in every other transmembrane sequence to charged residues, starting with the first, cleaved signal sequence

A. Deleting the first signal sequence completely would convert the next membrane-spanning domain into an internal start-transfer signal and would invert the orientation of the protein B. Changing the hydrophobic amino acids to charged amino acids destroys the ability of the sequence both to act as a signal sequence and to become a membrane-spanning sequence. Therefore, the adjacent membrane-spanning domain will now become an internal start-transfer sequence and the protein will be inverted, as seen above in part A. The mutated signal sequence would not get cleaved off, because it would remain on the cytoplasmic side of the membrane and signal peptidase is found only inside the ER C. Mutating every other membrane-spanning region so that they are now charged (and thus cannot span the membrane) would decrease the number of transmembrane regions and increase the size of the loops between membrane-spanning regions

What would happen in each of the following cases? Assume in each case that the protein involved is a soluble protein, not a membrane protein. A. You add a signal sequence (for the ER) to the N-terminal end of a normally cytosolic protein. B. You change the hydrophobic amino acids in an ER signal sequence into charged amino acids. C. You change the hydrophobic amino acids in an ER signal sequence into other hydrophobic amino acids. D. You move the N-terminal ER signal sequence to the C-terminal end of the protein.

A. The protein will now be transported into the ER lumen. B. The altered signal sequence will not be recognized and the protein will remain in the cytosol. C. The protein will still be delivered into the ER. It is the distribution of hydrophobic amino acids that is important, not the actual sequence. D. The protein will not enter the ER. Because the C-terminus of the protein is the last part to be made, the ribosomes synthesizing this protein will not be recognized by the signal-recognition particle (SRP) and hence not carried to the ER.

Using genetic engineering techniques, you have created a set of proteins that contain two (and only two) conflicting signal sequences that specify different compartments. Predict which signal would win out for the following combinations. Explain your answers. A. Signals for import into the nucleus and import into the ER. B. Signals for export from the nucleus and import into the mitochondria. C. Signals for import into mitochondria and retention in the ER.

A. The protein would enter the ER. The signal for a protein to enter the ER is recognized as the protein is being synthesized and the protein will end up either in the ER or on the ER membrane. Cytosolic nuclear transport proteins recognize proteins destined for the nucleus once those proteins are fully synthesized and fully folded. B. The protein would enter the mitochondria. For a nuclear export signal to work, the protein would have to end up in the nucleus first and thus would need a nuclear import signal for the nuclear export signal to be used. C. The protein would enter the mitochondria. To be retained in the ER, the protein needs to enter the ER. Because there is no signal for ER import, the ER retention signal would not function.

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

Given Figure Q15-34, which of the following statements must be true? (a) The N-terminus of this protein is cytoplasmic. (b) The C-terminus of this 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. (d) None of the above.

B

Molecules to be packaged into vesicles for transport are selected by ________. (a) clathrin. (b) adaptins. (c) dynamin. (d) SNAREs.

B

Which of the following statements about the endoplasmic reticulum (ER) is false? (a) The ER is the major site for new membrane synthesis in the cell. (b) Proteins to be delivered to the ER lumen are synthesized on smooth ER. (c) Steroid hormones are synthesized on the smooth ER. (d) The ER membrane is contiguous with the outer nuclear membrane.

B

Which of the following statements about the protein quality control system in the ER is false? (a) Chaperone proteins help misfolded proteins fold properly. (b) Proteins that are misfolded are degraded in the ER lumen. (c) Protein complexes are checked for proper assembly before they can exit the ER. (d) A chaperone protein will bind to a misfolded protein to retain it in the ER.

B

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 moves through the protein translocator in the outer membrane of these organelles, the protein diffuses in the lumen 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

Which of the following statements is true? (a) Lysosomes are believed to have originated from the engulfment of bacteria specialized for digestion. (b) The nuclear membrane is thought to have arisen from the plasma membrane invaginating around the DNA. (c) Because bacteria do not have mitochondria, they cannot produce ATP in a membrane-dependent fashion. (d) Chloroplasts and mitochondria share their DNA.

B

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

Figure Q15-48 (a) The oligosaccharide should have been added to the serine instead of the asparagine. (b) The oligosaccharide should have been added one sugar at a time. (c) The oligosaccharide needs to be further modified before it is mature. (d) The oligosaccharide needs a disulfide bond.

C

Figure Q15-57: Given this diagram, 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.

C

In which cellular location would you expect to find ribosomes translating mRNAs that encode ribosomal proteins? (a) the nucleus (b) on the rough ER (c) in the cytosol (d) in the lumen of the ER

C

Most proteins destined to enter the endoplasmic reticulum _________. (a) are transported across the membrane after their synthesis is complete. (b) are synthesized on free ribosomes in the cytosol. (c) begin to cross the membrane while still being synthesized. (d) remain within the endoplasmic reticulum.

C

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.

C

Vesicles from the ER enter the Golgi at the ______. (a) medial cisternae. (b) trans Golgi network. (c) cis Golgi network. (d) trans cisternae.

C

Which of the following organelles is not part of the endomembrane system? (a) Golgi apparatus (b) the nucleus (c) mitochondria (d) lysosomes

C

Which of the following statements about nuclear transport is true? (a) mRNAs and proteins transit the nucleus through different types of nuclear pores. (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 have water-filled passages that small, water-soluble molecules can pass through in a nonselective fashion. (d) Nuclear pores are made up of many copies of a single protein.

C

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

Which of the following statements about vesicular membrane fusion is false? (a) Membrane fusion does not always immediately follow vesicle docking. (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.

C

Which of the following statements is true? (a) Proteins destined for the ER are translated by a special pool of ribosomes whose subunits are always associated with the outer ER membrane. (b) Proteins destined for the ER translocate their associated mRNAs into the ER lumen where they are translated. (c) Proteins destined for the ER are translated by cytosolic ribosomes and are targeted to the ER when a signal sequence emerges during translation. (d) Proteins destined for the ER are translated by a pool of cytosolic ribosomes that contain ER-targeting sequences that interact with ER-associated protein translocators.

C

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. (d) Mitochondrial proteins cross the membrane in their native, folded state.

C

Your friend has just joined a lab that studies vesicle budding from the Golgi and has been given a cell line that does not form mature vesicles. He wants to start designing some experiments but wasn't listening carefully when he was told about the molecular defect of this cell line. He's too embarrassed to ask and comes to you for help. He does recall that this coat proteins cell line forms coated pits but vesicle budding and the removal of don't happen. Which of the following proteins might be lacking in this cell line? (a) clathrin (b) Rab (c) dynamin (d) adaptin

C

Your friend works in a biotechnology company and has discovered a drug that blocks the ability of Ran to exchange GDP for GTP. What is the most likely effect of this drug on 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.

C

For each of the following sentences, choose one of the two options enclosed in square brackets to make a correct statement. New plasma membrane reaches the plasma membrane by the [regulated/constitutive] exocytosis pathway. New plasma membrane proteins reach the plasma membrane by the [regulated/constitutive] exocytosis pathway. Insulin is secreted from pancreatic cells by the [regulated/constitutive] exocytosis pathway. The interior of the trans Golgi network is [acidic/alkaline]. Proteins that are constitutively secreted [aggregate/do not aggregate] in the trans Golgi network.

Constitutive, constitutive, regulated, acidic, do not aggregate

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; use each word or phrase only once. The __________________ makes up about half of the total cell volume of a typical eukaryotic cell. Ingested materials within the cell will pass through a series of compartments called __________________ on their way to the __________________, which contains digestive enzymes and will ultimately degrade the particles and macromolecules taken into the cell and will also degrade worn-out organelles. The __________________ has a cis and trans face and receives proteins and lipids from the __________________, a system of interconnected sacs and tubes of membranes that typically extends throughout the cell. cytosol Golgi apparatus nucleus endoplasmic reticulum lysosome peroxisomes endosomes mitochondria plasma membrane

Cytosol, endosomes, lysosome, Golgi apparatus, endoplasmic reticulum

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

D

Different glycoproteins can have a diverse array of oligosaccharides. Which of the statements below about this diversity is true? (a) Extensive modification of oligosaccharides occurs in the extracellular space. (b) Different oligosaccharides are covalently linked to proteins in the ER and the Golgi. (c) A diversity of oligosaccharyl transferases recognizes specific protein sequences, resulting in the linkage of a variety of oligosaccharides to proteins. (d) Oligosaccharide diversity comes from modifications that occur in the ER and the Golgi of the 14-sugar oligosaccharide added to the protein in the ER.

D

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

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

Where are proteins in the chloroplast synthesized? (a) in the cytosol (b) in the chloroplast (c) on the endoplasmic reticulum (d) in both the cytosol and the chloroplast

D

Which of the following choices reflects the appropriate order of locations through which a protein destined for the plasma membrane travels? (a) lysosome ◊ endosome ◊ plasma membrane (b) ER ◊lysosome ◊plasma membrane (c) Golgi ◊ lysosome ◊ plasma membrane (d) ER ◊ Golgi ◊ plasma membrane

D

Which of the following protein families are not involved in directing transport vesicles to the target membrane? (a) SNAREs (b) Rabs (c) tethering proteins (d) adaptins

D

Which of the following statements about a protein in the lumen of the ER is false? (a) A protein in the lumen of the ER is synthesized by ribosomes on the ER membrane. (b) Some of the proteins in the lumen of the ER can end up in the extracellular space. (c) Some of the proteins in the lumen of the ER can end up in the lumen of an organelle in the endomembrane system. (d) Some of the proteins in the lumen of the ER can end up in the plasma membrane.

D

Which of the following statements about disulfide bond formation is false? (a) Disulfide bonds do not form under reducing environments. (b) Disulfide bonding occurs by the oxidation of pairs of cysteine side chains on the protein. (c) Disulfide bonding stabilizes the structure of proteins. (d) Disulfide bonds form spontaneously within the ER because the lumen of the ER is oxidizing.

D

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

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Eukaryotic cells are continually taking up materials from the extracellular space by the process of endocytosis. One type of endocytosis is __________________, which uses __________________ proteins to form small vesicles containing fluids and molecules. After these vesicles have pinched off from the plasma membrane, they will fuse with the __________________, where materials that are taken into the vesicle are sorted. A second type of endocytosis is __________________, which is used to take up large vesicles that can contain microorganisms and cellular debris. Macrophages are especially suited for this process, as they extend __________________ (sheetlike projections of their plasma membrane) to surround the invading microorganisms. chaperone Golgi apparatus pseudopods cholesterol mycobacterium rough ER clathrin phagocytosis SNARE endosome pinocytosis transcytosis

Pinocytosis, clathrin, endosome, phagocytosis, pseudopods

Name two types of protein modification that can occur in the ER but not in the cytosol.

Proteins in the ER can undergo disulfide bond formation. Proteins in the ER can undergo glycosylation.

Name three possible fates for an endocytosed molecule that has reached the endosome.

Recycled to the original membrane Destroyed in the lysosome Transcytosed across the cell to a different membrane

Fill in the list below. Not all words or phrases will be used; use each word or phrase only once. Proteins are transported out of a cell via the __________________ or __________________ pathway. Fluids and macromolecules are transported into the cell via the __________________ pathway. All proteins being transported out of the cell pass through the __________________ and the __________________. Transport vesicles link organelles of the __________________ system. The formation of __________________ in the endoplasmic reticulum stabilizes protein structure. Carbohydrate Golgi apparatus disulfide bonds hydrogen bonds endocytic ionic bonds endomembrane lysosome endoplasmic reticulum protein endosome secretory exocytic

Secretory OR exocytic, endocytic, endoplasmic reticulum, Golgi apparatus, endomembrane, disulfide bonds

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.

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?

Those destined for lysosomes Those destined for secretory vesicles Those destined for immediate delivery to the cell surface

Name the membrane-enclosed compartments in a eukaryotic cell where each of the functions listed below takes place. A. photosynthesis B. transcription C. oxidative phosphorylation D. modification of secreted proteins E. steroid hormone synthesis F. degradation of worn-out organelles G. new membrane synthesis H. breakdown of lipids and toxic molecules

a. Photosynthesis = chloroplast b. Transcription = nucleus c. Oxidative phosphorylation = mitochondrion d. Modification of secreted proteins = Golgi apparatus and rough endoplasmic reticulum (ER) e. Steroid hormone synthesis = smooth ER f. Degradation of worn-out organelles = lysosome g. New membrane synthesis = ER h. Breakdown of lipids and toxic molecules = peroxisome

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; use each word or phrase only once. Plasma membrane proteins are inserted into the membrane in the __________________. The address information for protein sorting in a eukaryotic cell is contained in the __________________ of the proteins. Proteins enter the nucleus in their __________________ form. Proteins that remain in the cytosol do not contain a __________________. Proteins are transported into the Golgi apparatus via __________________. The proteins transported into the endoplasmic reticulum by __________________ are in their __________________ form. amino acid sequence Golgi apparatus sorting signal endoplasmic reticulum plasma membrane transport vesicles folded protein translocators unfolded

endoplasmic reticulum, amino acid sequence, folded, sorting signal, transport vesicles, protein translocators, unfolded