Exam 2 in ppt questions

Figure Q15-31 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 cytoplasm* (b) in the ER lumen (c) inserted into the ER membrane (d) degraded by signal peptidase

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.

In stage 1 of photosynthesis, a proton gradient is generated and ATP is synthesized. Where do protons become concentrated in the chloroplast?

(a) *thylakoid space* (b) stroma (c) inner membrane (d) thylakoid membrane

The enzyme ribulose bisphosphate carboxylase (Rubisco) normally adds carbon dioxide to ribulose 1,5-bisphosphate. However, it will also catalyze a competing reaction in which O2 is added to ribulose 1,5-bisphosphate to form 3-phosphoglycerate and phosphoglycolate. Assume that phosphoglycolate is a compound that cannot be used in any further reactions. If O2 and CO2 have the same affinity for Rubisco, which of the following is the lowest ratio of CO2 to O2 at which a net synthesis of sugar can occur?

(a) 1:3 (b) 1:2 (c) *3:1* (d) 2:1

15-28 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.*

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.

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.

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.

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.*

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.*

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.*

Which of the following organelles is not part of the endomembrane system?

(a) Golgi apparatus (b) the nucleus (c) *mitochondria* (d) lysosomes

Stage 2 of photosynthesis, sometimes referred to as the dark reactions, involves the reduction of CO2 to produce organic compounds such as sucrose. What cofactor is the electron donor for carbon fixation?

(a) H2O (b) NADH (c) FADH2 (d) *NADPH*

Which of the following statements is not true about the possible fates of glyceraldehyde 3-phosphate?

(a) It can be exported from the chloroplast to the cytosol for conversion into sucrose. (b) It can be used to make starch, which is stored inside the stroma of the chloroplast. (c) It can be used as a precursor for fatty acid synthesis and stored as fat droplets in the stroma. (d) *It can be transported into the thylakoid space for use as a secondary electron acceptor downstream of the electron-transport chain.*

If you add a compound to illuminated chloroplasts that inhibits the NADP+ reductase, NADPH generation ceases, as expected. However, ferredoxin does not accumulate in the reduced form because it is able to donate its electrons not only to NADP+ (via NADP+ reductase) but also back to the cytochrome b6-f complex. Thus, in the presence of the compound, a "cyclic" form of photosynthesis occurs in which electrons flow in a circle from ferredoxin, to the cytochrome b6-f complex, to plastocyanin, to photosystem I, to ferredoxin. What will happen if you now also inhibit photosystem II?

(a) Less ATP will be generated per photon absorbed. (b) ATP synthesis will cease. (c) *Plastoquinone will accumulate in the oxidized form.* (d) Plastocyanin will accumulate in the oxidized form.

15-43 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.

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.

Which of the following statements about proteins 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.

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

15-1 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.

Figure Q15-34 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 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.

(Figure Q15-48). Unfortunately, immune cells do not seem to recognize this synthesized glycoprotein. Which of the following statements is a likely explanation for this problem?

(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.

15-20 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.

Which of the following statements is true? II

(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.

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.

15-23 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.

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 cell line forms coated pits but vesicle budding and the removal of coat proteins don't happen. Which of the following proteins might be lacking in this cell line?

(a) clathrin (b) Rab (c) dynamin (d) *adaptin*

15-39 Molecules to be packaged into vesicles for transport are selected by ________.

(a) clathrin. (b) *adaptins.* (c) dynamin. (d) SNAREs.

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.

In the electron-transport chain in chloroplasts, ________-energy electrons are taken from __________.

(a) high; H2O. (b) *low; H2O.* (c) high; NADPH. (d) low; NADPH.

15-10 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*

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*

15-15 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*

15-54 Vesicles from the ER enter the Golgi at the ______.

(a) medial cisternae. (b) trans Golgi network. (c) *cis Golgi network.* (d) trans cisternae.

The photosystems in chloroplasts contain hundreds of chlorophyll molecules, most of which are part of _______________.

(a) plastoquinone. (b) *the antenna complex.* (c) the reaction center. (d) the ferredoxin complex.

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*

15-11 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.*

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) i*n the cytosol* (d) in the lumen of the ER

Photosynthesis is a process that takes place in chloroplasts and uses light energy to generate high-energy electrons, which are passed along an electron-transport chain. Where are the proteins of the electron-transport chain located in chloroplasts?

(a) thylakoid space (b) stroma (c) inner membrane (d) *thylakoid membrane*

The ATP synthase found in chloroplasts is structurally similar to the ATP synthase in mitochondria. Given that ATP is being synthesized in the stroma, where will the F0 portion of the ATP synthase be located?

(a) thylakoid space (b) stroma (c) inner membrane (d) *thylakoid membrane*

You discover a fungus that contains a strange star-shaped organelle not found in any other eukaryotic cell you have seen. On further investigation, you find the following.

1. The organelle possesses a small genome in its interior. 2. The organelle is surrounded by two membranes. 3. Vesicles do not pinch off from the organelle membrane. 4. The interior of the organelle contains proteins similar to those of many bacteria. 5. The interior of the organelle contains ribosomes.

From these results, match each of the transferases (A, B, C, D) to its subcellular location selected from the list below. (Assume that each location contains only one enzyme.)

1. central Golgi cisternae_-B 2. cis Golgi network-D 3. ER-A 4. trans Golgi network-C

15-53 Match the set of labels below with the numbered label lines on Figure Q15-53.

A. cisterna - 3 B. Golgi stack -1 C. secretory vesicle-5 D. trans Golgi network-4 E. cis Golgi network-2

Name the membrane-enclosed compartments in a eukaryotic cell where each of the functions listed below takes place.

A. photosynthesis- chloroplast B. transcription- nucleus C. oxidative phosphorylation-mitochondrion D. modification of secreted proteins- golgi and rough er E. steroid hormone synthesis- smooth er F. degradation of worn-out organelles- lysosomes G. new membrane synthesis- er H. breakdown of lipids and toxic molecules- peroxisomes

When you incubate some of these mutant fibroblasts in a medium in which normal cells have been grown, you find that the inclusion bodies disappear. Because of these results, you suspect that the constitutive exocytic pathway in normal cells is secreting lysosomal hydrolases that are being taken up by the mutant cells. (It is known that some mannose-6-phosphate receptor molecules are found in the plasma membrane and can take up and deliver lysosomal proteins via the endocytic pathway.) You incubate cells from each patient with medium from normal cells and medium from each of the other mutant cell cultures, and get the results summarized in Table Q15-65.

Strain A has protein accumulating in the ER, which means that this cell has a mutation that blocks transport from the ER to the Golgi apparatus. Strain B has secreted protein, and therefore is the wild-type control. Strain C has protein accumulating in the Golgi apparatus, and thus has a mutation that blocks exit of proteins from the Golgi apparatus. Strain D has protein accumulating in the cis Golgi network, and thus has a mutation that blocks the travel of proteins through the Golgi cisternae.

15-63 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.

If you shine light on chloroplasts and measure the rate of photosynthesis as a function of light intensity, you get a curve that reaches a plateau at a fixed rate of photosynthesis, x, as shown in Figure Q14-62.

Which of the following conditions will increase the value of x? (a) increasing the number of chlorophyll molecules in the antenna complexes (b) *increasing the number of reaction centers* (c) adding a powerful oxidizing agent (d) decreasing the wavelength of light used

Fibroblast cells from patients W, X, Y, and Z, each of whom has a different inherited defect, all contain "inclusion bodies," which are lysosomes filled with undigested material. You wish to identify the cellular basis of these defects. The possibilities are:

W—3 (defect in mannose-6-phosphate receptor) X—2 (defect in phosphotransferase) Y—1; Z—1 (defect in lysosomal hydrolases); these will be defects in two different lysosomal acid hydrolases

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.

15-38 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.

15-2 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.

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.

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.

15-21 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.

15-61 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.

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.