MOLECULAR BIOLOGY OF THE CELL, SIXTH EDITION

Chapter 13 INTRACELLULAR MEMBRANE TRAFFIC

© Garland Science 2015

1. Reconstitution of vesicle transport in cell-free systems was historically carried out in the
presence of isolated “donor” and “acceptor” Golgi stacks. The donor stacks are isolated from
cells expressing a viral protein and lacking a processing enzyme. The protein can be transported
to the acceptor stacks (that do contain the processing enzyme) and be processed only in the
presence of an energy source (such as ATP) and a cytosolic fraction. The transport vesicles that
mediate this process are visualized by microscopy. Various compounds can be added to this
system to help understand the mechanism of transport. Two such compounds were added in early
experiments in the 1980s, both of which blocked transport of the viral protein and resulted in the
accumulation of transport vesicles. However, the accumulated vesicles following treatment with
one of these compounds (A) appeared to be coated, while those resulting from treatment with the
other compound (B) did not. If one of these compounds is a nonhydrolyzable GTP analog and
the other one is N-ethylmaleimide, which compound (A or B) do you think represents the GTP
analog? Write down A or B as your answer.

1. Indicate whether each of the following descriptions better applies to COPI- (1), COPII-
(2), or clathrin- (3) coated vesicles. Your answer would be a four-digit number composed of
digits 1 to 3 only, e.g. 1322.
( ) They mediate transport from the ER to the cis Golgi network.
( ) Their coat protein forms a three-legged structure called a triskelion.
( ) They are pinched off from their donor compartment by a dynamin collar.
( ) They are involved in retrograde transport in the Golgi apparatus.

1. Indicate which one of the indicated types of coat proteins (A, B, and C) in the schematic
diagram below corresponds to COPI, COPII, and clathrin, respectively. Your answer would be a
three-letter string composed of letters A to C only, e.g. CBA.
 A

1. Consider a perfectly assembled clathrin cage that is composed of 12 pentagons and 20

hexagons and therefore resembles a soccer ball. How many clathrin heavy chains are there in this
cage? Write down the number as your answer, e.g. 24.

1. Adaptor proteins select cargo proteins that will be incorporated into clathrin-coated
vesicles. An adaptor protein such as AP2 …
A. can induce membrane curvature even before clathrin molecules bind.
B. acts as a coincidence detector, assembling only when a number of requirements are
met.
C. binds to phosphoinositides in the cytosolic leaflet of the membrane.
D. alternates between a locked cytosolic form and an unlocked membrane-bound form.
E. All of the above.

1. Phosphoinositides mark different cellular membranes and play key roles in protein
trafficking inside the cell. Among them, PI(4,5)P2 is involved in receptor-mediated endocytosis
as well as phagocytosis at the plasma membrane. This phosphoinositide …
A. is bound by the adaptor protein AP2.
B. is bound by the GTPase dynamin.
C. is depleted from clathrin-coated vesicles to promote their uncoating.
D. All of the above.
1. Indicate whether each of the following descriptions better applies to COPI- (1), COPII-
(2), or clathrin- (3) coated vesicles. Your answer would be a four-digit number composed of
digits 1 to 3 only, e.g. 1322.
( ) They are uncoated by an hsp70 family protein, which is stimulated by the binding of
auxilin.
( ) They keep their coat proteins for a relatively long time, until they dock onto their
target membrane.
( ) Their uncoating depends on activation of an ARF-GAP.
( ) Their uncoating depends in part on activation of a Sar1-GAP.

1. Sort the following events to reflect the order in which they occur during the formation of
vesicles from the ER destined for the Golgi apparatus. Your answer would be a four-letter string
composed of letters A to D only, e.g. DACB.
(A) Sar1 GTP hydrolysis
(B) Sar1 GTP binding
(C) Sar1–Sec23 binding
(D) Sar1 membrane association

1. Indicate true (T) and false (F) statements below regarding intracellular vesicle transport.
Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF
( ) The plasma membrane is stiffer and flatter than most intracellular membranes, and its
deformation generally requires greater force.
( ) Large molecules such as collagen fibers of about 300 µm in length are highly packed
and coiled to fit into normal COPII vesicles of about 80 nm in diameter.
( ) Rab proteins are recruited to membranes following activation by Rab-GEFs.
( ) A Rab and its effector are always on two different membranes that will then fuse.

1. If this protein is unable to hydrolyze its bound GTP, invaginated clathrin-coated pits
accumulate but fail to pinch off from the plasma membrane. In neurons, long vesicle necks
collared by the protein are observed and presynaptic endocytosis is blocked. This protein …
A. contains a PI(4,5)P2 binding domain and a GTPase domain.
B. recruits other proteins to the neck of the vesicle.
C. may change the membrane lipid composition by recruiting lipid-modifying enzymes.
D. may directly distort the membrane using the energy from GTP hydrolysis.
E. All of the above.
1. Sort the following events to reflect the order in which they occur during vesicle docking
onto a target membrane, starting with an inactive Rab in the cytosol. Your answer would be a
four-letter string composed of letters A to D only, e.g. DACB.
(A) Rab is bound to its effector (tethering protein) on the target membrane.
(B) Rab is bound to its Rab-GDI.
(C) Rab is bound to the membrane in its GTP-bound form.
(D) Rab dissociates from the membrane.

1. Rab5 and Rab7 constitute a Rab cascade in the process of endosome maturation. One of
the Rab5 effectors is a Rab7-GEF, while one of the Rab7 effectors is a Rab5-GAP. Which of
these proteins would you expect to find in early endosomes? Write down Rab5 or Rab7 as your
answer.

1. Indicate whether each of the following descriptions better applies to t-SNAREs (T) or v-
SNAREs (V). Your answer would be a three-letter string composed of letters T and V only, e.g.
TVV.
( ) They are usually located on the target membrane.
( ) They are composed of a single polypeptide chain.
( ) They are usually associated with inhibitory proteins that can be released by Rab
proteins.

1. The transmembrane protein Tango1 is a packaging protein that helps some secretory
proteins leave the endoplasmic reticulum (ER) after synthesis. Knocking down Tango1 by RNA
interference impairs the incorporation of collagen VII, but not collagen I, into transport vesicles
destined for the Golgi apparatus. The protein contains a lumenal N-terminal SH3 domain and a
cytosolic C-terminal proline-rich domain. Which of the following proteins would you expect to
interact with the N-terminal and C-terminal domains of Tango1, respectively?
A. Procollagen VII; COPI components
B. Procollagen VII; COPII components
C. Procollagen I; COPI components
D. Procollagen I; COPII components
E. COPI components; procollagen I

1. In the following schematic diagram depicting the formation of vesicular tubular clusters
between the ER and the CGN, what major coat proteins are indicated by 1 and 2, respectively?
 1

2
!

A. COPI; COPII
B. COPI; clathrin
C. COPII; COPI
D. COPII; clathrin
E. Clathrin; COPII

1. The cytoplasmic C-terminal KKXX sequence of transmembrane proteins interacts with

…
A. t-SNAREs
B. v-SNAREs
C. AP2
D. COPI coatomers
E. COPII coatomers

1. A schematic drawing of the secretory and endocytic pathways is presented below.

Indicate which component in the drawing (A to J) corresponds to each of the following. Your
answer would be a 10-letter string composed of letters A to J only, e.g. HICDJABFGE.
 J

A
H

B C D E
F
G
!

( ) Early endosome
( ) Late endosome
( ) ER
( ) Lysosome
( ) cis Golgi cisterna
( ) medial Golgi cisterna
( ) trans Golgi cisterna
( ) cis Golgi network (CGN)
( ) trans Golgi network (TGN)
( ) Secretory vesicle

1. The Golgi apparatus is made up of an ordered series of compartments. To process N-

linked oligosaccharides, different Golgi compartments carry different enzymes that alter the
sugar chains sequentially. Which Golgi cisternae are normally responsible for the addition of
galactose and sialic acid, respectively, in complex oligosaccharides?
A. cis cisterna; medial cisterna
B. cis cisterna; trans cisterna
C. medial cisterna; trans cisterna
 D. medial cisterna; medial cisterna
E. trans cisterna; trans cisterna

1. Consider two N-linked oligosaccharide chains on the same protein. The first chain
contains three mannose residues and three negatively charged sialic acid residues, as well as
other residues. The second chain contains only two N-acetylglucosamine and eight mannose
residues. Which chain seems to have been added to the protein such that it is NOT fully
accessible to the processing enzymes in the Golgi apparatus? Which chain is Endo H-sensitive?
A. Chain one; chain one
B. Chain one; chain two
C. Chain two; chain one
D. Chain two; chain two

1. Indicate whether each of the following descriptions better applies to N-linked (N) or O-
linked (O) glycosylation. Your answer would be a four-letter string composed of letters N and O
only, e.g. OONO.
( ) It is abundant in proteoglycans.
( ) It involves the attachment of a preassembled block of oligosaccharide onto a protein.
( ) It is attached to a serine or threonine residue in the protein.
( ) It involves heavily sulfated sugars.

1. Indicate true (T) and false (F) statements below regarding glycosylation of proteins in the
endoplasmic reticulum and the Golgi apparatus. Your answer would be a four-letter string
composed of letters T and F only, e.g. TTTF
( ) Glycosylation can promote protein folding.
( ) The glycosylation state of a protein can determine its fate along the secretory
pathway.
( ) Glycosylation makes a protein more accessible to proteases and other proteins.
( ) Glycosylated proteins are generally more flexible.

1. Indicate whether each of the following descriptions better applies to the cisternal
maturation model (C) or the vesicle transport model (V) for the organization of the Golgi
apparatus. Your answer would be a four-letter string composed of letters C and V only, e.g.
CVCV.
( ) Golgi cisternae are static organelles.
( ) Golgi cisternae exchange material exclusively by retrograde vesicular transport.
 ( ) A cis Golgi cisterna becomes a medial cisterna which becomes a trans cisterna.
( ) Any protein that passes through the Golgi apparatus should be incorporated into
transport vesicles several times.

1. You have engineered a fusion protein composed of a cis Golgi resident protein and the
green fluorescent protein. Similarly, you have made a fusion protein composed of a trans Golgi
protein and the red fluorescent protein. You express these proteins in cells and follow individual
Golgi cisternae using fluorescence microscopy. You observe that each individual cisterna emits a
green, faint yellow, or red fluorescent signal at different times: it initially shows green
fluorescence, but the green fluorescent signal fades away with time, and instead red fluorescence
appears in the same cisterna. Additionally, you do not observe any red fluorescent cisterna that
becomes green over time. Do these observations agree better with the cisternal maturation model
(C) or the vesicle transport model (V) for the organization of Golgi stacks? Write down C or V as
your answer.

1. Aspartic acid residues resemble phosphorylated serine residues in proteins and also carry
a similar negative charge. As a result, a protein in which serine residues are mutated to aspartic
acid residues may mimic the function of the corresponding wild-type protein when those serines
are phosphorylated. Given that phosphorylation on serine residues in a number of Golgi matrix
proteins occurs during mitosis, would you expect that mutation of these serines to aspartic acids
would prevent Golgi stack formation in interphase (1) or prevent Golgi dispersion in mitosis (2)?
Write down 1 or 2 as your answer.

1. Indicate whether each of the following descriptions better applies to a BAR domain (B),
the outer shell of COPI coatomer (C), or a dynamin oligomer (D). Your answer would be a three-
letter string composed of letters B, C, and D only, e.g. CBD.
( ) It resembles a crescent.
( ) It resembles a collar.
( ) It resembles a cage.

1. An animal cell has been wounded and has a small rupture in its plasma membrane. Which
of the following is more likely to happen next?
A. The cell rapidly cleaves by cytokinesis.
B. The rate of receptor-mediated endocytosis is increased.
C. The rate of exocytosis is increased.
D. The rate of pinocytosis is increased.
 E. All of the above.

1. 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.

1. How many protons [or, more accurately, hydronium ions (H3O+)] are there in a spherical
lysosome that is about 0.6 µm in diameter and maintains an interior pH of about 5.0? Recall that
the volume of a sphere of radius r is calculated as V = 4/3 × π × r3, and that pH = –log [H+].
Avogadro’s constant is approximately 6 × 1023 molecules/mole.
A. About 700 ions
B. About 7000 ions
C. About 70,000 ions
D. About 700,000 ions
E. About 7,000,000 ions

1. What is the cellular function of plant vacuoles?

A. They store nutrients and waste products.
B. They help increase cell size and maintain turgor pressure.
C. They are used for degradation of cytoplasmic components.
D. They help maintain cytosolic pH.
E. All of the above.

1. You are studying the cellular basis of petal coloration in the flowering plant Ipomoea
tricolor. These plants have colorful petals due to the presence of pH-sensitive vacuolar
anthocyanins that change color from red/purple in acidic pH to blue at neutral pH. You treat
petals with either vanadate (a specific inhibitor of P-ATPases) or bafilomycin (a specific
inhibitor of V-ATPases) or both and compare the color with that of control petals, obtaining the
results shown in the table below. Which of the following conclusions is consistent with these
observations?

Treatment Color
 Control Red
Vanadate Blue
Bafilomycin Blue
Vanadate + bafilomycin Blue

A. Both P- and V-ATPases are required to sufficiently acidify the vacuoles in petal cells.
B. P-ATPases are sufficient for acidification of the vacuoles in petal cells.
C. V-ATPases are sufficient for acidification of the vacuoles in petal cells.
D. Neither P- nor V-ATPases are necessary for vacuole acidification in petal cells.

1. Which of the following pathways does NOT directly deliver materials to lysosomes?
A. Endocytosis
B. Exocytosis
C. Phagocytosis
D. Autophagy
E. Macropinocytosis

1. A mitochondrion has just been engulfed by a cup-shaped isolation membrane as it

undergoes mitophagy. Before lysosomal fusion, how many membranes separate the cytosol from
the matrix of the engulfed mitochondrion?
A. 2
B. 3
C. 4
D. 5

1. In Drosophila melanogaster, loss-of-function mutations in either Pink1 or Parkin show

similar phenotypes including impaired ability to fly, male sterility, and degeneration of
dopaminergic neurons. Transgenic overexpression of Parkin in mutants lacking Pink1
significantly ameliorates the loss-of-function phenotype, but overexpression of Pink1 cannot
rescue the Parkin loss-of-function phenotype. According to these findings, which protein is more
likely to act upstream of the other one? Assuming that the Parkin loss-of-function phenotype is
merely due to defects in autophagy, would you expect Parkin overexpression to also rescue an
ATG9 loss-of-function phenotype?
A. Parkin acts upstream of Pink1; yes
 B. Parkin acts upstream of Pink1; no
C. Pink1 acts upstream of Parkin; yes
D. Pink1 acts upstream of Parkin; no

1. How does the affinity of M6P receptor proteins for the mannose 6-phosphate marker
change between the TGN and early endosome? Which coat protein is mainly responsible for
their transport from the TGN to the endosome?
A. The affinity is higher in the TGN; clathrin
B. The affinity is higher in the TGN; retromer
C. The affinity is higher in endosomes; clathrin
D. The affinity is higher in endosomes; retromer

1. Which of the following is NOT correct regarding M6P receptors and KDEL receptors?
A. They both shuttle back and forth between different membrane-enclosed
compartments.
B. They are both transmembrane proteins.
C. They both release their soluble binding targets at lower pH.
D. They both prevent the escape of proteins to the cell exterior by the “default” pathway.

1. You know that a particular sequence at the C-terminus of the lectin ERGIC53 enhances
its exit from the endoplasmic reticulum (ER). You create two mutant versions of the protein, one
without the suspected sequence (1) and one in which the sequence is replaced with an ER
retention signal (2). You transfect a fibroblast cell line with a plasmid that encodes either wild-
type ERGIC53 (0) or one of the engineered versions of it (1 or 2). After inducing the expression
of the proteins, you lyse the cells and either treat the lysate with endoglycosidase H (Endo H) or
leave the lysate untreated, as indicated below. You then separate the proteins by SDS-PAGE and
perform a Western blot to detect the bands corresponding to ERGIC53. Your results are
represented in the following drawing. Which lanes (A to C) do you expect to correspond to each
of the proteins 0, 1, and 2, respectively? Your answer would be a three-letter string composed of
letters A to C only, e.g. CAB.
 Expressed A B C

Treated with Endo No Yes No Yes No Yes

1. What is the effect of defective or missing N-acetylglucosamine phosphotransferase on

lysosomal protein sorting?
A. Lysosomal proteins are secreted from the cell.
B. Lysosomal proteins are retained in the Golgi network.
C. Lysosomal proteins are retained in the ER.
D. Lysosomal proteins remain tightly bound to M6P receptors.
E. Nonfunctional lysosomal proteins accumulate in the lysosome.

1. Indicate whether each of the following descriptions better applies to receptor-mediated

endocytosis (R), phagocytosis (F), pinocytosis (P), or macropinocytosis (M). Your answer would
be a four-letter string composed of letters R, F, P, and M only, e.g. MMPF.
( ) This pathway depends on caveolin and cavin proteins.
( ) Pathogenic particles such as SV40, papillomavirus, and cholera toxin enter the cell
via this pathway.
( ) In animals, this pathway is normally limited to professional cells such as neutrophils.
( ) This pathway proceeds by the formation of highly ruffled regions in the plasma
membrane which then collapse, resulting in fluid uptake.

1. By forming over 100 pinocytic vesicles per minute, a macrophage ingests over 10% of its
own volume of fluid every half an hour. This is equivalent to ingesting about 100% of the
macrophage’s plasma membrane. If the average volume of a macrophage is about 450 µm3 and
its average surface area is about 750 µm2, what is the average diameter of the early pinocytic
vesicles in the cell? Assume spherical vesicles. The formulas for the volume (V) and surface area
(S) of a sphere of radius r are V = 4/3 × π × r3, and S = 4 × π × r2, respectively. Write down your
answer in nanometers, with no decimals, e.g. 830 nm.
1. Which endocytic process is best depicted in the following schematic diagram?

A. Receptor-mediated endocytosis
B. Pinocytosis
C. Macropinocytosis
D. Phagocytosis
E. Entosis

1. How can the formation of tubular structures, as opposed to spherical vesicles, in the early
endosomes facilitate recycling of membrane proteins such as cell-surface receptors?
A. By increasing surface area-to-volume ratio
B. By decreasing surface area-to-volume ratio
C. By enhancing the formation of intralumenal vesicles
D. By preventing the formation of intralumenal vesicles

1. During maturation of early endosomes to late endosomes, …

A. the vacuolar domain of the endosome is shed, whereas the tubular domain is retained.
B. the endosome migrates along actin filaments away from the cell interior.
C. the lumen of the endosome becomes more acidic.
D. intralumenal vesicles disappear.
E. All of the above.
1. 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.

1. Indicate whether each of the following membrane proteins releases its protein ligand (R),
remains bound to its protein ligand (B), or is degraded in the lysosome along with its protein
ligand (D) following receptor-mediated endocytosis. Your answer would be a three-letter string
composed of letters R, B, and D only, e.g. RBD.
( ) LDL receptor
( ) Transferrin receptor
( ) EGF receptor

1. Indicate whether each of the following processes is topologically similar (Y) or not
similar (N) to formation of intralumenal vesicles in multivesicular bodies. Your answer would be
a four-letter string composed of letters Y and N only, e.g. YYYY.
( ) Fission of peroxisomes
( ) Formation of clathrin-coated vesicles
( ) Budding of HIV from infected cells
( ) Cytokinesis

1. In mammals, colostrum (or “first milk”) is produced by the mother in late pregnancy and
shortly after giving birth to feed the newborn. In addition to nutrients, it is particularly rich in
antibodies that are absorbed through the intestinal epithelium and support the weak immune
system of the infant. Occasionally, some infants suffer from either respiratory acidosis or
alkalosis. In acidosis, the blood pH becomes acidic due to lack of sufficient ventilation, while the
opposite happens in alkalosis due to hyperventilation. Considering the molecular mechanism of
transcytosis in intestinal epithelia, which of these conditions—acidosis (C) or alkalosis (L)—
would you expect to interfere more with antibody absorption by transcytosis in these infants?
Write down C or L as your answer.
1. You are viewing a sample of pond water under the microscope. The sample contains a
variety of microorganisms, some moving faster than others. You spot a Paramecium that is being
followed by a Didinium almost as large as itself; the Paramecium initially swims away and tries
to escape, but Didinium, which moves in faster bursts, finally stops it and attaches firmly onto
the side of the Paramecium and proceeds to eat it. What type of endocytosis will ensue? Write
down the name of the process as your answer. Do not use abbreviations.

1. Sort the following events to reflect the order in which they occur during engulfment of an
antibody-coated microorganism by a neutrophil in the blood. Your answer would be a four-letter
string composed of letters A to D only, e.g. DACB.
(A) Rho-GEF activation
(B) Activation of Fc receptors
(C) Local PI(4,5)P2 production
(D) Local PI(3,4,5)P3 production

1. Indicate true (T) and false (F) statements below regarding secretory vesicles. Your answer
would be a four-letter string composed of letters T and F only, e.g. TTTF.
( ) Proteins destined for secretory vesicles (for regulated secretion) often aggregate in the
lumen of the TGN.
( ) The lumen of secretory vesicles is generally less acidic than the lumen of the TGN
from which they originate.
( ) A secretory vesicle starts recycling Golgi components only after it has budded from
the TGN and its coat proteins have disassembled.
( ) Secretory vesicles recycle Golgi components to the TGN in small clathrin-coated
vesicles.
1. Insulin is a secretory protein made by the β cells in the pancreas. This protein …
A. is released by the β cells in response to increased intracellular Ca2+ concentration.
B. is first synthesized as preproinsulin.
C. is stored as aggregates inside secretory vesicles in the β cells.
D. undergoes proteolytic cleavage before secretion.
E. All of the above.

1. In the simplified diagram below depicting exocytosis of synaptic vesicles, which

components (A to D) correspond to each of the following? Your answer would be a four-letter
string composed of letters A to D only, e.g. DBCA.
 A

D
C D Membrane fusion

C
!

( ) Ca2+
( ) Complexin
( ) Synaptotagmin
( ) SNARE complex

1. Neurotransmitters are retrieved from the synaptic cleft soon after their release from the
presynaptic axon terminal. Do you think treatment of neurons with the drug dynasore, a dynamin
inhibitor, would affect this retrieval positively (P) or negatively (N)? Write down P or N as your
answer.

1. A protein that is normally not expressed in epithelial cells has been induced in these cells
and has been engineered such that a GPI anchor is attached to it as it is processed in the ER.
Would you expect to find this protein in the apical (A) or basolateral (B) domain of the plasma
membrane in these cells? Write down A or B as your answer.

1. In the highly simplified diagram below, the energy landscape of secretory vesicle fusion
to the plasma membrane is shown in the presence or absence of appropriate SNARE complexes.
Which curve (A or B) do you think corresponds to the presence of SNARE complexes? Write
down A or B as your answer.
 A

Free energy
B

Progress of fusion
!
Answers
1. Answer: A

Difficulty: 3

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: GTP hydrolysis by ARF GTPases is required for the uncoating of COPI
vesicles. On the other hand, the NEM-sensitive components are involved in the later steps
of fusion and recycling.

2. Answer: 2331

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: Typically, transport vesicles from ER to CGN are COPII-coated, whereas

retrograde transport in the Golgi apparatus is mediated by COPI-coated vesicles.
Clathrin-coated vesicles are involved in traffic from the plasma membrane as well
between the endosomal and Golgi compartments, and require dynamin for pinching off
efficiently. Clathrin triskelions assemble into a basket-like cage that envelopes these
budding vesicles.

3. Answer: ACB

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: Please refer to Figure 13-5.

4. Answer: 180

Difficulty: 3

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: There is one triskelion at each vertex. The number of vertices is calculated as
follows:
 Number of vertices = [(12 × 5) + (20 × 6)] / 3 = 60

(There are five vertices around each pentagon and six vertices around each hexagon.
Each vertex is counted three times this way, the reason why we divide the sum by 3.)

Since each triskelion contains three heavy chains, the number of heavy chains equals 180.

5. Answer: E

Difficulty: 1

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: When bound to the phosphoinositide PI(4,5)P2, the adaptor protein AP2
changes conformation (or “unlocks”) and binds to cargo receptors in the membrane,
inducing membrane curvature. Since several requirements must be met for stable AP2
binding to a membrane, the protein only assembles at the right place and at the right time.

6. Answer: D

Difficulty: 1

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: AP2 adopts an open conformation once bound to PI(4,5)P2 in the plasma
membrane. Dynamin also has a PI(4,5)P2-binding domain which tethers the protein to the
membrane as a clathrin-coated bud grows. Once clathrin-coated vesicles pinch off from
the membrane, a PIP phosphatase that is co-packaged into the vesicles depletes PI(4,5)P2,
which weakens the binding of the adaptor proteins.

7. Answer: 3212

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: Uncoating of COPII-coated vesicles may occur upon docking at a target

membrane well after Sar1 hydrolyzes its bound GTP and is released. Clathrin- and COPI-
coated vesicles, in contrast, shed their coat soon after they pinch off, through the
activation of an uncoating ATPases or an ARF-GAP, respectively.
8. Answer: BDCA

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: A Sar1-GEF in the endoplasmic reticulum membrane activates Sar1 by

guanine nucleotide exchange; Sar1 then inserts an amphiphilic helix into the membrane,
one leaflet deep. Sar1 then recruits COPII coat proteins (and also a Sar1-GAP) and
initiates budding. Sar1 then hydrolyzes its GTP and dissociates following a delay;
however, if a sealed coat is already formed, Sar1 dissociation may not cause uncoating.

9. Answer: TFTF

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: Specific packaging proteins induce the formation of especially large COPII-
coated transport vesicles that can accommodate procollagen fibers. A Rab and its effector
can be on the same membrane or on different membranes.

10. Answer: E

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: It is dynamin.

11. Answer: BCAD

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: In its GDP-bound form, a Rab protein is bound to a Rab-GDP dissociation

inhibitor and kept in the cytosol. Once activated by a membrane-bound Rab-GEF and
bound to GTP, Rab molecules associate with the membrane through a lipid anchor and
 bind to their effector proteins. Finally, GTP hydrolysis results in Rab inactivation and
dissociation from the membrane.

12. Answer: Rab5

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: In this cascade, Rab5 is the upstream Rab that is replaced by Rab7 in the late
endosomes.

13. Answer: TVT

Difficulty: 2

Section: The Molecular Mechanisms of Membrane Transport and the Maintenance of

Compartmental Diversity

Feedback: A v-SNARE is typically found on vesicle membranes and is a single

polypeptide chain, whereas a t-SNARE is typically found on target membranes and is
usually composed of three proteins. The t-SNAREs are often associated with inhibitory
proteins that are released only when membrane fusion is necessary.

14. Answer: B

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: ER export is mediated by COPII-coated vesicles. Tango1 is likely to interact

with the type VII procollagen molecules.

15. Answer: C

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: ER-derived COPII-coated vesicles (1) fuse with one another to form the
vesicular tubular clusters, which in turn bud off transport vesicles coated with COPI (2)
for the retrieval of ER resident proteins.
16. Answer: D

Difficulty: 1

Section: Transport from the ER through the Golgi Apparatus

Feedback: By binding to the COPI coats, the retrieval signal mediates the retrograde
transport of the protein back to the ER.

17. Answer: HIAJCDEBFG

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: Please refer to Figure 13-3.

18. Answer: E

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: Addition of Gal and NANA has been shown to occur primarily in the trans
cisterna.

19. Answer: D

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: Chains one and two represent complex and high-mannose oligosaccharides,
respectively.

20. Answer: ONOO

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: In N-linked glycosylation, a preassembled block of oligosaccharide is attached

onto an asparagine side chain in the protein. O-linked glycosylation, in which sugars are
added to the hydroxyl groups in the side chains of serine, threonine, or other residues,
 often involves sulfated sugars and is responsible for the production of heavily-
glycosylation in proteoglycans.

21. Answer: TTFF

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: Chains of sugar have limited flexibility and therefore protrude from the protein
surface. As a result, the approach of other macromolecules to the protein is limited. At the
same time, lectins can recognize the sugar chain and control the proper folding of the
protein or send it down a particular sorting pathway.

22. Answer: VCCV

Difficulty: 2

Section: Transport from the ER through the Golgi Apparatus

Feedback: The cisternal maturation model views the Golgi cisterna as dynamic structures
that move through the Golgi stack with cargo in their lumen. In this model, retrograde
transport is responsible for carrying Golgi resident proteins back to an earlier
compartment as each cisterna matures. The vesicle transport model, in contrast, describes
Golgi cisternae as static structures. In this model, forward-moving vesicles carry forward-
moving cargo, and backward-moving vesicles retrieve escaped resident proteins.

23. Answer: C

Difficulty: 3

Section: Transport from the ER through the Golgi Apparatus

Feedback: The cisternal maturation model predicts that each cisterna matures over time,
acquiring new components (as well as red fluorescence) as it matures, and recycling old
components (green fluorescence) to the less mature cisternae by retrograde vesicle
transport. The vesicle transport model predicts that each cisterna remains stationary and
fluoresces either red (or yellow) or green during the entire period.

24. Answer: 1

Difficulty: 3

Section: Transport from the ER through the Golgi Apparatus

 Feedback: The mutant proteins mimic constitutively phosphorylated proteins, and
therefore recapitulate the mitotic Golgi fragmentation even in interphase.

25. Answer: BDC

Difficulty: 2

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: Coat proteins assemble into distinctive cages that coat many transport vesicles
in the cell. Dynamin helps pinch off budding clathrin-coated vesicles by assembling like
a collar around their neck. BAR-domain proteins bend membranes by binding and
imposing their curved shape on the underlying membrane.

26. Answer: C

Difficulty: 1

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: After a rupture in the plasma membrane of a cell, a temporary cell-surface

patch is made from locally-available membranes such as those of lysosomes in a process
that probably involves exocytosis and homotypic vesicle-vesicle fusion.

27. Answer: C

Difficulty: 1

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: Lysosomes vary greatly in size and shape, reflecting their various functions.
They maintain a low interior pH of about 4.5–5.0 using lysosomal V-type ATPases. Their
own membrane proteins are highly glycosylated to protect them from digestion by the
proteases in the lumen.

28. Answer: A

Difficulty: 3

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: The volume of the lysosome would be calculated as:

V = 4/3 × π × (0.3 × 10–6 m)3 = 1.1 × 10–19 m3 = 1.1 × 10–16 L

 At approximately pH 5, the concentration of hydronium ions is 10–5 mol/L. Therefore,
there is about 1.1 × 10–21 mole of these ions in this lysosome. This is equivalent to only
approximately 660 ions.
29. Answer: E
Difficulty: 1
Section: Transport from the trans Golgi Network to Lysosomes
Feedback: Vacuoles in plants are equivalent to lysosomes in animal cells, and are
remarkably versatile in function.
30. Answer: A
Difficulty: 2

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: Anthocyanins can be considered as pH indicators in this experiment, which

shows that blocking either type of ATPase would prevent the sufficient acidification
required for red coloration.

31. Answer: B

Difficulty: 1

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: Multiple pathways deliver materials to lysosomes for degradation.

32. Answer: C

Difficulty: 2

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: Two membranes from the cup-shaped structure and two membranes from the
original mitochondrion surround the mitochondrial matrix. After fusion of the outermost
membrane with the lysosomal membrane, the three inner membranes would be digested
away in the process of autophagy.

33. Answer: D

Difficulty: 3

Section: Transport from the trans Golgi Network to Lysosomes

 Feedback: Overexpression of a protein in a pathway can often rescue the loss of function
of upstream (but not downstream) proteins. Since ATG9 is involved in downstream steps
of mitophagy, Parkin overexpression is not expected to rescue an ATG9 loss-of-function
phenotype.

34. Answer: A

Difficulty: 2

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: In the trans Golgi network (TGN), mannose 6-phosphate (M6P) receptor
proteins bind to hydrolases that carry the M6P group and mediate their incorporation into
clathrin-coated vesicles destined for endosomes. In the lower pH of the endosome lumen,
the hydrolases are released and the receptor proteins are retrieved by incorporation in
retromer-coated vesicles.

35. Answer: C

Difficulty: 2

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: Whereas mannose 6-phosphate (M6P) receptors bind more tightly to their
targets at higher pH (tighter in the trans Golgi network compared to endosomes), KDEL
receptors bind more tightly to their targets at lower pH (tighter in the Golgi complex and
vesicular tubular clusters compared to the endoplasmic reticulum). The receptors also use
different coat proteins for transport.

36. Answer: CAB

Difficulty: 3

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: Endo H-resistance is a sign that the protein has been transferred to the Golgi
apparatus and has undergone processing. With wild-type protein (0, C), the protein shows
partial Endo H-sensitivity. In the absence of the exit sign (1, A), transport to the Golgi is
impaired, and most of the protein remains Endo H-sensitive. When an ER retention signal
is also added (2, B), the protein seems to be completely Endo H-sensitive.

37. Answer: A
 Difficulty: 1

Section: Transport from the trans Golgi Network to Lysosomes

Feedback: Because the lysosomal enzymes cannot be phosphorylated by the

phosphotransferase to create the mannose 6-phosphate (M6P) marker, they are not
segregated to the appropriate transport vesicles and are lost from the cell by secretion.

38. Answer: PPFM

Difficulty: 1

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: Caveolae, a type of pinocytic vesicles, contain caveolins and cavins as their
structural proteins, and constitute the main route of entry for several pathogens. Other
pathogens may enter the cell by macropinocytosis which involves the formation of
ruffles. Professional phagocytes in our body engulf foreign cells and particles by
phagocytosis.

39. Answer: 360 nm

Difficulty: 3

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: The cell internalizes 3000 vesicles every half an hour (i.e. 100 vesicles/min ×
30 min), which is equivalent to 45 µm3 in volume (i.e. 10% × 450 µm3) and 750 µm2 in
surface area (i.e. 100% × 750 µm2). Thus, the volume and surface area of each vesicle is,
on average, about 0.015 µm3 and 0.250 µm2, respectively. The ratio of volume to surface
area for a sphere is equal to r/3 where r is the radius. Hence, the diameter (2r) is equal to
(0.015 µm3/0.250 µm2) × 6 = 0.36 µm = 360 nm.

40. Answer: C

Difficulty: 1

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: Macropinocytosis does not operate continually and is typically induced only in
response to activation of cell-surface receptors by various stimuli. The ensuing activation
of intracellular signaling pathways results in changes in actin dynamics and the formation
 of cell-surface protrusions known as ruffles, which then collapse to form
macropinosomes.

41. Answer: A

Difficulty: 2

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: The geometry of such tubular structures can help enrich membrane proteins
over soluble proteins, due to the large membrane area enclosing a small volume.

42. Answer: C

Difficulty: 1

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: During maturation, the endosome sheds its tubular domains and retains its
vacuolar domains, the lumen of which becomes more acidic. The endosome moves along
microtubule tracks toward the cell interior, and acquires intralumenal vesicles for
membrane protein degradation. It also receives new components from the trans Golgi
network.

43. Answer: FFFT

Difficulty: 1

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: Low-density lipoprotein (LDL) receptors associate with clathrin-coated pits

and are internalized irrespective of ligand binding. They normally release their bound
LDL (if any) in the early endosomes and are recycled back to the plasma membrane.
Mutations that interfere with receptor-mediated endocytosis of LDL particles can cause
high blood cholesterol and lead to diseases such as atherosclerosis.

44. Answer: RBD

Difficulty: 2

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: LDL receptors release LDL in the low pH in early endosomes and are recycled
back to the cell surface. Transferrin receptors do not release transferrin in early
 endosomes: the low pH only results in the release of the bound iron, and the transferrin-
receptor complex is recycled. In contrast, most EGF receptors are not recycled and are
degraded in the lysosomes along with EGF.

45. Answer: NNYY

Difficulty: 2

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: Budding of HIV particles and cytokinesis are both equivalents to the formation
of intralumenal vesicles, as both involve budding away from the cytosolic surface of the
membrane.

46. Answer: C

Difficulty: 3

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: Acidification of the blood results in reduced antibody absorption because the
antibody receptors do not efficiently release their bound antibodies on the basal side of
the epithelial cells.

47. Answer: Phagocytosis

Difficulty: 1

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: Protozoa such as Didinium carry out phagocytosis as a form of feeding. This is
not the case in multicellular organisms, in which few cells are able to ingest large food
particles efficiently, and breakdown of food particles occurs mostly extracellularly in the
digestive tract.

48. Answer: BACD

Difficulty: 2

Section: Transport into the Cell from the Plasma Membrane: Endocytosis

Feedback: The ordered generation and conversion of phosphoinositides guides sequential

steps of phagocytosis. First, PI(4,5)P2 is produced by a kinase to induce actin
 polymerization and engulfment of the target particle. Then, another kinase converts
PI(4,5)P2 to PI(3,4,5)P3, which is required for the closure of the phagosome.

49. Answer: TFFT

Difficulty: 1

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: Secretory vesicles bud from the trans Golgi network (TGN) in a process that
involves highly concentrating the enclosed secretory proteins into aggregates. The
immature vesicles become more and more acidic, fuse with each other, and send clathrin-
coated vesicles back to the TGN, sometimes even before they have completed budding
from the TGN themselves.

50. Answer: E

Difficulty: 2

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: Starting from a pre-pro-protein (e.g. preproinsulin), the pre-peptide is cleaved

off in the ER, and the pro-peptide is cleaved later normally during maturation of secretory
vesicles. The formation and maturation of secretory vesicles at the TGN involves
selective segregation and concentration of secretory proteins such as insulin.

51. Answer: ACBD

Difficulty: 2

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: Calcium binds to synaptotagmin and activates the protein, which then
displaces complexin to relieve the block that complexin places on the metastable SNARE
complexes; this release leads to membrane fusion.

52. Answer: N

Difficulty: 2

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: Dynamin is required to complete the endocytosis of the clathrin-coated,

neurotransmitter-containing vesicles.
53. Answer: A

Difficulty: 2

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: By being preferentially concentrated in lipid rafts, the

glycosylphosphatidylinositol (GPI)-anchored protein is incorporated into transport
vesicles destined for the apical membrane.

54. Answer: B

Difficulty: 1

Section: Transport from the trans Golgi Network to the Cell Exterior: Exocytosis

Feedback: Similar to enzymes and other catalysts, SNARE complexes facilitate

membrane fusion by lowering the free-energy barrier. They also transition into a stable
conformation at the end of the process, requiring the energy of ATP hydrolysis to reset.
Thus, they also push the process forward by stabilizing the products.