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BIOL 331 Midterm > Endomembrane System (Ch. 8) > Flashcards

Endomembrane System (Ch. 8) Flashcards

1
Q

True/False? The endomembrane system is found in both eukaryotes and prokaryotes

A

False. Only found in eukaryotes

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2
Q

List the interrelated organelles of the endomembrane system

A
  • endoplasmic reticulum
  • Golgi complex
  • endosomes
  • lysosomes
  • vacuoles
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3
Q

What is the order of passage of proteins to be secreted through the biosynthetic pathway? (use some or all of the following):
Plasma membrane
Rough ER
Lysosome
Golgi complex
Free ribosomes

A

Rough ER, Golgi complex, plasma membrane

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4
Q

What are the broad categories of the transport of protein?

A
  1. Transport materials from donor compartment to recipient compartment
  2. Transport materials out of the cell (secretory pathway)
  3. Transport materials into the cell (endocytic pathway)
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5
Q

What is the purpose of vesicles?

A

To transport membrane-bound materials between organelles

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6
Q

Where do vesicles bud from?

A

The donor compartment

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7
Q

Where do vesicles fuse? What happens to the cargo and to the membrane? What about the membrane proteins?

A

Vesicles fuse with the recipient compartment, where the cargo is released. The vesicle membrane becomes a part of the recipient compartment’s membrane, along with the membrane proteins, however, these proteins may be returned to the donor compartment

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8
Q

What are sorting signals? What are they recognized by? What is their purpose?

A

Sorting signals can be amino acids or oligosaccharides. They are recognized by receptors in the membranes of budding vesicles. They direct proteins to the correct destination for travel

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9
Q

What are some biomolecules synthesized by the ER?

A
  • lipids/cholesterol
  • steroid hormones
  • secreted proteins
  • integral membrane proteins
  • glycosylation of proteins
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10
Q

What are the two types of secretion?

A

Constitutive and regulated

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11
Q

Describe constitutive secretion

A
  • occurs in most cells
  • materials are continually transported in secretory vesicles from their site of synthesis
  • contributes to the formation of the plasma membrane
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12
Q

Describe regulated secretion

A
  • materials are stored in membrane-bound compartments and only released in response to stimuli (nerve cells, endocrine cells)
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13
Q

What is the broad purpose of an early endosome?

A

They sort the cargo that comes from outside of the cell

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14
Q

What is the broad purpose of a late endosome?

A

They are more acidic than early endosomes and transport cargo to lysosomes for degradation

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15
Q

What is a lysosome?

A

A hydrolytic enzyme with roles in breakdown of material and organelle turnover. They are usually low in pH

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16
Q

Describe the pulse step of autoradiography

A

Pulse step: radio-labelled amino acids are incorporated in the digestive enzymes being synthesized. They are only exposed for a short amount of time

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17
Q

Describe the chase step of autoradiography

A

Chase step: cells are transferred to media with only unlabeled amino acids, so enzymes synthesized in this step will not be radio-labeled

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18
Q

What is the purpose of autoradiography?

A

To track the locations in which proteins appear chronologically

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19
Q

What were the findings of the pulse-chase experiment?

A

The labelled proteins first appeared in the RER after a 3 minute pulse. The proteins were then observed moving into the Golgi complex after a 17 minute chase. After a 100 minute chase, the proteins were then found in secretory vesicles

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20
Q

Why are mutant phenotypes important for the study of function?

A

They show how abnormal function affects the cell, allowing for the extrapolation of the wildtype phenotype contributes to regular function

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21
Q

What is the endoplasmic reticulum?

A

A system of membranes and vesicles that encloses the ER lumen (separated from the cytosol). It is divided into the smooth and rough ER

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22
Q

Describe the rough ER

A
  • has ribosomes bound on the cytosolic membrane surface
  • composed of a network of cisternae “flattened sacks”
  • continuous with the outer membrane of the nuclear envelope
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23
Q

Describe the smooth ER

A
  • lacks ribosomes
  • composed of interconnected, curved, tubular membranes
  • continuous with the RER
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24
Q

What are the functions of the smooth ER? In which cells is it most abundant?

A
  • extensive in skeletal muscles, kidney tubules, and steroid-producing endocrine glands
  • synthesis of steroid hormones
  • synthesis of membrane lipids
  • detoxification of organic compounds in the liver
  • sequestering calcium ions in skeletal and cardiac muscle - role is muscle contraction
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25
Q

What are the functions of the rough ER? In which cells is it most abundant?

A
  • extensive in cells with a role in protein secretion
  • protein synthesis
  • addition of sugars is initiated
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26
Q

What fraction of proteins are synthesized by the RER and free ribosomes, respectively?

A

1/3 and 2/3

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27
Q

Define co-translational translocation

A

Peptides move into the lumen of the ER as it is being synthesized by the ribosome

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28
Q

What kind of proteins are synthesized in the RER?

A
  • secreted proteins
  • integral membrane proteins and soluble proteins that reside in compartments of the endomembrane system
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29
Q

What kind of proteins are synthesized by free-floating ribosomes?

A
  • proteins that remain in the cytosol
  • peripheral proteins on the cytosolic surface of membranes
  • proteins transported to the nucleus, mitochondria, and chloroplast
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30
Q

Describe the steps of co-translational translocation for secreted proteins

A
  1. A free ribosome starts translation. A signal sequence is found at the N-terminal end of the new protein, composed of 6-15 hydrophobic amino acids
  2. A signal recognition particle (SRP) binds to the signal sequence AND the ribosome, which temporarily halts protein synthesis
  3. SRP binds with an SRP receptor found on the ER membrane
  4. The ribosome and protein are transferred from the SRP to the translocon, a transmembrane protein pore found in the ER membrane. This contact dislodges the plug found usually in the translocon
  5. The peptide enters the ER lumen, still attached to the ribosome. Once it is done being synthesized, the ribosome dislodges and the signal sequence is cleaved by signal peptidase. Protein chaperones (BiP) aid in folding
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31
Q

Which of the following is/are likely to have an N-terminal amino acid sequence recognized by SRP? (Select all that apply)
a) peptide hormones
b) steroid hormones
c) hydrolytic enzymes (heading for lysosome)
d) mitochondrial membrane proteins
e) phospholipids found in the lysosome membrane

A

A and C. Steroid hormones are lipid-based, mitochondrial membrane proteins are made by free-floating enzymes, and phospholipids are not proteins

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32
Q

How does integral-membrane protein synthesis differ from secreted protein synthesis?

A

SRP recognizes the hydrophobic transmembrane domain as the signal sequence. This domain does not pass through the pore; instead, it directly enters the lipid bilayer. A gate in the translocon then opens to allow the proteins to partition themselves according to their solubility properties

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33
Q

How is an integral membrane protein oriented if its N terminal end is negatively charged?

A

The N-terminal end is oriented inside the ER lumen, as this side of the membrane is positively charged. The cytoplasmic end (C terminal, in this case), is more abundant in positively charged amino acids because of the negatively charged PS and PI phospholipids that are on the cytosolic side of the membrane

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34
Q

What happens to a newly-synthesized transmembrane protein if the N terminal end is positively charged?

A

The translocon reorients the transmembrane domain so the N terminal end is facing the cytosol

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35
Q

True/False? The DNA sequence for a given glycoprotein encodes the instructions to assemble the carbohydrate chains that will become attached to the glycoprotein.

A

False. The DNA sequence is for the synthesis of the protein only and plays no part in carbohydrate synthesis. The special localization of enzymes, like glycosyltransferases, allows for the addition of carbohydrates onto proteins

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36
Q

Carbohydrate groups have roles as __________

A

Binding sites

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37
Q

What is the function of carbohydrate groups on glycosylated proteins?

A

They aid in proper folding, stabilization, and sorting proteins to different cellular compartments

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38
Q

What are the two types of glycosylation?

A

N-linked (Asn residue, initiated in RER) and O-linked (Ser or Thr, occurs in Golgi complex)

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39
Q

Explain the steps of N-linked glycosylation

A
  1. The first seven sugars (2 NAG, 5 mannose) are transferred one at a time to a lipid molecule (dolichol pyrophosphate), embedded in the ER membrane on the cytosolic side by glycosyltransferases
  2. Dolichol and the attached oligosaccharide is flipped across the membrane, into the lumen side
  3. The remaining molecules (3 glucose) are attached to dolichol on the cytosolic side and flipped once again into the lumen where they are attached to the growing oligosaccharide chain one by one
  4. The completed oligosaccharide is transferred to an Asn residue of the polypeptide currently being translated (happens at the same time as co-translational translocation) by oligosaccharyltransferase
40
Q

What is the amino acid sequence that is recognized by oligosaccharyltransferase?

A

X-Asn-X-Ser/Thr, where the second X cannot be proline

41
Q

What are the steps of quality control for misfolded proteins?

A
  1. Glucosidase I and II remove 2 glucoses
  2. The glycoprotein with one glucose is recognized by calnexin (membrane protein chaperone), which removes the glucose
  3. If the protein is misfolded, it is recognized by UGGT (a conformation sensing enzyme), which detects exposed hydrophobic residues and adds a glucose molecule so it can revisit calnexin
  4. If the protein is properly folded, it exits the ER
  5. If the proteins are unable to be properly folded after many attempts, the protein is ejected into the cytosol where they are degraded by proteosomes
42
Q

Which of the following would you expect to find as an integral membrane protein of the RER membrane, but would be absent from the SER membrane?
a) calcium ion channels
b) SRP
c) translocon
d) proteosome

A

C. Calcium ion channels are prevalent in the SER, SRP is not integral, and neither is the proteosome

43
Q

What happens to vesicles in the endoplasmic reticulum Golgi intermediate compartment (ERGIC)?

A

They fuse together to form vesicular tubular carriers (VTCs)

44
Q

How is the Golgi complex oriented? What is it made up of?

A

It is made up of cisternae arranged in a stack. Distinct compartments arranged from the cis face (closest to ER) and trans face (furthest from ER)

45
Q

What is the cis Golgi network (CGN)? What is its purpose?

A

An interconnected network of tubules. It acts as a sorting station that distinguishes between proteins that need to be returned to the ER and those that should proceed through the Golgi

46
Q

What is the trans Golgi network (TGN)? What is its purpose?

A

A network of tubules and vesicles. It acts as a sorting station where proteins are segregated into different types of vesicles (heading the the plasma membrane or other)

47
Q

Describe protein modification in the Golgi complex

A

The order of sugars incorporated depends on the location of specific glycosyltransferases in the membrane of the Golgi complex, which allows for high variation. O-linked carbohydrates are entirely assembled within the Golgi

48
Q

Explain model 1 (vesicular transport model) of the movement of materials through the Golgi complex. What is the supporting evidence?

A
  • Golgi cisternae are stable compartments
  • vesicles carrying cargo bud from one compartment and fuse with the next
    Evidence:
  • Golgi cisternae have different enzymes
  • lots of vesicles bud from the edges of Golgi cisternae
49
Q

Explain model 2 (cisternal maturation model) of the movement of materials through the Golgi complex. What is the supporting evidence?

A
  • cisternae form at the cis face and move towards the trans face, ‘maturing’ as they move
  • experimental evidence, so this is the stronger model
    Evidence:
  • drugs blocking vesicle formation at the ER leads to the Golgi complex disappearing
  • certain large materials (ex. collagen) move from cis to trans without ever appearing in vesicles
50
Q

What direction is anterograde movement in vesicle transport?

A

From cis to trans

51
Q

What direction is retrograde movement in vesicle transport?

A

From trans to cis

52
Q

Which protein acts as a ‘gatekeeper’ in the ER quality control system by catalyzing monoglucosylation onto incompletely folded glycoproteins, allowing them to be recognized by ER chaperones?
a) glucosidase
b) calnexin
c) UGGT
d) oligosaccharyltransferase

A

C

53
Q

According to the cisternal maturation model of transport through the Golgi complex, are COPII-coated vesicles required for movement from the cis to trans Golgi?

A

No, because they recruit cargo, but cargo does not have to be in a vesicle to be able to be transported

54
Q

What role does COPII play in cargo transport?

A

Selects and concentrates certain proteins for transport in vesicles by interacting with transmembrane proteins that have ‘ER export signals’ (cytosolic). It also bends the membrane

55
Q

What are some examples of cargo that need to be transported from the ER?

A
  • enzymes destined for the Golgi complex (glycosyltransferases)
  • proteins involved in vesicle docking and fusion (SNARE)
  • proteins that bind to soluble cargo (which are secreted)
56
Q

Explain Sar1 (first step of COPII coating)

A

It is a COPII G protein. Sar1-GDP is recruited by guanine exchange factor (GEF), where it becomes Sar1-GTP. It undergoes a conformational change so that it inserts into the cytoplasmic leaflet, which bends the membrane away from it

57
Q

Explain the Sec23/Sec24 dimer (second step of COPII coating)

A

It bends the membrane further after Sar1-GTP has been recruited. Sec24 is the primary adaptor protein that interacts with the ER export signals of the membrane proteins

58
Q

Explain Sec13/Sec31 (third step of COPII coating)

A

They form an outer structural cage after Sec23/Sec24 is recruited

59
Q

Explain the final step of COPII coating (after Sec13/Sec31)

A

Disassembly is triggered by the hydrolysis of GTP bound to Sar-1 (into GDP)

60
Q

What is COPI? What are its functions?

A

A protein complex called a coatomer, which forms a thick protein coat directly on the membrane. It includes a membrane-bending G protein (Arf1). Retrograde transport of Golgi resident enzymes (trans to cis) and ER resident proteins back to ER

61
Q

Where are retrieval signals found?

A

In proteins that reside in the ER that need to be returned to the ER after vesicle transport. They can be found in soluble ER proteins or ER membrane proteins

62
Q

What is the retrieval signal found in soluble ER proteins? Where in the vesicle transport system are they found?

A

KDEL (lys-asp-glu-leu). They shuttle between the cis Golgi and ER

63
Q

What is the retrieval signal found in ER membrane proteins? Which side of the membrane is it located on?

A

KKXX (lys-lys-X-X). It is located on the cytosolic side

64
Q

Describe the steps of vesicle fusion

A
  1. Movement of the vesicle toward the specific target component mediated by microtubules and motor proteins
  2. Tethering vesicles to the target compartment by rod-shaped/fibrous (longer) or the multiprotein complex (shorter) tethering proteins. G proteins (Rabs) recruit specific tethering proteins and interact with specific motor proteins
  3. Docking vesicles to the target compartment by SNARE protein complexes
  4. Fusion between vesicle and target membrane through interactions between t-SNAREs and v-SNAREs that pull the lipid bilayers together with enough force to cause fusion
65
Q

What are SNARE proteins? What is the function of t-SNAREs vs. v-SNAREs?

A

They are integral membrane proteins. v-SNAREs are put into transport vesicles during budding, which fuse with 3 t-SNAREs on the target membrane to make a 4-stranded bundle

66
Q

Name the 3 proteins involved with vesicle fusion specificity

A

Rabs, tethering proteins, and SNAREs

67
Q

What are two ways that resident ER proteins are maintained in the ER?

A
  1. Retrieval: COPI brings them back with KDEL or KKXX retrieval signals
  2. Retention: ER resident proteins usually don’t get packaged into COPII transport vesicles (those that don’t have the ER export signal)
68
Q

What is the environment of a lysosome’s interior? How is it maintained, and what is encased within a lysosome?

A

A lysosome’s interior is acidic (pH = 4.6), which is maintained through proton pumps (v-type H+ ATPase). Enzymes are encased within

69
Q

Identify the two roles of lysosomes

A
  1. Breakdown of material brought into the cell by endocytosis (phagocytosis)
  2. Organelle turnover (autophagy)
70
Q

What is organelle turnover? Are there any cells that would exhibit autophagy more than others?

A

It is the regulated destruction and replacement of the cell’s organelles in which the organelle is surrounded by an autophagosome, a double-membraned structure, which fuses with a lysosome. Starved cells exhibit increased autophagy to acquire nutrients

71
Q

What happens to the autophagosome after fusion with the lysosome?

A

The membrane is made a part of the lysosome and the contents are released

72
Q

Define a lysosomal storage disorder

A

Deficient lysosomal enzymes leads to accumulation of un-degraded materials like sphingolipids

73
Q

What is an example of a lysosomal storage disorder?

A

Tay-Sachs disease: the accumulation of G(M2) in lysosomes of brain cells

74
Q

Gaucher’s disease is caused by an accumulation of glucocerebroside. Which of the following would be the best treatment?
a) delivery of protease
b) delivery of nuclease
c) delivery of a sphingolipid-hydrolyzing enzyme
d) delivery of glucocerebroside

A

C. Glucocerebroside is a sphingolipid (Chapter 4)

75
Q

How does phosphorylated mannose (mannose-6-phosphate) act?

A

As a sorting signal, which directs N-linked proteins to the lysosome

76
Q

Describe the steps of targeting lysosomal enzymes to lysosomes

A
  1. Mannose residues on the enzymes are phosphorylated in the cis Golgi
  2. MPRs, connected to GGA adaptors, connected to clathrin, detect and capture proteins (lysosomal enzymes) with the mannose 6-phosphate signal in the TGN
  3. Formation of the clathrin-coated vesicle
  4. Clathrin coat is disassembled
  5. Vesicle fuses with endosome for sorting
  6. a) MPR (receptors) are returned to the Golgi
  7. b) Lysosomal enzymes are delivered to the lysosome
  8. MPRs are also found in the plasma membrane (capture lysosomal enzymes that are secreted into the extracellular space and return these enzymes to the lysosome). This is a separate process from steps 1-6
77
Q

Clathrin:

A

A coat protein that forms a structural scaffold

78
Q

GGA Adaptor:

A

Physically connects clathrin to MPRs. Has 3 binding domains: Arf1-GTP, clathrin, and cytosolic tails of the MPR receptors

79
Q

Mannose-6-phosphate (MPR):

A

Transmembrane protein that recognizes and captures proteins with the mannose-6-phosphate signal

80
Q

Arf1-GTP (during lysosomal targeting):

A

Binds to the membrane and initiates formation of the budding vesicle and binding of the other coat proteins. Induces membrane curvature when bound to GTP

81
Q

What is the default pathway for a vesicle?

A

Constitutive secretion

82
Q

Name four proteins that interact to form clathrin-coated vesicles to transport lysosomal enzymes:

A

Clathrin
GGA adaptor
Arf1-GTP
MPR (mannose 6 phosphate receptor)

83
Q

What would happen if the enzymes in the cis Golgi that add phosphate groups to 6-mannose residues on the carbohydrate chains of lysosomal enzymes were defective?

A
  • lysosomal enzymes will not make it to lysosome
  • will “probably” get secreted (default pathway)
84
Q

What are the two pathways of endocytosis?

A

Bulk-phase (pinocytosis) and receptor-mediated

85
Q

What is pinocytosis?

A

Non-specific uptake of extracellular fluids (and any molecules that may be present)

86
Q

What is receptor-mediated endocytosis?

A

Specific molecules binding to receptors on the extracellular surface of the plasma membrane (hormones, growth factors, certain nutrients)

87
Q

AP2 complex (adaptor):

A

Links cytoplasmic tails of plasma membrane receptors with clathrin

88
Q

What is the structure of clathrin?

A

A triskelion composed of 3 heavy and light chains

89
Q

Dynamin:

A

A G-protein required for the clathrin-coated vesicle to bud from the membrane. The subunits polymerize to form a ring and GTP hydrolysis induces a movement in the ring. The vesicle is cleaved and dynamin disassembles

90
Q

What is the recycling pathway?

A

House keeping receptors mediate uptake of materials that will be used by the cell. Receptors are first transported to an early endosome (neutral pH) for sorting. Ligands dissociate due to an acidic pH as the endosome matures. Receptors are concentrated into a recycling compartment of the early endosome and vesicles return the receptors to the cell surface to be used again

91
Q

What is the degradation pathway?

A

Signaling receptors bind ligands that affect cellular activities (hormones, growth factors, etc). First transported to early endosome for sorting, early endosome matures into late endosome (more acidic). Late endosome fuses with lysosome for receptor degradation

92
Q

Receptor degradation prevents:

A

The cell from being further stimulated by the hormone/growth factor

93
Q

Which molecule below is a GTP-binding protein that is required for the release of a clathrin-coated vesicle from the membrane on which it was formed?
a) Arf1
b) GGA adaptor
c) Dynamin
d) Clathrin
e) Sar1

A

C

94
Q

Which of the following are required for both anterograde and retrograde vesicle transport through the endomembrane system?
a) COPI
b) COPII
c) Sar1
d) v-SNARE proteins (in general)
e) more than one of the above is correct

A

D

95
Q

A transmembrane protein undergoes co-translational translocation in the RER and is inserted into the membrane with its C-terminal domain oriented into the RER lumen. This protein is transported to the plasma membrane.
a) Which end will be modified by N-linked glycosylation?
b) In which orientation will the protein be oriented in the Golgi?
c) In which orientation will the protein be oriented in the plasma membrane?

A

a) the C-terminal end
b) the C-terminal end faces the Golgi lumen
c) the C-terminal end faces the extracellular space

BIOL 331 Midterm (3 decks)

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