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BIO 2B03 > Module 5 > Flashcards

Module 5 Flashcards

(61 cards)

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1
Q

T or F: The Endoplasmic Reticulum is constantly changing shape and structure, undergoing fission and fusion, and migrating to new locations in the cell

A

True

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2
Q

Two types of endoplasmic reticulum

A

a) Rough Endoplasmic Reticulum
b) Smooth Endoplasmic Reticulum

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3
Q

T or F: the membranes of the rough and smooth ER are not continuous with each other

A

False, they are continuous.

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4
Q

Why is the rough endoplasmic reticulum considered rough?

A

Ribosomes dot the surface of the endoplasmic reticulum

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5
Q

What’s the function of the RER membrane?

A

a) site of co-translational transport
b) protein modification
c) formation of vesicles (that transport proteins from ER to Golgi)

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6
Q

What’s the function of the SER membrane?

A

a) site of fatty acid
b) phospholipid synthesis
c) carbohydrate metabolism
d) calcium is collected to regulate cytosolic calcium concentration

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7
Q

Post-Translational Modification (PTMs)

A

a) Glycosylation: covalent addition of polysaccharides
b) Protein Folding
c) Disulphide Bond Formation
d) Proteolytic Cleavage

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8
Q

Modifications to proteins targeted to the ER lumen and ER membrane work differently, what’s the difference?

A

ER Lumen Proteins: modifications can occur along the entire length of the protein
ER Membrane Proteins: only occur on the luminal portion of the protein

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9
Q

Protein Glycosylation

A

[def] the addition of a polysaccharide to a protein

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10
Q

N-linked Glycosylation

A

[def] the addition of a polysaccharide to the NH2 of the R-group of asparagine

a) the modified portion of the protein will remain on the luminal side or exoplasmic side of the membrane throughout transport

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11
Q

Disulphide Bonds

A

[def] covalent linkages between the sulfhydral groups (-SH groups) of two cysteine amino acid residues

a) essential to the formation of tertiary or quaternary structure
b) can occur within a single protein (intramolecular) or two different proteins (intermolecular)
c) common in secreted proteins and proteins on the outside surface of the cell membrane
d) UNIQUE to the eukaryotic ER lumen

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12
Q

Oxidizing Environment VS Reducing Environment

A

1) Oxidizing Environment: lumen favours spontaneous formation of disulphide bonds
2) Reducing Environment: cytoplasm favours the reverse reaction

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13
Q

RNAse A

A

[def] pancreatic ribonuclease A

a) contains four disulphide bridges
b) secreted into the intestine
c) aids in digestion of RNA by cleaving RNA into small pieces

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14
Q

PDI [def] [pathway]

A

[def] protein disulphide isomerase is resident ER protein that promotes disulphide bridge formation

[pathway]
a) oxidized PDI contains a disulphide bridge
b) oxidized PDI forms an intermediate with one of the cysteine residues in a protein
c) results in the formation of an intramolecular cysteine bond
d) reduced PDI is spontaneously converted back to oxidized form in the lumen

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15
Q

Protein Folding: Lectins

A

[def] family of proteins that recognize modified proteins and assist in protein folding

a) EX: calnexin, calreticulin
b) calnexin is found throughout the ER membrane

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16
Q

Protein Folding: BiP

A

a) ER-resident protein
b) member of HSP70 family
c) recognizes and binds to unfolded proteins
d) bind to proteins once they appear on the luminal side of the ER membrane during co-translational support
e) co-chaperones: HSP40, NEF (nucleotide exchange factor)
f) important for the unfolded protein response

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17
Q

Proteolytic Cleavage

A

[def] the cleavage of the peptide backbone of a protein

a) EX: all type I integral membrane proteins have the N-terminal signal sequence cleaved by a signal peptidase

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18
Q

What can trigger the unfolded protein response?

A

a) overproduction of proteins
b) delays in the protein processing steps
c) toxins
d) heat and denaturants
e) lack of nutrients

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19
Q

UPR

A

[def] unfolded protein response

a) slow down new protein translation
b) remove unfolded proteins from the ER for degradation via ubiquitinylation
c) increase production of chaperone proteins

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20
Q

Which proteins are essential to the UPR? [pathway]

A

BiP: chaperone that assists proper folding and prevents misfolding of proteins
Ire1: transmembrane protein

[pathway]
a) When BiP and Ire1 are associated, both inactive
b) BiP dissociates from Ire1 when there’s more unfolded proteins (higher affinity)
c) Unassociated Ire1 forms homodimers in the ER membrane, which act as endonucleases
d) Ire1 endonucleases cut unspliced Hac1 mRNA, leading to Hac1 protein synthesis
e) Hac1 protein serves as a transcription factor that activates transcription of genes that code for BiP, lectins, PDI, and signal peptidases, to further assist in folding

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21
Q

Anterograde Transport VS Retrograde Transport

A

Anterograde Transport: movement of proteins from the ER towards the cell membrane

Retrograde Transport: movement of proteins back towards the ER

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22
Q

Techniques for Studying Vesicular Transport

A

a) Pulse-Chase Labelling & visualization using immuno-TEM (mammalian cells)
b) Fluorescent Microscopy (mammalian cells)
c) Genetic Mutations that disrupt transport (yeast cells)

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23
Q

Pulse-Chase Labelling [system]

A

a) acinar cells are exocrine cells of the pancreas that produce enzymes into the digestive system
b) these secreted enzymes are tagged to track where they go once they leave the ER
c) involves tagging proteins for only a brief period of time, so only some proteins are labeled

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24
Q

Pulse-Chase Labelling [method]

A

PULSE: acinar cells are incubated in a medium with radioactive methionine, which will be incorporated into proteins (3 mins)
CHASE: some cells are washed and transferred to a medium with non-radioactive amino acids (varies in length)

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25
Pulse-Chase Labelling [time points]
TIME POINTS: different lengths of chase 3 MINS: cells are pulsed for 3 mins, no chase, proteins are all in the ER 20 MINS: cells are pulsed for 3 mins, chased for 17 mins when protein transport is happening, proteins are in the Golgi 120 MINS: cells are pulsed for 3 mins, chased for 117 mins, proteins are found in vesicles
26
T or F: a graph summarizes the location of labelled proteins during the experiment, it plots the length of chase against percentage of autoradiographic grains
True
27
Fluorescent Microscopy: VSV
[def] vesicular stomatitis virus a) carries a gene that codes for an envelope protein called the G-glycoprotein, which is synthesized in the host cell ER b) VSV-G can be tagged with GFP to visualize live host cells c) 32°C (permissive temperature), protein folds and transported to ER membrane d) 40°C (restrictive temperature), protein misfolds, retained in ER
28
T or F: In a graph tracking VSV-G over time, once cells shifts from restrictive to permissive temperatures, proteins move from the ER (0 min) to the Golgi (40 min), to the plasma membrane (180 mins), the fluorescence is also decreasing over time as fluorophores lose fluorescence
True
29
Yeast Invertase [system]
a) yeast invertase metabolizes sucrose by converting it into glucose and fructose, using hydrolysis b) little community of yeast cells help feed each other collectively
30
Yeast Invertase [method]
a) mutations were generated at random b) each gene mutation was called a sec mutant (secretory mutant) c) they looked for mutations where yeast cells failed to secrete invertase in restrictive temperatures d) invertase accumulates in secretory vesicles at the restrictive temperature
31
Sec Class Mutations
[def] five classes of mutations defined by the location at which the invertase protein accumulated [A] accumulates in the cytosol (EX: SRP, SRP receptor, signal sequence, invertase signal sequence) [B] accumulates in the ER [C] accumulates in ER-Golgi vesicles [D] accumulates in Golgi [E] accumulates in secretory vesicles
32
T or F: upstream mutations therefore mask the appearance of downstream phenotypes (mutations that are later in the pathway)
True
33
T or F: Golgi complex is comprised of a series of elongated, flat sacs called cisternae, vesicles transport proteins from RER to cis-cisternae and away from the trans-cisternae
True
34
Exocytosis
[def] vesicles fuse with the cell membrane to release proteins from the cell
35
Constitutive Secretory Pathway
a) used by proteins that are released immediately after protein synthesis and transport b) secretory vesicles move from trans-cisternae of Golgi straight to the cell membrane
36
Regulated Secretory Pathway
a) used by proteins that are kept in the cell until a signal triggers release b) secretory vesicles that hold proteins are called secretory granules
37
Endocytic Pathway
a) used by proteins that form lysosomes b) vesicles fuse with vesicles formed at the cell membrane called endosomes
38
How can you distinguish the membrane of the Golgi complex from other organelles?
Fluorescently-labelled wheat germ agglutinin, a lectin that recognizes N-linked polysaccharides found in the Golgi cisternae
39
T or F: The Golgi complex is not a single organelle but a region that contains a series of elongated vesicle sacs, called cisternae, there are also many mobile spherical vesicles associated throughout the Golgi
True
40
Anterograde Transport [2 models]
[def] movement of proteins from RER to cell membrane [model A] vesicles containing protein cargo move from cisterna to the next [model B] proteins stay in cisternae but the cisternae themselves are moving forward, requires the use of vesicles that move backwards
41
Which model of anterograde transport is correct, why?
a) model B - cisternal maturation b) cell membrane protein undergoing anterograde transport was only found in cisternae, not vesicles c) residential medial-Golgi protein that's moving both directions and found in vesicles
42
What are cisternae defined by?
Location within the complex EX: cis-Golgi become medial-Golgi, and medial-Golgi become trans-Golgi
43
T or F: Under the cisternal maturation model, new cis-cisternae are formed by coalescing vesicles from the ER, trans-Golgi network dissipates into secretory vesicles, and importantly, vesicles are used to re-sort Golgi proteins in the retrograde direction
True
44
Vesicular Trafficking [4 steps]
[step 1] vesicles form by a process called budding, where buds arise from the membrane of the donor compartment [step 2] cargo proteins are loaded into buds via cargo signal sequences and receptors [step 3] vesicles formation and release [step 4] vesicle docking and fusion to membrane of the recipient compartment
45
Coated Vesicles [types]
a) Clathrin vesicles: required for transport away from trans-Golgi network to endosomes, cell membrane, and endocytosis b) COP I vesicles: used for retrograde transport c) COP II vesicles: required for transport from RER to cis-Golgi network
46
Coat Proteins
[def] proteins that are used in the formation of a vesicle a) all coat proteins are small GTP-binding proteins with GTPase activity b) Active when bound to GTP c) Inactive when bound to GDP d) Active to Inactive requires GAP (GTPase activating protein) e) Inactive to Active requires GEF (genuine exchange factor)
47
STEP 1: Vesicle Formation [COPII model]
a) budding of a vesicle on a donor membrane b) Sar1-GDP: inactive cytosolic protein c) Sec12: transmembrane protein found on membrane of donor compartment (EX: ER) d) Sec12 acts as a GEF that facilitates the exchange of GDP for GTP on Sar1 e) Sar1-GTP becomes active, revealing a hydrophobic N-terminus that anchors Sar1 into the ER membrane f) Sar1 proteins interact with cytosolic COPII coat proteins, inducing a change in shape g) COPII proteins: Sec23 (binds directly to Sar1), Sec24 (indirectly), Sec13, Sec31
48
What's a difference between COPII vesicle formation and COPI & clathrin-coated vesicle formation?
ARF instead of Sar1
49
STEP 2: Loading Cargo
a) cargo receptors accumulate in the bud and pick up soluble proteins b) transmembrane proteins and Golgi enzymes also accumulate in the bud
50
STEP 3: Vesicle Completion & Release
a) GTP hydrolysis by Sar1 converts Sar1-GTP into Sar1-GDP b) Sar1 is no longer membrane-anchored, releasing both Sar1 and coat proteins in a process called uncoating c) Uncoated vesicle is recognized by a motor protein and carried along microtubules from the donor membrane to recipient membrane
51
How can you inhibit vesicle coat disassembly?
a) add a non-hydrolyzable form of GTP that maintains Sar1 in it's GTP-bound state b) alternatively, study a mutation in the Sar1 protein that inhibits GTPase activity
52
Vesicle Release [clathrin]
a) clathrin coat forms a polyhedral lattice using a collection of different clathrin proteins: clathrin heavy chains, clathrin light chains, adaptor proteins b) tri-scallion: three light chains and three heavy chains c) G-protein, dynamin, is required for release of clathrin-coated vesicles D) visualization occurs by adding non-hydrolyzable GTP or by creating mutants in dynamin GTPase activity
53
T or F: In the presence of GFP, dynamin forms polymers that assemble into spiral structures
True
54
Dynamic Function [two models]
[def] two models for how dynamin uses its structure to induce vesicle release [model 1] POPPASE: suggests that dynamin helices elongate and push the vesicle away [model 2] PINCHASE: suggests that dynamin helices constrict and squeeze the membrane
55
Which model of dynamin function is correct? Why?
a) dynamin-lipid tubules constrict upon addition of GTP (evidence for the pinchase model) b) dynamin has elongated along lipid-tubules (evidence for poppase model) c) conclusion, perhaps it's a combination of both models
56
Dynamin Function [fruit flies]
a) Drosophila melanogaster b) vesicle is formed during endocytosis at the cell membrane of a presynaptic neural cell c) neurotransmitters are loaded from the cytosol into vesicles that are formed from a presynaptic cell membrane d) vesicle fusion with the cell membrane releases neurotransmitters into the synaptic cleft e) in flies, the shibire gene codes for dynamin
57
How does temperature sensitive mutations impact flies?
a) temperature sensitive mutation in shibire gene disrupts the dynamin protein b) flies are fine at permissive temperature (25°C) but paralyzed at restrictive temperature (30°C) c) at 33°C, in the absence of functional dynamin, there's no transport of neurotransmitters in vesicles, due to an inability to form synaptic vesicles d) the phenotype can be reversed (normal after 30 mins)
58
STEP 4: Vesicle Docking & Fusion [secretory vesicle]
a) Rab GTPase controls vesicle docking b) Rab-GDP is found free in cytosol, while Rab-GTP is bound to vesicles by a hydrophobic anchor c) Rab-GTP associates with a receptor on the target membrane d) both membranes must fuse for cargo to be released into recipient compartment
59
Snare Complex [vesicle fusion]
a) vesicle fusion is mediated by membrane anchored proteins called SNARE proteins b) vesicle snares are anchored on the vesicle membrane (EX: VAMP) c) target snares are anchored to the target membrane (EX: syntaxin, SNAP25) d) SNARE COMPLEX: two SNAP25 helices, one syntaxin helix, and one VAMP helix e) NSF & alpha-SNAP unwind the four helices
60
What proteins need to be returned to the ER?
a) ER resident proteins b) v-SNARES c) COPII vesicle cargo receptors d) unfolded proteins
61
Specific signals of ER resident proteins that are required for loading into COPI vesicles [3]
a) Resident ER soluble proteins: KDEL b) Resident ER membrane proteins: KKXX c) Cargo acceptor from COPII vesicle: DXE

BIO 2B03 (10 decks)

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