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L2 Molecular Cell Biology > Vesicular trafficking > Flashcards

Vesicular trafficking Flashcards

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1
Q

What are the 3 main trafficking methods within cells?

A
  • Gated transport
  • Transmembrane transport
  • Vesicular transport
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2
Q

What kind of trafficking occurs between the nucleus and the cytosol?

A

Gated transport

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3
Q

What is the structure of the nuclear pore? (3)

A
  • Brings together the double nuclear membrane
  • Complex consists of nucleoporins
  • Each complex is made of 8 subunits with a central plug
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4
Q

What is the function of the nuclear pore? (3)

A
  • Involved in moving substances across the nuclear envelope
  • Histones are made at ribosomes in the cytoplasm and need to get into the nucleus to package the DNA
  • Ribosomal subunits are made in the nucleolus and have to be transported into the cytoplasm
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5
Q

What are the 2 processes by which substances are transported by the nuclear pore complex?

A
  • Diffusion
  • Active transport
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6
Q

What is required for active transport through the nuclear pore? (2)

A
  • Signal
  • ATP
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7
Q

What signal is required for active transport through the nuclear pore?

A

An amino acid sequence that is rich in lysine, arginine and proline

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8
Q

What is an example of a signal in transport through the nuclear pore? (2)

A
  • T-antigen of the SV40 virus contains the sequence Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val
  • Mutation of a single amino acid in the sequence prevents nuclear translocation
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9
Q

What experiment would show that an amino acid sequence is necessary and sufficient to cause nuclear transport?

A

Put the sequence onto a protein that wouldn’t normally enter the nucleus and show that it causes nuclear translocation

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10
Q

What experimental evidence shows that active transport is used in nuclear translocation? (2)

A
  • Cool cells so they can’t make ATP, inhibits mRNA transport out of the nucleus
  • In the absence of ATP proteins bind to the pore complex but aren’t translocated, add ATP and they appear in the nucleus
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11
Q

What are the 2 ways in which newly made membrane proteins can be translocated into the ER?

A
  • Co-translational translocation
  • Post-translational translocation
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12
Q

What is co-translational translocation?

A

Protein is being fed into the lumen of the ER as it is being translated by the attached ribosome

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13
Q

What is post-translational translocation?

A

Proteins are fully made in the cytoplasm by a free ribosome and then transported into the ER after translation

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14
Q

What is the most common way in which secreted/membrane proteins are transported into the ER?

A

Co-translational translocation

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15
Q

What is the signal hypothesis?

A

Protein made in the cytoplasm that are targeted to the ER use a signal to direct them to the ER membrane

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16
Q

What are microsomes?

A

Isolated ER membrane preparation

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17
Q

How is a soluble protein destined for secretion made via co-translational translocation? (5)

A
  • Translocator protein on the ER is usually closed
  • Ribosome translating the mRNA is closely associated with the translocator
  • Peptide signal in the protein causes the translocator to open and the protein is fed through into the ER lumen as it is being translated
  • Peptide signal is cleaved by a signal peptidase
  • Full translated polypeptide chain is folded by chaperones in the ER lumen
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18
Q

How are type I membrane proteins inserted into the ER? (3)

A
  • Start-transfer sequence is recognised by the translocator protein
  • Protein is fed through the translocator until it reaches a hydrophobic stop-transfer sequence
  • Start-transfer sequence is cleaved off and the stop-transfer sequence remains in the membrane so the N-terminus is in the ER and the C-terminus is in the cytosol
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19
Q

What is the difference between type I and type II transmembrane proteins?

A

Type I transmembrane proteins have a cytoplasmic C-terminus and an extracellular/luminal N-terminus whereas type II transmembrane proteins are the other way round

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20
Q

How are type II membrane proteins inserted into the ER? (3)

A
  • Signal sequence is recognised by the translocator
  • N-terminus end remains in the cytosol and the C-terminus end is fed through into the ER lumen
  • The signal sequence acts as the transmembrane domain
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21
Q

How is proper protein folded ensured in the ER? (3)

A
  • BiP chaperone associates with newly made proteins until they are folded correctly
  • Proteins are retained in the ER lumen until they are correctly folded
  • Misfolded proteins are reverse translocated into the cytoplasm and degraded
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22
Q

What is the function of glycosylation in the ER?

A

Ensures good quality control

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23
Q

How can protein misfolding cause disease?

A

CFTRdelta508 mutation causes misfolding in CFTR which is recognised by quality control machinery so the mutant CFTR is retained in the ER membrane

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24
Q

What is triggered by a high number of misfolded proteins in the ER?

A

Unfolded protein response (UPR)

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25
Q

What happens in the UPR? (3)

A
  • Stop translation
  • Upregulate synthesis of chaperones
  • Cells can recover but if the cell is overwhelmed apoptosis is triggered
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26
Q

Which method is used to get proteins into the mitochondrial matrix?

A

Post-translational translocation

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27
Q

How do proteins get into the mitochondrial matrix? (3)

A
  • Fully translated proteins have an N-terminal signal sequence which is recognised by the TOM complex on the outer mitochondrial membrane
  • Protein translocates into the matrix via the TIM23 complex on the inner mitochondrial membrane
  • Signal peptide is cleaved by signal peptidase
28
Q

What is the signal for mitochondrial translocation? (3)

A
  • Amphipathic alpha helix structure
  • One side of the structure is hydrophobic, other is hydrophilic
  • The hydrophobic residues bind in a hydrophobic groove in the receptor associated with the TOM complex
29
Q

How are proteins inserted into the outer mitochondrial membrane? (2)

A
  • Polypeptide translocates into the intermembrane space
  • Chaperones in the intermembrane space help to assemble the protein in the outer membrane with the SAM complex
30
Q

How are proteins inserted into the outer membrane of bacteria? (3)

A
  • Protein is translocated into the periplasmic space and associates with chaperones
  • Protein is inserted into the outer membrane via the BAM complex
  • Similar process to mitochondria
31
Q

What are the similarities between insertion of membrane proteins in mitochondria and chloroplasts? (4)

A
  • Both occur post-translationally
  • Both require energy
  • Use membrane potential as well as energy to drive the process
  • Signals are similar but the proteins aren’t mixed up in plant cells
32
Q

What can vesicles be coated with? (3)

A
  • Clathrin
  • COPI
  • COPII
33
Q

What are the essential components for transport vesicle formation? (3)

A
  • GTPase
  • Adaptor proteins
  • Coat
34
Q

What is the function of adaptor proteins? (3)

A
  • Recognise and select cargo
  • Link the coat to the ER membrane
  • Recognise motifs in the cytoplasmic domains of membrane proteins
35
Q

What GTPases are in the Ras superfamily? (5)

A
  • Ras
  • Rabs
  • Arfs
  • Ran
  • Rho
36
Q

How do small GTPases work? (3)

A
  • Inactive when bound to GDP
  • GEFs cause the exchange of GDP for GTP to activate the GTPase
  • GAPs cause hydrolysis of GTP to GDP to inactivate the GTPase again
37
Q

What is a GEF?

A

Guanine nucleotide exchanging factor

38
Q

What is a GAP?

A

GTPase activating protein

39
Q

Which GTPase is required for nuclear transport?

A

Ran

40
Q

How is Ran involved in nuclear transport? (6)

A
  • Ran-GDP is in the cytosol
  • Ran-GTP is in the nucleus because the GEF is localised to chromatin
  • Cargo binds to nuclear import receptors to enter the nucleus
  • Ran-GTP binds to the import receptor causing the cargo to dissociate in the nucleus
  • Ran-GTP bound to the receptor exits the nucleus, GAP causes GTP hydrolysis
  • Ran-GDP dissociates from the receptor which is free to pick up more cargo
41
Q

What kind of vesicles form at the exit sites of the ER?

A

COPII coated vesicles

42
Q

What are the components of COPII coated vesicles? (3)

A
  • GTPase: Sar1 (Arf family)
  • Adaptor: Sec23/24
  • Coat: Sec13/31
43
Q

How are COPII coated vesicles formed? (5)

A
  • Cargo exit signal binds to cargo receptor in the ER membrane
  • GEF in the ER membrane activates sar1
  • Allows recruitment of adaptor complex, sec23 binds to sar1, sec24 binds to the cargo
  • Adaptor sec23/24 complex recruits coat proteins sec13/31
  • Bud pinches off to form coated vesicle
44
Q

How are ER resident proteins excluded from budding vesicles?

A

High surface area to volume ratio of the bud

45
Q

What is the function of coat proteins?

A

Provide a structural scaffold

46
Q

How can ER be isolated from cells for reconstitution experiments? (4)

A
  • Homogenise cells
  • ER vesiculates into rough and smooth microsomes
  • Centrifuge the mixture in a tube with a gradient of increasing sucrose concentration
  • Smooth and rough microsomes float at different sucrose concentrations so can be separated
47
Q

How did reconstitution experiments demonstrate the components of COPII vesicles? (4)

A
  • ER membrane preparation containing ribophorin (known ER protein)
  • COPII vesicles containing p58 (known vesicle protein)
  • Vesicles and ER pellet at different sucrose concentration
  • Found that they needed to add cytosol, ATP and GTP to ER membrane in order to form COPII vesicles
48
Q

How are COPII vesicles disassembled? (3)

A
  • Sec23 acts as a GAP for sar1
  • GAP activity of sec23 is enhanced by recruitment of the coat sec13/31
  • Causes GTP hydrolysis, inactivation of sar1 and disassembly of the coat
49
Q

What are the 2 types of GTPase mutants?

A
  • GTP mutants (constitutively active, can’t hydrolyse GTP)
  • GDP mutants (can’t exchange GDP for GTP, sequester GEFs)
50
Q

What are COPII vesicles used for?

A

ER budding to deliver material to the Golgi complex

51
Q

What are COPI vesicles used for?

A

Delivers material in an anterograde and retrograde direction through the Golgi

52
Q

What are clathrin coated vesicles used for?

A

Delivers material from the TGN to lysosomes and also bud from the cell surface

53
Q

What cargo are COPII coated vesicles used for?

A

Newly synthesised proteins

54
Q

What cargo are COPI coated vesicles used for?

A

Retrieved and newly synthesised proteins

55
Q

What cargo are clathrin coated vesicles used for? (2)

A
  • Lysosomal proteins
  • Regulated secretory proteins
56
Q

Which GTPase is required for COPII vesicle formation?

A

Sar1

57
Q

Which GTPase is required for COPI vesicle formation?

A

Arf1

58
Q

Which GTPase is required for clathrin vesicle formation?

A

Arf1

59
Q

What is the structure of AP2 (adaptor protein)? (3)

A
  • 2 large subunits which bind the coat
  • 2 flexible appendage domains
  • 2 smaller subunits which recognise signals in transmembrane proteins
60
Q

Which proteins are important for endocytosis? (2)

A
  • AP2 adaptor
  • Clathrin coat
61
Q

How is large cargo packaged?

A

COPII coat is modified which sorts the cargo into tubular structures for transportation

62
Q

Which GTPase superfamily do the Rab GTPases belong to?

A

Ras superfamily

63
Q

What are the features of Rab GTPases? (3)

A
  • Cycle between GDP-bound Rab in the cytoplasm and GTP-bound Rab in membranes
  • Required for membrane fusion
  • Different ones are associated with specific membranes
64
Q

What is the role of Rabs in fusion?

A

Rab-GTP on a vesicle recruits a tethering protein which facilitates the formation of SNARE complexes by bringing the membranes close together

65
Q

What is the role of Rab cascades? (2)

A
  • GAP for the previous Rab can recruit the GEF for the Rab in the next compartment where the cargo is being delivered to
  • Allow movement of cargo between organelles
66
Q

What disease is caused by a Sec23A mutation? (2)

A
  • Cranio-lenticulo-sutural dysplasia
  • Problems with the secretory pathway results in issues with ECM formation
67
Q

What disease is caused by a Rab mutation? (2)

A
  • Charcot-Marie-Tooth 2B
  • Causes too much autophagy which inhibits neurite outgrowth

L2 Molecular Cell Biology (13 decks)

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