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BIO230 Midterm > Week 6 > Flashcards

Week 6 Flashcards

1
Q

What happens to most soluble and transmembrane proteins in the ER?

A

glycosylated (very rarely happens in the cytosol)

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2
Q

What are the types of glycosylation?

A
  • O-linked glycosylation
  • N-linked glycosylation
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3
Q

What is the precursor for N-linked oligosaccharides?

A
  • performed in the ER
  • transferred to the target protein by oligosaccharyl transferase to an ASN on a protein being synthesized
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4
Q

What is the sequence for N-linked glycosylation?

A

Asn-X-Ser or Asn-X-Thr (x = any amino acid except proline)

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5
Q

What happens to the N-linked oligosaccharide after it is transferred to the protein in the ER?

A
  • three glucoses are removed: 1 by glucosidase 1 and 2 by glucosidase 2 (one at a time)
  • removal of one mannose
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6
Q

Where are proteins glycosylated?

A

only on the ER lumen

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7
Q

How are glycosylated proteins transported?

A

via vesicles to the Golgi

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8
Q

What is N-linked glycosylation?

A

oligosaccharide is covalently attached to a nitrogen atom of an asparagine residue

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9
Q

What are the different types of Golgi cisternae?

A

Cis, Medial, and Trans
- each has different enzymes

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10
Q

What happens to proteins in the Golgi?

A
  • removes or adds sugars
  • results in different modifications to different proteins
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11
Q

What is the purpose of glycosylation?

A
  • tag to mark the state of protein folding
  • protect proteins on the cell surface from proteases
  • some glycosylated proteins have a role in cell adhesion
  • allows proteins to form the correct 3D structure
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12
Q

What role does calnexin play in glycosylation?

A
  • a chaperone protein that binds to glycosylated proteins in the ER
  • retains proteins that are still undergoing folding
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13
Q

How does calnexin work for normally folded proteins?

A
  • binds to glucose of unfolded protein after glucosidase 1 and 2 both removed 1 glucose
  • Glucosidase 2 removes second glucose
  • mannosidase removed
  • folded properly
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14
Q

How does calnexin work for incompletely folded proteins?

A
  • binds to glucose of unfolded protein after glucosidase 1 and 2 both removed 1 glucose
  • Glucosidase 2 removes second glucose
  • mannosidase removed
  • if not folded properly, glucosyl transferase bing
  • UDP is cut off to add UDP-glucose
  • protein enters the cycle again
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15
Q

How do vesicles move cargo between compartments?

A
  1. budding with cargo
  2. fusion to target
  3. release cargo
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16
Q

What are the cargo proteins in a vesicle?

A
  • transmembrane proteins
  • soluble proteins (some bound by transmembrane cargo receptors)
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17
Q

What are nascent transport vesicles?

A

new transport vesicles that have protein coats

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18
Q

What are the roles of protein coats?

A
  1. select cargo for vesicles
  2. give curvature to vesicles
  3. promote vesicle budding
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19
Q

What are the different protein coats?

A
  1. COP1-coated vesicles: from Golgi to ER, between different Golgi cisterna
  2. COP2-Coated vesicles: from ER to Golgi
  3. Clatherin-Coated vesicles: from Golgi and plasma membrane to endosome
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20
Q

What is the role of monomeric GTPases in vesicle formation?

A
  • crucial for the recruitment of coat proteins
  • cycle between an inactive GDP-bound state and an active GTP-bound state
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21
Q

How are monomeric GTPases regulated?

A
  • GEF (exchange of GDP-GTP, turn on)
  • GAP (hydrolysis of GTP-GDP, turns off)
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22
Q

What are the two main types of monomeric GTPases involved in vesicle formation?

A
  • ARF: COPI and clathrin-coated
  • Sar1: COPII-coated vesicles.
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23
Q

How is the formation of COP2-coated vesicles done?

A
  • Sar1-GEF in ER membrane recruits Sar1-GDP (off)
  • Sar1-GDP is exchanged for GTP (on), which exposes the amphipathic alpha-helix
  • Sar1-GTP is bound into the membrane
  • recruits coat protein subunits
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24
Q

What are the vesicle coat layers?

A
  • inner layer: binds to the membrane and selects cargo
  • outer layer: associates with the inner layer to promote polymerization of the coat
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25
Q

What do coat proteins need to select?

A
  • cargo
  • transmembrane cargo receptors
  • SNAREs
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26
Q

What are the COP1-coated vesicle layers?

A
  • inner: 4 subunits
  • outer: 3 subunits
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27
Q

How is the uncoating of COP1-coated vesicles done?

A
  • y-COP binds to Arf GAP
  • GTP hydrolysis (Arf-GTP –> Arf-GDP)
  • Arf-GDP detaches from the membrane and the coat is released
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28
Q

What are the COP2-coated vesicle layers?

A
  • Inner: 2 subunits
  • Outer: 2 subunits
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29
Q

How is the uncoating of COP2-coated vesicles done?

A
  • Sec 23 has GAP activity (stimulated by Sec13/Sec31)
  • GTP-hydrolysis (Sar1-GTP –> Sar1-GDP)
  • Sar1-GDP detaches from the membrane and the coat is released
29
Q

What are the Clatherin-coated vesicle layers?

A
  • Inner: different adaptor complexes
  • Outer: clathrin (6 subunits)
30
Q

How is the uncoating of Clatherin-coated vesicles done?

A
  • pinching off of vesicle requires dynamic (has GTPase activity)
  • uncoating requires Hsp70 and auxillin
31
Q

What are triskelions?

A
  • basic structural units of clathrin-coated vesicles
  • three heavy chains and three light chains that come together to form a basket-like structure
32
Q

How is vesicle specificity determined?

A
  1. proteins for docking and tethering the vesicle to the target membrane (Rab GTPase and Rab effectors)
  2. Proteins for catalyzing vesicle fusion with the target membrane (SNAREs)
33
Q

What are Rab GTPases?

A
  • monomeric GTP-binding proteins
  • help in the docking and tethering of vesicles to their target membranes
34
Q

How do Rab GTPases function in vesicle docking?

A
  • functions by binding to their effectors when they are in the GTP-bound form (Rab-GTP)
  • binding facilitates the docking of the vesicle to the target membrane
35
Q

What are Rab effectors?

A
  • proteins that interact with Rab GTPases
  • provide specificity and facilitate the interactions
36
Q

How do Rab GTPases contribute to vesicle specificity?

A

by having a large variety of effectors that recognize different Rab proteins

37
Q

What are the steps of Rab GTPases and Rab effectors mediating vesicle docking?

A
  1. Rab-GTP binds Rab effector
  2. Rab-GTP + Rab effector
    - dock and tether vesicles
    - V-SNAREs and t-SNAREs are brought togther
38
Q

What are v-SNAREs?

A
  • proteins located on the membrane of transport vesicles
  • crucial role in the process of vesicle fusion with target membranes by interacting with t-SNAREs
39
Q

What are t-SNAREs?

A
  • proteins found on the target membrane
  • interact with v-SNAREs to facilitate the fusion of the vesicle with the target membrane
40
Q

What is the specificity of v-SNAREs and t-SNAREs?

A
  • many different types of v-SNAREs and t-SNAREs
  • specificity ensures that vesicles fuse only with the correct target membranes
41
Q

How do v-SNAREs and t-SNAREs promote vesicle fusion?

A

helical domains of these SNAREs coil around each other, effectively locking the two membranes together

42
Q

What happens after v-SNAREs and t-SNAREs fuse?

A
  • need to dissociate the SNARE complex
  • NSF and adaptor proteins unravel helical domains of SNARES
43
Q

What is the structure of the Golgi?

A

Cis Face
- cis-Golgi network
- cis cisterna
- medial cisterna
- trans cisterna
- trans-Golgi network
Tans Face

44
Q

How do cargo proteins go from the ER to the cis Golgi network?

A
  • cargo packaged in COP2-coated vesicles (bud from ER exit sites)
  • most cargo has exit signals
  • COP2-coated vesicles bud from the ER exit site, then shed their COP2 coat
  • Fuse with each other from vesicular tubular clusters
  • vesicular tubular clusters move to the Golgi apparatus
45
Q

How does retrieval transport occur?

A
  • occurs using COP1-coated vesicles (move back to ER)
  • vesicles from vesicular tubular clusters and the Golgi go to the ER
46
Q

What do retrieval transport vesicles contain?

A
  • escaped ER-resident proteins (most ER resident proteins have ER retrieval sequences)
  • proteins involved in vesicle budding from ER
47
Q

What kind of signal do soluble ER-resident proteins contain?

A

a retrieval signal (KDEL) and are bound by the KDEL receptor
- packages into COP1-coated transport vesicles

48
Q

What kind of signal do membrane ER-resident proteins contain?

A

a retrieval signal
- Ex. KKXX at. C-terminus
- signal bound by COP1 coats
- packages into vesicles

49
Q

Describe the pH dependency of the KDEL receptor.

A
  • KDEL receptor has a high affinity for KDEL at the acidic pH found in the Golgi = bind ER-resident proteins
  • receptor has a low affinity at neutral pH = release of the bound proteins
50
Q

How do KDEL receptors cycle?

A
  • between ER and Golgi
  • at vesicular tubular clusters, Golgi = high affinity
  • ER = low affinity for KDEL
51
Q

How is the retrieval of ER-resident proteins from the Golgi regulated?

A
  • pH (V-type ATPase H+ pump)
  • binds in acidic pH, releases at neutral pH
52
Q

What happens to ER and Golgi resident proteins that don’t have retrieval signals?

A
  • proteins end up in the right compartment
53
Q

What are the possible mechanisms for the proper sorting of ER and Golgi proteins without retrieval sequences?

A
  1. different transport rates
  2. Proteins retained in resident compartments
54
Q

What is an example of proteins that transport at different rates?

A

some Golgi enzymes cycle between the ER and Golgi, but transport to the ER at a slower rate

55
Q

What is an example of proteins that are retained in the resident compartment?

A

proteins that function in the same compartment from large complexes, which prevents packaging into transport vesicles

56
Q

What are the models of transport through the Golgi apparatus?

A
  1. Vesicular transport model: cargo moves via transport vesicles
  2. Cisternal maturation model: cisternae move through the Golgi and mature as they progress
57
Q

How does the vesicular transport model occur?

A
  1. COP1-coated transport vesicles with cargo move forward from one Golgi cisterna to the next
  2. Retrograded transport vesicles (COP1) return escaped resident ER protein and Golgi enzymes
58
Q

How does the cisternal maturation model occur?

A
  1. cisternae move through the Golgi apparatus
    - Vesicular Tubular Clusters from the ER (fuse to become the cis Golgi network)
    - Each cisterna becomes the next cisterna
    - existing trans cisterna move to the TGN
  2. Retrograded transport by COP1 vesicles
    - move Golgi enzymes and ER resident proteins back
59
Q

What is the similarity between the two models of transport through the Golgi?

A
  • Retrograde transport by COP1 vesicles
60
Q

Which model of transport occurs through the Golgi?

A
  • both may occur
  • some cargo move rapidly in transport vesicles
  • other cargo move more slowly through cisternal maturation
61
Q

What is the Trans Golgi Network (TGN)?

A

complex network of membranes and vesicles that serves as a major branch point for sorting proteins and lipids destined for various cellular locations

62
Q

What types of cargo are sorted at the TGN?

A

both soluble proteins and transmembrane proteins
- packages lysosomal hydrolases needed for lysosome function and degradation of macromolecules

63
Q

Where do TGN vesicles go?

A

transported to late endosome (late endosomes gradually mature into lysosomes)

64
Q

What are the roles of acid hydrolases?

A
  • degrade marcomolcules
65
Q

Where are acid hydrolases synthesized?

A
  • synthesized in ER and processed in the Golgi
66
Q

When are acid hydrolases active?

A

acidic pH (~5), regulated by proton pump

67
Q

How are lysosomal hydrolases synthesized and processed?

A
  • N-linked oligosaccharides added in the rough ER
  • then transported to the Golgi apparatus
  • mannose residue phosphorylated = M6P in the cis Golgi
68
Q

How are lysosomal hydrolases tagged for transport to the lysosome?

A
  • tagged with a mannose-6-phosphate (M6P) marker during their processing in the Golgi apparatus
69
Q

What role do M6P receptors play in the transport of lysosomal hydrolases?

A
  • bind to lysosomal hydrolases (at a neutral pH) that have been tagged with M6P
  • vesicular transport with clathrin coat with M6P receptors embedded in membrane
  • receptors package the hydrolases into vesicles for transport to late endosomes (matures into lysosome)
70
Q

What happens to lysosomal hydrolases once they reach the lysosome?

A

M6P receptor releases at acidic pH
- remove phosphate (optional)
- lysosomal hydrolase precursor

71
Q

How is the M6P receptor retrieval performed?

A
  • M6P receptor is in budding
  • retromer coat
  • transport vesicle goes back to trans Golgi

BIO230 Midterm (6 decks)

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