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Cell biology > Week 6 > Flashcards

Week 6 Flashcards

1
Q

cargo

A

solubles carried between compartments by vesicles

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2
Q

coats perform what 2 functions?

A
  1. cargo sorting: concentrate specific membrane proteins in a specialized membrane patch ⇒ select the right cargo
  2. shaping vesicles: assembly into curved basket like structures ⇒ determine shape and size of the vesicle
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3
Q

clathrin coated vesicles

A

transport from plasma membrane, transport from golgi to endosomes
- composed of triskelion
- binds to the adaptor protein AP2 which is bound to a cargo receptor in the membrane

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4
Q

COPI coated vesicles

A

transport from the golgi to the ER membrane

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5
Q

COPII coated vesicles

A

transport from the ER to the golgi membrane
- 2 adaptor proteins are Sec23 and 24 where Sec23 binds to Sar1 and Sec24 binds to the cargo receptor which induces membrane curvature
- the recruit COPII to the outer coat and this starts the bud formation (Sec13/31 are on outside)

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6
Q

retromer coated vesicles

A

transports from endosomes to the golgi

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7
Q

how do adaptor proteins bind to the membrane?

A

they first bind to a PIP and then they bind to a cargo receptor protein. Later on the coat layer binds to the adaptor protein as the vesicle is formed

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8
Q

bud formation

A

the shaping of the early vesicle as it is circularized but still attached to the membrane by fission proteins

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9
Q

Dynamin

A

small GTPase that forms a ring around the neck of the bud
- Brings the 2 non cytosolic leaflets into close proximity and allows membrane fusion (vesicle formation)

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10
Q

which PIP does the AP2 adaptor protein interact with

A

PI(4,5)P2 => AP2 rearranges and binds to the cargo receptors which induces a membrane curve

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11
Q

what molecular classification is a Phosphatidylinositol (PI)

A

it is a lipid and relatively rare on the cytosolic leaflet => this undergoes phosphorylation to form phosphoinositides (PIPs) which are distinct to different organelles and recruit specific binding proteins
- without phosphate it is just PI

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12
Q

T/F PIP distribution determines which adaptors and cargo proteins will be incorporated into a vesicle?

A

True => different membranes have different PIPs

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13
Q

Coat recruitment of GTPases (2 examples)

A

monomeric GTPases which regulate recruitment of coat proteins and trigger the reaction of coat assembly
- ARF: COPI and clathrin at the golgi
- Sar1: COPII at the ER

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14
Q

Sar1-GEF; what happens when it is activated?

A

embedded in the ER membrane and in an active state vs Sar1-GAP is inactive in the cytosol
- the hydrophobic tail is exposed from the GTP conformation so that the tail inserts into the ER membrane to recruit the 2 COPII adaptor proteins

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15
Q

which 2 protein classes regulate vesicle targeting?

A
  1. Rab => specify where the vesicles will go and only bind to certain places in the cell
  2. SNARE => help with membrane fushion between v-SNARE proteins on the vesicle membrane and t-SNARE proteins on the target membrane
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16
Q

How does Rab work?

A

when it is in its GTP bound state and active, it is attached to a vesicle and searching for its Rab effector protein counterpart on the target membrane
- Rab will flip its tail and insert into the membrane when active just like Sar1 and ARF and will bind to the Rab on the target membrane
- Rab will dissociate when the vessicle is docked and will be joined with a GDI which inhibits activity

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17
Q

How do SNARE proteins work?

A

when Rab binds to its effector molecule, then the v-SNARE on teh vesicle will intertwine with the t-SNARE on the target membrane to form a trans complex between the two
- this complex is energetically favorable and this is used to pull the snares closer and expel water so the two leaflets can make contact and form new bilayers that fuse

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18
Q

different between V and T SNARES

A

v- snare = vesicle and is composed of a single protein
t-snare = target and is composed of 2-3 proteins

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19
Q

in SNARE membrane fushion which membrane will fuse first?

A

the cytosolic leaflet fuses first and then the lumen leaflet will begin to form gaps where it fuses too

20
Q

forward vs retrieval transport (describe both in detail)

A

forward goes from the ER to the golgi and retrieval happens from the golgi to the ER
- in forward transport cargo has exit signals on their cytosolic tails that bind to the adaptor proteins Sec23 and 24
- the vesicles will bud off and when the COPII coat is removed, they will form vesicular tubular clusters and attach to motor proteins on microtubules going toward the golgi
- in retrograde transport the vesicled but off from the cis golgi via COPI coats and resident proteins go back to the ER to be used again if they accidentally escaped

21
Q

what are ER retrieval signals

A

retention signals like KKXX for ER resident membrane proteins that bind directly to COPI coats whereas KDEL binds to the resident protein and then to a KDEL receptor which binds COPI coats
- these vesicles are transported back to the ER
- retrieval can happen at the vesicular tubular cluster or on the cis and medial golgi

22
Q

how does KDEL bind?

A

the golgi is more acidic so KDEL has a high affinity to capture KDEL proteins but there is a low affinity in the ER where they are unloaded

23
Q

cisternae

A

the golgi apparatus has an ordered set of membrane enclosed compartments
- Proteins from the ER generally enter the cis face and exit at the trans face but there is bidirectional movement
- the golgi is a sorting center for proteins going into vesicles

24
Q

what is the major function of the golgi?

A

glycosylation => N-glycosylation forms the core structure but is modified further in the golgi as well as O-linked oligosaccharides being modified in the golgi
- proteins are modified in successive stages

25
2 classes of N-linked oligosaccharides in mammilian glycoproteins
1. complex oligosaccharides: terminal region containing a variable number of GlcNAc, glucose, and sialic acid (negative chg) heterogenous 2. high mannose oligosacharides: add mannoses
26
what proteins are involved in O-linked glycosylation?
mucin and proteoglycans where sugar residues are added to serine or threonine residues
27
lysosomal hydrolases
enzymes degrade all kinds of macromolecules like proteins, lipids, sugars, etc. - Lysosomes have a more acidic pH ⇒ the most acidic in the cell
28
types of transport from golgi (3)
(lysosomes, secretory vesicles, plasma membrane) 1. Transport to lysosomes: mannose 6-phosphate (M6P) - Signal mediated diversion needs certain cargo going to the lysosome - Can be anything but is usually enzymes for protein degradation 2. Regulated secretory pathway: cargo is initially stored in secretory vesicles - Extracellular signals stimulate their secretion - Specialized secretary cells 3. Constitutive secretary pathway: transport of proteins form TGN in a steady stream default pathway and found in all cells
29
how do golgi target lysosomes?
using a mannose 6 phosphate group attached to the N-linked oligosaccharides of lysosomal hydrolases in the cis golgi => recognized by certain cargo receptors called M6P receptors on lysosomal hydrolases - this is on an endosome which carry the proteins to the lysosome - this is done through clathrin coats - endosomes are more acidic than the golgi which is how receptors are released
30
Immature secretory vesicles
come from the trans golgi network through clathrin vesicle coats and the clathrin coat will leave with some of the empy portions of the vesicle membrane to go back to the golgi - makes the vesicle smaller and more consicely filled with cargo - cargo concentration will increase as secratory vesicles will mature
31
what types of potentially harmful molecules are inactive precursors cleaved for activation?
- protein hormones - neuropeptides - enzymes - cleavage can occur in secretory vesicles or extracellular space
32
what can be used to control the amount of cell curface?
exocytosis
33
4 examples when more surface is needed
1. Cytokinesis: when 1 cell divides to 2 ⇒ requires a lot more membrane 2. Phagocytosis: the cell is engulfing another material which required more membrane as well ⇒ supplied by exocytosis 3. Plasma membrane repair: requires membrane by exocytosis as an extreme case 4. Cellularization: after fertilization, there is not cell division but nuclear division in a single cell until at a certain stage a new amount of membrane comes in to create cells and borders between them ⇒ requires a lot of new membrane at once
34
endocytosis definition + (4 types)
the process in which the plasma membrane invaginates and encloses some type of cargo - Opposite process of exocytosis where something from outside comes inside after capture ⇒ retrograde transport - most of the time the goal is to put them back into the lysosome to get degraded 1. Pinocytosis 2. Receptor mediated endocytosis 3. Macropinocytosis 4. Phagocytosis
35
what do endocytic vesicles fuse with?
fuse with early endosomes where cargo is sorted - Early --> multivesicular body --> late --> endolysosome --> lysosome - may be recycled back to the plasma membrane via recyling endosome or can be transported to the golgi at any stage before endolysosome/lysosome stages - there is no recycling after the early endosome stage
36
multivesicular bodies
developing late endosomes that do not recycle - Proteins destined for degradation are internalized in intraluminal vesicles which form multivesicular bodies
37
pinocytotic vesicles
places on the membrane where cells ingest bits of the plasma membrane and extracellular fluid (cellular drinking) - Most pinocytosis is mediated by clathrin coated vesicles
38
receptor mediated endocytosis
grabs specific molecules => this occurs at the plasma membrane but is the same concept as what we learned before and goes to an early endosome - Provides a selective concentration mechanism for taking up molecules form the extracellular space
39
how does cholesterol transport occur?
Low density lipoproteins (LDLs) - Enclosed by phospholipids and cholesterol esters are embedded inside the lipid tails - this is associated with clathrin coated pits by binding to the adaptor protein AP2
40
explain the process of receptor mediated endocytosis of LDL
cholesterol and other lipids are packed into lipid protein particles for efficient transport 1. LDL is captured by LDL receptor 2. LDL-LDL receptor are transported as clathrin coated vesicles 3. In endosomes, the LDL disassociated from its receptor in low pH environment 4. LDL receptors are recycled back to the plasma membrane from early endosomes 5. LDL is transported to endolysosomes where cholesterol esters are hydrolyzed and cholesterol is released - LDL goes into the lysosome where it gets degraded and then hydrolyzed to be released into the cell as free cholesterol
41
what happens when uncaptured LDL circulat ein the blood?
atherosclerosis => strokes and heart attacks from blocked arterial blood flow
42
Acid hydrolases
in a lysosome and require acid environment for optimal activity ⇒ work at pH of 4.5-5.0
43
Endolysosomes
late endosomes fuse with preexisting lysosomes to form structures
44
pathways to deliver materials to lysosomes (4)
1. Endocytosis 2. Phagocytosis 3. Macropinocytosis 4. Autophagy
45
macropinocytosis
(clathrin independent) triggered in response to binding of specific ligands to surface receptors - ruffles of actin filled membrane protrusions form and collapse onto the cell to form macropinosomes in a non-specific closure - Trapped cargo is transported to late endosomes or endolysosomes for degradation
46
phagocytosis
ingest large particles like microorganisms, old or dead cells via large vesicles - Carried out by professional phagocytes like macrophages (ingest RBCs) and neutrophils
47
autophagy
closure of double membrane around a target where the autophagosome will fuse with a lysosome - an organelle is marked with ubiquitin dependent receptors on the autophagosome membrane where the ubiquitylated membrane protein is on the organelle

Cell biology (15 decks)

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