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The Dynamic Cell > Compartmentalisation and Intracellular Trafficking - Block 6 > Flashcards

Compartmentalisation and Intracellular Trafficking - Block 6 Flashcards

1
Q

What is the function of the ER?

A

> Lipid and protein synthesis//PT modification

> Protein processing and sorting

> Quality control

> Calcium storage

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2
Q

What is the function of the Golgi complex?

A

> Protein modification

> Complex polysaccharide synthesis

> Sphingolipid synthesis

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3
Q

What is the function of a lysosome?

A

> Hydrolysis and storage of proteins

> Ion storage

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4
Q

What is the function of a vacuole?

A

> Storing waste products (storage vacuole)

> Degradation and nutrient release (lytic vacuole)

> Maintaining turgor

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5
Q

What is the function of an endosome?

A

> Retrieval//sorting of endocytosed material

> Transport to Golgi

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6
Q

What are the 3 main methods of protein transport?

A
  1. Gated transport (import & export complexes)
  2. Protein translocation (via translocation complexes)
  3. Vesicular transport (mem-bound vesicles)
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7
Q

What are the 3 main stages of vesicular transport?

A
  1. Vesicle budding from the donor compartment
  2. Vesicle transfer between donor and target
  3. Fusion of vesicle with target
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8
Q

What occurs during vesicle budding (VT stage 1)?

A

> Cargo is selected

> Bud formation with coat proteins

> Scission of bud from the donor compartment

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9
Q

What occurs during vesicle transfer (VT stage 2)?

A

Microtubules help transfer the vesicle to the donor

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10
Q

What occurs during vesicle fusion (VT stage 3)?

A

> Rab proteins pull in the correct vesicles

> SNARE proteins help merge lipid bilayers in order to fuse

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11
Q

Which way is the material moving in anterograde trafficking?

A

Forwards

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12
Q

Which way is the material moving in retrograde trafficking?

A

Backwards

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13
Q

How can the order of compartents be determined experimentally?

A

> Modern method: GFP attached to the protein of interest

> Previously: the pulse-chase method, using a radioactive amino acid

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14
Q

How do vesicles “know” where to go?

A

> “Lipid postcode”

The position of the PO4 group on a phosphoinositide (PIP) gives it a unique identity. Different organelles are enriched with different PIPs, which recruit different proteins, giving each organelle its own identity and specificity.

> “Protein tour guides”

Rab proteins mediate lipid recognition.

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15
Q

What is the activity of Rab proteins?

A

> They mediate recognition of the lipids

> They “mark” organelles

> They are small GTPases

> They are regulated by Activator Proteins and Exchange Factors

> They guide vesicles to their target membrane

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16
Q

What can regulate the activity of Rab proteins?

A

> Activator proteins

> Exchange factors

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17
Q

What are the 1st and 2nd levels of vesicle fusion specificity?

A

1st - Rab proteins

2nd - SNARE proteins

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18
Q

What is the difference between V-SNARE ans T-SNARE proteins?

A

> V-SNARE proteins are involved with vesicle membranes

> T-SNARE proteins are involved with the target membranes

> > Only specific combinations of SNARE proteins can mediate fusion <

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19
Q

What kind of complex do a t-SNARE and v-SNARE protein form, and what does it do?

A

It forms the trans-SNARE helical complex, and it acts like a zip to pull the vesicle down, overcoming the repulsion caused by lipid membrane contact.

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20
Q

What studs the surface of the ER membrane?

A

Ribosomes - protein synthesis sites

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21
Q

What is the role of the rough ER?

A

> Protein synthesis, folding and PT-modification

> “Rough” refers to the ribosome studding

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22
Q

What is the role of the smooth ER?

A

> Synthesis of new lipid

> “Smooth” means devoid of ribosomes

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23
Q

What is a GPI Anchor?

A

> A PT-modification

> A phosphate and fatty acid//polysaccharide, which is embedded in the membrane

> Attaches protein to the membrane

> Reversible modification: can be cleaved

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24
Q

What is N-Glycosylation?

A

> A PT-modification

> Type of glycosylation occurring in the ER

> Additon of an ogliosaccharide to a protein

> Occurs on specific Asp residues

> Occurs after disulphife bond formation in the ER, facitlitated by ER’s oxidising environment

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25
Q

What is the purpose of N-Glycosylation?

A

Quality control: single glucose molecules allow the lectin family of chaperones to identify and bind to proteins that aren’t folded properly (as indicated by exposed glucose molecules added by glucosyl transferases to signify this). Once the protein is correctly folded the sugar is trimmed and it can escape the ER.

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26
Q

What happens to proteins that are unable to be correctly folded?

A

The mannose trimming is like a timer; the protein folding faster than the ogliosaccharide is degraded means it will escape the ER.

An incorrectly folded protein with many glucoses on it is recognised by special lectins, and are translocated out of the ER to the proteosome for destruction.

The disulphide bonds are removed so the PP chain can get through the Protein Translocator Complex into the cytosol.

Ubiquitin machinery then targets and marks it for degredation.

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27
Q

Where on the ER membrane to newly generated phospholipids end up?

A

The cytosolic side of the ER membrane.

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28
Q

What does phospholipid synthesis require?

A

> G3P and Fatty AcylCoA are combined as the first step

> Cytosolic precursors are also required

29
Q

How are phospholipids ordered correctly on the cytosolic face of the ER membrane?

A

> Phospholipids are only added to one side of the membrane.

> Scramblase enzymes flip phospholipids to create symmetry

30
Q

How are phospholipids ordered correctly in the plasma membrane?

A

> New membrane is delivered by exocytosis

> A monolayer is formed by flippase enzymes, which flip phospholipids

31
Q

How does correctly-folded cargo leave the ER?

A

> COPII-coated vesicles form from special ER exit sites (ribosome-free).

> The Sar1 GTPase enzyme is recruited by Sar1-GEF, which is embedded in the membrane. This means active Sar1 is now embedded in the membrane.

> The Sar1 binds to a mediating protein, Sec23, which is part of a Sec23//24 complex. The Sec24 is bound to a cargo receptor which contain the cargo.

> This complex recruits Sec13//31 complexes, which form the COPII coat. This results in an inner and outer coat.

> Over time and with more recruitment, this bud invaginates and forms a free vesicle. The coat then falls off as the GTPs on the GTPases are hydolysed, and so the vesicle is able to fuse with the target membrane.

32
Q

What kinds of cargo leave the ER?

A

> Protein with an ER Exit signal

> Soluble protein with ER Exit signal which binds to cargo receptors

> Accidental Cargo: ER resident proteins (no exit signal) which will be returned to the ER

33
Q

What happens if phospholipid symmetry of a membrane is not maintained?

A

This is a mark of destruction, so phagocytes would destroy that cell.

34
Q

What is homotypic fusion?

A

Fusion of membranes from the same compartment.

35
Q

What is heterotypic fusion?

A

Fusion of membranes from different compartments.

36
Q

What is the intermediate between the ER and the Golgi?

A

The vesicular tubular cluster.

37
Q

How is the vesicular tubular cluster transported to the golgi?

A

It is attached to a motor protein which transports it via a microtubule.

38
Q

When is a COPI-coated vesicle formed?

A

For transport vesicle formation from the VTC during the retrieval pathway.

39
Q

When is a COPII-coated vesicle formed?

A

For transport vesicle formation from the ER during ER exit.

40
Q

How is a COPI-coated vesicle formed?

A

> The ARF1 GTPase enzye is recruited,

> The whole coat forms at once with the addition of a multi-protein coatomer, as opposed to sequential addition seen in COPII-coated vesicles.

> ARF proteins perfom the scission of the vesicle.

41
Q

How are ER proteins retrieved back to the ER from the VTC?

A

> ER membrane proteins have an AA sequence that enables them to bind directly to the COPI coat.

> Soluble ER proteins cannot be directly recruits, so they have a KDEL(//HDEL) sequence which binds to a KDEL(//HEDL) receptor, which can bind to the COPI coat.

42
Q

Why are the organelles in the secretory pathway sequentially more acidic, from the ER to the VTC to the Golgi?

A

> KDEL receptors need to have a higher affinity for Soluble ER Proteins the closer the VTC gets to the Golgi,

> The KDEL receptor affinity is therefore dependant on pH, so a lower pH increases its affinity,

> The KDEL receptor can then release the Soluble ER Protein once it is back in the neutral pH of the ER and its affinity is low.

43
Q

Why do new vesicles fuse with the cis Golgi network (CGN)?

A

This is the side of the Golgi that faces inward towards the ER and nucleus of the cell.

44
Q

What is the difference between a Glycosyltransferase enzyme and a Glycosidase enzyme?

A

> Glycosyltransferase ADDS sugar molecules

> Glycosidase REMOVES sugar molecules

45
Q

What are the differences between N-linked-Glycosylation and O-linked-Glycosylation?

A

> N-linked-Glycosylation links the sugar to an N on an asparagine residue;
O-linked-Glycosylation links the sugar to an O on a serine or threonine residue.

> N-linked-Glycosylation adds a whole “tree” of branching sugars at once, so it is a large modification;
O-linked-Glycosylation adds one sugar at a time, so it is a somewhat smaller modification.

> N-linked-Glycosylation occurs in both the ER and Golgi;
O-linked-Glycosylation only occurs in the Golgi.

46
Q

What are some roles of protein glycosylation in the Golgi?

A

> Marking the progress of a protein through the secretory pathway,

> Protecting against hydrolysis,

> Cell-cell recognition for adhesion,

> Modifying the cell’s antigenic//functional properties.

47
Q

How is biochemical activity segregated in the Golgi?

A

Via its five segments:

  1. Cis Golgi network
  2. Cis cisterna
  3. Medial cisterna
  4. Trans cisterna
  5. Trans Golgi network
48
Q

What are the two hypothetical models for transport through the Golgi?

A
  1. Cisternal Maturation Model - Dynamic; the VTC moves from cis to trans, maturing by gaining and losing different enzymes, and the cargo stays in the same lumen.
  2. Vesicle Transport Model - long-lived vesicles which bud and fuse to the next section. Each section maintains its complement enzymes & retrograde transport retrieves any escaped enzymes.
49
Q

What evidence is there for the first Golgi transport model, the Cisternal Maturation Model?

A

> Fluorescent labelling of Golgi enzymes resulted in Golgi stacks changing colour over time, suggesting that their enzyme complements were changing.

> Some large cargo was tracked, and was only found moving through the cisternae and not the vesicles, suggesting that the cisternae move.

50
Q

What evidence is there for the second Golgi transport model, Vesicle Transport Model?

A

> Golgi enzymes were found as cargo in COPI vesicles, which implies budding vesicles transports the cargo between sections.

> When membrane proteins were expressed in a way that caused them to aggregate and not work, the soluble cargo moved through anyway, suggesting they can bud anyway.

51
Q

What are the 3 routes a protein could take when leaving the trans Golgi network (TGN) in an ANIMAL cell?

A
  1. (DEFAULT) Constutuative Secretion - Unlabelled proteins are packaged into vesicles & fused with plasma membrane.
  2. Lysosome - Often enzymes go here to degrade things.
  3. Regulated secretion - Shall be secreted, but not yet (spatial and temporal control), only until the right signal is received.
52
Q

How are proteins targeted for transport to the Lysosome?

A

A Mannose-6-Phosphate (M6P) tag is attached, and the Phosphate residue is cleaved once the protein arrives in the lysosome so it doesn not travel back with the receptor.

53
Q

What do lysosomes contain, and what kind of pH do they have?

A

They have high content of hydrolytic enzymes.

Their pH is low, pH 5, as this is the pH at which the enzymes can function. This is a safety mechanism so that if the enzymes end up in the cytosol, they cannot degrade anything.

The pH is maintained by a H+ pump.

54
Q

How does a lysosome work?

A

> The late endosome contains enzymes and intralumental vesicles,

> The endosome fuses with a lysosome to form an endolysosome intermediate, where the contents are digested.

> When everything but the enzymes is digested, the lysosome is now formed once again.

55
Q

What are the 3 routes a protein could take when leaving the trans-Golgi network (TGN) in a PLANT cell?

A
  1. Secretion (unmarked)
  2. Lytic vacuole (NTPP sorting signal)
  3. Storage vacuole (CTPP sorting signal)
56
Q

What are some examples of regulated secretion?

A

> Hippocampal neuron

> Adrenal cell

> Histamine release

> Pancreatic β cells (insulin in response to excess glucose)

> > Regulated secretion means vesicle fusion only occurs in response to a specific signal <

57
Q

How does insulin secretion occur in a pancreatic β cell?

A
  1. When glucose circulation is high, the GLUT2 transporter moves it into the cell,
  2. The glucose is metabolised, leading to a high ration of ATP,
  3. The ATP bind to the Na/K-ATPase channels, closing it and creating a buildup of K+ ions,
  4. This creates a positive charge, and depolarisation of the membrane, which activates voltage-gated Ca channels, letting Ca flow into the cell,
  5. This Ca is the signal for the secretory vesicles to fuse to the membrane and release insulin.
58
Q

What are the five stages of neurotransmitter release?

A
  1. Docking,
  2. Priming I - interaction of SNARE complexes,
  3. Priming II - SNARE complexes pull vesicle close, and complexin blocks the SNARE bundle to act like a break, holding the vesicle in a primed state until the cell gets the final Ca signal,
  4. Fusion Pore Opening - Ca flows in and binds to its sensor protein, synaptotagmin, which causes exocytosis,
  5. Fusion complete - Synaptotagmin changes conformation and disturbs plasma membrane by inserting residues; complexin and Ca are released and the vesicle is fused.
59
Q

Describe the Synaptic Vesicle Life Cycle

A

> > Components are recycled locally in the presynapse «

  1. Vesicle is refilled by a pump with proton motor force (ATP&raquo_space; ADP)
  2. Vesicle is trafficked to terminal
  3. Vesicle is docked & primed
  4. Ca increase causes neurotransmitter release; EXOCYTOSIS occurs

> > Plasma membrane now has extra membrane, and also contains transporter proteins that need not be there «

  1. ENDOCYTOSIS (e.g. Clathrin-mediated) occurs; vesicles invaginate from membrane with help of a clathrin-coated pit
  2. GTPase (e.g. Dynamin 1) mediates vesicle scission
  3. Vesicle uncoated & the cycle begins again
60
Q

What are the steps of clathrin-mediated endocytosis?

A
  1. Nucleation
  2. Invagination
  3. Fission (by dynamin)
  4. Uncoating
61
Q

What protein regulates cargo selection in the FORMATION of a clathrin-coated vesicle (step 1)?

A

> > an AP2 tetramer «

The core σ and μ domains in the centre; μ domain binds to cargo

α and β “appendage” domains pull in the clathrin coat

62
Q

What proteins regulates cargo selection in the MEMBRANE INVAGINATION of a clathrin-coated vesicle (step 2)?

A
  1. Clathrin - 3 light and 3 heavy chains
  2. BAR domain proteins - sense membrane curvature (can somertimes mediate membrane binding.
  3. ENTH domain family
63
Q

What protein regulates cargo selection in the SCISSION of a clathrin-coated vesicle (step 3)?

A

A GTPase, specifically dynamin, coils round the neck & constricts (oligomerisation & “power stroke”)

64
Q

What protein mediates cargo selection in the UNCOATING of a clathrin-coated vesicle (step 4)?

A

HSC70 proteins break down shell, using ATP

65
Q

How are phagocytosis and pinocytosis mediated?

A

Via the formation of a continuously-polymerising actin-rich pseudopods.

66
Q

How can viruses exploit the endomembrane system?

A

They can hitch a lift or specifically stimulate many endocytic pathways, most commonly CM Endocytosis.

67
Q

What does a virus do once it is inside the cell?

A

Take over protein and DNA synthesis

Take over secretory pathway

68
Q

How are endosomes transported around the cell?

A

Via microtubule-mediated transport

69
Q

What has happened to the early lysosome when matures into the mature endosome, and why can this process only go one way?

A

> > Maturation enables it to fuse with lysosome «

> Controlled via a Rab protein cascade

> Shift features & function to that of a late endosome

  1. GTP Exchange Factor (GEF) activates first Rab, removing GDP and allowing GTP to bind.
  2. Rab can now bind to effectors, activating fuctions in that organelle that shift endosome identity. It also now recruits the GEF for the next Rab in the cascade.
  3. The next Rab is activated, activatiting functions and recruiting the next GEF, but it also recruits a GTPase Activating Protein (GAP) for the first Rab protein, which stimulates hydrolysis of the first Rab, turning it off.

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