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Eukaryotic Cell Biology > Chapter 13 > Flashcards

Chapter 13 Flashcards

1
Q

What is vesicular transport?

A

The exchange of components between membrane compartments by the budding of transport vesicles from a donor compartment followed by fusion of the vesicle to the target compartment

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2
Q

Vesicular transport is the exchange of components between membrane compartments by the budding of transport vesicles from a donor compartment followed by what?

A

Fusion of the vesicle to the target compartment

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3
Q

Identify A and B

A

A: Donor compartment B: Target compartment

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4
Q

In eukaryotes, transport along the secretory and endocytic pathways occur by what?

A

The fusion of topologically equivalent membrane bound compartments

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5
Q

This flow of material between topologically equivalent membrane compartments is highly what? (3 answers)

A

Organized, balanced, and directional

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6
Q

The flow of material between topologically equivalent membrane compartments allows for what? (3 answers)

A
  1. The secretion of select proteins, 2. The uptake of extracellular material 3. The remodeling of the plasma membrane
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7
Q

The secretory pathway (red arrows) includes the outward movement of material from what? (3 answers)

A
  1. The ER to the Golgi 2. The Golgi to the plasma membrane 3. The Golgi to the lysosome
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8
Q

The endocytic pathway (green arrows) is uptake of what? Their fusion with what?

A

The uptake of plasma membrane material and their fusion with the lysosome

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9
Q

The retrieval pathway is what?

A

The movement from the plasma membrane to the Golgi and from the Golgi to the ER

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10
Q

Formation of transport vesicles requires a what? where?

A

A specialized ‘protein coat’ on the outside of the membrane vesicle

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11
Q

The specialized ‘protein coat’ perform what two main functions?

A
  1. Selects the membrane proteins required for transport 2. Generates the shape of the vesicle by influencing the curvature of the membrane
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12
Q

What is flat and stiff due to its cholesterol rich composition and its attachment to the underlying cytoskeleton?

A

The plasma membrane

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13
Q

For the plasma membrane, what are essential for the generation of the force required to introduce membrane curvature?

A

Coat proteins

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14
Q

What based vesicle formation is less dependent on coat-proteins for membrane curvature as vesicles form at curved regions of the membrane?

A

Golgi based

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15
Q

For the Golgi, coat proteins are primarily used for what?

A

Cargo selection

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16
Q

What are the 3 major types of coated vesicles distinguished by their coat proteins?

A
  1. Clathrin-coated vesicles 2. COPI-coated vesicles 3. COPII coats
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17
Q

What vesicles were the first identified and the best characterized coat type?

A

Clathrin-coated vesicles

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18
Q

What vesicles form on buds that exit from the Golgi

A

COPI-coated vesicles

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19
Q

Vesicles form at the plasma membrane and are ssential for endocytosis?

A

Clathrin-coated vesicles

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20
Q

What form on vesicles leaving the ER

A

COPII coats

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21
Q

Identify pathway A (in green):

A

Clathrin

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22
Q

Identify pathway B (in blue):

A

COPI

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23
Q

Identify pathway C (in red):

A

COPII

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24
Q

The formation of transport vesicles are mediated by the formation of what? where?

A

A specialized ‘protein coat’ on the cytosolic side of the membrane vesicle.

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25
Q

Specialized ‘protein coats’ on the cytosolic side of the membrane vesicle perform what two main functions?

A
  1. Select the membrane proteins required for transport 2. Generate the shape of the vesicle by influencing the curvature of the membrane
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26
Q

In general, there are 3 types of coated vesicles which are distinguished by their coat proteins with each type of coat being used for what?

A

Different transport steps

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27
Q

What kind of transport do clathrin-coated vesicles perform?

A

Plasma membrane mediated endocytosis

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28
Q

Where do COPI coated vesicles exit from?

A

They exit from the Golgi cisternae

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29
Q

Where do COPII coated vesicles exit from?

A

They exit from the ER

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30
Q

In general, coat formation requires what four things?

A
  1. Coat-recruitment GTPases 2. Adaptor proteins 3. Cargo receptors4. Coat proteins
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31
Q

What are monomeric GTPases that are responsible for the recruitment of coat proteins to the membrane surface for vesicle formation?

A

Coat-recruitment GTPases

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32
Q

What links the coat proteins to the vesicle membrane and interacts with cargo receptors.

A

Adaptor proteins

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33
Q

Not all coated vesicles have adaptor proteins as some cargo may directly bind to what?

A

Coat proteins

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34
Q

What are transmembrane proteins that capture specific soluble cargo for packaging into the vesicle?

A

Cargo receptors

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35
Q

What are proteins that form a cage-like structure over the vesicle to promote membrane curvature and bud formation?

A

Coat proteins

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36
Q

Give the four steps of protein coating

A
  1. Coat assembly and cargo selection 2. Bud formation 3. Vesicle formation 4. Uncoating
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37
Q

Give the steps in the formation of COPII coated vesicles

A
  1. Coat-recruitment GTPases 2. Recruitment of adaptor proteins 3. Recruitment of cargo 4. Assembly of coat proteins vesicle budding
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38
Q

What are found at high concentrations in the cytosol in an inactive GDP-bound form (Sar1-GDP)?

A

Coat-recruitment GTPases

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39
Q

When coat-recruitment GTPases interact with a specific membrane bound guanine exchange factor (GEF), their bound GDP is replaced with what?

A

GTP

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40
Q

Upon binding GTP, what undergoes a conformational change that exposes its amphiphilic helix leading to insertion into the outer leaflet of the ER membrane?

A

Sar1

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41
Q

The mechanism of activation and membrane tethering is common for what?

A

Other coat-recruitment GTPases.

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42
Q

What are coat-recruitment GTPases?

A
  1. They members of the monomeric GTPases 2. Their activity is regulated by the state of the guanine nucleotide bound 3. They are similar to Ran-GTP and nuclear transport
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43
Q

Give the steps for protein binding to ER using GTPases

A
  1. SAR-GDP - The GDP is replaced with GTP by Sar1-GEF 2. Sar1 undergoes conformational change that exposes it’s alpha helix 3. It is inserted into outer leaflet of ER membrane
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44
Q

When the coat recruitment protein associates with the membrane it recruits what molecules to the ER membrane?

A

Adaptor molecules

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45
Q

The adaptor molecules bind to what?

A

The carboxy terminal tail domain of select transmembrane “receptor” proteins

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46
Q

Proteins bound to these transmembrane receptors are selected as the what?

A

Vesicle cargo

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47
Q

GTP- and membrane-bound Sar1 recruits what two adaptor molecules to the membrane?

A

The Sec23 and Sec24 adaptor molecules

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48
Q

Which adaptor molecule (Sec23 or Sec24) has affinity for the C-terminal tails of receptor proteins and is therefore tethered to the vesicle cargo.

A

Sec24

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49
Q

Which adaptor molecule (Sec23 or Sec24) can bind to multiple receptors? How many of them?

A

Sec24, one

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50
Q

Identify 1 - 5

A

1: Sec24 2: Sec23 3. Sar1-GTP 4. Cargo receptor 5. Cargo

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51
Q

What two coat proteins assemble to form the outer shell of the coat?

A

Sec13 and Sec31

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52
Q

The subsequent recruitment of additional adaptor proteins and outer coat proteins by membrane-bound GTP-Sar1 promotes

A

Membrane deformation and vesicle formation.

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53
Q

Once in the cytosol, hydrolysis loss of GTP by Sar1 results in what? (2 answers)

A

The disassembly of the coat-adaptor complex and generation of a naked vesicle.

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54
Q

It is thought that Sar1 has a slow rate of GTP hydrolysis. What is it that influences coat disassembly?

A

Time

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55
Q

What kind of vesicles form only if bud formation occurs faster than Sar1 GTP hydrolysis?

A

Fully formed vesicles

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56
Q

What are the molecular players in COPII coat formation?

A
  1. Coat recruitment GTPase: (Sar1) 2. Adaptor proteins: (Sec23 and 24) (dimer) 3. Coat protein: (Sec13 and 31) (tetramer) 4. Cargo receptors: (Select transmembrane domain proteins)
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57
Q

Formation of COP1 coated vesicles utilizes what components? (3 answers)

A
  1. Coat recruitment proteins 2. Adaptors 3. Cargo receptors
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58
Q

What does ARF mean?

A

ADP-ribosylation factor

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59
Q

ARF, or ADP-ribosylation factor, is used as the what?

A

The coat recruitment protein

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60
Q

What is the first step of the formation of COI vesicles?

A

ARF is recruited to the membrane through the exchange of its bound GDP for GTP through a membrane bound GEF

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61
Q

What is the second step of the formation of COI vesicles?

A

Binding of GTP induces a conformational change that triggers membrane insertion

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62
Q

What is the third step of the formation of COI vesicles?

A

Membrane bound ARF recruits coat proteins for coat formation and adaptors for cargo selection

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63
Q

What is the last step of the formatin of COI vesicles?

A

Assembly of sufficient coat proteins results in vesicle formation. GTP hydrolysis of ARF leads to coat disassembly in the cytosol

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64
Q

What are the molecular players in clathrin coat formation:

A
  1. Coat recruitment: (GTPase ARF1) 2. Adaptor proteins: (20 different adaptor proteins) (AP) 3. _-arrestin 4. Coat protein: (Clathrin complex) 5. Cargo receptors: (Transmembrane proteins)
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65
Q

Coat recruitment GTPase ARF1 is involved in the formation of what two kinds of coats?

A

COPI and clathrin coats

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66
Q

COPI and clathrin vesicles utilize a common coat recruitment GTPase. How do they differ?

A

1.Their use of adaptor proteins, cargo receptors, and coat proteins. 2. They form on distinctly different membrane surfaces. 3. The final membrane ‘pinching off’ process requires an additional protein factor

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67
Q

What kind of vesicles were the first transport vesicles identified and hence, the best characterized?

A

Clathrin-coated vesicles

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68
Q

Clathrin-coated vesicles are involved in what? (2 answers)

A
  1. The endocytosis of transmembrane receptors 2. The delivery of lysosomal hydrolases from the TGN to the lysosome.
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69
Q

What does TGN mean?

A

Trans Golgi Network

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70
Q

Clathrin-coated vesicles are composed of what?

A

Clathrin

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71
Q

Each subunit contains three large and three small polypeptide subunits arranged in a three-legged structure called a what?

A

Triskelion

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72
Q

Clathrin triskelons assemble into a cage-like structure that promotes the formation of what?

A

Membrane vesicles

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73
Q

The last step in the formation of an internalized clathrin-coated vesicle requires a membrane tethered GTPase called what?

A

Dynamin

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74
Q

What kind of structure does dynamin assemble into around the neck of a forming bud?

A

A ring-like structure

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75
Q

Activation of dynamin and its associated proteins, leads to what two events?

A
  1. The ‘pinching off’ of the vesicle 2. Release into the cytosol.
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76
Q

In the cytosol the coat is released through the activity of what multiple proteins?

A
  1. HSC70, 2. cytosolic Hsp70 chaperone, 3. Auxillin, 4. A PIP phosphatase enzyme whose activity weakens the binding of the adaptor proteins to the membrane
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77
Q

What is essential for the formation of completely endocytosed vesicles?

A

Functional dynamin

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78
Q

What is X?

A

Dynamin

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79
Q

Because of a mutation in dyamin in the nerve cells of the fruit fly, Drosophila, the clathrin vesicles fail to release. This failure causes an accumulation of clathrin vesicles and leads to what?

A

Paralysis due to a failure in synaptic vesicle recycling.

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80
Q

What are available that are capable of interacting with a single coat protein?

A

Multiple adapter proteins

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81
Q

Even a single coat type can carry many different cargos depending on what? (2 answers)

A

The adaptor and the site of vesicle formation

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82
Q

What is another membrane vesicle type that assembles on endosomes. It is involved in the retrieval of endosomal proteins back to the trans-Golgi network and is dedicated to a specific cargo: transmembrane receptors like the mannose 6-phosphate receptor?

A

Retromer

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83
Q

Retromer formation occurs on endosomal membranes only when what three conditions have been met?

A
  1. It is bound to the cytoplasmic tails of specific cargo receptors, 2. It directly interacts with a curved phospholipid bilayer, and 3. It binds to the endosomal marker, phosphoinositide (PI(3)P)
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84
Q

Retromer formation can therefore only occur when and where?

A

At a defined time and on a defined membrane

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85
Q

Give some examples of retromers?

A
  1. Vps29 2. Vps35 (cargo binding) 3. Vps26 4. Snx1 (PI(3)P binding)
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86
Q

What cargo does retromer coat proteins cover?

A

Transmembrane proteins

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87
Q

What can undergo cycles of phosphorylation and dephosphorylation?

A

Sugar heads

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88
Q

Different organelles in the secretory pathway contain distinct sets of what due to the unique localization of PIP kinases and PIP phosphatases?

A

Phosphoinositides

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89
Q

Many of the proteins involved in vesicular transport recognize different what?

A

PIP species

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90
Q

Differential PIP pattern establishes a highly controlled flow of what?

A

Vesicular trafficking

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91
Q

What proteins are monomeric GTPases associated with the membranous organelles of the secretory pathway. They are selectively distributed to different organelles and act as guides for vesicular transport?

A

Rab proteins

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92
Q

Rab cycles between what two forms based on the status of their guanine nucleotide?

A

Cytosolic and membrane bound

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93
Q

When bound to GDP, Rab is what?

A

Inactive and cytosolic.

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94
Q

When bound to GTP, Rab is what?

A

Active and tightly associated with membrane.

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95
Q

What kind of Rab is found on both transport vesicles and target membrane.

A

Activated Rab

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96
Q

The specificity of vesicle-membrane fusion is controlled by what? Found where?

A

Protein markers found on the surface of the vesicle

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97
Q

Protein markers on the surface of the vesicle are recognized by specific receptors found only These markers are recognized by specific receptors found only where?

A

On the Correct target membrane

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98
Q

Rab proteins are example factors that act as what?

A

Surface markers

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99
Q

Monomeric GTPases cycle between cytosolic and membrane bound forms depending on what?

A

The guanine nucleotide bound

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100
Q

In the cytosol (membrane free), Rab is in a what form?

A

A GDP bound form

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101
Q

When activated by a membrane bound Rab-specific GEF, Rab exchanges GDP for what and becomes tightly bound to the what?

A

GTP, membrane

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102
Q

Membrane bound GTP-Rab recruits additional proteins called “what” to facilitate membrane tethering and fusion between the transport vesicles and target membrane?

A

Rab effectors

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103
Q

Membrane bound GTP-Rab recruits additional proteins called “what” to facilitate what? (2 answers)

A

Membrane tethering and fusion between the transport vesicles and target membrane

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104
Q

Individual Rab proteins can interact with multiple “Rab effectors” providing additional layers of what?

A

System flexibility.

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105
Q

Once a vesicle has been tethered to a target membrane by a Rab effector protein, what happens next?

A

The two lipid bilayers must be brought in close proximity to facilitate fusion and vesicle unloading.

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106
Q

A fusion event is mediated by another group of proteins called what?

A

SNAREs.

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107
Q

Give the steps of Rab mediated vesicle capture:

A
  1. Tethering 2. Docking 3. Fusion
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108
Q

What proteins are membrane bound proteins that mediate the fusion of transport vesicles with their target organelle?

A

SNARE proteins

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109
Q

What does SNARE stand for?

A

Soluble NSF Attachment Receptor

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110
Q

There are over 60 different SNARE proteins that are generally broken down into what two complementary sets:

A
  1. v-SNARE (vesicle) 2. t-SNARE (target)
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111
Q

Where are v-SNARE proteins found?

A

On transport vesicles

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112
Q

Where are t-SNARE proteins found?

A

On target compartments

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113
Q

SNAREs have what two important roles:

A
  1. They provide specificity to the transport process by ensuring that only correctly targeted vesicles fuse to a membrane, 2. They catalyze the membrane fusion reaction between vesicle and target.
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114
Q

The nomenclature of v-SNARE and t-SNAREs has become obsolete as more and more what proteins have been identified?

A

SNARE

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115
Q

Which SNARE (v-SNARE or t-SNARE) are single polypeptide chains and always a transmembrane protein?

A

v-SNARE

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116
Q

Which SNARE (v-SNARE or t-SNARE) has two to three polypeptide chains; one of which is always a transmembrane protein; they others may, or may not, be transmembrane proteins.

A

t-SNARE

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117
Q

v-SNARE association with t-SNARE forms a what?

A

4-_-helix bundle

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118
Q

The 4-_-helix bundle is so stable that even elevated temperatures and strong detergents are unable to do what to them?

A

Pry them apart

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119
Q

The availability of SNAREs for membrane fusion are regulated by what?

A

Rab proteins.

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120
Q

t-SNAREs in target membranes are often associated with inhibitory proteins that must be released prior to their interaction with what?

A

v-SNAREs

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121
Q

Rab proteins and their effector proteins control what?

A

The release of these inhibitory proteins and ultimately membrane fusion.

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122
Q

Identify A, B and C

A

A: v-SNARE (synaptobrevin) B: t-SNARE (Snap25) C: t-SNARE (syntaxin)

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123
Q

Intertwined SNARE complexes catalyze membrane fusion using the energy released when the _-helices do what? Excluding any what?

A

Wrap around each other to pull the two membranes together excluding any water.

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124
Q

In close contact, the outer lipid bilayer will fuse first, followed by what fusion?

A

Inner bilayer fusion

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125
Q

Give the steps of SNARE mediated vesicle membrane fusion:

A
  1. Water is released 2. Stalk formation 3. Hemifusion 4. Fusion
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126
Q

The interaction between v- and t-SNARE proteins is very strong, so strong that the complex needs to be physically pried apart after what?

A

Membrane fusion.

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127
Q

What use the energy of ATP hydrolysis to unravel the SNARE complex to prepare them for the next round of fusion?

A

The cytsolic proteins, NSF and SNAP

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128
Q

What does NSF stand for?

A

N-ethylmaleimide-sensitive factor

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129
Q

What does SNAP stand for?

A

Soluble NSF attachment protein

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130
Q

Proteins destined for organelles in the secretory pathway include what organelles?

A

The ER, the Golgi, the lysosome, the plasma membrane or proteins destined for secretion from the cell

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131
Q

Proteins start by co-translational transport into the ER through the what?

A

Sec61 membrane transport channel

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132
Q

In the ER, these proteins move along in the pathway by what?

A

Vesicle mediated transport

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133
Q

Proteins imported into the ER are processed how?

A

Amino terminal signal removed, modified by glycosylation, and correctly folded

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134
Q

Only proteins that are correctly folded ER can do what?

A

Leave the ER

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135
Q

What system ensures that only folded proteins are selectes as cargo for incorporation into transport vesicles?

A

The calreticulin/calnexin chaperone system

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136
Q

Proteins targeted to the Golgi or later organelles in the secretory pathway will leave the ER in what vesicles?

A

COPII coated vesicles.

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137
Q

Vesicles bud from specialized sites on the ER that lack ribosomes called what?

A

Transitional ER or ER exit sites

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138
Q

Cargo selection is an active one; soluble proteins contain amino acids sequences that are recognized by what? Function as what?

A

Transmembrane proteins that function as receptors for COPII transport.

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139
Q

Proteins that are found at high concentrations can also get packaged in what? Without what?

A

Transport vesicles without selection

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140
Q

Proteins intended as ER resident proteins can be mistakenly incorporated into what?

A

Transit vesicles

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141
Q

These accidental passengers are returned to the ER through the what?

A

The ‘retreival’ pathway

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142
Q

Identify A - D

A

A: Forming ER transport vesicle

B: Sar1-GTP

C: Subunits of COPII coat

D: Chaperone proteins (bound to folded or misfolded proteins)

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143
Q

In addition to the calreticulun/calnexin monitoring system, unassembled proteins can be retained in the ER by what?

A

The ER lumenal chaperone BiP

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144
Q

How is an IgG antibody composed/assembled/transported in the ER?

A
  1. It is composed of two large heavy chain polypeptides (dark green) and two smaller light chain molecules (light green) 2. Only when the protein is fully assembled can it exit the ER through transport vesicles
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145
Q

What binds to ER export signals preventing their recruitment into budding vesicles?

A

BiP

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146
Q

When assembled ,the BiP is released exposing the ER export signal promoting transport to the what?

A

Golgi

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147
Q

Quality-control steps place pretty strict rules on the continued movement of proteins through the what?

A

The secretory pathway

148
Q

For some proteins, what percentage of the protein synthesized never makes it past this checkpoint and are degraded

A

90%

149
Q

The stringent monitoring system can have a significant downside; Name one resulting illness?

A

Cystic fibrosis

150
Q

Many of cystic fibrosis patients have a deletion in the gene that codes the what?

A

The plasma membrane channel, CFTR

151
Q

CFTR encodes what?

A

A 12 transmembrane domain chloride channel

152
Q

CFTR localizes where?

A

The plasma membrane of epithelial cells

153
Q

CFTR maturation is very inefficient; only what percentage of the WT protein passes ER quality control?

A

25%

154
Q

Mutant CFTR protein is significantly slowed in folding and never leaves the what? Is targeted for what?

A

The ER and is targeted for degradation

155
Q

Mutated CFTR protein can function as a what channel if it made it to the plasma membrane, but because it takes too long to fold in the ER it never makes it out of this organelle

A

Chloride channel

156
Q

Soon after budding from tER sites, COPII coats are disassembled from the vesicles and they begin to fuse, in a SNARE dependent manner, to form a “Pre-Golgi” compartment called the what?

A

Vesicular tubular cluster

157
Q

Vesicular tubular clusters are not ‘true’ ER or Golgi as they lack what?

A

The required processing enzymes of these compartments.

158
Q

What proteins, moving along microtubule tracks, transports this ‘enlarged’ vesicle to the cis Golgi network to deliver the enclosed cargo.

A

Motor proteins

159
Q

Shortly after generation, vesicles bud off of the vesicular tubular cluster in a COPI dependent manner to return material to the ER by the what?

A

Retrieval pathway

160
Q

Material returned to the ER include what?

A
  1. ER resident proteins that were accidentally packaged into transport vesicles, 2. Cargo receptors that participated in the selection of cargo for transport
161
Q

Identify A-D

A

A: COPII coat

B: Motor protein

C: Vesicular tubular cluster

D: COPI coat

162
Q

The retrieval pathway is a what kind of process?

A

A signal sequence dependent process

163
Q

ER proteins that accidentally get packaged can be selected for transport where?

A

Back to the ER

164
Q

ER retrieval signals for membrane proteins consists of a highly conserved what sequence located within their carboxy terminus?

A

KKXX (Di-lysine motif)

165
Q

Soluble proteins contain what sequence?

A

The conserved KDEL amino acid sequence

166
Q

For soluble proteins, the KDEL sequence directs its interaction with what?

A

Membrane bound KDEL receptor proteins

167
Q

Both di-lysine motif containing transmembrane proteins and KDEL containing soluble proteins bound to KDEL receptors are packaged into what? For their retrograde transport where?

A

COPI coated vesicles for their retrograde transport back to the ER

168
Q

Not all proteins returned to the ER contain what kind of signal?

A

Retrieval signal

169
Q

The presence of a retrieval signal increases the efficiency of what?

A

Retrograde transport

170
Q

Identify A and B

A

A: COPII coat B: COPI coat

171
Q

Identify 1, 2 and 3

A
  1. cis Golgi network
  2. Golgi stack
  3. trans Golgi network
172
Q

Identify 1, 2 and 3

A
  1. KDEL
  2. Empty KDEL receptor
  3. COPI coat
173
Q

Proteins destined for the Golgi enter the stacks from what face?

A

The cis face

174
Q

What face in the Golgi is closest to the nucleus?

A

The cis face

175
Q

In what kind of cells, the Golgi is a single complex composed of many stacks?

A

Mammalian cells

176
Q

In what kind of cells, the Golgi are often many stacked complexes throughout the cytoplasm

A

Plant cells

177
Q

Proteins that enter the cis side of the Golgi move forward into the what or are returned to the what by the retrieval pathway?

A

Forward: Golgi network Return: ER

178
Q

Identify the five functional domains of the Golgi (A-E):

A

A: cis Golgi network (CGN)

B: cis cisterna

C: medial cisterna

D: trans cisterna

E: trans Golgi network (TGN)

179
Q

Identify the two faces of the Golgi (1 and 2):

A
  1. cis face
  2. trans face
180
Q

At the trans face of the Golgi, where can the proteins go?

A

They can be returned to an earlier compartment or moved along to the next destination

181
Q

If the proteins leave the trans face of the Golgi, where can they go?

A

Lysosomes, secretory vesicles, or the plasma membrane

182
Q

What are organized stacks of distinct biochemical compartments responsible for the successive modification and sorting of proteins as they move from the cis to the trans cisternae?

A

The Golgi

183
Q

The Golgi are organized stacks of distinct biochemical compartments responsible for what as they move from the cis to the trans cisternae?

A

The successive modification and sorting of proteins

184
Q

The spatial and biochemical compartmentalization of the Golgi is not absolutely necessary since each processing enzyme can only accept what as a substrate after it has been properly processed by the proceeding enzyme?

A

A glycoprotein

185
Q

Each compartment of the Golgi has a unique role in modifying the what that pass through the Golgi stacks?

A

The proteins

186
Q

Spatial distribution in the Golgi of each enzyme establishes an ‘ordering’ component to these post translational modifications with processing occuring in a stepwise manner in what direction?

A

Cis to trans direction

187
Q

What kind of modifications happen in the cis Golgi network?

A

Phosphorylation of oligosaccharides on lysosomal proteins

188
Q

What kind of modifications happen in the cis cisterna?

A

Removal of Man (mannose)

189
Q

What kind of modifications happen in the medial cisterna?

A

Removal of Man (mannose) and addition of GlcNAc (N-Acetylglucosamine)

190
Q

What kind of modifications happen in the trans cisterna?

A

Addition of Gal (galactose) and NANA (N-acetylneuraminic acid)

191
Q

What kind of modifications happen in the trans Golgi network?

A

Sulfation of tyrosines and carbohydrates

192
Q

What kind of sugar moiety gets added to substrate proteins in the ER?

A

An N-linked sugar moiety

193
Q

A 14 sugar oligosaccharide is initially trimmed in the ER and further modified where? What is removed and added?

A

In the Golgi with sugars removed and added

194
Q

The Golgi is also responsible for what? It is the addition of sugars to serine and threonine residues

A

O-linked glycosylation

195
Q

What is removed in step 1?

A
  1. Glucosidase I 2. Glucosidase I (two of them) 3. ER Mannosidase
196
Q

What is removed in step 2?

A

Golgi Mannosidase I (three of them)

197
Q

What is added in step 3?

A

N-acetylglucosamine transferase I

198
Q

What is removed in step 4?

A

Golgi Mannosidase II (two of them)

199
Q

What is added in step 5? What is the end result?

A
  1. N-acetylglucosamine 2. 5 UDP 3. 3 CMP Complex oligosaccharide
200
Q

The enzymes responsible for N-linked gylcosylation are found in the ER and the process utilizes what kind of enzymes?

A

Both soluble and membrane bound enzymes

201
Q

The enzymes responsible for O-linked addition are found in the Golgi and the process utilizes what kind of enzymes?

A

Only membrane bound enzymes

202
Q

All Golgi resident proteins are what kind of proteins?

A

Single-pass transmembrane proteins

203
Q

Which modification (N-linked or O-linked) occurs en bloc; the 14 sugar moiety is added in one step to a protein substrate?

A

N-linked

204
Q

Which modification (N-linked or O-linked) is through the addition of one sugar molecule at a time?

A

O-linked

205
Q

N-linked addition is through the amino group of a what?

A

An asparagine

206
Q

O-linked modification occurs on the hydroxyl residue of what?

A

Serine and threonine

207
Q

What kind of glycosylation is A (N-linked or O-linked)?

A

N-linked (N-linked addition is through the amino group of an asparagine)

208
Q

What kind of glycosylation is B (N-linked or O-linked)?

A

O-linked (O-linked modification occurs on the hydroxyl residue of serine and threonine)

209
Q

What are the two prevailing models for how the Golgi is able to maintain its polarized structure and how proteins are moved from one cisterna to another?

A
  1. Vesicular Transport Model 2. Cisternal Maturation Model
210
Q

The vesicular transport model states that the Golgi cisterna are what?

A

Stable membrane compartments with their associated membrane-bound enzymes

211
Q

The vesicular transport model states that proteins move through these stacks in sequence in what direction? What are the proteins carried by?

A

From the cis to the trans and are carried by transport vesicles

212
Q

According to the vesicular transport model, the forward movement through the stacks (red arrows) is mediated by what?

A

COPI coated vesicles

213
Q

(Vesicular transport model) The selection of cargo at different points along the pathway is facilitated by the use of different what?

A

Adaptor proteins

214
Q

(Vesicular transport model) What pathway is responsible for the return of escaped and recycled proteins back to the ER

A

The retrieval pathway

215
Q

According to the Cisternal maturation model, The Golgi stacks are what? What moves? What direction?

A

Dynamic such that the Golgi stacks migrate from the cis to the trans face of the apparatus

216
Q

(Cisternal maturation model) Vesicular tubular clusters fuse to become the what?

A

cis Golgi network

217
Q

(Cisternal maturation model) Each stack progressively matures to become the next compartment such that the secretory vesicles that leave the ER eventually mature to become the what?

A

trans Golgi network.

218
Q

(Cisternal maturation model) Everything moves forward as the what matures?

A

Cisternae

219
Q

(Cisternal maturation model) The flow of material in what direction has a significant role in maintaining Golgi function?

A

Retrograde

220
Q

(Cisternal maturation model) The COPI based retrograde traffic is essential for what?

A

The collection and return of enzymes back to earlier stacks where they function

221
Q

The two models are not mutually exclusive and it is likely that transport occurs in what way?

A

Through a combination of both pathways

222
Q

What transport model is this (vesicular or cisternal maturation)?

A

Vesicular transport

223
Q

What transport model is this (vesicular or cisternal maturation)?

A

Cisternal maturation model

224
Q

What membrane bound organelle is involved in intracellular digestion?

A

Lysosome

225
Q

The lysosome contains >40 acid what which are active only at acidic pH?

A

Hydrolases

226
Q

Besides the hydrolases, the lysosome contains what?

A

Lipases, nucleases, phosphatases, and glycosidases

227
Q

The membrane proteins of the lysosome are highly what?

A

Glycosylated

228
Q

The low pH of the lysosome is maintained by the what which pumps protons into the organelle?

A

Vacuolar H+ ATPase

229
Q

What is used to drive transport of small metabolites out of the lysosome?

A

Generated membrane potential

230
Q

The end-products of digested macromolecules (amino acids, sugar, nucleotides) are exported from the what? Into the what? For what purpose?

A

From the lysosome and into the cytosol for recycling

231
Q

The acid proteases in the lysosome require low pH for activity; Would they be active if they were to escape into the cytosol ?

A

No

232
Q

What are highly glycosylated which protects them from digestion by lysosomal proteases?

A

Lysosomal membrane proteins

233
Q

What generates a membrane potential which used to drive the transport of metabolites out of the lysosome?

A

The proton gradient

234
Q

The membrane potential facilitates the export of what?

A

End-products

235
Q

The lysosome has how many membranes?

A

One

236
Q

The lysosome is found in what kind of organisms?

A

All eukaryotes

237
Q

How are lysosomes generated?

A

They are generated from the Golgi apparatus as well as material by endocytosis from the plasma membrane

238
Q

The vacuole takes up to how much volume in a plant cell?

A

30%

239
Q

What are the functions of a vacuole? (4 answers)

A
  1. Storage of nutrients and waste products 2. Maintains cytosolic pH through regulation of H+ flux 3. Controls turgur pressure
240
Q

What does a vacuole contain?

A

It contains hydrolytic enzymes

241
Q

Material degraded by lysosomes are acquired from what 3 sources?

A
  1. Phagocytosis 2. Endocytosis 3. Autophagy
242
Q

What is the uptake of large extracellular molecules/microbes?

A

Phagocytosis

243
Q

What is the internalization of plasma membrane proteins?

A

Endocytosis

244
Q

What is the disposal of old intracellular organelles or microbes?

A

Autophagy

245
Q

The hydrolytic enzymes responsible for the degradation of these materials are provided by what?

A

Vesicular transport from the ER-Golgi based secretory pathway

246
Q

Which route (A, B or C) shows endocytosis?

A

B

247
Q

Which route (A, B or C) shows autophagy?

A

C

248
Q

Give the steps that lysosomal proteins take from translation to the ER?

A

1.Translation on cytosolic ribosomes 2. SRP recognition and co-translational transport into the ER via the Sec61 channel

249
Q

While in the ER, what happens to the lysosomal proteins?

A

They are modified by N-linked oligosaccharide addition

250
Q

Where and by what are lysosomal proteins transported out of the ER?

A

Into the cis Golgi network by COPII coated vesicles

251
Q

In the cis Golgi, what is added to the lysosomal proteins? By what?

A

N-acetyl glucosamine (GluNac) is added to the mannose residue of the N-linked oligosaccharide by N-acetyl glucosamine phosphotransferase

252
Q

In the trans Golgi, the N-acetyl glucosamine is removed from the lysosomal protein to generate what?

A

Mannose 6-phosphate (M6P)

253
Q

Mannose 6-phosphate modified proteins are recognized by transmembrane receptors which in turn are recognized by what? For assembly into what?

A

Adaptor proteins for assembly into clathrin-coated vesicles

254
Q

Clathrin-coated vesicles bud from what?

A

trans Golgi Network

255
Q

Coat proteins are lost upon hydrolysis of what?

A

GTP bound ARF

256
Q

Uncoated vesicles fuse with the what?

A

The early endosome

257
Q

The low pH of the pre-lysosomal compartment (pH 6.0) leads to what?

A

The disassociation of the M6P receptor and its cargo.

258
Q

The empty receptors are recycled back to the what?

A

trans Golgi Network

259
Q

At the lower pH the phosphate group on the mannose sugar is hydrolyzed which prevents what?

A

Tts recycling back to the Trnas Golgi Network with the receptor.

260
Q

Early endosomes then deliver their contents to what?

A

Lysosomes

261
Q

pH influences what binding?

A

M6P receptor-cargo binding

262
Q

At pH 6.5-6.7, the pH of the TGN, M6P receptors bind or release cargo?

A

Bind cargo

263
Q

M6P binds or releases cargo at more acidic pH?

A

Releases cargo

264
Q

Give the steps in the targeting pathway for lysosomal proteins?

A
  1. Addition of P-GlcNac
  2. Uncovering of the M6P signal
  3. Binding to M6P receptor
  4. Receptor-Dependent transport
  5. Dissociation at acidic pH
  6. Removal of phosphate
  7. Receptor recycling
265
Q

The mannose-6-phosphate tag acts as a marker for what?

A

Lysosomal targeting

266
Q

Since mannose-6-phosphate is added to an N-linked oligosaccharide with a terminal mannose residue and all glycoproteins leaving the ER contain this carbohydrate modification, the Golgi enzymes responsible for mannose-6-phosphate addition must recognize something in addition to the oligosaccharide. What contributes to their recognition?

A

A specific cluster of neighboring amino acids on the surface of a target protein(signal patch)

267
Q

The N-acetyl glucosamine phosphotransferase enzyme contains what two functional sites:?

A
  1. One responsible for recognizing the surface ‘signal patch’ 2. A second site that binds UDP-GluNac and the N-linked oligosaccharide
268
Q

After the transfer of GluNAc phosphate to the mannose residue a second enzyme catalyzes the removal of what? To generate what?

A

The removal of N-acetylglucosamine to generate mannose 6-phosphate

269
Q

What is the process by which cells take up extracellular macromolecules

A

Endocytosis

270
Q

The two main types of endocytosis differ according what?

A

The size of the vesicles formed during the uptake process

271
Q

What are the two types of endocytosis?

A
  1. Phagocytosis 2. Pinocytosis
272
Q

What is the uptake of large molecules such as microorganisms and dead cells?

A

Phagocytosis (cell eating)

273
Q

In what kind of organisms, this process supplies nutients and is viewed as a mode of ‘feeding’?

A

In protozoans

274
Q

In what kind of organisms, phagocytosis is carried out by specialized cells such as macrophages and neutrophils

A

Mammalian cells

275
Q

To be phagocytosed, the material to be ingested must be recognized by what?

A

Surface receptors

276
Q

Once recognized by surface receptors, binding triggers pseudopod formation through what?

A

Actin polymerization and re-organization

277
Q

To complete engulfment, the actin network at the base of the pseudopod is depolymerized by the activity of a PI-3 kinase that converts PI(4,5)P2 to what which promotes actin reorganization?

A

PI(3,4,5)P3

278
Q

This is phagocytosis. What is X and Y?

A

X: PI(4,5)P2 Y: PI (3,4,5)P3

279
Q

What kind of endocytosis is carried out by all eukaryotes and is a continual process used for the ingestion of fluid and solutes?

A

Pinocytosis

280
Q

What varies by cell type but can range as high as 3% of its plasma membrane/minute?

A

Rate of membrane internalization

281
Q

What is mediated by clathrin-coated vesicles

A

Pinocytosis

282
Q

To ensure no change in cell size endocytosis is balanced by what?

A

Exocytosis

283
Q

Extracellular fluid internalized by this process is called what?

A

Fluid-phased endocytosis

284
Q

What is the specific uptake of molecules from the extracellular fluid by clathrin coated pits?

A

Receptor mediated endocytosis

285
Q

Extracellular molecules bind to transmembrane receptors and accumulate in coated pits for entry into the cell by what?

A

Clathrin-coated vesicles

286
Q

Receptor binding allows for the efficient concentration of ligands to ensure that even minor components in the extracellular fluid are what?

A

Endocytosed

287
Q

>25 receptors may participate in receptor mediated endocytosis; all use what for internalization?

A

Clathrin

288
Q

Signals in the what terminus of these receptors interact with adaptor proteins in the clathrin-coat?

A

Carboxy

289
Q

Association with adaptor proteins results in clathrin-coated pits preferentially collecting a subset of what?

A

Plasma membrane receptor

290
Q

Give an example of receptor mediated endocytosis?

A

The uptake of cholesterol in mammalian cells

291
Q

Most cholesterol is transported in the blood in what?

A

Low density lipoproteins (LDLs)

292
Q

Each LDL particle is composed of what? (3 answers)

A
  1. ~1,500 cholesteryl ester molecules 2. Cholesterol containing phospholipid monolayer 3. 500 kD protein that mediates binding to LDL receptors
293
Q

Give the the steps of LDL particle binding to LDL receptors (3 steps)

A
  1. With low intracellular levels of cholesterol, the cell increases plasma membrane levels of the LDL receptor 2. These receptors diffuse in the plane of the membrane until they associate with clathrin-coated pits 3. The receptors are rapidly internalized, regardless of their ligand binding status
294
Q

With high intracellular levels of cholesterol, the cell decreases synthesis of what?

A

LDL receptors

295
Q

Individuals with defects in the gene coding for the LDL receptor are unable to aquire cholesterol from the what?

A

Circulating blood

296
Q

Individuals with defects in the gene coding for the LDL receptor are unable to aquire cholesterol from the circulating blood. These individuals have an increased risk of what?

A

A heart attack from coronary artery disease

297
Q

Give two identified LDL receptor mutations

A
  1. Receptors that lack extracellular LDL binding sites, 2. Receptors that are unable to bind to clathrin coat proteins,
298
Q

Once internalized, vesicles are targeted to the what?

A

The early endosome

299
Q

The acidic pH of the early endosome releases what particles from their receptors?

A

The LDL particles

300
Q

Once the LDL particles are released, what happens to the receptors?

A

They are recycled back to the plasma membrane

301
Q

How many trips does a single LDL receptor make into the cell during its lifetime?

A

Hundreds

302
Q

LDL particles released in the early endosome are targeted to the what in a multi step process?

A

The lysosomes

303
Q

In the lysosome, LDL is degraded to what? For use in what process?

A

Free cholesterol for use in membrane biosynthesis

304
Q

Give the steps of receptor mediated endocytosis

A
  1. endocytosis 2. uncoating 3. fusion with endosome 4. fusion with lysosome
305
Q

Give the steps in the recycyling of receptors?

A
  1. Budding off in transport vesicles 2. Return of LDL receptors to plasma membrane
306
Q

Are all endocytosed receptors returned to the plasma membrane?

A

No

307
Q

Endocytosed receptors with their bound ligands have 1 of 3 fates when they reach the early endosomal compartment. What are they?

A

A. In transcytosis the endocytosed receptors are returned to another domain of the plasma membrane. B. The transferrin receptor follows the recycling pathway C: Signaling receptors (epidermal growth factor receptor, or EGF receptor) are degraded along with their bound ligand in the lysosome

308
Q

The early endosome acts as a what for the endocytic pathway?

A

Sorting station

309
Q

Endosomal compartments are heterogeneous, membrane-enclosed tubes that extend from the what to the what?

A

Cell periphery (early endosomes) to a perinuclear location (late endosomes)

310
Q

The presence of vacuolar H+ ATPases generates endosomes that are acidic; ranging from a pH of 6.0 for the what?

A

The early endosomes

311
Q

The presence of vacuolar H+ ATPases generates endosomes that are acidic; ranging from a pH of 6.0 for the early endosomes to pH 5 for the what?

A

Lysosome

312
Q

Identify structures A - D

A

A: Early endosome

B: Late endosome

C: Endolysosome

D: Lysosome

313
Q

What is the movement of macromolecules from one domain of the plasma membrane to another and cccurs most often in polarized cells?

A

Transcytosis

314
Q

What movement requires material be endocytosed and targeted to the early endosomes?

A

Transcytosis

315
Q

(Transcytosis) In the early endosome the material is moved to an intermediate compartment called what?

A

A recycling endosome

316
Q

Recycling endosomes serve as what? For what?

A

An intracellular storage compartment for membrane proteins whose subsequent targeting to the plasma membrane can be regulated

317
Q

Give an example of transcytosis:

A

The acquision of maternally provided antibodies

318
Q

In the newborn, what are removed from ingested milk through the activity of receptors localized on the apical side of gut epithelial cells?

A

Antibodies

319
Q

Under the acidic conditions of the lumen of the gut, maternally provided antibodies do what?

A

Bind to their receptor and are endocytosed by clathrin-coated pits for targeting to the early endosome

320
Q

The antibody-receptor complex is then targeted to the what which targets vesicles to the basolateral domain of the plasma membrane?

A

Recycling endosome

321
Q

Once presented to the neutral pH of the extracellular fluid, the antibodies dissociate from their receptors entering the newborns what?

A

Bloodstream

322
Q

The transport of material from the recycling endosome to the plasma membrane can be what kind of event?

A

A regulated event

323
Q

In muscle or fat cells the recycling endosome is an intracellular store for what?

A

Plasma membrane glucose transporters

324
Q

Plasma membrane glucose transporters can be relocalized to what to increase glucose uptake by the cell under specific conditions such as insulin signaling?

A

the plasma membrane

325
Q

What is this transport system?

A

Transcytosis

326
Q

What is a mechanism for transcellular transport in which a cell encloses extracellular material in an invagination of the cell membrane to form a vesicle, then moves the vesicle across the cell to eject the material through the opposite cell membrane by the reverse process?

A

Transcytosis

327
Q

What transport process uses vesicles that fuse with the plasma membrane to deliver material to the plasma membrane and for extracellular secretion

A

Exocytosis

328
Q

What two pathways do transport vesicles that leave the trans Golgi network?

A
  1. The constitutive secretory pathway, or 2. The regulated secretory pathway
329
Q

What pathway has vesicles that continually fuse with the plasma membrane, delivers both soluble secretory proteins and new material to the plasma membrane and operates in all cell types?

A

Constitutive secretory pathway

330
Q

What pathway are present only in secretory cells specialized for the on demand delivery of hormones, neurotransmitters, or digestive enzymes?

A

Regulated secretory pathway

331
Q

What pathway is this? Proteins are selected in the trans Golgi network for storage in secretory vesicles.

A

Regulated secretory pathway

332
Q

This pathway has vesicles that retain high concentrations of materials until an extracellular signal stimulates their fusion with the plasma membrane. What is it?

A

Regulated secretory pathway

333
Q

What pathway is A?

A

Constitutive secretory pathway

334
Q

What pathway is B?

A

Regulated secretory pathway

335
Q

The trans Golgi network is responsible for sorting proteins into one of three pathways. What are they?

A
  1. Proteins with a mannose-6-phosphate will be diverted to the lysosome. 2. Proteins in the regulated secretory pathway are targeted for storage in secretory vesicles where they will remain until a extracellular signal is received for their release 3. Proteins are delivered to the cell surface in a constitutive manner
336
Q

Secretory vesicles form where?

A

At the trans Golgi network

337
Q

Proteins destined for regulated secretion are packaged through what? Mediated by what?

A

A selection mechanism mediated by protein aggregation

338
Q

Secretory proteins contain patches of amino acids that promote their what?

A

Aggregation

339
Q

Aggregated proteins are segregated into secretory vesicles which fuse to form what?

A

Immature secretory vesicles

340
Q

Immature secretory vesicles become what through the fusion of additional secretory vesicles coupled with the continuous retrieval of membrane back to the TGN?

A

Mature secretory vesicles

341
Q

The recycling of membrane concentrates vesicle contents and increases the concentration of what?

A

Membrane localized ATP driven protonpumps

342
Q

What activity acidifies this compartment leading to the further condensation of enclosed aggregated material?

A

V-type ATPase

343
Q

Give the structures of the secretory pathway

A
  1. Golgi 2. trans Golgi network 3. Immature secretory vesicle 4. Mature secretory vesicle
344
Q

Densely packed secretory granules contain what? Localized where?

A

Large amounts of electron dense material that are typically localized adjacent to the plasma membrane

345
Q

Upon receipt of an external signal, these vesicles fuse with the plasma membrane releasing their contents to what?

A

The extracellular space

346
Q

Extracellular signals are what? That bind to what? To generate what?

A

Chemical messengers (hormone) that bind to plasma membrane receptor to generate an intracellular signal

347
Q

An example cue for exocytosis is the increase in intracellular what? Generated by what?

A

Intracellular calcium generated by voltage gated calcium channels

348
Q

Membrane fusion events associated with regulated exocytosis are balanced by what? To prevent what?

A

Endocytosis to prevent an increase in plasma membrane surface area

349
Q

Endocytic events remove secretory vesicle membrane proteins for what? (2 answers)

A

Recycling or targeted lysosomal degradation

350
Q

Give the steps in exocytosis of secretory vesicles

A
  1. Docking 2. Fusion 3. Release
351
Q

Most cells are what, having 2 or more distinct plasma membrane domains that serve different functions and therefore require the delivery of a different set of proteins?

A

Polarized

352
Q

The segregation of proteins destined for the apical versus the basolateral surface of a cell occurs where?

A

In the TGN, and not before.

353
Q

Work in polarized epithelial cells have shown that proteins from the ER that are destined for different domains travel where and how?

A

Through the ER and the cis and medial Golgi together

354
Q

Only at what are proteins segregated into vesicles for transport to the apical or basolateral surface of a cell?

A

The trans Golgi network

355
Q

What transport has coat protein recognition in the Trans Golgi Network and sortings signal in C-terminus of proteins?

A

Basolateral membrane transport:

356
Q

What transport has GPI modified proteins accumulate in a modified lipid environment of the TGN

A

Apical membrane transport

357
Q

In one case, targeting is directed by an amino acid sequence within the C-terminus of the cargo protein. In the other, it is the association of the protein with what?

A

A particular lipid environment in the TGN that influences its targeting.

358
Q

In most epithelial cells, the apical plasma membrane proteins are linked to the lipid bilayer through the attachment of a what?

A

GPI anchor

359
Q

GPI anchored proteins are thought to associate with glycosphingolipids in

A

Lipid rafts

360
Q

Lipid rafts help select specific cargo molecules in the TGN for transport to the what?

A

Apical domain of the plasma membrane

361
Q

Proteins targeted to the basolateral membrane contain sorting signals in their cytosolic tail which are recognized by coat proteins for what?

A

Packaging into transport vesicles transported to the basolateral membrane.

362
Q

What pathway has proteins that are delivered to all regions of the cell surface indiscriminately?

A

Indirect targeting pathway

363
Q

Proteins are selectively retained at their location or actively removed and retargeted to what?

A

Their appropriate membrane domain

364
Q

The retargeting of proteins from one plasma membrane domain to another occurs through what?

A

Transcytosis

365
Q

What kind of proteins are retrieved by endocytosis, transported to the early endosome and then redirected to their correct membrane domain?

A

Incorrectly localized membrane proteins

366
Q

The indirect targeting pathway is used only in certain cells such as what cells for the redirection of proteins to the apical domain that line the bile ducts

A

Liver hepatocytes

Eukaryotic Cell Biology (7 decks)

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