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BIOL1006 > Protein sorting > Flashcards

Protein sorting Flashcards

1
Q

Label the structures in this cell

A
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2
Q

Tell me the types of proteins produced in the ER?

A
  • Transmembrane proteins
  • hydrolytic enzymes
  • growth factors
  • extracellular matrix
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3
Q

What types of proteins have to go through the RER?

A

Those that are membrane bound

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4
Q

After the proteins are produced in the ER, where are they then trafficked to in the cell?

A

The golgi

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5
Q

After proteins are processed in the Golgi, what happens to them?

A

They are then trafficked out through secretory vesicles destined for the plasma membrane or vesicles destined for lysosomes

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6
Q

Whats the Biosynthetic pathway?

A

An interconnected route from the RER –> Golgi –> secretory vesicle –> secretion at apical domain

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7
Q

what does the SER synthesise?

A

fatty acids and phospholipids

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8
Q

Tell me about the polarity of Acinar cells and how this is known?

A

They are polarised (this is shown by the presence of the apical and basal domain)

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9
Q

Label the structure of the Golgi complex

A
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10
Q

What happens between the stacks of golgi?

A

The processing of proteins e.g. glycosylation and folding

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11
Q

What does cis golgi mature to?

A

Medial then trans golgi

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12
Q

Is the golgi constantly replenishing and how does it do this?

A

Yes

its constantly folding forwards and backwards via budding off and replenishing certain areas

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13
Q

Which part of the golgi complex recieves proteins from the RER?

A

The cis region

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14
Q

Are products able to go forwards and backwards between the ER and golgi?

A

yes

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15
Q

Tell me what occurs during exocytosis in the cell?

A

A vesicle that may derive from the golgi fuses with the plasma membrane and released its contents into the extracellular space, and vesicle membrane becomes part of the plasma membrane

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16
Q

Tell me what occurs during endocytosis in the cell?

A

A region of the plasma membrane is internalised, forming a vesicle whose contents derive from the extracellular space

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17
Q

What do endocytosis and exocytosis processes in the cell require?

A

Fission/ fusion via different mechanisms

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18
Q

What type of organelle are lysosomes in animals?

A

a degradative organelle

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19
Q

whats the end point of endocytosis, phagocytosis and autophagy?

A

Lysosomes

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20
Q

Whats endocytosis definition?

A

Invagination of plasma membrane involved in the uptake of extracellular and transmembrane molecules

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21
Q

Whats the definition of Autophagy?

A

cytosolic degradation pathway of aggregated proteins, damaged organelles and invading pathogens.

Membrane forming around an intracellular component, isolating it

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22
Q

Are lysosomes and acidic or alkaline organelle?

Tell me some things it contains?

why is the environment this way?

A

The lysosome is an acidic organelle

it contains several hydrolytic enzymes (acid hydrolases)

For protein degfradation and subsequent re-use of amino acids

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23
Q

Whats the pH of the lysosome and how is this achieved?

Why does it have to be around this pH?

A

Acidic state (pH 5)

Achieved by H+ ion ATP-ase pump and Cl- ion channel (decoupling the electro gradient from H+ being pumped in) allows the continual pump of H+ ions

Has to be acidic to function properly e.g. correct enzyme function

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24
Q

What does the Endoplasmic reticulum produce/ process and send out?

A

proteins and lipids

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25
Q

What are the two types of ER?

What identifiable feature allows you to work out the different?

A

Smooth endoplasmic reticulum: no ribosomes attached

Rough endoplasmic reticulum: ribosomes attached

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26
Q

Tell me the function of the SER?

A

synthesised fatty acids and phospholipids

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27
Q

Tell me the function of the RER?

A

synthesises, processes and sorts; proteins, lysosomal proteins and membrane proteins

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28
Q

Label the structures of this RER

A
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29
Q

What ribosomes do secreted proteins, integral membrane proteins, and proteins destined for ER, Golgi, or lysosome begin on before attaching to the ER?

A

cytosolic riboosomes

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30
Q

Whats a Secretory protein?

A

contains an ER signal sequence, and segment of hydrophobic residues at the N-terminus

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31
Q

Whats the translocon?

Whats its function?

A

A channel on the ER membrane.

A central channel thats lined with hydrophobic residues which allows the transit of growing polypeptides into the ER

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32
Q

Whats the role of the signal peptidase in the ER membrane?

A

It cleaves the ER signal sequence from the secretory protein after N-terminus enters the ER lumen

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33
Q

What does the signal sequence bind to during translocation at the ER?

A

SRP (Signal-recognition particle)

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34
Q

Tell me the steps to protein translocation at the ER?

A
  1. Signal sequence binds SRP
  2. SRP binds SRP receptor in ER
  3. Delivery of complex to translocon
  4. Translocation begins ‘co-translationally’
  5. Signal sequence cleavage by signal peptidase
  6. Protein modifications then occur within ER lumen
  7. Once GDP binds its dissociates
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35
Q

Where does translation of integral membrane protein’s occur?

A

On the ER membrane

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36
Q

What does each integral membrane protein have which is unique to them?

A

They each have a unique orientation (topology; where the N and C termius lie) with respect to the lipid bilayer membrane

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37
Q

Where do the integral membrane protein have to be located in order to be translated on the rough ER?

A
  • ER
  • Golgi
  • Lysosomes
  • plasma membrane
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38
Q

Whats the final orientation of membrane proteins determined by?

A

During translation at the ER membrane they stay in that particular orientation to their final destination

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39
Q

Name the 5 major classes of integral membrane proteins synthesised on the rough ER

A
  • Type I
  • Type II
  • Type III (signal-anchor type II)
  • Tail-anchored proteins (C-terminal anchor)
  • Type IV (polytopic)
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40
Q

For Type I integral membrane proteins give some examples of them and tell me where the N/C terminus lie?

A

C terminus in cytosol (cytoplasm)

N terminus in ER lumen

examples:

  • LDL receptor
  • influenza
  • HA protein
  • insulin receptor
  • Growth hormone receptor
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41
Q

For type II integral proteins, tell me about the orientation of the terminal’s

provide some examples

A

C terminus in ER lumen

N terminus in cytoplasm

Examples:

  • Asialoglycoprotein receptor
  • transferrin receptor
  • Golgi galactosyltransferase
  • Golgi sialyltransferase
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42
Q

For type III integral proteins, tell me about the orientation of the terminal’s

provide some examples

A

C termius is in the ER lumen

N terminus in cytoplasm

Examples:

  • Cytochrome p450
43
Q

For tail-anchored integral proteins, tell me about the orientation of the terminal’s

provide some examples

A

C terminus is in the ER lumen

N terminus is in the cytoplasm

examples:

  • v-SNARE
  • t-SNARE
44
Q

For type IV integral proteins, tell me about the orientation of the terminal’s

provide some examples

A

C terminus is in the ER lumen

N terminus is in the cytoplasm

Examples:

  • G protein-coupled receptors
  • Glucose transporters
  • Voltage-gated Ca2+ channels
  • ABC small molecule pumps
  • CFTR (Cl-) channel
  • sec61
45
Q

How might the type IV proteins differ?

A

May have a different number of helices or different orientation of N- and C- terminus

46
Q

what signal sequence do type I membrane proteins contain?

A

An N-terminal signal sequence

47
Q

in type I membrane proteins, what allows insertion into the membrane and how does it do this?

A

stop transfer anchor sequence with hydrophobic amino acids allows insertion into membrane by preventing new chain from migrating farther into ER lumen

48
Q

How does the stop transfer sequence move in type I proteins and where does it anchor?

A

Stop transfer anchor sequence moves laterally between translocon subunits and becomes anchored in phospholipid bilayer

49
Q

Tell me the steps to the type II membrane protein insertion at the ER?

A
  1. internal signal-anchor sequence is synthesised on a cytosolic ribosome
  2. This signal-anchor sequence is then bound by an SRP, which directs the complex to the ER membrane
  3. This hydrophobic signal-anchor sequence is not located at N-terminus and not cleaved
  4. New polypeptide chain becomes oriented in translocon with N-terminal portion toward cytosol, mediated by positively charged residues
  5. As chain is elongated, internal signal-anchor moves laterally out of translocon and anchors into phospholipid bilayer
50
Q

What is type III membrane insertion at the ER similar to, but how is it different?

A

It is similae to type II membrane protiens, except positively charged residues are on the C-terminal side of the signal-anchor sequence

51
Q

As the positively charged residues are on the C-terminal side of the signal-anchor sequence in type III proteins, what does this mean for its orientation?

A

It causes the transmembrane portion to be orientated in the translocon with C-terminus orientated towards the cytosol (cytoplasm)

52
Q

For type III proteins, where does the elongation of the C-terminal protion of the polypeptide occur?

A

In the cytosol

53
Q

Tell me the two things used to determine the orientation of ER membrane proteins?

A
  • Internal stop-transfer anchor sequence (STA)
  • internal signal-anchor sequence (SA)
54
Q

Tell me about the internal stop-transfer anchor sequence

A

stops passage of polypeptide chain through translocon and becomes transmembrane segment (hydrophobic)

55
Q

Tell me about the internal signal-anchor sequence ?

A

ER signal sequence and membrane anchor

56
Q

What type of delivery is ER to golgi transport?

A

Vesicular delivery

57
Q

When transporting proteins between the ER and golgi, what must it pass through and where is this located?

A

The Vasicular tubular cluster

this is found between the ER and golgi

58
Q

What acts to maintain the distinct composition of the ER and golgi and what is it made up of?

A

KDEL receptors

This is made up of the 4 amino acids; lysine (K), Aspartic acid (D), Glutamic acid (E) and Leucine (L)

59
Q

What are the names of the coats on the ER/Golgi that initiate transport between the two

which one is found on what organelle?

what is the coat’s role?

A

The two coats are: COPII and COPI

COPII: found on the ER and moves things from ER –> Golgi (forward only)

COPI: found on the Golgi and moves things from Golgi –> ER (backward only)

60
Q

What does the difference in pH between the ER and golgi influence?

What effect does high and low pH cause?

A

It influences the binding of KDEL containing protein to their receptors

Low pH: favours binding in Golgi

High pH: In ER triggers the dissociation of protein-receptor interaction in ER (pH determines the interaction)

61
Q

Does the ER or golgi have a higher pH ?

A

Higher pH in ER

62
Q

Tell me the steps secretory pathway

A
  1. protein synthesis on bound ribosomes; co-translational transport of proteins into or across ER membrane
  2. Budding and fusion of ER-to-golgi vesicles (surrounded by a COPII coat) to form Cis-golgi
  3. Retrograde Golgi-to-ER transport (vesicles surorunded by COPI coat)
  4. cisternal maturation
  5. retrograde transport from later to earlier Golgi cisternae
  6. constitutive secretion
  7. regulated secretion
  8. sorting to lysosomes
  9. endocytosis
63
Q

Tell me how newly synthesises ER proteins are modified

A
  • Disulphide bonds
  • Glycosylation
  • proteolytic cleavage
  • assembly of multi-subunit proteins
64
Q

What do all of the modification of ER proteins promote/ ensure?

A

Folding of secretory proteins and ensure stability of these proteins once in the extracellular environment

65
Q

What does protein glycosylation allow a cell to do?

A

Produce a number of different, distinct molecules on the cell surface which may act as a basis for specific interaction during cell-cell adhesion or communication

66
Q

When can’t protein enter the golgi/ exit ER?

A

When they arent folded properly.

There is a quality control mechanism to ensure this

67
Q

What are the two types of glycosylation?

A
  • N-linked
  • O-linked
68
Q

Where does N-linked protein glycosylation start and continue to?

A

Starts in the ER and continues into the golgi

69
Q

What does N-linked glycos. allow?

A

A more complex arrangement of carbohydrates

70
Q

whats the function of dolichol lipid in N-linked glycos?

A

it delivers oligosaccharide tree distinct orientation and composition onto asparagine residue on newly synthesised proteins

71
Q

what is the oligosaccharide tree made from?

A
  • 3 glucose
  • 9 mannose
  • 2 N-acetylglucosamine
72
Q

In order to create a more specific composition on the oligosaccharide tree, what occurs?

A

enzymatic trimming

73
Q

Whats often critical in protein function?

A

The unique pattern of glycosylation

74
Q

For N-linked glycos. how does the processing begin in the ER (3 steps)?

A

The removal of glucoses in ER

Then a mannosidase removes a specific mannose in ER

Mannose trimming then occurs as proteins move from ER to golgi

75
Q

is vesicle transport required between golgi compartments?

A

no

76
Q

For N-linked glycos. what occurs in each compartment of the golgi?

A

Cis: golgi mannosidase removes 3 mannoses

Medial: 3 GlcNAc added, 2 mannoses removed

Trans: 3 galactose added, addition of N-acetylneuramic acid to each galactose

77
Q

Tell me what occurs for protein modification in each section of the golgi?

A

A lot of modification occurs in the cis-golgi network

78
Q

Whats added to proteins which helps target them to lysosomes?

A

Mannose-6-phosphate (M6P)

79
Q

What generate’s M6P residues?

A

The N-linked oligosaccharides generated in the ER, undergoes processing in cis-golgi to generate M6P residues

80
Q

What occurs through the M6P residues?

A

segregation and sorting or lysosomal enzymes occurs in the trans-golgi through binding to the M6P receptor

81
Q

Name the mechanism that helps to get phosphate groups onto the carbon chain (it is cleaved off later once done)?

A

N-acetylglucosamine

82
Q

The M6P addition that directs proteins to lysosomes is generated where?

A

in the cis-golgi

83
Q

What does the M6P residue interact with?

A

M6P receptor in the trans-golgi which directs the protein to vesicles destined for lysosomes

84
Q

draw the structure of the M6P

A
85
Q

vesicles containing the M6P complexes are transported where?

A

to the lysosome

86
Q

What helps to dissociate the protein from the receptor in the lysosomal targeting of proteins?

A

The low pH of the lysosome

(dissociates in low pH and high affinity interactions in high pH)

87
Q

Lysosomal proteins are processed and stay where?

A

in the lysosome

88
Q

View image below

A
89
Q

Once the proteins are budded off of the golgi, where can they be directed?

A

either the apical or basal domain

90
Q

define transcytosis

A

Transcytosis (also known as cytopempsis) is a type of transcellular transport in which various macromolecules are transported across the interior of a cell.

91
Q

What are the 3 pathway which are possible for the post-golgi trafficking of transmembrane receptors in epithelial cells

A
  1. recycling to the same domain on plasma membrane
  2. transcytosis from one domain of plasma membrane to another
  3. degradation of lysosome
92
Q

Label this LDL receptor and its components

A
93
Q

What are the 2 parts that the Low-density lipoprotein (LDL) is made from?

A
  1. amphipathic shell (hydrophobic and hydrophilic regions) composed of phospholipid monolayer, cholesterol, and protein (apolipoprotein B)
  2. hydrophobic core mostly containing cholesterol esters (Apolar core)
94
Q

What are the steps to the endocytosis of LDL receptor

A
  1. Cell surface LDL receptors bind to an apoB protein embedded in phospholipid outer layer of LDL particles; Neutral pH allows the motif attached to the LDL receptor to wrap around the ApoB protein
  2. Clustering of occupied receptors occurs in coated pits (clathrin)
  3. Endocytic vesicles containing LDL-receptor complexes traffic within the cell to an acidic late endosome, causing a conformational change in the LDL receptor resulting in release of LDL particle
  4. Late endosome fuses with lysosome to deliver ligand, resulting in proteins and lipids of the free LDL particle to be broken down to their individual parts (cholesterol, amino acids, fatty acids) by enzymes in lysosome
  5. pH lowers as its trafficked. From neutral –> pH 5(low pH= low affinity)
  6. in low pH environment the LDL complex closes
95
Q

How is Ferrotransferin formed?

A

Apotransferring + 2Fe3+ –> Ferrotransferrin

96
Q

Tell me about the affinity of the Ferrotransferrin?

A

Ferrotransferrin form has a high affinity for receptor at neutral pH

97
Q

what is transferrin?

A

A ligand

98
Q

At low pH what is lost from transferrin?

A

Iron

The iron is reduced

99
Q

What does Apotransferrin have a high affinity for?

A

receptor at low pH

100
Q

What does Apotransferrin mean?

A

Transferrin with no iron bound to it

101
Q

Following the release of Fe3+ in low pH, what does the ligand remain bound to?

A

The receptor at pH 5-6 and the ligand-receptor complex is returned to cell surface

102
Q

At what pH does Apotransferrin dissociate from the receptor?

A

7

103
Q

When does Apotransferrin have a low affinity?

A

At neutral pH

BIOL1006 (5 decks)

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