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My Packs: (WIZEPREP) (BIO 2382) > Chapter 3: 3.4 Vesicular Traffic - Protein Sorting > Flashcards

Chapter 3: 3.4 Vesicular Traffic - Protein Sorting Flashcards

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1
Q

How can proteins associate with membranes?

A
  1. Transmembrane
  2. Monolayer-associated
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2
Q

Define:

Transmembrane proteins

A

Extend through the bilayer; amphipathic

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3
Q

Define:

Monolayer-associated proteins

A

Associate with one monolayer

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4
Q

Describe:

Transmembrane proteins

A
  • Transmembrane segments are hydrophobic protein domains
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5
Q

What types of mono-layer associated proteins are there? Describe them

A
  1. Lipid-linked: Proteins which do not span the bilayer, but which are covalently attached to membrane lipids
  2. Protein-attached: Proteins which lie entirely outside of the bilayer, but form noncovalent interactions with other membrane proteins
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6
Q

In transmembrane proteins:

What are the transmembrane domains usually?

A

α-helices consisting of amino acids, with hydrophobic side chains
* Occasionally β-barrels (β-sheets in cylinder form)

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7
Q

In transmembrane proteins:

What might β-barrels or α-helices form in the membrane?

A

Pore

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8
Q

How can membrane proteins be classified?

A

Based on their integration with the membrane

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9
Q

List:

Types of membrane protein based on their integration with the membrane

A
  1. Integral protein
  2. Peripheral protein
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10
Q

Define:

Integral protein

A

Partially integrated with the cellular membrane; contain a hydrophobic domain

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11
Q

Define:

Peripheral protein

A

Associated with membrane components, but not integrated into the membrane and lack a hydrophobic domain

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12
Q

For integral protein:

  1. Examples
  2. How they can be separated from membrane
A
  1. Transmembrane and monolayer-associated proteins
  2. By detergents
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13
Q

Define:

Detergents

A

Small, amphipathic molecules with a single hydrophobic tail

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14
Q

For peripheral proteins:

  1. Examples
  2. How they can be separated from membrane
A
  1. Lipid-linked and protein-attached proteins
  2. Exposure to salt or changes in pH
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15
Q

How do changes in pH cause peripheral proteins to separate from the membrane?

A

Disrupt protein-protein interactions but not the membrane itself

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16
Q

Define and describe:

Glycocalyx

A

A coating formed around some animal and bacterial cells
* Consists of polysaccharides attached to lipids (glycolipids) and proteins (glycoproteins, proteoglycans)

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17
Q

List:

Functions of glycocalyx

A
  • Protection of the cell from mechanical damage ia lubrication (sugars absorb water)
  • Cell-to-cell recognition, owing to the vast diversity of sugars and the proteins which recognize them (lectins)
  • Adhesion
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18
Q

What are the two strategies for partitioning cellular processes? Describe

A
  1. Enzyme complexes: Multiple enzymes which are required for a particular sequence of reactions are aggregated into a single, large complex
  2. Compartmentalization: Different processes and their associated enzymes/proteins are confined to different membrane-enclosed compartments (organelles)
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19
Q

For the following compartment, list the main function(s)

Cytosol

A
  • Many metabolic pathways
  • Protein synthesis
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20
Q

For the following compartment, list the main function(s)

Nucleus

A
  • DNA and RNA synthesis
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21
Q

For the following compartment, list the main function(s)

Endoplasmic Reticulum

A
  • Lipid and protein synthesis
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22
Q

For the following compartment, list the main function(s)

Golgi Apparatus

A
  • Modification, sorting, and packaging of proteins and lipids
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23
Q

For the following compartment, list the main function(s)

Lysosomes

A
  • Intracellular degradation
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24
Q

For the following compartment, list the main function(s)

Endosomes

A
  • Sorting of endocytosed materials
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25
Q

For the following compartment, list the main function(s)

Mitochondria

A
  • Oxidative phosphorylation, ATP synthesis
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26
Q

For the following compartment, list the main function(s)

Chloroplasts

A
  • Photosynthesis
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27
Q

For the following compartment, list the main function(s)

Vacuoles

A
  • Storage
  • Intracellular degradation
  • Control of cellular pH and pressure (in plants + fungi)
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28
Q

For the following compartment, list the main function(s)

Peroxisomes

A
  • Oxidation reactions
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29
Q

The ER is the entry point for…

A

Proteins detined for transport to organelles, or to the outside of the cell (secretion)

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30
Q

Define:

ER signal sequence

A

An N-terminal sequence of 8 or more hydrophobic amino acids, which directs the protein to the ER

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31
Q

In the ER signal sequence:

What is the function of the following:
1. Start signal
2. Stop signal

A
  1. Transfers protein synthesis into ER lumen
  2. Stops transfer and protein is synthesized outside of ER
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32
Q

Targeting to the ER:

Describe the structure and function of water-soluble proteins

A
  • Cross the ER membrane to end up in the ER lumen (interior)
  • Destined for secretion or for the lumen of other organelles
33
Q

Targeting to the ER:

Describe the structure and function of transmembrane proteins

A
  • Embedded in the ER membrane
  • Destined for membranes of the ER, of other organelles, or the plasma membrane
34
Q

Targeting to the ER:

How many populations of ribosomes are there? What are they?

A

2
1. Membrane-bound ribosomes
2. Free ribosomes

35
Q

Targeting to the ER:

Where are membrane-bound ribosomes located?

A

Attached to the cytosolic side of the rough ER membrane

36
Q

Targeting to the ER:

What do membrane-bound ribosomes do?

A

Synthesize proteins which are translocated (moved) to the ER

37
Q

Targeting to the ER:

How are proteins moved into the ER?

A

Addition of amino acids
* Provides necessary thrust to move the protein into the ER

38
Q

Targeting to the ER:

What is co-translational trafficking?

A

Ribosomes translating ER-target proteins can move to the ER membrane before translation is complete
* The protein can insert into the ER while being translated

39
Q

Targeting to the ER:

Where are free ribosomes located?

A

Localized to the cytosol, not ER-localized

40
Q

Targeting to the ER:

What do free ribosomes do?

A

Synthesize proteins that are not translocated to the ER

41
Q

Targeting to the ER:

What is post-translational trafficking?

A

Depending on localization signal:
1. Could go to nucleus, mitochondrion, chloroplast, or peroxisomes
2. If no localization signal, the protein remains in the cytosol

42
Q

What proteins guide newly-made protein (plus ribosome) with an ER signal sequence to the ER membrane?

A
  1. Signal Recognition Particle (SRP)
  2. SRP Receptor
43
Q

True or False:

Protein guide newly made proteins with and ER signal sequence to the ER membrane

A

Partially true, it also guides the ribosomes

44
Q

Describe:

Signal Recognition Particle (SRP)

A

Cytosolic protein which binds the ER signal sequence and associated ribosome

45
Q

Describe:

SRP Receptor

A

Protein embedded in the ER membrane which binds the SRP-ribosome complex

46
Q

What does the SRP receptor do?

A

Embeds the ER start signal into the membrane which is cleaved after the protein is released

47
Q

What is protein targeting?

A

The biological mechanism by which proteins are transported to their appropriate destinations within (or outside) the cell

48
Q

List:

Membrane-enclosed compartments of eukaryotic cells (8)

A
  • Cytosol
  • Endoplasmic Reticulum
  • Golgi Apparatus
  • Late endosome
  • Lysosome
  • Early endosome
  • Cell Exterior
  • Secretory Vesicles
49
Q

State the first 4 steps of:

The translocation process

A
  1. SRP binds ribosomes with a growing polypeptide displaying an N-terminal signal sequence
  2. The SRP-ribosome complex engages with the SRP receptor on the ER membrane
  3. The ribosome is passed from the SRP receptor to a protein translocator on the ER membrane, and protein synthesis resumes at normal rates
50
Q

Fill in the blank:

Binding of SRP —– protein synthesis

A
  1. Slows
51
Q

Fill in the blank:

What happens when the SRP-ribosome complex engages with the SRP receptor on the ER membrane?

A

SRP dissociates, leaving the ribosome bound to the SRP receptor

52
Q

Define:

Start-transfer sequence

A

SRP binds ribosomes with a growing polypeptide displaying an N-terminal signal sequence

53
Q

Fill in the blank:

The ER signal sequence binds to a ——- in the ———— while the growing ———– is threaded through the ——-

A
  1. Channel
  2. Translocator
  3. Polypeptide
  4. Channel
54
Q

In step 4 of the translocation process:

What happens to soluble proteins?

A

Once the C-terminus passes through the translocator channel, the protein is released into the ER lumen

55
Q

In step 4 of the translocation process:

What happens to transmembrane proteins?

A

An internal hydrophobic stop-transfer sequence causes the translocator to release the growing polypeptide chain into the lipid bilayer

56
Q

In step 4 of the translocation process:

In transmembrane proteins:
1. What causes the translocator to release the growing polypeptide chain?
2. How is the polypeptide chain released?

A
  1. Stop-transfer sequence
  2. Laterally into bilayer
57
Q

True or False:

Some proteins have multiple transmembrane domains

A

True

58
Q

In step 4 of the translocation process:

In proteins with multiple transmembrane domains, besides stop-transfer sequences what else will they have?

A

An internal hydrophobic start-transfer sequences (besides the ER signal sequence)

59
Q

In step 4 of the translocation process:

In proteins with multiple transmembrane domains, what’s the relationship between stop-transfer and start-transfer sequences?

A

They are paired together:
* Stop-transfer and start-transfer sequences are paired

60
Q

What is the final step in the translocation process?

A

Once protein synthesis is complete:
* N-terminal ER signal sequence is cleaved and degraded
* Internal start-transfer sequences of proteins with multiple transmembrane domains, however, are not degraded

61
Q

How can the orientation of proteins in the ER membrane be predicted?

A

By using:
1. Protein domain diagrams
2. Hydropathy plots

62
Q

True or False:

Both start and stop transfer sequences are hydrophilic

A

False, they are both hydrophobic

63
Q

How are hydropathy plots read?

A

From the N-terminus to the C-terminus

64
Q

What can you predict from hydropathy plots?

A
  • Domain structure
  • Orientation of the protein
65
Q

How is it decided if a protein is translocated to the ER lumen?

A

The N-terminal start transfer sequence is cleaved
* If no other transmembrane domains, the protein is translocated to the ER lumen

66
Q

State:

The C terminal end of the protein, if the last transmembrane domain is:
1. A stop transfer sequence
2. A start transfer sequence

A
  1. C terminal end of the protein is in the cytosol
  2. C terminal end of the protein is in the ER lumen
67
Q

True or False:

Internal start transfer sequences are cleaved

A

False, they are not cleaved but instead stay in the membrane

68
Q

If the internal start transfer sequences stay in the membrane, where do the N-terminal and C-terminal regions remain?

A
  • N-terminal region remains in the cytosol
  • C-terminal region is in the ER lumen
69
Q

How do we get this arrangement?
1. N-terminal region remains in the ER lumen
2. C-terminal region remains in the cytosol

A

Can be achieved with:
1. N-terminal start transfer sequence (cleaved)
2. An internal stop transfer sequence

70
Q

What will happen when there’s a combination of internal start transfer sequence and internal strop transfer sequences?

A

Results in multiple passes through the membrane

71
Q

In targeting to lysosome:

Proteins are sorted from the —– but made in –

A
  1. Golgi
  2. ER
72
Q

In targeting to lysosome:

What signal binds to cargo protein?

A

M6P signals

73
Q

In targeting to lysosome:

What does M6P bind to?

A

Binds to clathrin coat AP-3 to target for lysosome

74
Q

True or False:

M6P is pH sensitive

A

True

75
Q

How is M6P pH sensitive?

A
  1. At 6.5, binds to cargo
  2. At low pH (like in the lysosomal environment), detaches from the cargo so it can be recycled
76
Q

In protein targeting to mitochondria:

Proteins are made in…

A

The cytosol

77
Q

True or False:

Protein targeting to mitochondria is part of the endomembrane system

A

False, it is not

78
Q

In protein targeting to mitochondria:

State the receptors on the membrane

A

Two membranes, therefore two receptors:
1. Tom receptor on outer membrane
2. Tim receptor in inner membrane

79
Q

In protein targeting to mitochondria:

How long is the signal peptide?

A

20-50 amino acids

My Packs: (WIZEPREP) (BIO 2382) (20 decks)

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