Chapter 3: 3.4 Vesicular Traffic - Protein Sorting Flashcards
1
Q
How can proteins associate with membranes?
A
- Transmembrane
- Monolayer-associated
2
Q
Define:
Transmembrane proteins
A
Extend through the bilayer; amphipathic
3
Q
Define:
Monolayer-associated proteins
A
Associate with one monolayer
4
Q
Describe:
Transmembrane proteins
A
- Transmembrane segments are hydrophobic protein domains
5
Q
What types of mono-layer associated proteins are there? Describe them
A
- Lipid-linked: Proteins which do not span the bilayer, but which are covalently attached to membrane lipids
- Protein-attached: Proteins which lie entirely outside of the bilayer, but form noncovalent interactions with other membrane proteins
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)
7
Q
In transmembrane proteins:
What might β-barrels or α-helices form in the membrane?
A
Pore
8
Q
How can membrane proteins be classified?
A
Based on their integration with the membrane
9
Q
List:
Types of membrane protein based on their integration with the membrane
A
- Integral protein
- Peripheral protein
10
Q
Define:
Integral protein
A
Partially integrated with the cellular membrane; contain a hydrophobic domain
11
Q
Define:
Peripheral protein
A
Associated with membrane components, but not integrated into the membrane and lack a hydrophobic domain
12
Q
For integral protein:
- Examples
- How they can be separated from membrane
A
- Transmembrane and monolayer-associated proteins
- By detergents
13
Q
Define:
Detergents
A
Small, amphipathic molecules with a single hydrophobic tail
14
Q
For peripheral proteins:
- Examples
- How they can be separated from membrane
A
- Lipid-linked and protein-attached proteins
- Exposure to salt or changes in pH
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
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)
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
18
Q
What are the two strategies for partitioning cellular processes? Describe
A
- Enzyme complexes: Multiple enzymes which are required for a particular sequence of reactions are aggregated into a single, large complex
- Compartmentalization: Different processes and their associated enzymes/proteins are confined to different membrane-enclosed compartments (organelles)
19
Q
For the following compartment, list the main function(s)
Cytosol
A
- Many metabolic pathways
- Protein synthesis
20
Q
For the following compartment, list the main function(s)
Nucleus
A
- DNA and RNA synthesis
21
Q
For the following compartment, list the main function(s)
Endoplasmic Reticulum
A
- Lipid and protein synthesis
22
Q
For the following compartment, list the main function(s)
Golgi Apparatus
A
- Modification, sorting, and packaging of proteins and lipids
23
Q
For the following compartment, list the main function(s)
Lysosomes
A
- Intracellular degradation
24
Q
For the following compartment, list the main function(s)
Endosomes
A
- Sorting of endocytosed materials
25
# For the following compartment, list the main function(s)
Mitochondria
* Oxidative phosphorylation, ATP synthesis
26
# For the following compartment, list the main function(s)
Chloroplasts
* Photosynthesis
27
# For the following compartment, list the main function(s)
Vacuoles
* Storage
* Intracellular degradation
* Control of cellular pH and pressure (in plants + fungi)
28
# For the following compartment, list the main function(s)
Peroxisomes
* Oxidation reactions
29
The ER is the entry point for...
Proteins detined for transport to organelles, or to the outside of the cell (secretion)
30
# Define:
ER signal sequence
An N-terminal sequence of 8 or more hydrophobic amino acids, which directs the protein to the ER
31
# In the ER signal sequence:
What is the function of the following:
1. Start signal
2. Stop signal
1. Transfers protein synthesis into ER lumen
2. Stops transfer and protein is synthesized outside of ER
32
# Targeting to the ER:
Describe the structure and function of **water-soluble proteins**
* Cross the ER membrane to end up in the ER lumen (interior)
* Destined for secretion or for the lumen of other organelles
33
# Targeting to the ER:
Describe the structure and function of **transmembrane proteins**
* Embedded in the ER membrane
* Destined for membranes of the ER, of other organelles, or the plasma membrane
34
# Targeting to the ER:
How many populations of ribosomes are there? What are they?
2
1. Membrane-bound ribosomes
2. Free ribosomes
35
# Targeting to the ER:
Where are membrane-bound ribosomes located?
Attached to the cytosolic side of the rough ER membrane
36
# Targeting to the ER:
What do membrane-bound ribosomes do?
Synthesize proteins which are translocated (moved) to the ER
37
# Targeting to the ER:
How are proteins moved into the ER?
Addition of amino acids
* Provides necessary thrust to move the protein into the ER
38
# Targeting to the ER:
What is **co-translational trafficking**?
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
# Targeting to the ER:
Where are free ribosomes located?
Localized to the cytosol, not ER-localized
40
# Targeting to the ER:
What do free ribosomes do?
Synthesize proteins that are not translocated to the ER
41
# Targeting to the ER:
What is post-translational trafficking?
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
What proteins guide newly-made protein (plus ribosome) with an ER signal sequence to the ER membrane?
1. Signal Recognition Particle (SRP)
2. SRP Receptor
43
# True or False:
Protein guide newly made proteins with and ER signal sequence to the ER membrane
Partially true, it also guides the ribosomes
44
# Describe:
Signal Recognition Particle (SRP)
Cytosolic protein which binds the ER signal sequence and associated ribosome
45
# Describe:
SRP Receptor
Protein embedded in the ER membrane which binds the SRP-ribosome complex
46
What does the SRP receptor do?
Embeds the ER start signal into the membrane which is cleaved after the protein is released
47
What is protein targeting?
The biological mechanism by which proteins are transported to their appropriate destinations within (or outside) the cell
48
# List:
Membrane-enclosed compartments of eukaryotic cells (8)
* Cytosol
* Endoplasmic Reticulum
* Golgi Apparatus
* Late endosome
* Lysosome
* Early endosome
* Cell Exterior
* Secretory Vesicles
49
# State the first 4 steps of:
The translocation process
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
# Fill in the blank:
Binding of SRP ----- protein synthesis
1. Slows
51
# Fill in the blank:
What happens when the SRP-ribosome complex engages with the SRP receptor on the ER membrane?
SRP dissociates, leaving the ribosome bound to the SRP receptor
52
# Define:
Start-transfer sequence
SRP binds ribosomes with a growing polypeptide displaying an N-terminal signal sequence
53
# Fill in the blank:
The ER signal sequence binds to a ------- in the ------------ while the growing ----------- is threaded through the -------
1. Channel
2. Translocator
3. Polypeptide
4. Channel
54
# In step 4 of the translocation process:
What happens to soluble proteins?
Once the C-terminus passes through the translocator channel, the protein is released into the ER lumen
55
# In step 4 of the translocation process:
What happens to transmembrane proteins?
An internal hydrophobic stop-transfer sequence causes the translocator to release the growing polypeptide chain into the lipid bilayer
56
# 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?
1. Stop-transfer sequence
2. Laterally into bilayer
57
# True or False:
Some proteins have multiple transmembrane domains
True
58
# In step 4 of the translocation process:
In proteins with multiple transmembrane domains, besides stop-transfer sequences what else will they have?
An internal hydrophobic start-transfer sequences (besides the ER signal sequence)
59
# In step 4 of the translocation process:
In proteins with multiple transmembrane domains, what's the relationship between stop-transfer and start-transfer sequences?
They are paired together:
* Stop-transfer and start-transfer sequences are paired
60
What is the final step in the translocation process?
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
How can the orientation of proteins in the ER membrane be predicted?
By using:
1. Protein domain diagrams
2. Hydropathy plots
62
# True or False:
Both start and stop transfer sequences are hydrophilic
False, they are both hydrophobic
63
How are hydropathy plots read?
From the N-terminus to the C-terminus
64
What can you predict from hydropathy plots?
* Domain structure
* Orientation of the protein
65
How is it decided if a protein is translocated to the ER lumen?
The N-terminal start transfer sequence is cleaved
* If no other transmembrane domains, the protein is translocated to the ER lumen
66
# State:
The C terminal end of the protein, if the last transmembrane domain is:
1. A stop transfer sequence
2. A start transfer sequence
1. C terminal end of the protein is in the cytosol
2. C terminal end of the protein is in the ER lumen
67
# True or False:
Internal start transfer sequences are cleaved
False, they are not cleaved but instead stay in the membrane
68
If the internal start transfer sequences stay in the membrane, where do the N-terminal and C-terminal regions remain?
* N-terminal region remains in the cytosol
* C-terminal region is in the ER lumen
69
How do we get this arrangement?
1. N-terminal region remains in the ER lumen
2. C-terminal region remains in the cytosol
Can be achieved with:
1. N-terminal start transfer sequence (cleaved)
2. An internal stop transfer sequence
70
What will happen when there's a combination of internal start transfer sequence and internal strop transfer sequences?
Results in multiple passes through the membrane
71
# In targeting to lysosome:
Proteins are sorted from the ----- but made in --
1. Golgi
2. ER
72
# In targeting to lysosome:
What signal binds to cargo protein?
M6P signals
73
# In targeting to lysosome:
What does M6P bind to?
Binds to clathrin coat AP-3 to target for lysosome
74
# True or False:
M6P is pH sensitive
True
75
How is M6P pH sensitive?
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
# In protein targeting to mitochondria:
Proteins are made in...
The cytosol
77
# True or False:
Protein targeting to mitochondria is part of the endomembrane system
False, it is not
78
# In protein targeting to mitochondria:
State the receptors on the membrane
Two membranes, therefore two receptors:
1. **Tom** receptor on outer membrane
2. **Tim** receptor in inner membrane
79
# In protein targeting to mitochondria:
How long is the signal peptide?
20-50 amino acids
