Chapter 13 Flashcards
What is vesicular transport?
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
Vesicular transport is the exchange of components between membrane compartments by the budding of transport vesicles from a donor compartment followed by what?
Fusion of the vesicle to the target compartment
Identify A and B
A: Donor compartment B: Target compartment
In eukaryotes, transport along the secretory and endocytic pathways occur by what?
The fusion of topologically equivalent membrane bound compartments
This flow of material between topologically equivalent membrane compartments is highly what? (3 answers)
Organized, balanced, and directional
The flow of material between topologically equivalent membrane compartments allows for what? (3 answers)
- The secretion of select proteins, 2. The uptake of extracellular material 3. The remodeling of the plasma membrane
The secretory pathway (red arrows) includes the outward movement of material from what? (3 answers)
- The ER to the Golgi 2. The Golgi to the plasma membrane 3. The Golgi to the lysosome
The endocytic pathway (green arrows) is uptake of what? Their fusion with what?
The uptake of plasma membrane material and their fusion with the lysosome
The retrieval pathway is what?
The movement from the plasma membrane to the Golgi and from the Golgi to the ER
Formation of transport vesicles requires a what? where?
A specialized ‘protein coat’ on the outside of the membrane vesicle
The specialized ‘protein coat’ perform what two main functions?
- Selects the membrane proteins required for transport 2. Generates the shape of the vesicle by influencing the curvature of the membrane
What is flat and stiff due to its cholesterol rich composition and its attachment to the underlying cytoskeleton?
The plasma membrane
For the plasma membrane, what are essential for the generation of the force required to introduce membrane curvature?
Coat proteins
What based vesicle formation is less dependent on coat-proteins for membrane curvature as vesicles form at curved regions of the membrane?
Golgi based
For the Golgi, coat proteins are primarily used for what?
Cargo selection
What are the 3 major types of coated vesicles distinguished by their coat proteins?
- Clathrin-coated vesicles 2. COPI-coated vesicles 3. COPII coats
What vesicles were the first identified and the best characterized coat type?
Clathrin-coated vesicles
What vesicles form on buds that exit from the Golgi
COPI-coated vesicles
Vesicles form at the plasma membrane and are ssential for endocytosis?
Clathrin-coated vesicles
What form on vesicles leaving the ER
COPII coats
Identify pathway A (in green):
Clathrin
Identify pathway B (in blue):
COPI
Identify pathway C (in red):
COPII
The formation of transport vesicles are mediated by the formation of what? where?
A specialized ‘protein coat’ on the cytosolic side of the membrane vesicle.
Specialized ‘protein coats’ on the cytosolic side of the membrane vesicle perform what two main functions?
- Select the membrane proteins required for transport 2. Generate the shape of the vesicle by influencing the curvature of the membrane
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?
Different transport steps
What kind of transport do clathrin-coated vesicles perform?
Plasma membrane mediated endocytosis
Where do COPI coated vesicles exit from?
They exit from the Golgi cisternae
Where do COPII coated vesicles exit from?
They exit from the ER
In general, coat formation requires what four things?
- Coat-recruitment GTPases 2. Adaptor proteins 3. Cargo receptors4. Coat proteins
What are monomeric GTPases that are responsible for the recruitment of coat proteins to the membrane surface for vesicle formation?
Coat-recruitment GTPases
What links the coat proteins to the vesicle membrane and interacts with cargo receptors.
Adaptor proteins
Not all coated vesicles have adaptor proteins as some cargo may directly bind to what?
Coat proteins
What are transmembrane proteins that capture specific soluble cargo for packaging into the vesicle?
Cargo receptors
What are proteins that form a cage-like structure over the vesicle to promote membrane curvature and bud formation?
Coat proteins
Give the four steps of protein coating
- Coat assembly and cargo selection 2. Bud formation 3. Vesicle formation 4. Uncoating
Give the steps in the formation of COPII coated vesicles
- Coat-recruitment GTPases 2. Recruitment of adaptor proteins 3. Recruitment of cargo 4. Assembly of coat proteins vesicle budding
What are found at high concentrations in the cytosol in an inactive GDP-bound form (Sar1-GDP)?
Coat-recruitment GTPases
When coat-recruitment GTPases interact with a specific membrane bound guanine exchange factor (GEF), their bound GDP is replaced with what?
GTP
Upon binding GTP, what undergoes a conformational change that exposes its amphiphilic helix leading to insertion into the outer leaflet of the ER membrane?
Sar1
The mechanism of activation and membrane tethering is common for what?
Other coat-recruitment GTPases.
What are coat-recruitment GTPases?
- 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
Give the steps for protein binding to ER using GTPases
- 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
When the coat recruitment protein associates with the membrane it recruits what molecules to the ER membrane?
Adaptor molecules
The adaptor molecules bind to what?
The carboxy terminal tail domain of select transmembrane “receptor” proteins
Proteins bound to these transmembrane receptors are selected as the what?
Vesicle cargo
GTP- and membrane-bound Sar1 recruits what two adaptor molecules to the membrane?
The Sec23 and Sec24 adaptor molecules
Which adaptor molecule (Sec23 or Sec24) has affinity for the C-terminal tails of receptor proteins and is therefore tethered to the vesicle cargo.
Sec24
Which adaptor molecule (Sec23 or Sec24) can bind to multiple receptors? How many of them?
Sec24, one
Identify 1 - 5
1: Sec24 2: Sec23 3. Sar1-GTP 4. Cargo receptor 5. Cargo
What two coat proteins assemble to form the outer shell of the coat?
Sec13 and Sec31
The subsequent recruitment of additional adaptor proteins and outer coat proteins by membrane-bound GTP-Sar1 promotes
Membrane deformation and vesicle formation.
Once in the cytosol, hydrolysis loss of GTP by Sar1 results in what? (2 answers)
The disassembly of the coat-adaptor complex and generation of a naked vesicle.
It is thought that Sar1 has a slow rate of GTP hydrolysis. What is it that influences coat disassembly?
Time
What kind of vesicles form only if bud formation occurs faster than Sar1 GTP hydrolysis?
Fully formed vesicles
What are the molecular players in COPII coat formation?
- 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)
Formation of COP1 coated vesicles utilizes what components? (3 answers)
- Coat recruitment proteins 2. Adaptors 3. Cargo receptors
What does ARF mean?
ADP-ribosylation factor
ARF, or ADP-ribosylation factor, is used as the what?
The coat recruitment protein
What is the first step of the formation of COI vesicles?
ARF is recruited to the membrane through the exchange of its bound GDP for GTP through a membrane bound GEF
What is the second step of the formation of COI vesicles?
Binding of GTP induces a conformational change that triggers membrane insertion
What is the third step of the formation of COI vesicles?
Membrane bound ARF recruits coat proteins for coat formation and adaptors for cargo selection
What is the last step of the formatin of COI vesicles?
Assembly of sufficient coat proteins results in vesicle formation. GTP hydrolysis of ARF leads to coat disassembly in the cytosol
What are the molecular players in clathrin coat formation:
- Coat recruitment: (GTPase ARF1) 2. Adaptor proteins: (20 different adaptor proteins) (AP) 3. _-arrestin 4. Coat protein: (Clathrin complex) 5. Cargo receptors: (Transmembrane proteins)
Coat recruitment GTPase ARF1 is involved in the formation of what two kinds of coats?
COPI and clathrin coats
COPI and clathrin vesicles utilize a common coat recruitment GTPase. How do they differ?
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
What kind of vesicles were the first transport vesicles identified and hence, the best characterized?
Clathrin-coated vesicles
Clathrin-coated vesicles are involved in what? (2 answers)
- The endocytosis of transmembrane receptors 2. The delivery of lysosomal hydrolases from the TGN to the lysosome.
What does TGN mean?
Trans Golgi Network
Clathrin-coated vesicles are composed of what?
Clathrin
Each subunit contains three large and three small polypeptide subunits arranged in a three-legged structure called a what?
Triskelion
Clathrin triskelons assemble into a cage-like structure that promotes the formation of what?
Membrane vesicles
The last step in the formation of an internalized clathrin-coated vesicle requires a membrane tethered GTPase called what?
Dynamin
What kind of structure does dynamin assemble into around the neck of a forming bud?
A ring-like structure
Activation of dynamin and its associated proteins, leads to what two events?
- The ‘pinching off’ of the vesicle 2. Release into the cytosol.
In the cytosol the coat is released through the activity of what multiple proteins?
- HSC70, 2. cytosolic Hsp70 chaperone, 3. Auxillin, 4. A PIP phosphatase enzyme whose activity weakens the binding of the adaptor proteins to the membrane
What is essential for the formation of completely endocytosed vesicles?
Functional dynamin
What is X?
Dynamin
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?
Paralysis due to a failure in synaptic vesicle recycling.
What are available that are capable of interacting with a single coat protein?
Multiple adapter proteins
Even a single coat type can carry many different cargos depending on what? (2 answers)
The adaptor and the site of vesicle formation
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?
Retromer
Retromer formation occurs on endosomal membranes only when what three conditions have been met?
- 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)
Retromer formation can therefore only occur when and where?
At a defined time and on a defined membrane
Give some examples of retromers?
- Vps29 2. Vps35 (cargo binding) 3. Vps26 4. Snx1 (PI(3)P binding)
What cargo does retromer coat proteins cover?
Transmembrane proteins
What can undergo cycles of phosphorylation and dephosphorylation?
Sugar heads
Different organelles in the secretory pathway contain distinct sets of what due to the unique localization of PIP kinases and PIP phosphatases?
Phosphoinositides
Many of the proteins involved in vesicular transport recognize different what?
PIP species
Differential PIP pattern establishes a highly controlled flow of what?
Vesicular trafficking
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?
Rab proteins
Rab cycles between what two forms based on the status of their guanine nucleotide?
Cytosolic and membrane bound
When bound to GDP, Rab is what?
Inactive and cytosolic.
When bound to GTP, Rab is what?
Active and tightly associated with membrane.
What kind of Rab is found on both transport vesicles and target membrane.
Activated Rab
The specificity of vesicle-membrane fusion is controlled by what? Found where?
Protein markers found on the surface of the vesicle
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?
On the Correct target membrane
Rab proteins are example factors that act as what?
Surface markers
Monomeric GTPases cycle between cytosolic and membrane bound forms depending on what?
The guanine nucleotide bound
In the cytosol (membrane free), Rab is in a what form?
A GDP bound form
When activated by a membrane bound Rab-specific GEF, Rab exchanges GDP for what and becomes tightly bound to the what?
GTP, membrane
Membrane bound GTP-Rab recruits additional proteins called “what” to facilitate membrane tethering and fusion between the transport vesicles and target membrane?
Rab effectors
Membrane bound GTP-Rab recruits additional proteins called “what” to facilitate what? (2 answers)
Membrane tethering and fusion between the transport vesicles and target membrane
Individual Rab proteins can interact with multiple “Rab effectors” providing additional layers of what?
System flexibility.
Once a vesicle has been tethered to a target membrane by a Rab effector protein, what happens next?
The two lipid bilayers must be brought in close proximity to facilitate fusion and vesicle unloading.
A fusion event is mediated by another group of proteins called what?
SNAREs.
Give the steps of Rab mediated vesicle capture:
- Tethering 2. Docking 3. Fusion
What proteins are membrane bound proteins that mediate the fusion of transport vesicles with their target organelle?
SNARE proteins
What does SNARE stand for?
Soluble NSF Attachment Receptor
There are over 60 different SNARE proteins that are generally broken down into what two complementary sets:
- v-SNARE (vesicle) 2. t-SNARE (target)
Where are v-SNARE proteins found?
On transport vesicles
Where are t-SNARE proteins found?
On target compartments
SNAREs have what two important roles:
- 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.
The nomenclature of v-SNARE and t-SNAREs has become obsolete as more and more what proteins have been identified?
SNARE
Which SNARE (v-SNARE or t-SNARE) are single polypeptide chains and always a transmembrane protein?
v-SNARE
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.
t-SNARE
v-SNARE association with t-SNARE forms a what?
4-_-helix bundle
The 4-_-helix bundle is so stable that even elevated temperatures and strong detergents are unable to do what to them?
Pry them apart
The availability of SNAREs for membrane fusion are regulated by what?
Rab proteins.
t-SNAREs in target membranes are often associated with inhibitory proteins that must be released prior to their interaction with what?
v-SNAREs
Rab proteins and their effector proteins control what?
The release of these inhibitory proteins and ultimately membrane fusion.
Identify A, B and C
A: v-SNARE (synaptobrevin) B: t-SNARE (Snap25) C: t-SNARE (syntaxin)
Intertwined SNARE complexes catalyze membrane fusion using the energy released when the _-helices do what? Excluding any what?
Wrap around each other to pull the two membranes together excluding any water.
In close contact, the outer lipid bilayer will fuse first, followed by what fusion?
Inner bilayer fusion
Give the steps of SNARE mediated vesicle membrane fusion:
- Water is released 2. Stalk formation 3. Hemifusion 4. Fusion
The interaction between v- and t-SNARE proteins is very strong, so strong that the complex needs to be physically pried apart after what?
Membrane fusion.
What use the energy of ATP hydrolysis to unravel the SNARE complex to prepare them for the next round of fusion?
The cytsolic proteins, NSF and SNAP
What does NSF stand for?
N-ethylmaleimide-sensitive factor
What does SNAP stand for?
Soluble NSF attachment protein
Proteins destined for organelles in the secretory pathway include what organelles?
The ER, the Golgi, the lysosome, the plasma membrane or proteins destined for secretion from the cell
Proteins start by co-translational transport into the ER through the what?
Sec61 membrane transport channel
In the ER, these proteins move along in the pathway by what?
Vesicle mediated transport
Proteins imported into the ER are processed how?
Amino terminal signal removed, modified by glycosylation, and correctly folded
Only proteins that are correctly folded ER can do what?
Leave the ER
What system ensures that only folded proteins are selectes as cargo for incorporation into transport vesicles?
The calreticulin/calnexin chaperone system
Proteins targeted to the Golgi or later organelles in the secretory pathway will leave the ER in what vesicles?
COPII coated vesicles.
Vesicles bud from specialized sites on the ER that lack ribosomes called what?
Transitional ER or ER exit sites
Cargo selection is an active one; soluble proteins contain amino acids sequences that are recognized by what? Function as what?
Transmembrane proteins that function as receptors for COPII transport.
Proteins that are found at high concentrations can also get packaged in what? Without what?
Transport vesicles without selection
Proteins intended as ER resident proteins can be mistakenly incorporated into what?
Transit vesicles
These accidental passengers are returned to the ER through the what?
The ‘retreival’ pathway
Identify A - D
A: Forming ER transport vesicle
B: Sar1-GTP
C: Subunits of COPII coat
D: Chaperone proteins (bound to folded or misfolded proteins)
In addition to the calreticulun/calnexin monitoring system, unassembled proteins can be retained in the ER by what?
The ER lumenal chaperone BiP
How is an IgG antibody composed/assembled/transported in the ER?
- 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
What binds to ER export signals preventing their recruitment into budding vesicles?
BiP
When assembled ,the BiP is released exposing the ER export signal promoting transport to the what?
Golgi