MCB Final PQ Exam 3

What is a vesicle?

A membrane bubble.

How is a vesicle formed from an existing membrane?

By budding or pinching off from a donor membrane.

What is the source membrane for a budding vesicle called?

The donor membrane.

Where does a vesicle place cargo after fusing with its destination?

Into the target organelle.

How can cargo travel from the ER to the cell exterior without crossing a membrane?

Inside vesicles.

What direction is movement from the nucleus toward the outside of the cell?

Anterograde.

What direction is movement from the cell surface toward the nucleus?

Retrograde.

Is endocytosis retrograde or anterograde?

Retrograde.

Is retrieval or recycling retrograde or anterograde?

Retrograde.

Is secretion retrograde or anterograde?

Anterograde.

What property of sugars permits phosphorylation at several locations?

They are polar.

How does phosphate addition change molecular charge?

It adds negative charge.

What type of molecule is glycerol-based in these notes?

A lipid.

What does fatty-acid tail bond order control?

Biochemical properties.

How are biochemical properties of fatty-acid tails controlled?

By the bond order of their hydrophobic tails.

What membrane feature helps determine organelle identity and curvature?

Lipid composition.

What membrane feature selectively recruits trafficking proteins?

Lipid composition.

How do Rab proteins help define membrane compartments?

Their spatial compartmentalization defines them.

What regulates progression of vesicle transport by Rab proteins?

Rab GTPase regulation.

Where is active Rab-GTP located?

On a membrane.

What does membrane-bound Rab-GTP help coordinate?

Budding; translocation; and docking or fusion.

Where is inactive Rab-GDP located?

In the cytosol.

What keeps Rab-GDP cytosolic?

Rab GDP Dissociation Inhibitor or GDI.

Why must Rabs be recycled?

They must return to their donor compartments.

How does a protein coat help form a vesicle?

It shapes the bud and concentrates cargo on the donor membrane.

Which route does COPII coat support?

ER to Golgi transport in the anterograde direction.

Which route does COPI coat support?

Golgi-internal traffic and retrograde transport back to the ER.

Which routes can clathrin coat support?

Golgi to endosome or plasma membrane and inward from the plasma membrane.

In what special context is Retromer noted in the source material?

Certain viral infections.

What does COP stand for?

Coat Protein Complex.

How can coat identity affect a vesicle?

Different coats produce different-sized vesicles.

What limits how many proteins fit in a transport carrier?

The capacity of a vesicle.

What gives a vesicle its structure and shape?

Coat proteins.

What evolutionary relationship is suggested for coat proteins?

They are structurally similar to nuclear pore proteins or NUPs.

How do the inner and outer layers of a coat assemble?

Sequentially.

What is the COPII inner layer?

Sar1 GTPase with Sec23 and Sec24.

What is the COPII outer layer?

Sec13 with Sec31.

How is COPI organized compared with COPII?

COPI is a single layer built around Arf1 and COP subunits.

What makes up a clathrin coat's inner layer?

AP adaptor complexes such as AP1 through AP5.

What makes up a clathrin coat's outer layer?

Clathrin heavy and light chains.

How does a GEF promote coat assembly?

It stimulates budding or coat recruitment while the GTPase is GTP-bound and membrane-associated.

How does a GAP promote coat removal?

It stimulates uncoating; the GDP-bound GTPase leaves the membrane.

Which GTPase GEF and GAP define the COPII system?

Sar1; Sec12; and Sec23.

Which GTPase GEFs and GAPs define the COPI system?

Arf1; ArfGEFs; and ArfGAPs.

How is AP1 recruited for clathrin traffic?

By Arf1.

How is AP2 recruited for clathrin traffic?

By phospholipid PIP2.

What was Arf required for in the cholera-toxin study?

Modification of adenylate cyclase.

What forms can vesicular cargo take?

Soluble cargo; membrane-associated cargo; or tethering and fusion machinery.

How can soluble cargo enter a vesicle?

By binding a coat receptor; binding an adaptor to a coat receptor; or bulk flow without a receptor.

Which coat recognizes ER-export signals on the cytosolic face?

COPII.

What are examples of ER-export signals used with COPII?

Di-acidic export signals.

Which coat recognizes KDEL and KKXX return-to-ER signals?

COPI.

Where is the COPI KKXX return signal found?

At the cargo C-terminus.

Which coat can recognize linear motifs conformational signals and modifications?

Clathrin.

What cargo receptor is associated with COPII?

Sec24.

What cargo receptor is associated with COPI?

Arf1.

What cargo receptors are associated with clathrin?

Various adaptor proteins.

How do BAR domains bend the plasma membrane?

Their positively charged helices attract negatively charged phospholipid heads.

What vesicle-forming event can gentle membrane bending begin?

Budding of a clathrin-coated vesicle.

How do COPI and COPII coats drive budding?

By coat polymerization.

Why does clathrin-mediated budding need actin?

Large clathrin-coated vesicles need an additional pushing force.

What is scission in vesicle transport?

The pinching off of a vesicle through strong membrane-curvature distortion.

Which factors are associated with scission in COPII COPI and clathrin traffic?

Sar1 for COPII; Arf1 for COPI; and dynamin with epsin for clathrin.

What must occur before a vesicle can travel on the cytoskeleton?

It must be uncoated.

How does COPII uncoat?

GTP hydrolysis produces Sar1-GDP.

How does COPI uncoat?

GTP hydrolysis produces Arf1-GDP.

How does a clathrin coat uncoat?

ATP hydrolysis by auxilin and Hsc70.

What direction of movement is associated with dynein in these notes?

Toward the Golgi or anterograde transport.

What direction of movement is associated with kinesin in these notes?

Toward the nucleus or retrograde transport.

What motor proteins are associated with clathrin traffic?

Kinesin; dynein; and myosin.

Besides the centrosome what can function as an MTOC?

The Golgi.

Which microtubule end is anchored at the Golgi?

The minus end.

What is the anterograde route through the Golgi?

ER to cis Golgi to trans Golgi.

What is the retrograde route through the Golgi?

Trans Golgi to cis Golgi to ER.

How do tethering proteins enable SNARE-mediated fusion?

They bring a vesicle close enough to the target membrane for SNAREs to interact.

What does SNARE stand for?

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor.

Does SNARE composition dictate compartment identity like Rab composition?

No.

What energy source is needed to unwind SNAREs?

ATP.

Where are v-SNAREs found?

On vesicles.

Where are t-SNAREs found?

On target compartments.

What charged residues can occupy the central position of a SNARE helix?

Glutamine or arginine.

How does co-translational ER insertion begin?

SRP recognizes a nascent protein at a rough-ER ribosome.

What machinery is required for co-translational ER insertion?

SRP; the SRP receptor; and the gated Sec61 translocator.

How does post-translational ER insertion begin?

Translation occurs on a free ribosome.

What machinery supports post-translational ER insertion?

Cytosolic chaperones; Sec61; and ER-lumen chaperones such as BiP.

About what proportion of proteins need to pass through the ER?

About 30 percent.

What components make up the Signal Recognition Particle?

One noncoding RNA and six proteins.

Why can SRP bind a signal sequence?

Its methionine-lined binding pocket is hydrophobic.

What does SRP binding do to a ribosome?

It pauses translation by covering the eEF entry site and exit tunnel.

What drives a nascent polypeptide through Sec61 during co-translational insertion?

Continued translation elongation.

Where does Sec61 deliver the nascent polypeptide?

Into the ER lumen.

How are SRP and its receptor unusual as GTPases?

They do not use GEFs or GAPs.

What does a sorting sequence allow a protein to enter?

The Sec61 translocator.

How does BiP support post-translational translocation?

It uses ATP to pull the protein into the ER lumen.

What does BiP stand for in ER import?

Binding protein.

How do COPII and COPI differ in route and cargo-sorting purpose?

COPII exports cargo from ER to Golgi; COPI returns KDEL or KKXX cargo from Golgi to ER.

How do the three pinocytosis modes differ in coat budding mechanism and speed?

Clathrin uses amphiphysin plus actin and is fast; caveolin uses lipid composition and is slow; no coat uses actin membrane ruffles and is induced.

How is the cholesterol-uptake particle organized?

A phospholipid monolayer surrounds it; apolipoprotein B protrudes at the surface; and cholesteryl esters occupy the core.

How does the phagocytosis diagram connect recognition to engulfment?

Antibodies on a bacterium bind Fc receptors; PI3-kinase changes PI(4 5)P2 to PI(3 4 5)P3; and actin forms the pseudopod.

How are t-SNAREs and v-SNAREs distinguished on the Golgi-to-lysosome clathrin route?

Two syntaxins plus VTI1 are t-SNAREs; VAMP is the v-SNARE.