Chapter 11 Anki

Why is pH important in endosomes?

pH changes the conformation.
It separates receptors from their ligands for recycling.

Why do we need flippases?

Synthesis of phospholipids only occurs in one side of the layer.

Where are sphingomyelin and glycolipids synthesized?

In the Golgi apparatus.

Where are nuclear proteins translated?

On free ribosomes in the cytosol

Where are ER proteins identified to be brought into the ER?

ERGIC or Golgi transports them back into the ER.

Whats the pH of the Golgi in the cis compared to the trans location?

• Cis: More basic near ER around pH 7

• Trans around ph 6-6.5

What’s the recycling process called? Explain process

Autophagy: Cellular materials are enveloped in a membrane and then fused with a lysosome. Degraded and recycled.

What's this process

Autophagy: learn mechanism

What's the role of calreticulin?
What does it recognize + process:

Has a folding sensor that checks for proper folding by monitoring exposed hydrophobic regions. 

Recognizes hydrophobic parts of proteins

1. If nothing is found, process is passed on to the Golgi.
2. If severely misfolded, the protein is targeted for degradation by ERAD. 

What's the function of the basolateral side?

Transport of molecules out of the cell into the body.

What's the defense process of lysosomes?

Lysosome's can fuse with endocytic vesicles –capture pathogens –> degrades of the invaders.

What structure prevents intestinal leaks on both apical and basolateral sides?

Tight junctions

What small GTP-binding protein helps vesicle formation?

Arf (ADP-ribosylation factor)

What signals directs nuclear proteins to the nucleus?

NLS: Nuclear Localization Signal, recognized by importins. 

What side is polarized and faces the intestine? What's its function?

Apical side: Focuses on nutrient absorption and digestion via microvilli

What recognizes the signal sequences? Function

Signal Recognition Particle (SRP)
Role: This directs “nascent” proteins to the ER via interactions with the SRP receptor.
"nascent": proteins in process of being translated by ribosome. 

What proteins drive vesicle formation?

Clathrin, COPI, and COPII coat proteins.

What protein initiates autophagy?

Atg9, which docks at the ER membrane.

What process degrades the proteins? Details of process

The ER-associated degradation (ERAD) Process: 
1. Misfolded protein are identified
2. Returned to the cytosol
3. Degraded by the ubiquitin-proteosome system

What pinches the membrane to form a vesicle?

Dinamine

What makes epithelial cells polarized?

They have distinct apical and basolateral (sides) domains with different functions.

What is transport vesicle composed of?

1. Membrane proteins
2. Lumenal secretory proteins + receptors
3. Donor Membrane

What is the translocon?

A channel in the ER membrane through which nascent proteins are translocated during translation.

What is the structure of sphingomyelin?

Ends up in?

A phosphorylcholine head group and a tail.

Ends up in the plasma membrane

What is the structure of glycolipids? Ends up in?

Structure: Has a sugar residue head and tail. 
Ends up in membrane.

SAME AS SPHINGOMYELIN

What is the Signal Hypothesis? Does the signal remain on the protein in the ER?

Proteins have a N-terminal signal sequence that directs ribosomes to the ER for translocation. The signal comes out once in the ER, its removed.

What is the precursor for sphingomyelin and glycolipids?

Ceramide, which is made in the ER.

What is Gaucher Disease? 

Lysosomal storage disease, where the glucocerebrosidase enzyme is dysfunctional. 

What is chathrin?

A miltimeric protein complex with a triskeleton structure consisting of 3 arms that extend from the central hub.

What is autophagy?

The process of recycling cellular components through autophagosome formation.

What is a signal sequence?

Include a stretch of hydrophobic residues preceded by one or two basic residues.

What is a phagophore?

The growing double membrane that engulfs cytoplasmic material during autophagy.

What is a lysosome? What do all proteins in lysosome end up as?

Digestive enzyme.
All proteins end up as a sugar called Mannose-6-phosphate.

What happens when protein folding is inefficient? Sent to...

Sent to the proteosome (trash)

What happens when it gets to the target membrane?

1. The transport vesicle then docks at its target membrane

2. The coat is removed.

3. The vesicle fuses with its target.

What happens when glucocerebrosidase is defective?

Substrates build up in lysosomes, causing cellular dysfunction.

What happens to the signal peptide after a protein enters the ER?

It is cleaved off by signal peptidase

What happens to early endosomes?

1. Transport vesicles carrying acid hydrolases from the trans-Golgi network 

2.  Then fuse with late endosomes

3. Then these mature into lysosomes as they acquire a full complement of lysosomal enzymes.

What happens if the system gets overwhelmed from an overload of misfolded proteins?

Activates the UPR (unfolded protein response)

1. Expands the ER production of chaperones
2. Inhibits translation
3. Slows process down

*** IF CELL DOESN'T CATCH UP, CELL PROGRAMED DEATH**

What facilitates turning the phospholipids into the inner membrane?

Flippases: Allows for the passage of polar head groups through the membrane.

What does the illustrations show about clathrin assembly?

Shows how a clathrin coat dives membrane warping during vesicle budding. 

What does glucocerebrosidase normally do?

It breaks down the glycolipid into glucosylceramide & ceramide

What do these other proteins take? Name of Pathway?

Secretory Pathway: If protein follows through, it could be completely secreted from the pathway

What do the three receptors do?

All three activate transcription of UPR target genes

PERK phosphorylates eIF2 which globally reduces translation. 
     - Reduces exchange of GTP/GDP

What determines the final dimensional conformation of the protein?

The primary sequence

What chaperon facilitates folding within the ER?

BiP

What changes as endosomes mature?

The pH decreases

What causes Atg9 vesicle docking?

Interaction between Atg9’s cytosolic domain and Atg protein complexes.

What can the enzymes in lysosomes degrade?

Biomolecules including proteins, lipids, nucleic acids, and carbohydrates.

What are the directions of vesicle transport for COPI, COPII, and Clathrin?

COPI: trans-Golgi → cis-Golgi → ERGIC → ER

COPII: ER → ERGIC → cis-Golgi

Clathrin: trans-Golgi → endosome/lysosome/cell surface and back

What are tail-anchored proteins, and how are they inserted?

Proteins with a C-terminal transmembrane domain inserted post-translationally via the GET pathway to the ER.
     - C-terminus inserted in membrane via GET
     - Requires ATP to function

What are proteins that decide to stay in the ER called?

ER resident protein

What are lysosomes?

Membrane-bound organelles in eukaryotic cells are filled with a variety of hydrolytic enzymes.

The primary function is to break down and recycle various cellular materials.

What are GPI Anchors?

The addition of glycolipids to the C-terminus of proteins anchors them to the membrane.

     - Anchors proteins to membranes (esp. outer leaflet)

     - Different proteins can end up in the same location and be processed the same way because they share this anchor.

     - Anything that is cytosolic stays inside (cytosol region) of an organelle.

Vesicle is transported by ______ proteins and _______ filaments to its target.

motor, cytoskeletal

Vesicle docking and fusion: Process

1. Rab proteins on vesicle membrane binds to tethering factor on target membrane.
2. Once they get close they form a complex (bind) between SNAREs
     - v-SNAREs: membrane –>targets t-SNAREs (receptors)
3. Uncoat the membrane of the vesicle.
4. The coiled-coiled formation between SNAREs tighten and zip together, bringing the vesicle and target membrane into close proximity. 
5. Membrane fuses

True or False: Vesicular transport is how protein are moving back and fourth between different sites. 

True. 

True or False: The Smooth ER is abundant in cells with acitve lipid metabolism 

True 

Transport to and retrival from the Golgi facilitated by:

Transport vesicles

Translocon: True or False
Transmembrane particles can wiggle its way out of the channel into the membrane of the ER.

True: Because of hydrophobic properties.

Translation on free ribosome remains in what organelles?
ER-bound ribosomes?

Free ribosomes: Translate proteins – stay in the cytosol, nucleus, or mitochondria.
ER-bound: Secretion, insertion into membranes, or delivery to other organelles 

The fusing of the autophagosome's outer membrane and a lysosome produces a ______

autolysosome

The expanded membrane forms a _________ that encapsulates cytoplasmic substance

phagophore

Structure of a proteoglycan: 

A core protein modified with long sugar chains called glycoaminoglycans (GAGs).

Smooth ER: Synthesis of hydrophobic phospholipids process:

1. Glycerol phospholipids are synthesized in ER from cystolic precursors
2. 2 fatty acids linked to CoA carrier joins to G3P, yields phosphatidic acid (PA)
3. PA instered into the membrane
4. Phosphotase turns PA into diacylglycerol
5. Different polar head groups can then be attached to diacylglycerol to generate a variety of phospholipids. 

Smooth ER: Does it contain ribsosomes? Translation

No and no

Smooth ER: Are the membrane lipids hydrophobic or hydrophilic? How are they synthesized?

Hydrophobic; synthesized in association with already existing membranes (ER) rather than in cytosol.

Smooth ER is also the site of _______ synthesis, from __________ in the ER

hormone, cholesterol

Secretory Pathway: 

ER –> Golgi Apparatus –> Secretory Vesicles –> Cell exterior

EGSX (Hint) Goes in order

Route of Protein Export FROM the Golgi Apparatus. 4 Methods

Proteins sorted in the trans-golgi network.

1. Lysosome: Go there
Example: Mannose-6-phosphate receptor
1. Receptor recognizes protein with mannose-6-phosphate sugar
2. Brings it to vesicle that goes to the lysosome.

2. Plasma Membrane: membrane
     - Either brought directly or via recycling endosomes.

3. Regulated Secretion: Secrete
     - Proteins sorted in distinct seculatory granules.

4. Lysosomes pt.2: Turn into it
    - Proteins can be targeted to late endosomes to turn into lysosomes. 

Review: Nuclear Protein are imported to the nucleus by _____. This is followed by translation on _____ __________.

Importins, "free ribosomes".

Quality Control in the ER: When UPR activated: _ receptors are activated.

3 Receptors:

1. 1. IRE1

2. 2. ATF6

3. 3. PERK

Proteins, other than nuclear proteins, are trafficked differently.
These proteins include:

1. Plasma Membrane proteins
2. Secreted proteins
3. ER proteins
4. Golgi proteins
5. Lysosomal proteins

Proteins synthesized in _____ ER. Phospholipids in the _____ ER

rough, smooth

Orientation of membrane proteins:

Once inserted, the orientation is fixed (cytosolic side stays cytosolic).
But the N and C terminus can be in either direction or go through the membrane multiple times.

Organelles pH: Importance and pHs

Think different pH important: you dont want it folding at the wrong location.
     - pH: Helps tell it if its in the right pH to start folding. 
**Mitochondria: only site where pH is higher with a 7.8 or 7.4. Basic.

Once encapsulated and phagophore detaches, it forms a double membrane called an __________

Autophagosome

Lysosomes can release their contents in the cytoplasm, leading to ___ ______

cell death

Lysosomes are a "digestive system" of the cell, breaking down: 2 Things

1. External materials brought into the cell
2. Worn-out cellular components

Key Study: What was the purpose of the pulse-chase experiment in pancreatic cells?

To trace the pathway of newly synthesized protein as they move through the cell for secretion (pathway)

Key Study: Process of the Experiment:

1. "Pulse-labeled" newly synthesized proteins with radioactive "hot" AAs

2. "Chased" with non-radioactive "cold" AAs

3.  Tracked the location of the radioactive protein through time. (Golgi)

Inside the autolysosome, the inner membrane and its contents are _______

digested.

Insertion of a protein with multiple transmembrane sequences:

During translation the protein bypasses several times trough the translocon, everytime the transmembrane domains can slip past the translocon.

Insertion of membrane protein via internal transmembrane sequence

Protein is inserted to ER and it mentains that orientation.

2 scenrios just know 

1. N comes out and then back in, then back in, when ends inside lumen.

2. N-terminus comes back out again into the cytosol.

Insertion of a transmembrane protein with a cleavable signal: 

Protein is inserted to ER and it maintains that orientation.

     - Either N or C terminus can be inside the ER lumen.

In the liver, smooth ER has enzymes that metabolize _____-_____ compounds

lipid-soluble

If Arf wasn't for the lipid anchor, what would it be?

A transmembrane protein

How does the smooth ER detoxify drugs?

Contains enzymes that metabolize lipid-soluble compounds. (last flashcard)

Detox enzymes INACTIVATE drugs. Concerts them into water-soluble compounds. Eliminated in urine. 

How does the autophagosome membrane expand? 2 Reasons

Autophagosome precursor forms from vesicles forming together.

1. By receiving lipids from the ER via Atg2
2. Fusing with ER-derived vesicles.

How does microvilli increases nutrient absorption on the apical membrane?

Microvilli that increase surface area.

How does clarithin complex form? Structure name?

Three arms of clathrin interact with each other to form interlaced complexes.
Forms a lattice structure.

HOW are the proteins identified to be brought into the ER? Protein example?

These proteins have targeted sequence at the carboxyl terminus that directs retrival back to the ER. 

Protein example: KDEL

How are proteins targeted to the ER?

Signal Hypothesis

How are proteins targeted for export from the ER?

1. Some have carbohydrate signals that direct transport into vesicles
2. Unmarked proteins can also be transported out of ER.

Golgi Apparatus: Function

Proteins from the ER are processed and sorted for transport to endosome, lysosomes, the plasma membrane, or section.

Protein ex: Glycolipids, Sphingomyelin

Golgi Apparatus Structure: (from ER) top–>down

Composed of flattened membrane-enclosed sacs (cisternae) and vesicles.

1. cis: Vesicles that come IN from the ER
2. medial: 
3. trans: Exit part of the Golgi, sorting takes place
     - pH is all different in these 
4. Trans Golgi Network 

Glycolipids: Process of N-linked oligosaccharides in the Golgi.
What does it play an important role in? How do we distinguish?

Begins in the ER; further modifed in the Golgi.
PLAYS IMP. ROLE IN:
 

Distinguish factor: Different combination of sugars

Function of Proteoglycans:

Main: To be added to the Golgi.

• Tissue hydration and resilience

• Extracellular Matric Structure

• Cells signaling

• Cell adhesion

• Barrier Function

• Joint Lubrication

Formation of Clathrin-coated vesicles: Process

1. Arf GEF turns Arf1/GDP to GTP 
2. Adaptor protein (Arf, Clathrin, Receptors) recognizes GTP
3. Receptor chooses what goes into vesicle, picks up adaptor
4. Dynamin constricts the neck of the vesicle and drives membrane fission.

ER is also a major site of cholesterol and ceramide. What does ceramide get turned into in the Golgi?

Ceramide gets turned into glycolipids or sphingomyelin in the Golgi.