Protein Sorting

Question 1

Where is a terminal start-transfer sequence of a transmembrane protein?

Answer 1

N-terminus as it gets to translocator

Question 2

What is the stop-transfer sequence of a protein?

Answer 2

The area where the protein stops and leaves translocator

Question 3

Is the stop-transfer sequence hydrophilic or hydrophobic?

Answer 3

Hydrophobic

Question 4

What common domain serves as the membrane-spanning part of the stop transfer signal?

Answer 4

A single alpha helix

Question 5

What’s an internal signal sequence?

Answer 5

Signal sequence not on the end of a protein

Question 6

In an internal signal sequence, what determines if the n-terminus or c-terminus will be on the ER lumen side?

Answer 6

Positively charged amino acids > cytosol

Negatively charged > lumen

Question 7

What part of a double-pass transmembrane protein would get stuck in a membrane?

Answer 7

Start + stop transfer sequence

Question 8

What sequences are present in multipass proteins that get stuck in membranes?

Answer 8

Lots of start & stop transfer sequences

Question 9

How does ‘rough ER’ get its name?

Answer 9

It’s the part with a lot of polyribosome sequences on it

Question 10

What does a signal sequence do to a channel once it gets to it?

Answer 10

Pushes out the plug in the channel

Question 11

What ways can a protein get stuck in the membrane?

Answer 11

Single-pass, double-pass, multipass

Question 12

What ways can a protein get stuck in the membrane?

Answer 12

Single-pass, double-pass, multipass

Question 13

What functions does the ER have besides helping protein synthesis?

Answer 13

Add N-linked oligosaccharides

Question 14

What does ‘N-linked’ oligosaccharide mean?

Answer 14

Attached to nitrogens of asparagine side chains

Question 15

Why do proteins have oligosaccharides added to them?

Answer 15

Signal pathway recognition

Question 16

Where does dolichol hang out?

Answer 16

lipid bilayer of ER membrane

Question 17

What does dolichol do?

Answer 17

It’s a carrier that pre-assembles oligosaccharides for protein transfer

Question 18

Why are proteins glycosylated? (in golgi)

Answer 18

Help fold proteins, help for cell recognition / adhesion

Question 19

What does ‘o-linked’ oligosaccharide mean?

Answer 19

Attached to hydroxyl oxygen of serine, threonine, tyrosine, or other oxygens

Question 20

What adds glucose to proteins that aren’t completely folded?

Answer 20

glucosyl transferase

Question 21

What does calnexin do?

Answer 21

ER chaperone, binds to proteins with single terminal glucose

Question 22

When a protein is fully folded, can it still have an oligosaccharide on it?

Answer 22

Yes, N-linked

Question 23

What is a cycle of adding glucose and then trimming it for?

Answer 23

To get the protein folded properly

Question 24

Where is the protein as oligosaccharides are getting attached?

Answer 24

Still going through Cytosol/ER lumen membrane

Question 25

What happens to misfolded proteins?

Answer 25

Get ubiquitin attached to them, then sent to proteosome to get rekt

Question 26

What ubiquitinates misfolded proteins?

Answer 26

E3 ubiquitin ligase

Question 27

What's the unfolded protein response?

Answer 27

Signalling protein to get more expression of ER proteins that fold new proteins properly

Question 28

How does the unfolded protein response turn on?

Answer 28

Accumulation of misfolded proteins signals transcription activation in nucleus

Question 29

What's a GPI anchor?

Answer 29

Protein that binds to C-terminus of some membrane proteins

Question 30

How are lipid bilayers assembled in the ER?

Answer 30

Binding protein attaches ot fatty acid, then it binds to ER membrane Polar head gets modified Lipids leave

Question 31

What needs to happen for lipids to flip from one side to another?

Answer 31

Enzymes have to catalyze 'Scramblases' equilibrate to create symmetry (one-way) Flippases do the same (two-way)

Question 32

How do cholesterol / ceramide get produced?

Answer 32

ER makes them

Question 33

When is a signal sequence on a single-pass transmembrane protein useful a second time before cleavage?

Answer 33

It gets recognized by protein translocator and then acts as start-transfer signal

Question 34

What distinguishes start and stop transfer sequences in multipass transmembrane proteins?

Answer 34

Nothing really, it's just based on which sequence goes in first ('relative order in growing polypeptide chain')

Question 35

How might a protein stay in the ER after translation?

Answer 35

KDEL / KDEL receptor: amino acid sequence at c-terminus of protein keeps it there

Question 36

What does 'glycosylated' mean?

Answer 36

Carbohydrates (sugars) are added to something

Question 37

What does an oligosaccharyl transferase do?

Answer 37

Helps attach sugar precursors (glycosylate) to proteins in lumen rom dolichol

Question 38

What's the temporal progression of a new dolichol lipid look like?

Answer 38

Attach to lipid bilayer > phosphorylated at cytosol side > sugars added at cytosol side > FLIPS > more sugars added to chain on lumen side > 14 sugars total on it

Question 39

What adds sugars to N-glycosylation sites?

Answer 39

oligosaccharyl transferase

Question 40

What's the sugar system that lets proteins get folded properly?

Answer 40

Glucose trimming (glucosidase) > glucose addition (glucosyl transferase) > folding (calnexin/reticulum) until it's folded

Question 41

What marks time a protein has spent in the ER?

Answer 41

N-linked oligosaccharides - proteins that can fold faster than sugar is removed don't get degraded

Question 42

If there are so many misfolded proteins that calnexin/reticulin can't bind them fast enough, what happens?

Answer 42

UPR (unfolded protein response): Sensors (IRE1, PERK, ATF6) sense the misfolded proteins and activate gene expression

Question 43

Where on proteins do GPI anchors attach?

Answer 43

C-terminus

Question 44

Why are scramblases necessary for bilayer formation?

Answer 44

Lipids are added to bilayer from cytosol side, so ER side doesn't have any heads. Scramblases need to flip them to make the bilayer equilibrate

Question 45

What do flippases do?

Answer 45

Also flip lipids, but specific lipid heads to create asymmetry

Question 46

What is ceramide? How is it made? Where?

Answer 46

Just the head of a lipid, useful for signalling. Condense serine with a fatty acid. Made in ER