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BIOL 331 > Unit 3 (post-test 1) > Flashcards

Unit 3 (post-test 1) Flashcards

1
Q

what are more than half of animal membranes associated with

A

Over half are associated with the ER

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2
Q

where in the cell is the ER?

A

Extends enough such that all regions of the cytosol are close to at least one part of its membrane.

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3
Q

what do we call the lumen of the ER?

A

ER cisternal space

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4
Q

does the ER make lipids?

A

yes

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5
Q

where is Ca+ stored in the cell?

A

in the ER

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6
Q

What kind of proteins are initially sent to the ER?

A

Proteins that are
-on the outside of the cell
-resident to ER lumen
-resident to golgi
-resident to lysosomes
-resident to other endomembrane system compartments

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7
Q

Explain the difference between the rER and the sER

A

rER has ribsomes. It is where protein comes in and is made.
Smooth ER is where vesicles bud off (this part is called “transitional ER” It also makes lipids and stores calcium.

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8
Q

What kind of cell would have more rER? What kind of cell would have more sER? Which of the two ERs is more common to have more of?

A

More rER: cells that secrete a lot of protein
More sER: cells that do lots of lipid metabolism ex:hypatocytes which need lipoproteins OR that use Ca+2 ex: muscle cells that use it for contraction/relaxation

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9
Q

how do we isolate the ER and its two parts?

A

Homogenize cells to break the ER into small pieces
Due to their membrane, these pieces will autoreseal into closed vesicles called microsomes
Use gradient centrifugation to isolate (uses sugar gradient that causes things to move to their level of equal density after centrifugation)
The rough ER will isolate itself bc its heavy
the smooth ER will remain with the other organelles (golgi, endosome and mitochondria)

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10
Q

how did we learn about the ER signal sequence?

A

Microsomes act like mini ERs for cell-free experiments
In an experiment done with no microsomes an ER protein was found to be bigger than when it is normally secreted by a cell
This is bc the N-terminal leader peptide gets cut off when its in a cell
We thus hypothesis that this peptide is a signal sequence that directs to the ER membrane and is then cleaved via signal peptidase after translation.

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11
Q

what does SRP stand for?

A

Signal-Recognition Particle

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12
Q

What is the SRP

A

complex of 6 diff proteins + a small RNA that acts as a receptor for signal peptide.

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13
Q

Where can we find SRP?

A

It cycles between the cytosol and the ER membrane where it binds the SRP receptor

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14
Q

How can SRP bind multiple different signal shapes/sizes?

A

It has a flexible and large hydrophobic pocket of Met (flexible/unbranched a.a.) residues

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15
Q

What is a signal peptide?

A

A central stretch of 8-9 hydrophobic a.a.

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16
Q

what role does the SRP play in protein import?

A

It has a pause domain to ensure ER-destined proteins are never fully transcribed in the cytosol (could be bad if its a hydrolase)
It prevents misfolding
It means we don’t need chaperones to keep the protein unfolded

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17
Q

in what order does SRP binding occur?

A

SRP binds protein signal sequence
SRP binds SRP receptor
Everything (including the ribosome) is brought to the ER membrane protein translocator
SRP and SRP receptor released
Translocator does its job
*works with a polyribosome too
*once translation is done, the ribosome leaves to be free but the mRNA stays to be used by an ever-changing ribosome population

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18
Q

explain how the ER signal sequence is used twice

A

Firstly it is used to bind the SRP then, it is used to bind the translocator to open its pore.

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19
Q

which form of transport requires energy in the ER? Co-translational or post-translational

A

Post-translational

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20
Q

Explain what the ER protein translocator is

A

A protein made of 4 sec61s (the Sec61 complex) and its associated complexs. It has a small pore created via alpha helices and is gated by a short alpha helix such that it is closed when it rests. The pore allows unfolded soluble proteins through and a side opening to allow proteins into the membrane.

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21
Q

how does post-translational transport happen in the ER

A

Sec 62 and SEc 63 are transmembrane proteins on the lumenal side. They bring BiP chaperone proteins (which have a high affinity for unfolded proteins) onto the polypeptide chain. Bip then uses ATP to bind and unbind the polypetide as it comes out. This prevents it from slipping back in and promotes FWD motion so that more Bips can bind.

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22
Q

Is post- or co-translational transport more common in the ER?

A

Co-transport is.

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23
Q

How do bacteria push proteins through their ER translocator?

A

Sec A ATPase which is a motor protein attatched to the translocator.

24
Q

how do soluble proteins get into the ER

A

Signal binds pore
Polypeptide moves through the pore of the translocator as a loop.
Once protein grows to a certain length, the ER signal peptidase cleaves the signal
Signal release into membrane where it is degraded by membrane-bound ER proteases.

25
Q

how do single pass transmembrane proteins with an internal signal sequence get into the ER

A

-signal sequence is never cleaved it is simply a signal to start translocating
-orientation depends on short +ly charged a.a. stretch.
-this stretch ends up on the cytosolic side always
-a.as are R, K or H

26
Q

How do single-pass transmembrane proteins with a N-terminal signal sequence get into the ER

A

signal binds pore
once 2nd and hydrophobic a-helix sequence tries to cross, it is anchored in the membrane (this is after the OG signal is cleaved)
lateral gate releases protein into membrane

27
Q

how do multipass transmembrane proteins get into the ER membrane?

A

“Start” sequence signals for the polypeptide to enter as a loop. “Stop” sequences signal for the ER translocator to push the polypeptide into the lipid membrane. Continues until no more start sequences.

28
Q

what are the 2 types of ribosomes? How are they similar?

A

Free ribosomes are in the cytosol and make all other nucleas-coded proteins
Membrane-bound ribosomes are on the rER membrane and translate proteins with an ER signal sequence.

29
Q

what is a polyribosome

A

When multiple ribosomes are translating the same mRNA

30
Q

What are ER resident proteins

A

Proteins that are meant to stay in the ER ex: BiP

31
Q

what signal do ER resident proteins carry? Where is it?

A

KDEL at the C-terminus

32
Q

What are ER membrane proteins like? What anchors them in the membrane? where do they mostly reside?

A

They are anchored with a C-terminal tail and exist mostly in the cytosol.

33
Q

Explain how the ER creates lipid bilayers and how these bilyars differ from the other ones

A

They are always made on the cytosol side as this is where the substrates and active sites are. These bilayers have equal PL distribution in both leaflets due to scramblase which catalases random flip-flopping.

34
Q

Why are golgi, plasma and other non-ER membranes asymetric?

A

flipasses recognize PLs with free NH2 groups in their heads (PS, PE) and they move them to the cytosolic side

35
Q

How is the PM (plasma membrane) enriched with PS?

A

lipid transfer proteins move lipids between the ER and the PM at regions where the 2 membranes are very close.

36
Q

Explain how glycosylation can act as a timer for proteins in the ER

A

Sugar is slowly being trimmed and its final trimmed form signals for removal of the protein

37
Q

How are PERK, ATF6 and IRE1 regualted?

A

BiP binds them to supress their activity but is titrated away when levels of unfolded protein are high.

38
Q

What do PERK, ATF6 and IRE1 do?

A

They control the unfolded protein response pathways

39
Q

what is retrotranslocation

A

Deportation from ER to be degraded by proteosome due to failiure to fold

40
Q

what are the 2 types of glycosylation? which is more common where?

A

N-linked and O-linked.
Most in ER are N-linked.
All in cytosol are O-linked

41
Q

Does glycosylation affect the way a protein folds

A

Yes. Some need N-linked to fold properly (although it doesn’t really matter where the sugar attatches)

42
Q

how many euk. proteins are glycosylated? How many ER proteins are glycosylated. How many are N-linked?

A

50%.
Most
90%

43
Q

where does the N-linked sugar get added? How is it added?

A

to NH2 groups on Asn residues typically in an NXS or NXT sequence where X is any a.a but proline.
Added en bloc.

44
Q

what is the base sugar added to ER proteins as they enter?

A

Chain of 14 sugars including
-3 glucoses
-9 mannoses
-2 N-acetylglucosamines

45
Q

What is the olgiosaccaride of N-linked glycosylation linked to?

A

the lipid dolichol

46
Q

How do we ensure every ER protein that needs to be N-linked gets its sugar?

A

Each translocator has its own copy of oligosaccharyl transferase so it can add the sugar directly as the protein enters (active site on the lumenal side)

47
Q

what is the typical modification given to the sugar on N-linked ER proteins?

A

Chop off 3 glucoses and one mannose

48
Q

How do proteins get a GPI anchor?

A

They have a signal in their hydrophobic C terminus + a few adjacent residues on the lumenal side.
Their transmembrane domain is cleaved off as an attatchement is made

49
Q

How do you take off a GPI anchor?

A

phospholipases

50
Q

How would you describe the shape of the ER?

A

Labrithn of branching tubules and flattened sacs that is continuous with the outer membrane of the nuclear envelope.

51
Q

What happens when the ER has too much unfolded protein?

A

Unfolded protein response

52
Q

What do the 3 parallel signaling pathways that happen during UPR do? What happens if they fail.

A

STOP protein production
UPREGULATE ER resident regulaory components ex: ER chaperones
ACTIVATE ER resident regulaory components ex: ER chaperones

If they fail: apoptosis

53
Q

What happens in a cell when there are too many unfoled proteins

A

Heat Shock response: upregulates chaperone trasncription

54
Q

What is needed for retrotranslocation?

A

Chaperones
Energy
PDI to break bad S-S bonds
Translocator

55
Q

what is the max faliure rate for some proteins?

A

80%

BIOL 331 (12 decks)

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