Exam 2

Question 1

ER Signal Sequence

Answer 1

20 Hydrophobic AA

Question 2

Why is ER Signal Sequence Cleaved?

Answer 2

Unnecessary & Hydrophobic AA would disrupt folding

Question 3

SRP

Answer 3

Signal Recognition Particle

Question 4

P54

Answer 4

54 kDa subunit of SRP, binds ER sequence and SRP receptor via (hydrophobic) Van der Waals, binds GTP

Question 5

P68/P72

Answer 5

Binds translocon

Question 6

G proteins

Answer 6

Can bind and hydrolyze GTP

Question 7

P9/P14

Answer 7

Binds to the ribosome, reaches into the ribosome to pause translation

Question 8

SRP Receptor

Answer 8

Located on the ER, can bind SRP*GTP (SRP + Ribosome + GTP complex) after it has bound GTP to itself

Question 9

Docking of the ribosome to the ER

Answer 9

P68/P72 transfers the ribosome to the translocon, opening the ribosome-gated translocon. P54 and SRP receptor hydrolyze GTP to dissociate.

Question 10

Non-hydrolyzable GTP

Answer 10

GMPPNP, GTP-(gamma)S

Question 11

Secretory Pathway Translation

Answer 11

SRP release resumes translation, ER Signal Sequence is cleaved by a signal peptidase, once translation is finished the ribosome dissociates and the translocon closes

Question 12

Length of ER Signal Sequence

Answer 12

20 AA

Question 13

Type 1 Membrane Protein

Answer 13

Stop-transfer anchor sequence is in the middle of the mRNA. The hydrophobic anchor sequence alpha helix diffuses out of the translocon into the membrane. This stops the transfer and anchors the protein in the membrane. N (amine) terminus is outside the cell and C terminus is inside the cell.

Question 14

Type 2 Membrane Protein

Answer 14

No ER Signal Sequence so nothing is cleaved. The alpha helix acts as the (internal) signal sequence to which SRP binds. The protein is translated until the alpha helix is exposed, to which P54 binds and SRP brings to the ER. The C terminus is outside the cell and N terminus is inside the cell.

Question 15

Why do proteins fold?

Answer 15

Because it is thermodynamically favorable to have hydrophobic portions tucked inside the protein because of the water surrounding it.

Question 16

BiP

Answer 16

Tugs protein into the ER and prevents it from exiting back into the cytosol. It is a Hsc protein, so its expression increases during heat shock to prevent denaturing and promote proper folding. It is a signal that the protein has been improperly folded.

Question 17

BiP binding

Answer 17

BiP binds to hydrophobic sequences, only 3 out of a group of 7 AA need to be hydrophobic for BiP to bind. In order to bind, BiP must hydrolyze ATP.

Question 18

BiP binding sites

Answer 18

Sec63 and Ire1

Question 19

GSH and GSSG

Answer 19

GSH is reduced, GSSG is oxidized (bound). Ratio in the cytosol is 50:1 and ratio in the ER is 1:1.

Question 20

PDI

Answer 20

Corrects improper disulfide bonds

Question 21

N-linked Glycosylation

Answer 21

Sugars are added to XNXS/T. Gluc3Man9 is initial glycosylation. Converted to Gluc1Man9, which tethers to CNX and CRT to remain in the ER. After folding, it is converted to Man8. If correctly folded, it enters vesicle as Man8. If not, it is re-glycosylated into Gluc1Man9 for re-folding or into Man5-6 for ERADication. In the cis-golgi, glycosylation signature is Man5.

Question 22

Proteasome

Answer 22

Degrades proteins

Question 23

Lysosome

Answer 23

Degrades any structure

Question 24

Ubiquitin

Answer 24

Binds to a cytosolic protein that is to be degraded by the proteasome.

Question 25

What happens when misfolded proteins accumulate in the ER?

Answer 25

Ire1 forms a dimers, which splices Hac1 mRNA. Hac1 transcription factor activates expression of BiP, PDI, CNX, and CRT. Once levels are normal, BiP binds to Ire1 which ends splicing.

Question 26

CFTR

Answer 26

ATP gated channel

Question 27

Lumacaftor

Answer 27

Corrector

Question 27

Ivacaftor/kalydeco

Answer 27

Potentiator (potentiates CFTR activity)

Question 28

Trikafta

Answer 28

Ivacaftor and 2 correctors

Question 29

Orkambi

Answer 29

Ivacaftor and Lumacaftor

Question 30

Classes of CFTR Mutations

Answer 30

Class 1: Early stop codon, no function
Class 2: Improper folding / unable to leave the ER (still functional)
Class 3: Gating, Even when ATP is bound it doesn’t open
Class 4: Conductance of the channel
Class 5: Reduced amount of protein