Protein Sorting

Question 1

default localization of proteins in eukaryotic cell

Answer 1

cytosol, transport is required for any protein that resides anywhere other than cytosol
for ER localized proteins, after the removal of the signal sequence, the protein will be transported, by default, to golgi and subsequently to plasma membrane

Question 2

gated transport

Answer 2

between topologically equivalent compartments through selective gates (b/n nucleus and cytosol)

Question 3

transmembrane transport

Answer 3

between topologically distinct compartments across a lipid bilayer (b/n cytosol and ER)

Question 4

vesicular transport

Answer 4

between topologically equivalent compartments via membrane-enclosed transport intermediates (ER to Golgi to plasma membrane or cell exterior)

Question 5

4 things needed for protein transport

Answer 5

signal sequence, transport machinery, directionality, energy source

Question 6

signal sequence

Answer 6

amino acid sequence within protein that indicates where protein should go; nuclear localization sequence- positively charged amino acids lysine and arginine; ER signal sequence- at N-terminus of hydrophobic amino acids and signal sequence is cleaved once N-terminus has reached inside of ER; membrane proteins- need additional signal sequence also of hydrophobic amino acids (stop-transfer sequence) that becomes inserted into ER membrane during translation (some proteins cross membranes multiple times so are “stitched” into ER membrane via series of start and stop transfer sequences

Question 7

transport machinery

Answer 7

other proteins that function to recognize/transport protein bearing particular signal sequence (nuclear pore complex, SRP, SRP receptor, translocation channel, signal peptidase, coat proteins, Rab proteins, tethering proteins, SNAREs)

Question 8

nuclear transport

Answer 8

via nuclear pores, active transport- energy spent (1 GTP hydrolyzed per round), molecule greater than 40 KDA, must have NLS; passive diffusion- no energy spent, molecular less than 40 KDA

Question 9

necessary

Answer 9

if something is necessary for a process, that means the process will not occur in the absence of that thing; to determine if something is necessary- “take it away” experiment (if process no longer happens-> necessary, still happens- not necessary)

Question 10

sufficient

Answer 10

if something is sufficient for a process, then that thing should be able to trigger/induce/cause that process to occur under conditions where the process does not normally occur; to determine if something is sufficient- “add it” experiment (if process is induced-> sufficient, not induced-> not sufficient)

Question 11

ER co-translational transport

Answer 11

ribosomes docked at rough ER translate proteins that are being inserted into ER as they are being synthesized, proteins may stay in ER membrane or lumen or be transported to Golgi, lysosome, plasma membrane or secreted from cell, membrane proteins are inserted first into ER membrane and soluble proteins are inserted first into ER lumen

Question 12

signal recognition particle (SRP)

Answer 12

soluble cytosolic particle of 6 proteins and 1 RNA that binds and pauses ribosomes translating a protein with a signal sequence

Question 13

SRP receptor

Answer 13

protein anchored in ER membrane that recruits SRP (and associated ribosome)

Question 14

translocation channel

Answer 14

complex of membrane-anchored proteins that form aqueous pore in ER membrane. only opens once it binds to signal sequence

Question 15

signal peptidase

Answer 15

protease enzyme responsible for cleaving signal sequence

Question 16

vesicle transport

Answer 16

transfers soluble and membrane proteins from 1 compartment to another, maintaining topological equivalence (bc there is a way to exchange materials)

Question 17

how can membrane transport occur without mixing everything together if all these membrane-bound compartments are distinct and unique?

Answer 17

different pathways, and membrane/protein composition of vesicles is not random, specific membranes/proteins are recruited or excluded from budding vesicles bc vesicles are “coated” and coat proteins recruit specific proteins to vesicle

Question 18

how do vesicles know which membrane to fuse with

Answer 18

complementary sets of proteins on vesicle and target membrane: vesicles find their target membrane via complementary Rab proteins, tethering proteins and SNAREs and after docking SNARE proteins catalyze membrane fusion