L4 Protein Trafficking

Question 1

what is a signal sequence (signal peptide)

Answer 1

part of protein that is targeted to the secretory pathway

necessary and sufficient for ER lumen targeting (name sounds generic but this is only referring to sequence to target ER)

short stretch of a.a that is eventually cleaved by peptidase > matured protein is shorter than original genome sequence

Question 2

process of synthesis of soluble secretory proteins at RER

Answer 2

signal is always at 5’ end of coding sequence > gets translated via ribosome first

once signal polypeptide translated > recognised by SRP and binds > translation halted

SRP binds to SRP receptor at ER membrane to bring ribosome close to ER > SRP dissociates > translation continues > protein threads through translocon (channel on ER membrane) into ER lumen

protein immediately folded > signal sequence is cleaved > ready for translocation to Golgi

Question 3

two directions of vesicle trafficking

Answer 3

anterograde (forward) transport: moves vesicles from ER to Golgi then to PM; uses coat protein COPII; purpose is to deliver newly synthesised proteins and lipids to destinations

retrograde (reverse) transport: moves vesicles from Golgi back to ER; uses coat protein COPI; purpose is to retrieve and recycle trafficking machinery components and resident enzymes that had accidentally escape

Question 4

properties of vesicle trafficking

Answer 4

reversible

specificity achieved by tethering proteins v-SNARES and t-SNARES pairing

requires dynamic shaping and fusion of membranes

topology conservation: orientation of membrane proteins maintained throughout transport

Question 5

different types of vesicle coats

Answer 5

COPI: mainly at Golgi

COPII: mainly at ER

clathrin: mainly at plasma membrane for endocytosis and transport between Golgi and lysosomes

size of transport vesicle: 50-100nm

function of coats:
- help membranes form vesicles by physically shaping it
- cargo protein selection

Question 6

what is essential for the assembly of COPII coat

Answer 6

Sar1 GTPase

Question 7

what is the maturation model of Golgi trafficking

Answer 7

model suggests that cargo moves through Golgi by progressive maturation of Golgi cistern rather than vesicle mediated transport between stable cisternae

Question 8

explain how maturation model works

Answer 8

cargo enters Golgi from ER via COPII vesicles > enter cis Golgi

cisternae mature progressively from cis to trans with cargo moving through each maturation stage

no vesicles transport cargo between cisternae, instead membrane maturation occurs

at trans Golgi, cargo sorted into vesicles for delivery to final destinations

ER proteins recycled back to ER if they escaped to golgi

Question 9

clathrin dependent endocytosis

Answer 9

clathrin forms cage around membrane on cytoplasmic side > deforms membrane to form bud

adapter proteins help clathrin capture specific cargo

as clathrin polymerises > membrane curves further > form vesicle > dynamin pinches off vesicle

clathrin removed > vesicle uncoats > cargo transported to early endosomes

Question 10

what happens to ligand and LDL receptor during endocytosis of LDL and LDL receptor

Answer 10

ligand will be degraded but receptor will be recycled

Question 11

process of clathrin dependent endocytosis of EGF

Answer 11

EGF binds to EGF receptor > receptor dimerisation and activation

EGF-EGFR complex internalised into cell via clathrin coated vesicles > vesicle uncoats and fuses with early endosomes

Question 12

process of phagocytosis

Answer 12

only takes place in special cells like macrophages

special form of endocytosis where large endocytic vesicle, phagosome is formed > fuse with lysosome > enclosed contents digested

Question 13

process of autophagy

Answer 13

takes place in all cells

to dispose obsolete organelles in lysosome

after autophagosome is formed > fuse with lysosome > degradation

Question 14

properties of nucleocytoplasmic trafficking

Answer 14

signal mediated using nuclear localisation signal and nuclear export signal

process of trafficking passed through nuclear pore complex

vesicles not involved

membrane remodelling not required

it is not a membrane trafficking process

Question 15

charged amino acids

Answer 15

+ve: lysine, arginine, histidine

-ve: aspartic acid, glutamic acid

Question 16

polar amino acids

Answer 16

serine, threonine, tyrosine, asparagine, glutamine

Question 17

non polar amino acids

Answer 17

glycine, alanine, valine, cysteine, proline, leucine, isoleucine, methionine, tryptophan, phenylalanine