Liu Flashcards
Where are Ran-GAP and Ran-GEF located and what do they do?
Ran-GAP: cytosol, hydrolysis of Ran-GTP to Ran-GDP
Ran-GEF: nucleus, dissociation of GDP from Ran-GDP, which is quickly exchanged for GTP
A signal sequence is an amino acid chain that directs a protein to a certain organelle. What is the 3-D structure made up of multiple internal amino acid sequences known as?
signal patch
Proteins destined for the mitochondria have an N-terminal signal/leader sequence with many _____ amino acids. They are transported across the outer membrane by ____ proteins and across the inner membrane by ____ proteins.
positively charged (K, R); TOM complex, TIM complex
Transport into ____ occurs co-translationally, whereas transport into ____, ____, and ____ occurs post-translationally.
ER; mitochondria, nuclei, peroxisomes
Proteins destined for ____ have a specific 3-amino acid import sequence on their ___ terminus.
peroxisomes, C-terminus
*Even large oligomeric proteins do NOT have to be unfolded for transport to peroxisomes.
Transport into ____ requires fully synthesized but unfolded peptides and the use of chaperones and ATP.
mitochondria
What is a microsome?
small ER particle resulting from homogenization of cells, either a rough microsome (RER) or a smooth microsome (SER). Rough microsomes are denser due to their ribosome content.
How do SRPs help translocate proteins to the ER?
Signal recognition particles (SRPs) are proteins that bind the N-terminal signal sequence of the protein being imported and the ribosome itself, causing a pause in translation. The ribosome-SRP complex binds the SRP receptor on the ER membrane, and the nascent peptide is fed through a nearby Sec-61 translocator complex. The SRP dissociates and translation continues concurrent with translocation.
For soluble proteins, ER signal sequences are recognized twice. Why? Comment on their hydrophobicity.
Signal sequences are hydrophobic and are bound by hydrophobic signal-binding domains of the SRP, which brings the ribosome/nascent peptide to the SRP receptor on the ER membrane. Then they bind the Sec61 translocator complex at the hydrophobic start-transfer-peptide-binding site, which opens the pore and allows translocation of the soluble peptide.
How are transmembrane proteins embedded in the ER membrane?
Start-signal binding at start-signal-peptide-binding site, translation and translocation, then stop-signal binding at stop-signal-peptide-binding site, and termination of translocation fixing the peptide to the membrane and leaving a cytoplasmic domain in the cytosol.
A mutation in which protein of the ER-associated degradation pathway causes autosomal recessive juvenile Parkinson’s (AR-JP)? What is its substrate?
Parkin (an E3 ubiquitin ligase); Pael receptor (a transmembrane protein normally degraded by Parkin that accumulates in AR-JP and damages the ER)
What are the 3 major classes of glycoproteins (based on the nature of the linkage between their polypeptide chains and their oligosaccharide chains)?
- O-linked: Glycosidic bond between Ser/Thr OH and a sugar such as N-acetylgalactosamine (GalNAc-Ser[Thr])
- N-linked: Glycosidic bond between amide nitrogen of Asn and N-acetylglucosamine (GlcNAc-Asn)
- GPI-anchored: C-terminal amino acid joined to an oligosaccharide (via a phosphorylethanolamine moiety), which in turn is linked to phosphatidylinositol (via glucosamine).
What are the three subtypes of N-linked glycoproteins? What do they all have in common? How is the oligosaccharide added to the polypeptide?
complex, hybrid, high mannose; pentasaccharide core Man3(GlcNAc)2; the oligosacch. group is transferred from a Dolichol-P-P-oligosaccharide complex to the Asn of the peptide chain using oligosaccharide transferase whenever the sequence Asn-X-Thr/Ser occurs
Which drug inhibits the formation of the dolichol-P-P-oligosaccharide complex necessary for N-linked glycosylation?
tunicamycin
The GPI anchor is assembled independently and then transferred to the ______ end of its acceptor protein, thereby cleaving the transmembrane acceptor protein on the ____ side of the membrane, leaving a small hydrophobic peptide within the membrane.
C-terminal, ER lumen
What are the 3 major types of vesicle coats and what route do their vesicles primarily take?
COP I: Golgi –> ER (mostly)
COP II: ER –> Golgi
Clathrin: Membrane Golgi
Describe the structural framework of a clathrin coat.
Clathrin is the major coat protein that provides the mechanic force needed for budding and is the framework of the coat.
3 light chains and 3 heavy chains -> 3-legged triskelion -> clathrin cage
Adaptins - coat proteins that link clathrin cage with transmembrane receptor
What are adaptins?
Coat proteins that link clathrin with various transmembrane receptors. There are at least 4 types of adaptins, each specific for a different set of cargo receptors.
clathrin–adaptin–cytoplasmic domain of transmembrane receptor–membrane–extracellular domain–cargo
Which protein is used in endocytotic vesicle budding?
Dynamin creates a collar around the vesicle and pinches it off, clathrin coat quickly dissociates
Small GTPases are involved in the recruitment of coat proteins from the cytosol to the different membranes (Golgi, ER, plasma). ____ is responsible for ____ and ____ coat assembly at Golgi membranes. _____ is responsible for _____ coat assembly at the ER membrane.
ARF, COP-I, clathrin
Sar1, COP-II
When vesicle encounters the correct target membrane, the binding of ____ to _____ causes the vesicle to remain bound for long enough to allow ___ to hydrolyze its GTP, which locks the vesicle onto the target membrane (“docking”). These, together with ___ induce the two membranes to fuse. A similar fusion process is employed in _____ receptors.
t-SNARE, v-SNARE, Rab-GTP; NSF; chemokine
Resident ER proteins are retrieved by ____ receptors. They are packaged in ____-coated vesicles for retrograde transport back to the ER.
KDEL (recognize K-D-E-L sequence on proteins), COP-I
What happens to proteins secreted from the ER that don’t have a KDEL sequence? KDEL sequence at C terminus?
not retrieved (cytosol?); stay in ER
What is the”default” secretory pathway, constitutive or regulated?
constitutive
