Protein Sorting

• loss of rigid cell wall in ancient anaerobic archaeon facilitates horizontal gene transfers • digestion of other prokaryotes (archaeal and bacterial) further increases horizontal gene transfers and cell membrane folds in forming primitive nuclear membrane • aerobic bacterium is engulfed (retains both membranes and its DNA) = mitochondrion • chloroplasts are created when a photosynthetic bacterium later is engulfed

• inner- original bacteria; outer- cell that engulfed (primitive eukaryote) • cytosol • took place in plasma membrane (outer) in bacteria • they were original intact cells • just the important ones necessary to perform functions in the mitochondria; not enough to sustain life • mitochondria was engulfed before current genetic code was the universal code • it evolved parallel to the nucleus; mitochondria were world of their own -what happens in one compartment doesn’t have to happen in the other. mutation rates in mitochondria DNA is much greater than nuclear genome

• nuclear pore complex (NPC) • nucleus/cytosol • equivalent • Yes

• translocator proteins • cytosol –> organelle • different • Yes

• vesicle • organelle –> organelle • equivalent • No

• located on cargo to be moved direct traffic flow • signal patch consolidates many scattered sequences (next to each other after protein folding) • biochemical properties are more important than amino acid identity • recognized by complementary receptors on targeted organelle • necessary and sufficient for protein targeting • may be removed by a signal peptidase after protein reaches final destination

rich in K and R + charge located internally

amphipathic located internally

+ charge located on N-terminus

hydrophobic core located on N-terminus

KDEL helps proteins stay in ER or helps to return to ER if escapes mixed biochemical features located on C-terminus

nuclear export signal (NES)

nuclear localization signal (NLS)

nucleoporins (NUPs)

• scaffold: structural, stabilize membrane • ring: anchor to membrane • channel: connectors and gates (FG repeats) • fibrils: neither structural or symmetrical; interact with proteins

tethers active genes to the NPC interact with nuclear lamins regulation of transport

• nuclear localization signal (NLS) • • charged amino acids (K, R) • multiple internal sites • Nuclear Import Receptors (NIR): cytosolic proteins; ferry cargo into nucleus; also called importins; direct or indirect recognition

• nuclear export signal (NES) • amphipathic helices • internal • nuclear export receptors (NER): nuclear proteins; ferry cargo into cytosol; recycled back to nucleus; also called exportins; recognition must be indirect when cargo is RNA

nucleus to cytosol and back these cargo proteins may have both and NES and NLS

• phosphorylation • proteolysis • inhibitor proteins

karyopherins

GTP

monomeric G protein (GTPase)

found in cytoplasm catalyzes removal of phosphate bound to Ran-GTP