gated transport: into/out of the nucleus from the cytoplasm

transmembrane transport: unfolded proteins go from the cytosol into the organelles

veisular transport: membrane-bound vessicles transport proteins from one organelle/compartment to another

1. be integrated into the cell membrane

2. be transported out of the cell

3. go into a particular organelle

- linear (transmembrane transport)

- "patch" conformational (depends on the protein being folded) (vesicle and nuclear/gated transport)

- rough ER: covered in ribosomes

- smooth ER: no ribosomes; involved in lipid metabolism

- transitional ER: where the vessicles exit from on the way to the golgi

- pulls the polypeptide sequence through the translocon

- blocks translocon when there's no protein bound

- assisted protein folding

- formation of disulfide bonds

- assembly of subunits into multimers

- cleavage (if needed)

- addition of sugars (glycoproteins are made)

- happens as proteins are transferred into the ER

- helps keep them from aggregating

- provides signals for subsequent sorting

the four sections of the golgi:

- cis golgi (recieves molecules from the ERGIC)

- medial golgi stack (modifications)

- trans golgi stack (modifications)

- trans golgi network (sorting and distribution)

anterograde: all ER proteins are marked by default to export to the golgi

retrograde: therefore, the ones that need to end up in the ER have to be taken BACK

1. direct transport (normal, continuous vessicle transport)

2. endosomic recycling

3. regulated secretory pathways (proteins hang out in the vessicles until they get signals to be secreted)

COPII-coated vessicles

vs. 

COPI-coated vessicles

vs.

clathrin-coated vessicles

COPII: carry secretory proteins from the ER->ERGIC->golgi

COPI: opposite of that (from golgi->ERGIC->ER)

clathrin: transport in BOTH directions between trans-golgi-network and endosomes/lysosomes/plasma membrane

SNARE: v-SNARE and t-SNARE match up and bind each other to fuse the vessicle and the organelle membranes.

Rab (specific for each interaction) hydrolyzes (GTP->GDP) when this has been done successfully

- about 50 degradative enzymes

- these only function at low pH (around 5),which is lower than the general cell

- a proton pump keeps the pH low in the lysosomes

EARLY ENDOSOME:

- accepts material from outside (endocytotic pathway)

--> the stuff to be recycled gets passed to the RECYCLING ENDOSOMES and are then sent out to the plasma membrane again

--> the stuff to be thrown away gets sent to the LATE ENDOSOME

- which also gets lysosomal-bound proteins from the golgi

then the late endosome fuses with or matures into the lysosome

phagocytosis: specialized cells (like macrophages) absorb  bacteria, debris, etc. into PHAGOSOMES, which then merge with the lysosomes to form PHAGOLYSOSOMES

autophagy: the cell digests its own organelles/macromolecules to cope with starvation

- fibrous mesh that provides structural support

- bound to embedded proteins in the inner nuclear membrane

- contains fibrous proteins called LAMINS

- proteins that make up the nuclear lamina

- three genes

- two lamins coil around each other in the alphahelical regions to make a coil

- these interact to form a mesh

- mind to inner membrane proteins and also CHROMATIN

- form nuclear lamina and ALSO a loose network within the cell

- large, complex, composed of more than 30 proteins

- have eightfold symmetry around a central channel

- small molecules go through them by PASSIVE TRANSPOSRT

- macromolecules (RNA and proteins) go through them by  a selective, energy-dependant mechanism 

- GTP binding protein

- enzymes for hydrolyzing to GDP are on the cytoplasmic side, while enzymes for exchange to GTP are on the nuclear side, so it's bound to GTP in the cytoplasm and GDP on the inside of the nuclear membrane

- binds to cargo/importin complex to get the importin to drop the cargo on the inside

- exportins bind to cargo, promoted by Ran-GTP

- when Ran-GTP is hydrolized to Ran-GDP, cargo dissociates

- proteins are tagged for export by NUCLEAR EXPORT SIGNALS

Ran-GEF exchanges Ran-GDP for Ran-GTP in the nucleus

Ran-GAP exchanges Ran-GTP to Ran-GDP in the cytosol

- transcription factors/other proteins associate with the nuclear proteins and mask their nuclear localization signals

- phosphorylation near nuclearl localization signal

section in the nucleus where ribosomes are assembled and ribosomal RNA is transcribed.

- has over 300 proteins and lots of snoRNAs (small nucleolar RNAs) which are involved in pre-rRNA processing

DNA in nucleus is transcribed, sent outside the nucleus, translated to form ribosomal proteins.

- these re-enter the nucleus, then the nucleolus, where they join with rRNA to form the halves of the ribosomes.

- these are then exported back out; they come together in the cytoplasm or the rough ER

the amino-terminal sequences by which proteins are targeted to the mitochondria

- these bind to receptors on the outside of the mitochondria - Tom complexes.

- some are inserted between the membranes.

- if not, they then bind to Tim complexes on the INNER membrane.

heat shock proteins

- these unfold the proteins so they can get through the translocase complexes of Tom and Tim

- and refold them when they reach their destinations.

THIS IS COUPLED WITH ATP HYDROLYSIS

instead of presequences they have multiple internal import signals

- as they are passed through Tom40, they are bound and escorted by Tiny Tims

- these stay with them through Tim22

- when they exit LATERALLY and end up embedded in the inner membrane.

- some are coded for by mitochondrial DNA

- some are coded for by NUCLEAR DNA

- evidently some of these were translated to the nucleus from the original prokaryotic ancestor of mitochondria.

- there are TONS of mitochondrial proteins, and mitochondria from different cells have different proteins, but we don't know all that much about them. 

- mitochondrial DNA is passed down exclusively from the female line.