-associated with cytosolic face of ER membrane

1) remain assciated with membranes

2) entrapped in small vesicular organelles

3) secreted from the cell

-not bound to any membrane

-produce proteins that are found in nucleoplasm, cytosol, mitochrondria/chloroplast, cytoskeleton

-proteins are synthesized on ER membrane bound ribosomes

-incorporated into membrane or moved into lumen of the organelle

-materials to golgi for modification and sorting

-transported via vesicles to organelles

-plasma membrane secreted from cell

-collection of membranous tubules and flattened sacs that extend throughout the cytoplasm of eukaryotes

-continuous and enclose a "lumen", or internal channel

-extends into a series of large flattened sacs

-"resident" RER membrance and lumenal components are involved in protein processing

a) protein translocation into/across membrane

b) protein folding

c) protein modification- primarily glycosylation

d) protein packaging for transport along the membrane/secretory pathway

-elongated, tubular structures

a) fatty acid/phospholipid synthesis

b) steroid and steroid hormone synthesis

c) initial fat oxidation

d) glycogen metabolism

e) detoxification reactions

f) storage of materials

-membrane lipids hydrophobic

-synthesize new lipid, thus, new membrane in association with preexisting membrane

-eukaryotes: membrane/lipid factory in the SER

-initial steps occur in cytoplasm 

-fatty acid synthase produces a short chain fatty acids by the condensation of acetate groups 

-initial products held in the cytosol within an acyl carrier protein by esterification to the hydrophilic Coenzyme A

-hydrophobic fatty acid tails inserted into the cytoplasmic leaflet of the SER membrane 

-integral/peripheral SER: enzymes involved in phosphoglyceride synthesis

1) phospholipid exchange proteins

2) in bulk along with proteins from the RER as part of membrane vesicles that bud from the ER

-localized, pancake-like stack of ribosome-free, flattened, sac-like membranes

-individual sacs: cisternae- usually dialated or swollen at their margins where they contain granular material

-surrounding cisternae on all sides- numerous vesicles that arise from and fuse with margins of cisternae

-closely associated with and form from the RER via vesicle flow

-face of the golgi closest to the ER: cis

-the opposite: trans

a) covalently coupling protein and lipid components

b) modifying proteins with sulfate, phosphate, acetyl groups, etc

c) removing, adding, or modifying the carb components attached to membrane/secretory proteins

d) sorting proteins for delivery to the final destination

-secretory proteins transfer across ER membranes

-begins on free cytoplasmic ribosomes

-info needed to target through pathway to ultimate location is encoded into the amino acid sequence of the protein

-info that targets a protein (and ribosome synthesizing it)

-string of about 30 amino acids at amino terminal (beginning) of the protein

a) up to 7 polar N-terminal amino acids, 3 are +

b) next a string of 6-12 hydrophobic amino acids

c) peptidase recognition and cleavage site

-as protein synthesized, nascent peptide exits through subunit tunnel

-after 40 amino acid have been added the amino terminal will produce into the cytoplasm

-signal recognized by "signal recognition particle" (SRP)

-ribonucleoprotein particle composed of 6 proteins and a small cytoplasmic RNA (scRNA)

functions: 

1) recognize and bind to the hydrophobic core of the signal sequence 

2) arrest further translation. this stops synthesis at about 70 aa, preventing improper folding/positioning of nascent polypeptide

3) promote the interaction of the ribosome/peptide/SRP complex with the ER membrance and entrance of the peptide into the membrane/secretory pathway

-transmembrane protein resident in the RER, which has a cytoplasmic projection, and functions as an SRP binding site

-binds the SRB/ribosome complex and directs the ribosome to a position above a protein translocation channel- "translocon"

-transfer the "signal sequence" of the nascent peptide from the grasp of the SRP to the mouth of the translocon

-lock the opening of the large subunit tunnel to the top of the translocon- intro to translocon opening

-release the SRP from the complex, making it available to guide another nascent membrane/secretory protein to the ER

-opening of translocon channel

-ribosome is free to resume protein synthesis

-result: nascent protein begins to be inserted through the membrane

-through a protein lined channel not through the lipid

-simple chain of amino acids with no 2^o structure

-powered primarily by peptide bond formation by the ribosome and secondarily by "chaperone pulling" from the lumen to ER

-"signal" is anchored at the translocon channel the protein moves through as loop

-original N-terminal "signal sequence" cleaved off

-accomplished by a special enzyme: signal peptidase, which is associated with lumenal surface of the translocon

-allow the new protein to be released into the RER lumen for further processing

-pathway accepts integral membrane proteins, especially those destined for the ER, golgi, vesicle-endomembrane system, nuclear envelope, plasma membrane

-proteins directed into the pathway by the same N-terminal "signal sequence" as secreted proteins

-moved part way through and then must be precisely anchored in the lipid bilayer; controlled by targeting sequences

-20 to 25 hydrophobic amino acids

-longer than "signal sequence", spans the bilayer as an alpha helix

-translocon recognizes sequence and "pops-open" lengthwise allowing the hydrophobic segment to float out into lipid bilayer

-ribosomes released, allowing synthesis in the cytoplasm

-result: protein anchored in the membrance with a portion in the ER lumen and still growing portion in the cytoplasm

-like the ER signal: positively charged aa on one end of a string of hydrophobic amino acids, recognized by the SRP and directed to the ER 

-unlike ER signal: not at the N-terminal nor built-in cleavage site

-similar to "stop transfer"- string of hydrophobic aa here is 20-25, sufficient to span the membrane as an alpha helix

-proper folding and formation of multi-subunit proteins assisted by group of lumenal proteins aka "chaperones"

-formation of disulfide bonds which helps maintain the subunit structure of proteins exposed to harsh extracellular enviro

-initial addition of carbohydrate modifying groups

-packaging into vesicles for transport along the membrane/secretory pathway

-cisternae modify

-primary protein modification: glycosylation

-to asparagine

-begins in the ER with addition of a complex polysaccharide and adjustments of teh sugar groups

-to serine

-occurs primarily in the golgi and involves a 3 step addition of a small polysaccharide unit

1) golgi localization

2) ER-golgi exchange

3) lysosomal tageting 

4) secretion

maintained two ways:

1) attachment to a specific region of cytoskeleton

2) size dependent prevention of golgi protein entrance into transport vesicles

some proteins are inadvertently packaged and sent to golgi- must be sent back to the ER

ER lumen proteins: via an ER specific sequence KDEL. proteins with this tag are bound by amembrane embedded receptor protein, repackaged into transport vesicles, and returned to ER

-ER membrane proteins that escape display a dibasic (Lys:Lys) signal which induces the formation of COPI coated vesicle which returns to the ER

1) lysosomal enzymes inserted through the ER membrane into lumen where they are glycosylated in an N-linked fashion with a high-mannose carb and shipped to golgi

2) cis golgi: these proteins recognized by shape. phosphotransferase enzyme adds a phosphate to a sugar group creating a "mannose-6-phosphate"

3) after transport the tagged protein will bind to an integral membrane "mannose-6-phosphate-receptor" protein that directs incorporation into chathrin (roughly) coated transport vesicles 

4) vesicle is transported through cytosol and fuses with a "CURL endosome". V-type  H+ ATPase pumps acidify this CURL including M6P-R to release its enzyme- phosphate then removed

1) small but membrane rich "tubule" carrying the M6P-R for recycling into the golgi

2) vesicle that entraps the now free lysosomal enzyme which then fuses with a mature lysosome delivering fresh enzyme that can be activated when needed

carries out routine, ongoing delivery of proteins to the plasma membrane as well as secretion to the extracellular space of normal materials (components of extracellular matrix)

-possibly a default mechanism

-future work may reveal specific signals since some proteins taking this path are ultimately delivered to very specific locations

-in the cis golgi

-steps: 

a) specific amino acid sequence on the protein to be secreted binds to a "granin" protein that resides in the lumen of cis golgi 

b) upon reaching the trans golgi the local high H+ and Ca++ concentration in the lumen causes the granin proteins to aggregate carrying their cargo (secretory) protein with them into an insoluble "granule" within trans golgi cisternae

c) specific transmembrane receptor proteins bind to the granin containing granules and induce their incorporation into clathrin coated vesicle

d) vesicles carrying their specific protein bud off the golgi and travel to the region under the plasma membrane where they are stored as secretory vesicles

e) responding to the regulated signal, the vesicles fuse with the plasma membrane and release contents

1) bind to cytoplasmic "tails" of integral membrane proteins. some are functional membrane proteins destined for residence in another organelle. others are receptors/carriers for soluble proteins in the lumen

2) deform the membrane creating a pit, bud and vesicle

-ARF hydrolyzes its GTP releasing the coat from the vesicle allowing the vesicle to travel to its destination

-COP I coated vesicles shuttle cargo among cisternae of the golgi and from the cis golgi back to the ER

-composed of 4 protein subunits 

-regulated by a Sar/GTP protein 

-function in a similar fashion as COP I but are responsible for shutting materials from ER to cis golgi

1) trans golgi membrance for transport either to the lysosome or for regulated secretion

2) plasma membrane for endocytosis

a) outer honeycomb lattice of "clathrin"

b) inner shell of adaptin proteins which crosslink specific transmembrane receptor proteins to the forming clathrin cage

1) recognizes sequence tags on the cytoplasmic extensions of plasma membrane receptors used for endocytosis

2) recognizes sequence tags on receptors of the trans golgi, which carry materials destined for lysosome or secretion

-recognizes a receptor/cargo combo then recruited into a "clathrin coated pit"

-pit is then separated from originating membrane with the help of a dynamin/GTP motor protein

-released vesicle then sheds its clathrin coat prior to transport to final destination

-each vesicle formed at trans golgi has specific protein content 

-in order to maintain cellular organization/function the vesicle must be directed to one and only one type of cell compartment

-divided into two classes 

a) v-snares specifically incorporated into forming vesicles with assistance of adaptin and/or coat proteins

-inactive untl coat proteins removed

-then become able to interact with second class of SNARE, t-SNARES

-tSNARES- specific target snares, exist on each receiving organelle membrane

-interact with one another

-distinct combos permitted, insuring certain vesicles can interact with certain organelles

-family of proteins with separate members on each variety of organelle/vesicle

-involved in SNARE process, regulate interaction

-regulate the assembly/disassembly of SNARE complexes

-"zippering" of v/t SNARE amphipathic helices drive vesicle/target membranes into contact, inducing ;lipid mixing and ultimately membrane fusion which delivers the contents to target organelle

-basic method of nutrition in unicellular heterotrophs

-defense mechanism by specialized cells of many multicellular organisms

-plasma membrane of phagosome which then fuses with a lysosome creating a phagolysosome within which engulfed material is killed and digested via oxygen radicals/hydrolytic enzymes

-small chemicals can then be transported to cytoplasm and non-digestible debris eliminated by exocytosis

-nonspecific uptake of extracellular fluid

-occurs continually in certain cell types and tends to internalize any molecules that are enclosed by the vesicle forming at plasma membrane

-appears to be important in recycling membrane components brought the plasma membrane during secretory process

1) external materials are captured by an integral membrane receptor

2) receptor/cargo complexes associate with adaptins that recruit clathrin to the cytosolic surface of the plasma membrane. clathrin deforms the membrane into a "pit" that concentrates recpetor/cargo complexes. ultimately pinch off as clathrin

3) vesicles then fuse with CURL-early endosomes. acidification leads to release of cargo by receptors. endosomes then divide into two segments, one carrying the receptor back to the plasma membrane and the other carrying the cargo deeper into the cell

4) transport vesicles can fuse with lysosomes and late endosomes. cargo is processed by hydrolysis or chemical modification. products of this acticity used for internal cellular activities