Ch 13 Cell Bio

Front 1

what gives organelles its unique molecular address

Back 1

it is the specific combination of marker molecules on its membrane

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purpose of coated vesicles

Back 2

1. concentrates specific membrane proteins in a specialized membrane patch that then gives rise to the vesicle membrane, helps in selecting the appropriate molecules for transport
2. the coat form a deformed membrane patch and molds the forming vesicles into uniform size and shape, leads to curvature of the membrane

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clathrin coated vesicles

Back 3

mediate transport from the golgi apparatus and from the plasma membrane, removed after the vesicle is formed

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COPI and COPII coated vesicles

Back 4

mediate transport from the ER (COPII) and the Golgi cisternae (COPI), composed of coat-protein subunits (7 for COPI and 4 for COPII)

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triskelion

Back 5

main structure of clathrin, formed from three large and three small polypeptide chains, assemble into a basketlike convex framework of hexagons and pentagons, N-terminal domain turns inward forming an interdiate shell, determines the geometry of the clathrin cage

Front 6

adaptin

Back 6

required to bind the clathrin coat to the membrane and to trap various transmembrane proteins/receptors (those that capture the soluble cargo for transport)

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dynamin

Back 7

GTP binding protein that helps in bud pinching to form a vesicle, assemble as a ring around the neck of each bud, recruits other proteins

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hsp70 and clathrin decoating

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a hsp70 family member, acts as an uncoating ATPase, uses ATP to peel off the coat

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auxillin

Back 9

thought to activate the ATPase, attached to the vesicle

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plasma membrane and vesicle transport

Back 10

plasma membrane is very stiff and flat due to its cholesterol rich lipid composition, clathrin coats need to produce considerable force to introduce curvature

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intracellular membranes and vesicle transport

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occurs preferentially at regions where the membrane are already curved, such as the rims of Golgi cisternae or membrane tubules

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coat-recruitment GTPases

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control the assembling of coats, assemble only when and where they are needed, include the ARF proteins and the Sar1 protein, usually found in high concs. in the cytosol in an inactive GDP bound state, when needed are activated by GEF to replace GDP with GTP, this exposes a hydrophobic tail causing it to bind to the donor membrane, inactivated by GAPs (thought to be like timework)

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ARF protein

Back 13

responsible for both COPI coat assembly and clathrin coat assembly at Golgi membranes, have hidden fatty acid chain

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Sar1 protein

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responsible for COPII coat assembly at the ER membrane, have hidden hydrophobic tail

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surface markers on transport vesicles and targets

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found no all transport vesicles, identify them according to their origin and type of cargo, targets display complementary receptors that recognize the appropriate markers

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SNARES

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seem to have a central role in providing specificity and in catalyzing the fusion of vesicles with the target membrane, there are v-SNARES (vesicular, syntaxin) and t-SNARES (target, synaptobrevin and Snap25), v-SNARES and t-SNARES wrap around each other forming trans-SNARE complexes

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Rabs

Back 17

work with other proteins to regulate the initial docking of the vesicle to the target membrane, monomeric GTPases, multiple types found on multiple organelles, cycle between the membrane and the cytosol, Rab-GDP is inactive and in the cytosol (bound to a GDI (GDP dissociation inhibitor), GEF on donor causes release of GDP to GTP, activates the Rab exposing a lipid group that binds to the membrane which allows the vesicle to bind to a Rab effector on the target, speed up the process complimentary SNAREs finding each other

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trans-SNARE-complex

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composed of t-SNARE and 2 v-SNARES interacting, syntaxin and synaptobrevin give one alpha helix to the complex while Snap25 gives 2 to form a 4 alpha helix complex

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NSF

Back 19

binds to the trans-SNARE complex via adaptor proteins for dissociation, ATP driven, allows for control of when t-SNAREs are free and activated

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fusion of membrane

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does not necessarily follow immediately after docking, when fusion does occur, want to bring them close to each other (1.5 nm) where lipids can jump from one bilayer to another, wrapping of the alpha helices provides the energy to overcome water barrier present, forms stalk  hemifusion  fusion

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exit signals on cargo receptors on ER

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can be used to concentrate cargo proteins into a vesicle

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how does BiP and calnexin keep misfolded proteins in the ER?

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they either cover up the exit signals or somehow anchor the protein in the ER, important bec. lots of proteins are misfolded, 90% of T cell receptor and acetylcholine receptors are misfolded

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homotypic fusion

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the fusion of membranes from the same compartment, v-SNARES and t-SNARES are contributed by both membranes

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heterotypic fusion

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a membrane from one compartment fuses with the membrane of a different compartment

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vesicular tubular clusters

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the structure formed when ER-derived vesicles fuse with one another, have a convoluted appearance, act as transport packages that bring material from the ER to the Golgi, relatively short lived because they move along microtubules to the golgi

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ER retrieval signals

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used in the retrieval pathway, resident ER proteins have signals that bind directly to COPI coats and are brought back to the ER if they leave (KKXX sequence)

Front 27

KDEL sequence

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a short retrieval signal at the C-terminal end, bind to KDEL receptors which package them into COPI coated vesicles for transport back into the ER, high affinity for KDEL receptors at the golgi and low affinity at ER (affinity regulated by [H+] at the respective sites regulated by H+ pumps, acidic in golgi and neutral in ER)

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other ways to retain ER resident proteins

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selective retention, can be anchored there independent of the KDEL signal, only those that leave the ER use the KDEL signal, some proteins bind to each other forming large complexes that are too big to enter vesicles (kin recognition)

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vesicles destined for the plasma membrane

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rich in cholesterol, fills the space between the kinked hydrocarbon chains of the lipids, vesicles must have long transmembrane segments

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cis face of golgi

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entry face, found closest to the ER

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trans face of golgi

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exit face, found furthest to the ER

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special compartments of the golgi

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1. cis Golgi network (CGN), intermediate compartment, composed of tubular structures
2. trans Golgi network (TGN), composed of cisternal structures, in cells specialized for secretion, this network has large vesicles for secretion (think goblet cell
between these two are cis cisterna, medial cisterna and trans cisterna (Golgi stack)

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complex oligosaccharides

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N-linked oligosaccharide attached in the golgi, has common core region derived from the ER added sugar containing two N-acetylglucosamines and three mannoses, has a terminal region attached to the core region that contains a variable number of copies (normally 2-4) of a special trisaccharide unit (N-acetylglucosamine-galactose-sialic acid (- charge)), occurs through trimming then adding new sugars, Endo H-resistant

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high mannose oligosaccharides

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N-linked oligosaccharide attached in the golgi, has common core region derived from the ER added sugar containing two N-acetylglucosamines and three mannoses, are trimmed but no new residues are added, remains in this form if the oligosaccharide is inaccessible by enzymes in the Golgi, Endo H-sensitive

Front 35

O-linked glycosylation

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glycosylation an occur on the OH groups of serine or threonine

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protegoglycans

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are made in the Golgi, involves the polymerization of one or more glycosaminoglycan chains via a xylose link onto serines, can become components of the extracellular matrix or plasma membrane

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in what type of organisms are N-linked glycosylation found

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present in eukaryotes and yeasts, but absent in prokaryotes

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functions of oligosaccharide addition to proteins

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protection from proteases, proper folding, cell-to-cell adhesion, regulatory roles

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functions of the different compartments of the Golgi

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1. cis Golgi network-sorting, phosphorylation of oligosaccharides on lysosomal proteins
2. cis cisternae-removal of Man
3. medial cisternae-removal of Man, addition of GlcNAc
4. trans cisternae-addition of Gal, addition of NANA (sialic acid)
5. trans Golgi network-sulfation of tyrosines and carbs, sorting

Front 40

vesicular transport model

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theory of how transport occurs through the Golgi, vesicles transport proteins between the cisternae, budding from one cisterna and fusing with the next, Golgi is static, with its enzymes held in place, retrograde flow returns ER and preceding compartment proteins, transport may be directional or random

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cisternal maturation model

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theory of how transport occurs through the Golgi, Golgi is viewed as a dynamic structure in which the cisternae themselves move through the Golgi stack as they mature into the next compartment in line, Golgi enzymes stay in their proper places through retrograde flow

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organization of the Golgi

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due mostly to matrix proteins that form a dynamic scaffold that helps organize the Golgi and microtubule cytoskeleton

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lysosomal enzymes

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all are acid hydrolases, optimal activity requires an acidic environment, lysosoome has a pH of about 5.0, kept at this pH through an H+ ATPase, lysosomal membrane proteins are usually highly glycosylated

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pathways to degradation

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1. endocytosis
2. autophagy
3. phagocytosis

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endocytosis

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endocytosis of material  early endosome (first place of lysosomal hydrolases, pH = 6)  late endosome  lysosome (formed from late endosomes through a gradual maturation process)

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autophagy

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used in the disposal of obsolete parts of the cell (i.e. mitochondria, which has a life of about 10 days), creates an autophagosome (which is a structure that has an organelle surrounded by membranes of unknown origin which then fuses with a lysosome)

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phagocytosis

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used in breaking down large particles and microorganisms, form phagosomes

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recognition of lysosomal proteins in the TGN

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these proteins carry a mannose 6-phosphate (M6P) which are added to the N-linked oligosaccharide as they pass through the CGN, recognized by M6P receptor proteins in TGN, then form vesicle w/ adaptins and clathrins, delivered to late endosome

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M6P receptor protein

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binds to M6P on proteins destined for lysosomes, bind at pH 6.5-6.7 and release at pH 6 (that of a late endosome)

Front 50

how does an enzyme know to add M6P to lysosomal enzymes and not others?

Back 50

the signal for adding the M6P unit resides in the polypeptide chain as a signal patch, two enzymes involved:
1. GlcNAc phosphotransferase, add GlcNAc-phosphate to one or two of the mannose residues on the oligosaccharide chain
2. responsible for cleaving the GlcNAc residue, leaving a M6P marker, leaves multiple M6P markers on multiple oligosaccharide chains, gives high affinity for M6P receptors

Front 51

lysosomal storage disease

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caused by genetic defects that affect one or more of the lysosomal hydrolases, results in an accumulation of undigested substrates in lysosmomes leading to nervous system consequences

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Hurler’s disease

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caused from a defect in or absence of an enzyme required for the breakdown of glycosaminoglycans

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inclusion-cell disease (I-cell disease)

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almost all of the hydrolytic enzymes are missing from the lysosomes of fibroblasts and their undigested substrates accumulate in lysosomes forming large inclusions in the patients’ cells, due to a missing GlcNAc phosphotransferase

Front 54

types of endocytosis

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phagocytosis and pinocytosis

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phagocytosis

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“cellular eating,” involves the ingestion of large particles, generally >250 nm in diameter, ingested with phagocytic cells (phagosomes), a triggered process, requiring that receptors be activated that transmit signals to the cell interior and initiate the response

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pinocytosis

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“cellular drinking,” involves the ingestion of fluid and solutes via small pinocytic vesicles (about 100 nm in diameter), constitutive reaction that occurs continuously

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three classes of white blood cells

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these act as professional phagocytes (those phagocytes that act in means other than nutrition), defense against infection by ingesting invading microorganisms
1. macrophages
2. neutrophils
3. dendritic cells

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residual bodies in lysosomes

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an accumulation of indigestible substances that remain in the lysosomes

Front 59

what triggers apoptosis

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when a cell dies, the membrane loses the asymmetric distribution of phospholipids, negatively charged phosphatidylserine is found on the outside of the wall where it triggers phagocytosis

Front 60

formation of pinocytic vesicles

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1. clathrin coated pits
2. caveolae-thought to form from lipid rafts (patches of the plasma membrane that are rich in cholesterol), major protein is caveolin, thought to collect cargo proteins from the lipid composition of the membrane as opposed to by the assembly of a cytosolic protein coat, can deliver products to endosomes or other side of the cell

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uptake of cholesterol

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mediated by receptor-mediated endocytosis, taken up as low-density lipoproteins (LDL), when body needs cholesterol it makes LDL receptors and places them into its plasma membrane, this pathway can become disrupted if an individual has a defect in their LDL receptor protein (defects cause receptors to lose their binding ability to adaptins and therefore clathrins and LDL can bind to the receptor but cannot be brought into the cell)

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possible fates for transmembrane receptor proteins (and bound ligands) that have been endocytosed

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1. recycled-taken back out the same plasma membrane domain
2. transcytosis-taken to the plasma membrane on a different domain
3. degradation-taken to a lysosome for degradation

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transferrin receptor

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may recycle its ligand as well as the receptor

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constitutive secretory pathway

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operates in all cells, continual secretion of soluble proteins, carry proteins and lipids automatically

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regulated secretory pathway

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specialized secretory pathway in which soluble proteins and other substances are initially stored in secretory vesicles for later release, used for cells that need to release a large amount of product on demand via a signal, normally localized

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separation of proteins prior to leaving the TGN

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sorted into where they are to go next: lysosome, secretory vesicles or cell exterior

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default pathway

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the pathway for protein transport to the cell exterior, does not need a signal like lysosome and secretory vesicles do

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secretory vesicles

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house the proteins for the regulated secretory pathway, INC the concentration of cargo as it matures, normally wait near the membrane until signaled for release

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maturation of secretory vesicles

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1. lead to increasing concentrations of cargo
2. proteolytically process many polypeptide hormones and neuropeptides that are synthesized as inactive ones (either the mature forms are too short for transfer or to slow their activation until needed)