BIOL300: Chapter 15

endomembrane system

ER, Golgi, endosomes, lysosomes, peroxisomes, transport vesicles, nuclear envelope

nuclear envelope

double membrane around the nucleus

nuclear pores

transport complexes through which information is exchanged between the nucleus and the cytosol

ER

new membrane synthesis (lipids) and production of endomembrane associated proteins and those bound for export

RER

ER with ribosomes: attached ribosomes active synthesize proteins

SER

ER without ribosomes: diverse functions depending on cell type:

-steroid hormone synthesis

-detoxification (ex: alcohol in liver cells)

-sequesters Ca2+ from cytosol--> selectively released for specific types of intracellular signaling events

Golgi apparatus

-receives proteins and lipids from the ER (COP coated vesicles)

-modifies these molecules (most often by glycosylation)

-reads sorting signals for shipping to cellular destinations

lysosomes

-contain diverse digestive enzymes active only at very low pH

-degrade and recycle worn-out biomolecules, organelles, and other waste material as well as molecules taken up by endocytosis

endosomes

receive ingested molecules via endocytosis and sort them to appropriate destinations; traffic may be recycled back to the plasma membrane or delivered to lysosomes to be degraded

peroxisomes

-close proximity to mitochondria

-oxidize long chain fatty acids for B-oxidation (beta) in mitochondria

-oxidize diverse additional substrates (toxins) using O2 as oxidizer; toxic byproduct H2O2 is then cleared by using it as an oxidizing agent for other reactions

mitochondria and chloroplasts

-not part of endomembrane system--> generate membrane components independently and do not receive transport vesicles from other organelles

transport vesicles

enclosed sacs that pinch from, transport between, and fuse with the membrane of endomembrane system organelles

signal sequence

-sorting signal composed of a unique amino acid sequence (4-60 AAs long) that is recognized by other cellular proteins and used as a mailing address for delivery or retention

-necessary and sufficient

nuclear lamina

meshwork of structurally supporting proteins

nuclear localization signal (NLS)

signal sequence that directs a protein from the cytosol into the nucleus

nuclear import receptor

cytosolic protein that recognizes proteins w/ NLS

importin

(cargo) the cytosolic protein with the nuclear import receptor

Ran

monomeric GTPase

Ran-GTP

Ran carrying a molecule of GTP

transporter outer membrane (TOM) complex

receptor protein within recognizes signal sequence

transporter inner membrane (TIM) complex

receptor within interacts with signal sequence inserted through TOM complex

chaperone

proteins inside the organelles that help pull the protein across the two membranes and refold it once inside; prevent misfolded or partially assembled proteins from leaving the ER

polyribosome

mRNA bound by multiple ribosomes at various stages of translation

signal recognition particle (SRP)

cytoplasmic protein that binds the ribosome and the ER signal sequence on the N-terminus --> helps to guide ER signal sequence to the ER membrane

SRP receptor

embedded in the ER membrane of the RER; recognizes the SRP

protein translocator

embedded in ER membrane; interaction releases the SRP from the ribosome; contains channel in which the the signal sequence remains bound to while the peptide translation continues

stop-transfer sequence

N-terminal signal sequence; signal to halt translocation and cleave the N-terminus

start-transfer sequence

internal signal sequence; starts protein translation; never removed from the polypeptide

vesicular transport

transport of proteins from the ER to the Golgi, from the Golgi to other compartments of the endomembrane system

coated vesicles

vesicles with distinctive protein composition coat on cytosolic surface

clathrin

well-known protein that makes up a protein coat; forms lattice-like network which eventually pinches the vesicle from the membrane

clathrin-coated vesicles

bud from the Golgi on the outward secretory pathway and the plasma membrane on the inward endocytic pathway

-Golgi --> lysosomes

-p.m. --> endosomes

clathrin-coated pits

form in which clathrin-coated vesicles start

adaptins

second class of coat proteins that work alongside clathrin; secure the clathrin coat to vesicle membrane and help select cargo molecules for transport

dynamin

GTP-binding protein; assembles ring around the neck of each deeply invaginated coated pit; along with other proteins, help pinch the vesicle from the membrane

COP-coated vesicles

class of coated vesicles; involved in transporting molecules between the ER and the Golgi apparatus and from one part of the Golgi apparatus to another

Rab proteins

monomeric GTPases; attached to the surface of cargo vesicle to initiate appropriate docking to the target membrane (correspond to tether on target membrane)

-over 70 encoded in the human genome

SNAREs

transmembrane proteins on the cargo vesicle; aid Rab proteins in identification (correspond to complementary SNAREs on the target membrane); promote fusion of the vesicle and the target membrane

v-SNAREs

vesicle-bound

t-SNAREs

target membrane bound

disulfide bonds

formed by the oxidation of pairs of cysteine side chains; stabilizes proteins against enzymatic activity and changes in pH outside of the cell

-do not form in cytosol due to reducing environment

glycosylation

-conversion of proteins (that enter the ER membrane or ER lumen) to glycoproteins by covalently attaching sugar additions

-protect from degradation; hold protein in ER until properly folded; guide the protein to appropriate organelle as a transport signal

glycocalyx

cells outer carbohydrate layer; generated by the glycosylation of proteins into glycoproteins

-involved in cell-cell recognition

dolichol

ER membrane specialized lipid in which the sugar complex is first assembled before being transferred to the protein

asparagine

side chain of the protein (amino group NH2) in which the sugar complex is attached to from the dolichol; in the N-terminus of the recipient protein

N-linked glycosylation

most common type of linkage found on glycoproteins (attached to the asparagine NH2 group)

O-linked glycosylation

less common type of linkage found on glycoproteins

-occurs in the Golgi rather than the ER where N-linked glycosylation occurs

health relevance of protein quality control mechanism

cystic fibrosis: (severe long damage) produces plasma-membrane transport protein which is slightly misfolded; even though mutant protein could function normally as a chloride channel if it reached the plasma membrane, still degraded because it does not fold properly

unfolded protein response (UPR)

occurs when quality control mechanism is overwhelmed; misfolded proteins accumulate in ER; prompts cell to produce more ER, including more chaperones and other proteins concerned with quality control

cis face

facing ER; receives COP coated vesicles

anterograde movement

proteins move through the medial cistern as they are processed by means of transport vesicles that bud from one cistern and fuse with the next in the stack

trans face

facing away from ER towards plasma membrane; completes processing of proteins and assembles clathrin-coated vesicles for export

retrograde movement

returns the enzymes, which moved with the COP coated vesicles in an anterograde fashion, to their appropriate positions in both the Golgi and ER

exocytosis

steady stream of vesicles budding from trans Golgi network and fusing with the plasma membrane

constitutive exocytosis pathway

operates continually -provides cell with newly made lipids and proteins to resupply/replace worn out membrane components and increase surface area for cell division

-secretes extracellular proteins that will become a part of the extracellular matrix or diffuse to signal or nourish other cells (these kinds of proteins do not possess a unique signal sequence)

regulated exocytosis pathway

only occurs in cells specialized for secretion -- hormones. digestive, or neurotransmitter producing cells

secretory vesicles

store secretions; bud off from trans Golgi and accumulate near plasma membrane and must wait for a release signal

-ex: excess of blood sugar triggers insulin release from pancreatic B-cells (beta)

endocytosis

taking up of fluid and molecules

endocytic vesicles

generated by clathrin-coated pits; delivered to endosomes

pinocytosis

engulfing small amounts of liquid and small molecules -clathrin-dependent (clathrin-coated pits)

-also used in receptor-mediated endocytosis

phagocytosis

ingestion of large molecules (microorganisms, cell debris)

-non-clathrin dependent

-used infrequently for nutrient uptake

phagocytic cells

cells of the immune system (white blood cells like macrophages and neutrophils) that fight invasion by foreign microorganisms

-Mycobacterium tuberculosis: evolved defenses against phagocytosis that inhibits membrane fusion that unites phagosomes and lysosomes

phagosomes

large vesicles of phagocytosis

pseudopods

sheetlike projections of the plasma membrane; engulf bacterium and fuse at their tips to form phagosome

-generated from the binding of antibody-coated bacteria to the surface receptors of the phagocytic cell

receptor-mediated endocytosis

macromolecules in the extracellular fluid bind to complementary receptors on the cell surface and enter the cell as receptor-macromolecule complexes in clathrin-coated vesicles

-provides selective concentration mechanism that increases the efficiency of internalization of particular macromolecules

-ex: take up of cholesterol to make new membrane

trancytosis

early endosome buds transport vesicles that deliver receptor/cargo to different plasma membrane locations

-a way to transport a signal or molecule across an epithelium like that found in the intestinal lining

mannose-6-phosphate

specific phosphorylated sugar group

-added in the ER and cis-Golgi network

-tags enzymes so when they arrive in the trans-Golgi they can be recognized by appropriate receptor --> permits lysosomal enzymes to be sorted and packaged into transport vesicles

autophagy

(additional pathway that supplies materials to lysosomes) degradation of worn-out intracellular organelles, or in response to nutrient depravation or the need to restructure cell (as during development)

autophagosome

enclosure of the organelle by a double membrane, which then fuses with a lysosome