Bio exam 2

endomembrane system

act as a coordinated unit; made of ER, Golgi complex, endosomes, lysosomes, and vacuoles; distinct compartments bounded by membrane barriers and contain specialized proteins for particular activities

vesicles in endomembrane system

package materials; bud from a donor membrane compartment; move via motor proteins on microtubules and microfilaments of cytoskeleton; fuse with the membrane of the acceptor compartment

biosynthetic pathway

proteins are synthesized in the ER, modified at the Golgi complex, and transported to various destinations

secretory pathway

proteins synthesized in the ER are discharged from the cell

endocytic pathway

materials move from the outer surface of the cell to compartments

constitutive secretion

materials are transported in secretory vesicles and discharged in a continual manner

regulated secretion

materials are stored in vesicles and discharged in response to a stimulus; occurs in endocrine cells (hormones), pancreatic acinar cells (digestive enzymes), and nerve cells (neurotransmitters)

liposomes

vesicles whose surface consists of an artificial bilayer that is created from purified phospholipids

uses of cell-free systems

can be used to study proteins that bind to the membrane to initiate vesicle formation, those responsible for cargo selection, and those that sever the vesicle from the donor membrane

secretory granules

large, densely packed, membrane-bound; store secreted materials

sorting signals

encoded in the amino acid sequence of the proteins or in the attached oligosaccharides; routes various cargo to appropriate cellular destinations

autoradiography

visualized biochemical processes by radioactively labeling molecules; "pulse-chase" experiment; determined ER as site of secretory protein synthesis

pulse phase

cells are exposed to a labeled compound (amino acids); labeled molecule is incorporated into the molecule or pathway being studied

chase phase

an unlabeled form replaces the labeled compound

insights from fluorescent proteins

GFP-"tagging" allows microscope viewing of protein movement in living cells; cells infected with strain of virus that has viral-GFP gene fusion; virus takes over the machinery of the cell; production/movement of viral proteins monitored via GFP

homogenization

fragments cytoplasmic membranes

microsomes

similar sized vesicles derived from the endomembrane system

mutant

organism in cultured cell with chromosomes containing one or more genes with abnormal protein function

RNA interference (RNAi)

used to inhibit mRNA translation into proteins; can be used to find genes involved in various steps of the secretory pathway

endoplasmic reticulum (ER)

network of membranes that penetrates much of the cytoplasm and has a lumen separated from the cytosol by a membrane; highly dynamic, 2 compartments share some proteins and activities

rough ER (RER)

ribosomes bound to its cytosolic surface; flatted sacs (cisternae) connected to neighbours by helicoidal membranes; continuous with the outer membrane of the nuclear envelope; near the basal surface, facing blood supply

smooth ER (SER)

lacks ribosomes; membranes are highly curved and tubular; continuous with RER

SER functions

steroid hormone synthesis in endocrine cells of the gonad and adrenal cortex; detoxification of organic compounds in the liver via oxygenases including the cytochrome P450 family; calcium ion sequestration and regulated release

RER functions

starting point of the biosynthetic pathway for secretory proteins; about 1/3 of proteins are synthesized at RER are released into ER lumen

co-translation translocation

process by which proteins are released into the ER lumen after synthesis

signal sequence

on the N-terminus of secretory proteins that directs the emerging polypeptide and ribosome to the ER membrane (then moves into cisternal space of ER through protein-lined, aqueous channel in ER membrane)

signal hypothesis

proteins contain built-in "address codes" for protein trafficking pathways throughout the cell

signal recognition particle (SRP)

recognizes the signal sequence; binds polypeptide and the ribosome, arresting synthesis;

SRP receptor

on ER membrane; recruits SRP/protein complex to ER membrane

translocon

protein channel embedded in the ER membrane; signal sequence is recognized and polypeptide is inserted into the translocon channel

G protein examples

SRP, SRP receptor

signal peptidase

removes the signal peptide from most nascent polypeptides; integral membrane protein

oligosaccharyltransferase

adds carbohydrates to polypeptides in ER; integral membrane protein

membrane biosyntheis in ER

membranes arise from pre-existing membranes; enzymatically modified as they move from ER to other cellular compartments; luminal/extracellular face established in the ER

how membranes change lipid composition

using lipid-modifying enzymes to convert a phospholipid to another; preferentially including or excluding phospholipid vesicles; exchanging lipids between organellar compartments using lipid transfer proteins

glycosyltransferases

catalyzes addition of sugars to an oligosaccharide; each transfers a specific monosaccharide to the growing end of the carbohydrate chain

proteasomes

degrade misfolded proteins

cytoskeleton

"skeletal system" of a eukaryotic cell; composed of microtubules, actin filaments, and intermediate filaments

functions of cytoskeleton

structural support and maintains cell shape; positions various organelles; directs the movement of materials and organelles; generates forces needed for ceullar locomotion; makes us essential part of cell division machinery

microtubule structure

hollow, relatively rigid, tubular; assembled from protein tubulin; arranged in longitudinal rows called protofilaments; 13 protofilaments aligned side by side in a circular pattern

protofilament structure

assembled from dimeric building blocks consisting of one a-tubulin and one B-tubulin subunit; the subunits fit tightly together, organized in linear array, assymetric and polar (plus end is B, minus end is a)

microtubule-associated proteins (MAPs)

increase stability and promote microtubule assembly by linking tubulin subunits togethr

microtubule function

provide mechanical support by resisting forces that might compress or bend the fiber; distribution helps determine shape of cell ; direct movement within the cell; tracks for motor proteins

microtubule motor proteins

kinesin and dynein

actin motor proteins

myosin

motor proteins

convert chemical energy to mechanical energy; move unidirectionally along cytoskeletal track in stepwise manner

kinesins

smallest and best understood; tetramer of two identical heavy and two identical light chains; globular heads bind microtubule and hydrolyze ATP; each head connected to a neck, a rodlike stalk, and a fanlike tail that binds cargo

processive

can walk along a microtubule for considerable distances without falling off

kinesin transport

trafficking routes defined by microtubules; tend to move in an outward direction toward the cell's plasma membrane

dynein

microtuble-associated motor in cilia and flagella; huge protein; two identical heavy chains; variety of intermediate and light chains; heavy chain has large globular force-generating head and microtubule-binding stalk; moves towards minus end (opposite of most kinesins)

dynein function

positions the spindle and moves chromosomes during mitosis; positions the centrosome and Golgi complex; moves organelles, vesicles, and particles through the cytoplasm

taxol

increases stability of microtubule and does not allow disassembly; inhibits mitosis

nucleation

initiation of a microtubule

microtubule-organizing centers (MTOCs)

site of nucleation; controls number and polarity of microtubules, number of protofilaments, and time and location of assembly

centrosome

best studied MTOC; in animal cells; contains centrioles surrounded by electron dense pericentriolar material (PCM); major site of initiation and remains at the center of cell's microtubular network

basal body

another type of MTOC that forms at the base of the cilium or flagellum; are identical in structure to centrioles; can turn into centrioles and vice versa

y-tubulin

critial protein needed for microtubule nucleation; shared by all MTOCs

dynamic properties of microtubules

can shorten, lengthen, disassemble, and reassemble

microtubule disassembly

initiated by posttranslation modifications, cold temperature, hydrostatic pressue, elevated Ca2+ concentration, and a variety of chemicals

katanin

enzyme that severs microtubules into shorter peices

assembly of of tubulin dimers

GTP molecule is bound to the B-tubulin subunit; GTP is hydrolyzed to GDP after the dimer is incorporated and the resulting GDP remains bound to assembled polymer

dissasembly of tubulin dimers

dimer enters the soluble pool, the GDP is replace by new GTP; this nucleotide exchange "recharges" the dimer, allowing it to again be a building block for polymerization

dynamic instability

growth and shrinkage of microtubules can coexist in the same region of a cell; a given microtubule can switch back and forth unpredictably between growing and shortening phases; inherent proerty of plus end

Chediak-Higashi syndrome (CHS)

disease caused by a microtubule polymerization defect; presents as recurrent pyogenic infections, partial albinism, and peripheral neuropathy

cilia

hairlike, sometimes motile organelles; project from surface of a variety of eukaryotic cells' move by sliding adjacent microtubular doublets relative to one another

motile cilia

usually occur in large numbers on a cell's surface, with coordinated beating activity; move fluid and particulate material through tracts

nonmotile cilia

usually one per eukaryotic cell; acts as a sensory organelle, monitoring mechanical and chemical properties of extracellular fluid

flagella

typically occur singly or in pairs; exhibit a variety of beating patterns, depending on cell type

axoneme

core of the cilium; contains array of microtubules that runs longitudinally through the entire organelle; 9 + 2 array

ciliopathies

a set of seemingly unrelated diseaes that all result from primary cilia defects; ex: polycystic kidney disease (PKD) and Bardet-Biedl Syndrome (BBS)

intermediate filaments

strong, flexible, ropelike fibers that provide mechanical strength to cells that are subjected to physical stress; divided into five major classes

plectin

protein that connects intermediate filaments to other cytoskeletal filaments; has a binding site for an IF at one end and another binding site at the other end

IF assembly/disassembly

tetrameric building blocks lack polarity; subunits incorporated into the filament's interior (not the ends); controlled primarily by subunit phosphorylation and dephosphorylation

keratin containing IFs

sturctural proteins of epithelial cells; tethered to the nuclear envelope in the center of the cell and anchored at the outer edge by desmosomes and hemidesmosomes; organize and maintain cellular architecture and absorb mechanical stress

neurofilaments

IFs located in the cytoplasm of neurons in bundles oriented parallel to the axon

actin structure

two-stranded structure with two helical grooves running along its length; can be organized into ordered arrays, highly branched networks, and tightly anchored bundles; "barbed" and "pointed" ends; major contractile muscle protein

actin filament assembly/disassembly

before incorporation, binds ATP; actin is an ATPase; ATP is hydrolyzed to ADP; nucleation occurs slowly, elongation is much more rapid; barbed end grows 10x faster than pointed end

uses of actin

cell locomotion, changes in cell shape, phagocytosis, cytokinesis

myosin

move toward barbed end of actin filament; all share characteristic motor (head) domain (contains site that binds actin filament and site that binds/hydrolyzes ATP); tail domains are highly diverse

conventional (type II) myosin

primary motors for muscle contraction; all move toward barbed end of actin filament; required for splitting cell in two during cell division, generating tension at focal adhesions, cell migration, and turning behavior of growth cones

myosin II structure

pair of globular heads that contain the catalytic site; a pair of necks, each with a single, uninterrupted a-helix and two associated light chains; a single, long, rod-shaped tail formed by the intertwining of long a-helical sections of the two heavy chains; tails point towards center of filament and heads point away from center (bipolar)

unconventional myosins

several are associated with various types of cytoplasmic vesicles and organelles

phalloidin

binds specifically to F-actin, preventing the filaments from depolymerizing; hyperstabalizes the actin filaments

skeletal muscle fiber

multinucleate cell

myofibrils

Microscopic protein filaments that make up muscle cells.

sarcomeres

contractile units within myofibrils, the smallest contractile unit of a muscle

cell locomotion uses

tissue and organ development, formation of blood vessels, development of axons, wound healing, protection against infection

lamellipodium

extended from the cell, adheres to the underlying substratum at specific points, providing temporary anchor sites for the cell to pull itself forward

cellular motility

stimulus is received at cell surface; activation of Arp2/3 complex by member of WASP/WAVE family; Arp 2/3 complex is site of nucleation; once (actin) filaments have formed, Arp 2/3 complex attaches to sides of filaments; bound complexes initiate side branching that extends outwards; push p.m. outwards as filaments polymerize

traction forces

occur at site where the cell grips the substrate and help pull the cell forward; greatest are just behind cell's leading edge (of lamellipodium)

growth cone

highly motile region of the cell that explores its environment and elongates the axon; contains lamellipodia and filapodia -> responds to stimuli, turns toward attractive factors and away from repulsive ones

golgi complex

processes, sorts, and ships proteins synthesized in the rough ER; membranous vesicles carry materials to and from; stack of flattened cisternae; assembly of carbohydrates found in glycolipids and glycoproteins

ERGIC

endoplasmic reticulum Golgi intermediate compartment; formed by transport vesicles fused with one another

cis face

golgi faces the ER

trans face

opposite side of golgi

cis Golgi network (CGN)

sorts proteins for the ER or the next Golgi station

trans Golgi network (TGN)

sorts proteins to the plasma membrane or various intracellular destinations

coated vesicles

carry materials between compartments; coat causes the membrane to curve and form a vesicle and selects the components to be carried by the vesicle

COPII-coated vesicles

move materials from the ER "forward" to the ERGIC intermediate compartment and Golgi complex

COPI-coated vesicles

move materials from ERGIC and Golgi "backward" to ER, or from the trans Golgi to the cis Golgi cisternae