biol 104

bulk flow vs signal mediated vesicular

transport (from the ER)

Bulk flow: typical exocytic pathway. Concentration in vesicle bud/vesicle = concentration in ER

Signal mediated: protein concentrated at exit sites. vesicle bud membrane has signal receptors, cargo has signal sequence, concentration is greater in vesicle bud / vesicle than in ER

Where are COPII COPI and Clathrin used?

COPII: ER to Golgi

COPI: golgi to ER, golgi to golgi

clathrin: endocytic pathway

What are the two functions of a clathrin coat?

concentrating specific membrane proteins (receptors) and shaping the vesicle

clathrin steps:

adaptors bind to receptors, clathrin binds to adaptors (function 1). veiscle buds and buds off, clathrin + adaptors fall off.

what is the structure of clathrin called?

triskelion

COPII asembly + bud formation

1)Sar-I gtpase bound to gdp comes into contact with membrane bound SAR GEF (in ER membrane)

2)exchanges gdp for GTP

3) SAR-I bound to GTP is now active, inserts into the membrane

4) SAR-I recruits adaptor proteins

5) adaptor proteins recruit COPII

6) the structure of COPII causes bud formation

what does a gtpase do?

gtp → gdp thorugh hydrolysis

what is GEF?

guanine exchange factor (gdp → gtp) through exchange

What is pinching and how does it work? (dynamin)

vesicle is budding off. dynamin assembles in spiral around pinch point. has GTPase activity. as it hydrolyzes bound GTP, its conformation changes and restricts.

COPII disassembly

SAR-1 GTP state –> SAR-1 GDP state = disassembly

How does the protein know where to go?

RAB protiens + V-snares in vesicle bind to specific organell docking proteins

NPC (nuclear pour complex) components

filled with f-g NPS (form mesch) (very small molecules can diffuse through) spagehtti noodles

nuclear transport factor (binding sites for FG nps and for cargo)

cytosolic fibrils

nuclear basket (nuclear side)

nuclearporin

protein of the NPC

what is the nuclear signal sequence? is there more than one?

binds to nuclear transport factors. yes!

GTP-binding proteins:

proteins that are either bound to GTP or GDP

GAP

GTP activating proteins – activate gtpase to hydrolyze GTP (into GDP)

where are gaps and gefs found?

gaps in cytosol, gefs in nucleus

draw ranGDP cycle / import cycle

what is acetylcholine?

neurotransmitter that enables communication between neurons and muscles

what is the axon?

a long extension of a neuron with microtubule tracks and motor proteins which deliver vesicles

what causes acetylcholine to be released?

an influx of calcium through ion channels prompts ach vesicles to bind to plasma membrane and be released into synapse

what is synapse?

area between neuron and muscle / receptor

ligand

extracellular chemical signal

general signaling sequence:

1) signal molecule binds to receptor protein (embedded in plasma membrane)

2) the receptor activates one or more intracellular signaling pathways

3)one or more of the intracellular signaling molecules alters the activity of the effector proteins + the cell

possible effector proteins:

metabolic enyme, transcription regulatory protein, cytoskeletal protein

Three types of signaling: (but really four)

contact-dependent, paracrine, synaptic (secretly paracrine), endocrine

describe contact-dependent signaling:

signal molecule is bound to surface of one cell. cells must kiss

paracrine (v autocrine)

signal molecule secreted, local different cell has receptor (autocrine: signal molecule secreted, picked up by same exact cell)

synaptic

performed by neurons, type of paracrine

endocrine

long distance paracrine

how can intracellular receptors going from one cell to another work?

small hydrophobic signals that can just get in there!

can the same signal molecule have different effects on different cell types?

yes

three major classes of cell surface receptors:

G-protein coupled receptors

receptor protein tyrosine kinases (enzyme)

ligand gated ion channels

G-protein coupled receptor features

1) 7 spanners

2) bind to heterotrimeric g-protein

enzyme coupled receptor

either receptor itself is an enzyme or it associates to an enzyme

single spanners usually

protein kinase + protein phosphateses

add phosphate, or remove phosphate group

heterotrimeric binding proteins

inactive: alpha bound to GDP, all three associated together

cAMP steps (8)

1) ligand binds to receptor

2) GDP molecule exchanged for GTP molecule in alpha unit, alpha unit activated

3)alpha unit associates to effector (a transmembrane protein). effector is activated

4) cAMP is produced from ATP

5)gtp is hydrolyzed by alpha unit, inactivated

6) g protein reforms

7) receptor is phosphorylated by a kinase

😎 arrestin binds to and inhibits GPCR (ligand still bound)

cMAP serves as a what

second signaling protein (amplifies signal)

protein-tyrosine kinases

phosphorylate tyrosine residues on target proteins

receptor tyrosine kinases:

activated directly by extracellular growth and differentiation factors to phosphorylate tyrosine residues on itself

RTK steps (4)

1) signal protein binds, dimerization occurs

2) kinase domains on each half phosphorylate the other or themselves

3) trans-autophosphorylation (automatic phospholiation) occurs

4) activates signal proteins for downstream signaling

What is a bad thing for cell signaling?

when it cannot be turned off (constitutively active)