BIOL 302 Exam 4

What are the two ways eukaryotic cells can separate processes that are incompatible?

aggregate the enzymes, confine processes within membrane-bound compartments

What is the function of the ER

major site for synthesis of new membranes

What is the function of the Golgi Apparatus?

receives/modifies proteins and lipids from the ER and dispatches them to other locations

What is the function of lysosomes?

sac of digestive enzymes, degrade worn-out organelles, macromolecules, particles

What is the function of perocisomes?

single membrane, has enzymes for oxidative reactions

What directs a protein to the organelle where it needs to go?

sorting signal

what are the three methods of transport for proteins to get into organelles

through nuclear pores, across membranes, by vesicles

how does protein sorting by vesicles work? (loaded from what into what?)

loaded from the lumen of 1 compartment of the endomembrane, discharged into the second

Which two organelles are connected into 1 membrane, thought to have happened when the plasma membrane invaginated in a prokaryotic cell?

nucleus/ER

What are the three jobs of nuclear pores?

traffic in both directions, binding sites for chromosomes, anchorage for nuclear lamina

What do nuclear transport receptors bind to?

nuclear localization signal on protein

what are the 5 steps for NTR recycling?

1.) NTR picks up cargo protein in cytosol and enters the nucleus

2.) Ran-GTP binds to NTR, causing release of cargo

3.) NTR-Ran-GTP complex exits the nucleus

4.) in the cytosol, GTP is hydrolyzed to GDP (triggered by accessory protein)

5.) Ran-GDP falls off NTR, which repeats process

What form are mitochondrial proteins imported in?

unfolded

What are the three steps of mitochondrial protein transport?

1.) signal sequence of precursor is recognized by a receptor in outer mitochondrial membrane

2.) Receptor complex/attached protein diffuse laterally to contact site, protein translocated across both membranes by protein translocator

3.) Signal sequence is cleaved off by signal peptidase, chaperone proteins help pull protein across membranes

What organelle has the most extensive membrane network?

ER

What happens to ribosomal subunits associated with the ER after they are done with protein synthesis

they are released to join the common pool

What two things direct a ribosome to the ER membrane

ER signal sequence and signal-recognition particle (SRP)

What are the 6 steps of ribosome movement to the ER membrane?

1.) SRP binds to ER signal sequence and ribosome, slows protein synthesis

2.) SRP complex binds to SRP receptor in ER membrane

3.) SRP is released, ribosome passed to translocation channel in ER membrane, inserts polypeptide chain into the membrane and starts transfer across

4.) Translocation channel binds signal sequence and transfers the rest of the polypeptide actively across the membrane as a loop

5.) During translocation, signal peptide is cleaved by signal peptidase

6.) signal is ejected into the bilayer and degraded, translocated polypeptide is released as soluble protein in ER lumen

3 steps for single pass transmembrane protein incorporation

1.) N-terminal ER signal sequence initiates protein transfer

2.) sequence enters translocation channel, protein is discharged sideways into the bilayer

3.) N-terminal signal sequence is cleaved, transmembrane protein stays anchored in the membrane

2 steps for double pass transmembrane protein incorporation

1.) internal ER sequence initiates transfer of polypeptide chain

2.) signal is recognized by SRP, brings ribosome to ER membrane - when stop transfer sequence enters channel, channel discharges both sequences into membrane

What is carried in a vesicle

soluble protein and membrane

What is the outward secretory pathway for vesicular transport

ER - Golgi - plasma membrane - endosome - lysosome

What is the inward endocytic pathway for vesicular transport

extracellular molecules ingested in plasma-membrane-derived vesicles - early endosome- late endosome- lysosome

What is the protein that shapes the membrane into a vesicle?

Clathrin

What are the 2 steps of Clathrin vesicle formation

1.) Cargo receptors carrying bound molecules are captured by adaptins, which bind Clathrin to cytosolic side of budding vesicles

2.) Dynamin proteins assemble around neck of vesicle, hydrolyze GTP and pinch off

What two things direct transport vesicles to target the membrane?

Rab proteins and SNAREs

How do Rab proteins and SNAREs direct transport vesicles to target a membrane? 3 steps

1.) Filamentous tethering protein on membrane binds to Rab protein on the surface of a vesicle

2.) v-SNARE on vesicle binds to complimentary t-SNARE on target membrane

3.) pairing draws 2 lipid bilayers into close proximity, the squeezing ousts water molecules and lets the bilayer become continuous

Where are most proteins glycosylated

the ER

What is it called when new proteins/lipids/carbs are delivered from the ER via golgi to cell surface by transport vesicles

exocytosis

What is the addition of oligosaccharide chains to the NH2 region of asparagine in polypeptide called?

glycolsylation

What is the word for the thing added during glycolsylation

N-linked oligosaccharide chain

What are the 2 steps to glycolsylation

1.) Each chain is transferred as an intact unit from a lipid

2) this is catalyzed by a membrane bound oligosaccharide protein transferase with the active site on luminal side of ER membrane

What type of proteins prevent misfolded or partially assembled proteins from leaving the ER?

chaperone proteins

What are the 3 steps of chaperone protein control?

1.) misfolded proteins trigger chaperone production and ER expansion

2.) Receptors trigger transcriptional regulator protein

3.) This protein translocates to nucleus and activates genes

What is the chaperone response called?

Unfolded protein response (UPR)

What is the golgi apparatus made of?

membrane enclosed sacs, each with a cis and trans face

Which side of the golgi do things enter from

cis golgi

In secretory cells, what is the unregulated/constitutive secretory pathway

used by soluble proteins, automatic, continually supplies plasma membrane with new lipids and proteins

In secretory cells, what is the regulated secretory pathway

use a signal to elicit secretion of products stored in secretory vesicles

What are the two types of endocytosis?

Pinocytosis and phagocytosis

What is pinocytosis

cellular drinking - small molecules and fluid

what is phagocytosis

cellular eating - large particles in phagosomes

What is the LDL pathway

transport of cholesterol

What is the 5 step pathway of cholesterol?

1.) transported in bloodstream bound to proteins forming LDL

2.) LDL binds to surface receptors, internalized in clathrin coated vesicle

3.) vesicles lose coat and fuse with endosomes, LDL dissociates in acidic environment

4.) LDL ends in lysosomes, degraded to release free cholesterol

5.) LDL receptors return to the membrane and are used again

what are the three possible fates of the receptor proteins?

1.) recycling back to apical plasma membrane

2.) degradation in a lysosome

3.) Transcytosis to another part of the membrane

What do lysosomes have to maintain pH difference?

hydrolytic enzymes and H+ pump

What are the 3 pathways to the lysosome for degradation?

1.) bacterium/large molecule is phagocytosed and enters lysosome

2.) endocytosed material goes from early to late endosome, then to lysosome

3.) mitochondria undergoes autophagy, becomes an autophagosome, and goes to lysosome

What is the process of converting extracellular signals into intracellular signals to elicit a response called?

signal transduction

What are the 4 reasons for cell communication?

survives, grow/divide, differentiate, die

What types of cell communication are long range

Endocrine and synaptic/neuronal

What types of cell communication are short range

paracrine and contact-dependant

What is the type of communication using hormones in the blood called?

endocrine

What is the type of communication using axons called?

synaptic/neuronal

What is the type of communication using local mediators called?

paracrine

what do cancer cells do to promote survival or proliferation?

autocrine signalling

What is the type of communication using contact called?

contact-dependant

What’s an example of contact dependent communication

Notch receptor

what protein binds to the notch receptor

Delta

What are the two categories of extracellular signals?

too big to cross the membrane/too hydrophobic and small/hydrophobic

What is the pathway of surface receptor pathways?

extracellular signalling molecule - receptor protein - intracellular signaling molecule - effector protein - target cell response

What do the effector proteins do? 1 or more of 4 options

1.) relay signal outwards

2.) amplify signal received

3.) integrate different signals

4.) Distribute signal to more than 1 pathway or protein

How does a kinase switch work?

signal in, kinase adds a phosphate from ATP, turning into ADP and turning on the switch. Protein phosphatase turns it off by releasing the phosphate

how does a GTP binding protein switch work?

Signal in, conformational change causes GDP to be released and GTP to bind, turning switch on. Later, GTP is spontaneously hydrolyzed and the phosphate is released, this turns the switch off

What are the three classes of cell-surface receptors

ion-channel coupled receptors, G-protein coupled receptors, enzyme coupled receptorsf

What do signal molecules do to an ion-channel-coupled receptor?

change the confirmation to an open/closed channel, results in changes in membrane potential/produces an electric current

What do signal molecules do to a G-protein coupled receptor?

activate membrane bound, trimeric GTP binding proteins which activate channel in membrane

What structure of a GPCR undergoes a conformational change to activate the G protein on the cytosolic side of the membrane?

7 pass transmembrane receptor protein

what are the subunits of G proteins called?

alpha, beta, upsilon (y)

In the unstimulated state, what part of the GPCR is bound to GDP?

alpha subunit

When is the GDP exchanged for GTP in an alpha subunit of a GPCR?

when ligand binds

What are the two domains of enzyme coupled receptors?

ligand binding domain (outside), enzyme/enzyme complex domain (cytosolic)

What are some examples of what enzyme coupled receptors do?

mediate reconfigurement to change shape of cell, respond to growth factors, etc

What is an important example of an enzyme coupled receptor?

Receptor tyrosine kinases (RTKs)

what does the cytoplasmic domain of an RTK do?

phosphorylates specific tyrosines on intracellular proteins

What does a signal do to the structure of an RTK?

causes 2 receptors to dimerize, activating kinases and letting them phosphorylate their tyrosines

what part of RTKs provide binding sites for intracellular signalling proteins

phosphorylated tyrosines

Activated WHAT forms large signalling compexes

RTKs

What is the small GTP binding protein bound by a lipid tail to cytoplasmic face of the plasma membrane

Ras

30% of human cancers have activating mutations of what protein resulting in inactivation in the GTPase activity

Ras

what protein docks on the phosphotyrosine and recruits Ras-activating protein to make Ras exchange GDP for GTP

Adaptor protein

What does Ras activate via the phosphorylation cascade?

MAP-kinase signaling molecule

MAP-kinase signaling molecule ahs how many kinase proteins?

three

what is the final kinase in the MAP kinase chain called?

Mitogen

what does mitogen signal

cell proliferation

What pathway is activated by RTKs

PI-3-kinase-Akt pathway

What does PI-3-kinase stand for

phosphoinositide 3 kinase

What protein, when activated, promotes cell survival by phosphorylating and inactivating the signaling protein “Bad”

Akt (protein kinase)

what does Bad inhibit?

BcI2

What does bad indirectly promote?

apoptosis

How does phosphorylated Bad promote cell survival?

blocking apoptosis

What are the 3 steps that allow Akt to stimulate cells to grow in size?

1.) Growth factor binds to an RTK, activating PI-3-kinase AtK pathway

2.) Akt indirectly activates Tor by phosphorylating and inhibiting protein that keeps Tor shut down

3.) Tor stimulates protein synthesis/inhibits degredation

what form of Ras transmits a signal even in the absence of extracellular signal molecules?

Constitutively active forms

Why does constitutively active Ras transmit a signal always?

cannot hydrolyze GTP

What are the three types of protein filaments we’re focusing on?

intermediate filaments, microtubules, actin filaments

What are the 5 things eukaryotes depend on the cytoskeleton to do?

1.) Adopt different shapes

2.) organize cellular components, including organelles

3.) provide transport machinery between organelles

4.) Interact mechanically with the environment

5.) Carry out coordinated movements

Which filament connects cells through desmosomes?

intermediate filaments

What do desmosomes/intermediate filaments provide the cell?

tensile strength

What does a monomer of an intermediate filament look like?

central rod domain with globular regions at each end

what is the final form of intermediate filaments?

helical array

what are the 4 categories of intermediate filaments?

1.) Cytoplasmic keratin

2.) Cytoplasmic vimentin

3.) Cytoplasmic neuro

4.) Nuclear lamins