Chapter 15

Cell Trafficking and Cell Structure

citric acid cycle, oxidative phosphorylation

what two metabolic processes take place in the mitochondria

houses genome, DNA replication, RNA synthesis

what are the 3 key functions of the nucleus

metabolic pathways, ribosomes doing translation, signaling pathways, cytoskeleton

what 4 things/processes happen in the cytosol

nuclear envelope

what is the ER continuous with

organelles, plasma membrane, export

where do the proteins made in the rough ER end up

synthesis of membrane lipids, Ca2+ storage

what are the 2 functions of the smooth ER

steroid hormone synthesis

what is unique about smooth ER in endocrine cells

detoxifies alcohol

what is unique about smooth ER in liver cells

sorting, modifying, and transporting lipids and proteins

what is the function of the golgi apparatus

recycled to plasma membrane, exported from cell, hydrolyzed in the lysosome

within the endosome, what are the possible fates of imported materials

endosome

where does every imported material go first in a cell

hydrolytic (allows it to digest materials)

what type of enzymes does a lysosome contain

imported macromolecules, unwanted organelles, unwanted proteins

what things does a lysosome digest

oxidative

what type of enzyme is a peroxisome filled with 

produces and removes H2O2, oxidizes and neutralizes toxic molecules, synthesizes phospholipids, beta-oxidation

what are the 4 functiosn of a peroxisome

endoplasmic reticulum, golgi apparatus, peroxisomes, lysosomes, endosomes, ECF

what is part of the endomembrane network and/or connected by vesicular transport

nuclear pores

what connects the cytosol to the nucleus

no

are mitochondria/choloroplasts connected to the endomembrane network

cytosol, nucleus (enters folded via pores), mitochondria/chloroplasts (enters unfolded)

where can a protein go after it is translated by cytosolic ribosomes and how does it enter alternate destinations

signal sequences (a short amino acid sequence within a protein read by sorting proteins)

what directs the sorting of any protein within a cell

ER signal sequence (8 to 15 hydrophobic amino acids)

what dictates where (cytosol or rough ER) a protein is translated by a ribosome and what is this made up of

import signal (at N-terminus, cleavage site nearby, removed during transport), membrane insertion signal (internal location, no cleavage site nearby, forms transmembrane alpha helix)

what two types of ER signal sequences are there and what are their differences

cytosol, nucleus, mitochondria, chloroplasts

where can a protein lacking an ER signal sequence end up

translocator

channel of translocating protein into ER

signal peptidase

this cleaves import signal from precursor protein within rough ER

signal recognition particle

what binds to an ER signal sequence

location of N-terminus and orientation, number of transmembrane regions (single pass or multipass protein)

what about the location of the first ER signal sequence determine the location/function of a protein, what about the total number of insertion signals

within the cytosol SRP binds to ER import signal on growing polypeptide chain and slowing translation, SRP binds to SRP receptor found on rER membrane causing ribosome to bind to protein translocator and ER import signal enters translocator, translation finishes as protein translocator closes, signal peptidase cleaves signal peptide and allows mature protein to fold in ER lumen

how do soluble ER proteins end up in the ER lumen while being translated by a ribosome in the cytosol

once insertion signal is translated on a growign peptide chain, SRP binds to the signal pausing translation and binds to SRP receptor, the protein and signal is pushed into the translocator as translation continues, after translation amino terminus stays in cytosol, there is a transmembrane alpha helix at the insertion singal, and the carboxyl region is in the ER lumen

how do transmembrane ER proteins end up in the ER lumen while being translated by a ribosome in the cytosol

ER soluble protein

for a growing polypeptide with one single ER signal at its N-terminus, will it be an ER soluble protein, single pass protein, or multipass protein

mitochondria, chloroplasts, inside nucleus, cytosol

once a protein is in the endomembrane network, where can it NOT go

there is a diffusion filter lined with disordered proteins, only small solutes and molecues that 1. can interact with the diffusion filter or 2. interact with a protein that can carry you in (nuclear import receptor)

why can’t all proteins enter the nucleus via nuclear pores

a nuclear protein will contain a nuclear localization signal (small amino acid sequence within the polypeptide) recognized by a nuclear import receptor that interacts with cytosolic fibrils and travels down pore proteins via binding to enter the nucleus, dropping its cargo and returning to the cytosol

how does a prospective nuclear protein enter the nucleus if it is unable to enter the nuclear pore by itself

Ran-GTPase

what protein is responsible for making sure imported proteins stay within the nucleus

Ran-GRP binds to a nuclear import receptor once it has entered the nucleus, displacing its protein, the receptor then enters the cytosol triggering Ran-GTPase activating protein (Ran-GAP) to hydrolyze GTP into inactive Ran-GDP which dissasociates from the nuclear import receptor, Ran-GDP enters the nucleus and is converted back to active Ran-GTP via Ran Guanine nucleotide exchange factor (Ran-GEF)

describe the cycle of Ran-GTP to Ran-GDP and how it drives nuclear import

Ran-GTP

which is higher in concentration within the nucleus: Ran-GTP or Ran-GDP

Ran-GTP

which can bind to a nuclear import receptor: Ran-GTP or Ran-GDP

a nuclear export receptor (exportin) bound to cargo cannot leave the nucleus without Ran-GTP also binding to it (Ran-GTP follows the same regeneration cycle as seen in nuclear import)

how does Ran-GTP drive nuclear export (don’t include regeneration cycle)

after mitosis (proteins need to be resorted into nucleus), transcription factor regulation (protein in nucleus = transcription on; protein out of nucleus = transcription off)

how is nuclear import and export crucial to a cell - 2 reasons

peroxisome

what is the only organelle that receives proteins from both the ER (endomembrane network) AND cytosol

folded proteins transport through pores in peroxisome, membrane proteins and lipids integrate via vesicular transport

how do peroxiomes take in proteins from cytosol, how do they from the ER

some are encoded in mitochondrai DNA and translated in mitochondria; most are encoded in nuclear genome, translated in cytosol, then imported unfolded after translation by import receptor protein recognizing its N-terminal signal sequence, after translocation the signal peptide is cleaved

how do mitochondrial (and chloroplasts) proteins end up in the mitochondria - 2 ways

outer membrane, inner membrane, intermembrane space, matrix

after being imported to the mitochondria, what are the 4 possible specific destinations a protein could end up based off of other signals and mechanisms

lipid-carrying proteins transfer them from ER

mitochondria have their own membrane and need lipids, how do lipids enter the mitochondria (hint they cant enter via vesicles)

proteins have specific signals and vesicles have specific surface targeting proteins

how is vesicle transport controlled, aka how does each protein end up in the right vesicle and location

clathrin

this is an outer coat protein which drives the budding of vesicle and helps to capture the correct cargo; is multidirectional

golgi (buds outwards to endomembrane network), plasma membrane (buds inwards during endocytosis to endosome)

what two locations can clathrin (a coat protein) be in and how does this determine the vesicles direction

adaptin

what confers cargo specificity to clathrin vesicles

• different types of these result in different destinations of the vesicle

1. cargo selection (cargo receptor recognizes signal sequences and binds to cargo; adaptins bind to the cargo receptors)

2. bud formation (clathrin binds to adaptins to form bud)

3. vesicle formation (dynamin a GTP binding protein releases the bud from the membrane)

4. uncoating (ATPases remove coat proteins - adaptin and clathrin)

5. naked transport vesicle is revealed (now targeting proteins can access vesicle)

what are the steps of vesicle budding and what proteins played a role

motor proteins, microtubules, vesicle specific

vesicles are often transported by ___ ___, usually along ____; motor proteins and direction are ____ specific

membrane

vesicle docking is ____ specific

1. tethering (specific Rab-GTPase on vesicle binds to a thethering protein on target membrane)

2. docking (vesicle-SNARE and target-SNARE interact)

3. fusion of membranes

describe the process of vesicle docking and include what proteins make this process membrane specific

the v and t-SNAREs interact to form a bundle of a-helices that wind together to squeeze out water, allowing membranes to get close enough to fuse together

how are v and t-SNARE proteins crucial to vesicle fusion

its toxin cleaves SNAREs prevent all docking and fusion of vesicles, resulting in weakness and paralysis, inabilty to breath (specifically from acetylcholine being unable to be released as a nt)

what affect does clostridium bolutlinum have on a cellular level and what affect does this have on the body

this temperature sensitive mutation misfunctions at higher temperatues and causes endocytosis to be blocked after bud formation of vesicles, paralysis results because neurotransmitters can’t be recycled

what affect does a dynamin mutation have on the body

glycosylation

what process creating a certain type of membrane and secreted proteins begins in the ER (hint: is N-linked, occurs during translation via oligosaccharyl transferase)

oligosaccharyl transferase

what enzyme moves a standard oligosaccharide to a growing peptide chain within the ER lumen, beginning glycosylation and creating an immature glycoprotein

disulfide bonds, glycosylation

what 2 modifications can occur to a protein within the ER

ECF (stabilize protein’s folded structure allowing it to remain functional longer)

where would a protein with disulfide bonds (created in the ER) likely end up: cytosol or ECF

are exported to cytosol as garbage and degraded in proteasome

if the ER only exports good proteins, what happens to proteins which failed folding

sudden increase in protein expression or a mutant protein accumulating, reduces demand on ER or increases ER capacity

within the ER, why would too many unfolded proteins accumulate, how is cell behavior altered to address this problem

excessive unfolded proteins bind to sensors on ER membrane, activated sensors inhibit protein syntehsis and slow the cell cycle, the expression of ER proteins is increases, including chaperones; apoptosis

within the ER, when too many unfolded proteins accumulate, what is inhibited and what is increased via the binding of what to what; lastly if this cycle continues for too long what happens to the cell as a whole

ER (requires an ER retention signal), golgi apparatus via vesicles

what two locations can a protein go after being folded and modified in the ER

endosome to lysosome, plasma membrane, ECF

where can proteins travel to after the golgi apparatus

constitutive secretion

this is the constant secretion of plasma membrane components and extracellular proteins (signals, enzymes, etc.) with no signal sequence required

specialized secretory

regulated secretion occurs in ____ ____ vesicles only and its exports are unique to the type of cell (ex: hormones, mucus, digestive enzymes, neurotransmitters)

selective aggregation, regulated vesicle fusion

what are the two types of regulated secretion a cell can do

selective aggresion

a type of regulated secretion in which secretory proteins aggregate in the golgi and are packed into a secretory vesicle at high concentrations and taken to ECF when the vesicle is full

regulated vesicle fusion

this type of regulated secretion is when secretory vesicles accumulate and wait at their final location for the signal required for fusion and release

hormones, neurotransmitters, action potential

what types of signals can trigger regulated vesicle fusion (a type of regulated secretion)

antitrypsin

this is a protease inhibitor secreted by the liver into the bloodstream, moderates the activity of secreted proteases

• protects lung tissue via inhibiting neutrophil elastase

lung disease

chronic obstructive pulmonary disease in younger pateients without a history of smoking

liver disease

cirrhosis and carcinoma without a viral hepatitis or alcohol abuse

decreased serum levels of antitrypsin

what is alpha-1 antitrypsin deficiency diagnosed

encodes a functional protease inhibitor but it cannot escape the ER due to misfolding (aka antitrypsin is not present in the blood)

what does the mutant gene do to antitrypsin

liver disease due to failed secretion of antitrypsin, lung disease due to overactive proteases

what are the effects and why of alpha-1 antitrypsin deficiency (an example of failed exocytosis)

endocytosis

when membrane components return to organelles and fluid is returned into the cell

• two types: pinocytosis and phagocytosis

pinocytosis

this type of endocytosis is when small vesicles form at plasma membrane and extracellular fluid and molecues are captured

• two types: non-selective and selective; both occur in the same vesicles

balances fluid and membrane loss from constitutive secretion

what is the purpose of non-selective pinocytosis

recycling to plasma membrane, transcytosis of recptor/cargo, degradation in lysosome

after endocytosis, all molecules go to the endosome; after that what 3 paths can a molecule go

ATP-driven H+ pumps acidify endosome and some receptors release cargo at low pH

what happens within the endosome

vesicle transport delivers hydrolytic enzymes, lysosomal proteins arrive from golgi, ATP powered H+ acidify the organelle as it moves away from the plasma membrane until the pH is 4.7-5.0

an endosome, with a pH of 5-6, eventually turns into a more acidic lysosome, how does this happen and what is the final pH

lysosome enzymes require a highly acidic environment to work, glycosylated membrane proteins facing the lumen

what prevents the lysosome from digesting the rest of the cell

phagocytic cell’s receptors recognize target, psuedopods engulf target, phagosome fuses with lysosome to be digested

describe the process of phagocytosis within an animal immune system

autophagy

when a cell eats parts of itself

extreme starvation, certain fate changes (ex: RBCs lose mitochondria), remove damaged organelles

in what examples would a cell do autophagy