Bio 210 Module 3

Where do cytoplasmic proteins fold and end up?

cytoplasm

What proteins don’t go to the cytoplasm?

proteins that go into the ER or are from the ER

What is a retention signal?

amino acid signal that tells a cell that a protein needs to stay in the ER

What proteins have a retention signal?

proteins that go into the ER

What signal do proteins leaving the ER have?

alternative localization signal, NOT a retention signal

What types of proteins does the ER import?

membrane and water soluble proteins

What are water soluble proteins, where do they go in the ER?

hydrophilic proteins, imported into the ER lumen

What is a lumen?

space inside an organelle

What are transmembrane proteins?

amphipathic proteins that span the membrane

What do proteins need to get into the ER?

ER localization signal

What is the difference between an ER retention signal and an ER localization signal?

an ER retention signal must stay on the protein the whole time for it to be in the ER, a localization signal just tells the protein it needs to head to the ER

What do proteins need to get through a lumen?

protein translocator

What is a protein translocator?

protein that helps move proteins through membranes, unfolds proteins to thread them through the translocator or else they would fold back up and can’t move through the membrane

Where is the ER localization signal (or signal sequence) located on a protein?

N terminus

What is a signal recognition particle (SRP)?

protein in cytosol that bings to ER signal and slows translation until a protein arrives at the ER

What is an SRP receptor?

receptor that finds and binds the SRP at the ER, it releases the SRP back to the cytosol, and opens the protein translocator so the protein can go through the ER membrane

What is signal peptidase?

transmembrane protiein that removes a signal peptide (signal sequence) via hydrolysis

Describe the steps of importing a water soluble protein into the ER

• An SRP binds to the signal sequence at the N terminus of a protein

• The SRP then slows down translation until it reaches an SRP receptor

• Once bound to the SRP receptor, the SRP is released into the cytosol and the protein’s signal sequence now binds to the protein translocator and it opens

• Translation resumes and the protein is translated through the protein translocator

• Once finished translating a signal peptidase removes the signal sequence via hydrolysis and the protein refolds in the ER

What is a single pass membrane protein?

membrane protein that passes once through the membrane

What is a double pass (or ____ pass) membrane protein?

protein that passes twice through the membrane, or however many times is indicated by the name

What do transmembrane proteins contain to regulate import to the ER?

have hydrophilic start and hydrophobic stop sequences so that hydrophobic regions stay in the membrane and hydrophilic regions don’t

Describe the steps of importing a single pass membrane protein into the ER

• a start sequence attaches to the protein translator and the protein threads through

• once a stop sequence is reached, the stop sequences recruits signal peptidase and it cleaves the start signal

• the protein is then ejected from the translator, and shifted in the membrane

Describe the steps of importing a multi pass membrane protein into the ER

• starts the same as a single pass, however there are multiple start and stop sequences that occur for the protein to thread through

• this time though there is NO signal peptidase that cleaves anything

What do proteins need to be exported from the ER?

need a transport signal to then export them via vesicle

What happens if proteins misfold in the ER?

• chaperones try and refold proteins to fix the problem, however this can cause a buildup of chaperones trying to fix tons of misfolded proteins

• the cell will try to make more lipids so there’s more membrane to make the ER larger

• eventually this is wasting energy on fixing the ER but it’s not helping so the cell will initiate apoptosis to avoid exploding and energy waste

What are cisternae?

golgi membrane pockets

What are the 3 cisternae levels in the Golgi?

trans, medial, and cis

In what direction do proteins enter and exit from the Golgi?

go from cis to trans

What happens to proteins when they exit the ER and go through the Golgi?

Golgi sorts proteins into vesicles by modifying them with sugars and lipids via enzymes

How are the cisternae of the Golgi organized, why does this organization exist?

organized by order of enzymes required for certain proteins, this happens because the cell is lazy, however enzymes can accidentally leave designated cisternae

What is the peroxisome?

organelle that imports a large amount of redox enzymes which produces a large amount of hydrogen peroxide, they digest toxins and synthesize some phospholipids, they have protein translocators in their membranes and receive proteins from the cytosol

What are lysosomes?

organelle that is full of proton pumps and has a low internal pH, it contains enzymes that work in acidic environments that can hydrolyze large molecules

What is the endomembrane system?

system of any membrane enclosed organelle in the cell working together; nucleus, ER, Golgi, endoscopes, lysosome, peroxisome, mitochondria/chloroplasts, etc.

What is a signal sequence?

amino acid sequence on the N terminal that tells a protein where to go, in most cases removed once protein has arrived where it needs to be, is necessary and sufficient to localize a protein

What does it mean for a signal sequence to be necessary?

it is needed for a protein to function

What does it mean for a signal sequence to be sufficient?

it is the minimum sequence a protein needs to have

What do proteins need to transport into the nucleus?

nuclear localization sequence (NLS) that tells the protein it needs to go to the nucleus

How do proteins transport into the nucleus?

• nuclear import receptors attach to the protein on the NLS

• the nuclear import receptor is grabbed by cytosolic fibrils and moves the cargo through a nuclear basket

• the protein bound to the receptor is replaced with Ran-GTP and the receptor can be reused

What is a nuclear pore?

perforation in membrane that forms a gate, it has cytosolic fibrils that act like a strainer and grab things

What are cytosolic fibrils?

proteins that act like a strainer and spider web to grab certain things entering the nuclear pore, made of alpha helices

What do cytosolic fibrils NOT bind to when a protein is imported into the nucleus?

does NOT bind to the nuclear localization signal

What are nuclear import receptors?

receptors that bind to a nuclear localization signal, they are grabbed by cytosolic fibrils and help in importing proteins into the nucleus

What is Ran-GTPs role in nuclear import of proteins?

molecule that has a higher affinity to the nuclear import receptor than a protein does, it swaps with the protein so that the protein can be delivered to the nucleus, Ran-GTP also allows for the receptor to be reused and move outside the cell with it, Ran-GTP hydrolyzes its GTP and dissociates so the receptor can be used again

How many membranes does the nucleus have, what are they?

2, outer and inner nuclear membrane

What is the outer nuclear membrane?

membrane that is around the nucleus and connects directly to the ER membrane

What is the nuclear lamina?

protein meshwork that gives structure to the nucleus, on the inner nuclear membrane

What is a guanyl activating protein (GAP)?

enzyme that shuts GTP off by promoting GTP hydrolysis

What is a guanyl exchange factor (GEF)?

enzyme that turns GTP on by promoting the exchange of GDP to GTP

What is the inner membrane space of the mitochondria?

space between the inner and outer membranes of the mitochondria

What is the mitochondrial matrix?

inner space of the mitochondria, has its own DNA and RNA machinery

How are proteins imported into the mitochondria?

• proteins have a localization sequence on the N terminus for the mitochondria

• signal sequence is recognized by a protein receptor which sits with a translocator on the outer membrane of the mitochondria

• the protein translocator will move in the membrane until it aligns with an inner membrane protein translocator

• the protein is then threaded through both translocators and is aided by chaperones so it doesn’t fold between membranes or get stuck in the inner membrane space

• the protein eventually refolds in the matrix and the signal sequence is hydrolyzed

What are the three mechanisms of protein transport?

nuclear pore into the nucleus, across membranes into membrane lumens, via vesicles

How are vesicles formed?

form a bud of a membrane, the membrane then has cargo receptors that to clathrin proteins with the help of adaptin, clathrin pulls the budding vesicle away from the membrane, and the membrane is then separated by dynamin

What functions do vesicle coat proteins serve?

structure of the vesicle, and capture proteins in the vesicle for transport

What are vesicle cargo receptors?

transmembrane proteins that bind a protein required for delivery via vesicle

What is adaptin?

protein that links cargo receptors to clathrin

What is clathrin?

protein that forms a structural basket when sequestered into a small area by adaptin

What does vesicle cargo contain that is crucial to cargo delivery?

cargo has a signal sequence for the cargo receptor and a delivery signal sequence

How does dynamin work to separate a vesicle from the membrane?

using GTP, it wraps around the remaining connected membrane and tightens down on it until the membrane separates, the membrane then reseals itself

What are the 3 steps to delivering a vesicle?

tethering, docking, and fusion

What is tethering of a vesicle?

the tethering protein on the target organelle attaches to the Rab protein on the vesicle, this creates a conformational change in the tethering protein

What is docking of a vesicle?

the v-SNARE on the vesicle and the t-SNARE on the target organelle bind and change conformations which brings the vesicle closer to the membrane

What is fusion of a vesicle?

the membrane of the vesicle breaks into the membrane of the delivery site (they basically fuse), this is an unfavorable event due to hydrophobic interactions so an enzyme is needed to help, luckily SNARE proteins catalyze the removal of water between the two membranes so they can fuse

What is a v-SNARE?

protein on a vesicle

What is a t-SNARE?

protein on target organelle that is supposed to receive a vesicel

What is autophagy?

quick fix, self eating method, creation of an autophagosome of internal organelles and degrades organelles, starts with eating the mitochondria since there’s such an abundant amount of ATP, fatty acids, and proteins

What happens if the cell doesn’t fix itself after autophagy?

apoptosis occurs

What is vesicular transport?

using vesicles to move proteins throughout the cell

What is a transport vesicle?

small pinched off membrane with proteins inside or in the membrane?

Where are soluble proteins held in a vesicle?

held inside the vesicle space

Where are insoluble proteins held inside a vesicle?

held inside the vesicle membrane

What is exocytosis (secretory pathway)?

where vesicles from the ER go to other organelles or the plasma membrane

How is exocytosis regulated vs unregulated?

regulated exocytosis requires the cell to receive a signal to release a vesicle, unregulated exocytosis just ships vesicles immediately

What is endocytosis (endocytic pathway)?

budding of membrane out of the plasma membrane and then internalized

What is phagocytosis?

from of endocytosis, the cell engulfs large particles (usually bacteria), cellular eating

What is pinocytosis?

cell takes in a little water and small particles, cellular drinking

How is neuron signaling an example of endo or exocytosis?

form of regulated exocytosis in which we release small packets of signal (neurotransmitters) to turn on the next neuron or muscle

How is lung surfactant an example of endo or exocytosis?

form of regulated exocytosis in which a receptor detects in more or less surfactant needs to be released, surfactant cells then release the surfactant to the lungs so they can properly hold pressure

How is the immune system an example of endo or exocytosis?

for exocytosis when antibodies are sent to the surface of the cell to detect antigens, form of endocytosis (phagocytosis) when engulfing and destroying antigens

What is IP3 stimulation?

IP3 is a ligand that causes calcium release

What are endocrine signals?

long distance signals, signals are deposited into the extracellular environment, form of exocytosis

What are paracrine signals?

short distance signals, signals are secreted to extracellular space for cells nearby

What are synaptic signals?

short distance signaling with long distance effects, between neurons or between a muscle and a neuron, utilize neurotransmitters

What is contact dependent signaling?

signaling between immediate neighboring cells, signal is membrane bound, cells have to touch in some way

What are autocrine signals?

signals from the cell to that same cell, cell signals itself

What are the five main types of receptors?

ligand-gated ion channels, G protein coupled receptors, catalytic receptors, intracellular receptors, and transmembrane proteins that release TFs

What are G protein coupled receptors (GPCRs)?

plasma membrane proteins that work via G proteins, the G protein is a regulator for the receptor

What is a catalytic receptor?

plasma membrane protein that can act like an enzyme

What are intracellular receptors?

transcription factors in the cytosol or nucleus that get activated by a ligand binding

What are transmembrane proteins that release TF?

transmembrane proteins that get cut and a portion of it goes to the nucleus and acts as a TF

What is intracellular signaling?

proteins that work together on the inside of the cell to cause some sort of signal

What is signal transduction?

conversion of a signal within a cell to a cellular response of some sort

What are the types of cellular responses to a signal?

survive, grow & divide, differentiate (become a specialized cell), relocate, apoptosis

What is a fast cellular response?

response in which everything needed for the pathway is already made so the cellular effect can start immediately

What is a slow cellular response?

response in which the cell needs to synthesize part of the pathway which means the cellular effect takes time

What are the steps of signal transduction?

• recognition: ligand binds to receptor

• transduction: ligand changes receptor causing effect, creation of a 2nd messenger

• transmission: 2nd messenger signals an effector protein

• modulation of the effector: effector activates enzymes to affect other enzymes/proteins, multiplier

• response: enzymes/proteins/ions do their job and cause something to happen in the cell

  • termination: response is turned off

What is cAMP?

secondary messenger, small molecule, ATP in which the last two P are ripped off and the third is tied down

How are slime molds an example of cell signaling? Discuss the signal pathway

form of autocrine, paracrine, and contact dependent signaling

• recognition: cells realizes its starving

• transduction: cell secretes cAMP

• transmission: other cells receive the cAMP signal via paracrine signaling and begin to clump and aggregate and form a mound

• modulation of the effector: this big clump of cells causes even more signals to be sent out that the cell is starving and a new one needs to be made, slug is formed

• response: a fruiting body is made and contact dependent signaling tells cells to differentiate to be certain parts

• termination: new spore is made, no longer starving

How many ligands can a receptor bind?

receptors can bind multiple receptors

How do receptors decide between competing ligands?

the receptor decides passed on the affinity and concentration of the ligand