w8 txtbk Flashcards
protein sorting
each compartment has a unique set of proteins that must be moved from the cytosol where they’re made to the compartment where they’ll be used
-depends on signals built into the AA sequence of the proteins
vesicular transport
some membrane-enclosed compartments in a eukaryotic cells communicate with each other by making small, membrane enclosed sacs called VESICLES
-these vesicles pinch off from one compartment and move through the cytosol and combine with another compartment = transport
membrane-enclosed organelles
any organelle in a eukaryotic cell that’s surrounded by a lipid bilayer
e.g. endoplasmic reticulum, golgi apparatus
structure of nucleus
-surrounded by double membrane known as nuclear envelope and communicates with the cytosol via nuclear pores that pierce the envelope
-outer nuclear membrane continuous with membrane of ER, a system of interconnected membrane sac and tubes
structure and function of ER
-system of interconnected membrane sacs that expand through most of cell
major site of synthesis of new membranes in cell
-large parts of the er have RIBOSOMES attaches and called rough ER
–ribosomes actively synthesize proteins that are inserted the ER membrane or delivered INTO the ER called LUMEN
smooth ER
-LACKS ribosomes
-highly developed for performing specific functions
e.g. site of steroid hormone synthesis in some endocrine cells of adrenal gland
-in many cells, smooth er can take Ca2+ from the cytosol –> involved in muscle contraction
cytosol function
contain many metabolic pathways, protein synthesis
nucleus function
contains main genome, dna and rna synthesis
ER function
synthesis of most lipids, synthesis of proteins for distribution to many organelles and to the plasma membrane
golgi appartus
modification, sorting and packaging of proteins and lipids for either secretion or delivery to another organelle
lysome function
intracellular degradation
endosome function
sorting of endocytosed material
mitochondria function
atp synthesis by oxidative phosphorylation
chloroplast function
atp synthesis and carbon fixation by photosynthesis
peroxisome function
oxidative breakdown of toxic molecules
organelle growth
requires a supply of new lipids to produce more membrane and a supply of proteins needed
(both membrane and soluble proteins that will be in the lumen/interior of organelle)
proteins in ER
major site of lipid and protein synthesis
-most proteins that enter the ER do WHILE being synthesized
–some proteins stay in there while others are moved by vesicles to plasma membrane or elsewhere
process by which proteins enter membrane-enclosed organelles from cytosol
-proteins made in cytosol are moved to diff locations in the cell by their specific address labels
-once at the right address, the proteins enter the membrane or interior LUMEN of designated organelle
how does the synthesis of proteins begin and what are the exceptions
-begins on ribosomes in the cytosol
the exceptions are the few mitochondrial and chloroplast proteins that are made on ribosomes inside organelles; others are made in cytosol and imported
how do you decide where any protein made in the cytosol goes
depends on its AA sequence, which can contain a SORTING SIGNAL
-directs protein to organelle in which it’s needed
what do proteins that lack sorting signals do
they remain as PERMANENT residents in cytosol
-those that do have one move from cytosol to their organelle
what’s the problem when a membrane-enclosed organelle imports a water-soluble protein to its interior
(either from the cytosol or from another organelle), problem is…
-protein must be transported across its membranes which’s normally IMPERMEABLE to hydrophilic macromolecules
transport of proteins moving from cytosol into nucleus
go from cytosol to nucleus by nuclear pores, which penetrate the inner and outer nuclear membranes
pores function as SELECTIVE GATES that actively transport specific macromolecules but also allows free DIFFUSION of smaller molecules
transport of proteins moving from cytosol into ER, mitochondria or chloroplasts
transported across organelle membrane by protein TRANSLOCATERS located in membrane
-unlike the transport thru nuclear pores, transported protein must UNFOLD for the translocator to guide it across the hydrophobic interior of the membrane
-bacteria have similar protein translocators in their plasma membrane, which they use to export proteins from cytosol to cell exterior
difference between transport of proteins from cytosol into nucleus AND transport from cytosol into er, mito or chloroplasts?
-unlike the transport thru nuclear pores, transported protein must UNFOLD for the translocator to guide it across the hydrophobic interior of the membrane
transport of proteins moving from er and from one compartment of endomembrane system to another
transported by TRANSPORT VESICLES, pinch off from the membrane of one compartment and then fuse with the membrane of a 2nd compartment
-in this process, transport vesicles deliver soluble cargo proteins, as well as the proteins and lipids that are part of the vesicle membrane
signal sequence function
AA that directs a protein to a specific destination
consequence of deleting a signal sequence from an er protein
converts it into a cytosolic protein
while placing an ER SIGNAL sequence at the beginning of a cytosolic protein REDIRECTS protein to the ER
proteins destined for the ER possess what
an N-terminal signal sequence that directs them to that organelle
nuclear pore structure & function
Function: channel through which SELECTED large molecules move between the nucleus and cytoplasm
Structure: contains extensive, unstructured regions where polypeptide chains are disordered, with meshwork that fills the center of the channel
=prevents the passage of big molecules but allows small, water-soluble molecules to pass freely and nonselectively b/w nucleus and cytosol
how can large molecules gain entry to a pore?
these large molecules and macromolecular complexes must display an appropriate SORTING SIGNAL
-signal sequence that directs protein from cytosol into nucleus is called nuclear localization signal (has sequences of positively charged lysines or arginines)
nuclear IMPORT receptor function
cytosolic proteins that recognize the nuclear localization signal on proteins destined for nucleus
-guide newly synthesized protein to nuclear pore by interacting with the tentacle-like fibrils
what does the nuclear import receptor do once it locates a pore
gains entry by grabbing onto short, repeated AA sequences within the tangle of nuclear pore proteins that fill center of channel
once nuclear pore is empty
-these repeated sequences bind to one another, forming a loosely packed gel
nuclear receptors shoulder their way thru this meshwork by pushing past repeat sequences, disrupting interactions and creating a temporary passageway thru pore
(temporary bc large molecules cant usually get past impermeable membrane)
once receptor delivers cargo to nuclear interior(LUMEN), empty receptor reenters nuclear pore, where it’ll go back to cytosol for reuse
what prevents nuclear import receptors from entering the nucleus empty-handed and then returning to the cytosol carrying nuclear proteins
like many cell processes that must be moved in one direction, movement is guided by the hydrolysis of a NUCLEOSIDE triphosphate (GTP)
hydrolysis of GTP
rxn mediated by GTPase called Ran
-ran exists in 2 forms, one with a molecule of GTP and the other GDP
each form is in a different place, gtp is in high conc. in the nucleus and gdp is in the cytosol
in the nucleus, gtp removes the nuclear protein from receptor, allowing imported protein to be released
the important receptor(now holding gtp) returns to cytosol, where GTP is hydrolyzed
ran-gdp has LESS desire for the import receptor so it dissociates and leaves receptor free to get another protein destined for nuclear
this way gtp hydrolysis drives nuclear transport
nuclear EXPORT receptor function
drive protein and rna traffic from nucleus to cytosol
-recognize nuclear export signals and also use Ran to combine the transport to an energy source
structure and function of proteins found in mitochondria and chloroplasts
these proteins usually have a signal sequence at their N-terminus that guide them to their destination
what do proteins need to do in order to enter a mito or chloroplast
proteins must cross both the inner and outer membranes that surround each of these organelles
-this translocation takes place at specialized sites where the 2 membranes are held closely tg, allowing the imported protein to cross both membranes at the same time
-each protein is UNFOLDED as it’s transported, and its signal sequence is removed AFTER translocation is complete
function of chaperone proteins
located inside the organelles and help pull protein across 2 membranes and refold it once it’s inside
structure and function of peroxisomes
membrane-enclosed organelles that are packed with enzymes that digest toxins and synthesize certain phospholipids, including those in myelin sheath
-acquire the bulk of their proteins thru selective transport from cytosol
-their signal sequence is recognized by receptor proteins in cytosol, and one escorts its cargo protein into the peroxisome before returning back to cytosol
consequence of mutations that block peroxisomal protein import
causes severe illness like zellweger syndrome (severe abnormalities)
structure and func of ER
serves as an ENTRY point for other organelles
-proteins destined for cell or organelles all enter ER from cytosol
-once in the ER lumen or embedded in ER membrane, individual proteins will NOT reenter cytosol during journey fwd
-get transported by transport vesicles from organelle to organelle within endomembrane
what are the 2 kinds of proteins transferred from cytosol to ER
water soluble: completely translocated across ER membrane and released into ER lumen
prospective transmembrane proteins: only partly translocated across ER membrane and become embedded in it
destination of water soluble and transmembrane proteins
-water soluble destined either for secretion or for the LUMEN of an organelle of the endomembrane system
-transmembrane proteins destined to reside in the membrane of one of these organelles or in the plasma membrane
regardless of this destination, these proteins both directed to ER by ER SIGNAL sequence(hydrophobic AA seq.), which’s also involved in the process of translocation across membrane
rough ER structure and function
when proteins enter ER, they get threaded across ER membrane before PP chain is completely synthesized
to accomplish this:
-ribosome synthesizing the protein must be attached to ER membrane
-such membrane-bound ribosomes thoroughly coat the surface of ER, creating rough ER
function of free ribosomes
unattached to any membrane and make the proteins encoded by nuclear dna
all of them differ only in what protein they are making at the time
when a ribosome is making a protein with an ER signal sequence(SS), SS directs ribosome to ER membrane
and because multiple ribosomes can simultaneously translate a single mRNA, mRNA molecules that encode a protein with an ER signal sequence become fastened to er membrane by PP chain that connect them to er membrane
why is no additional energy required for proteins with ER signal sequence
protein transport into most organelles is powered by nucleotide hydrolysis, but
proteins with ER SS are translocated AS they are being made
-elongation of each PP provides the thrust needed to push the growing chain thru ER membrane
what are the protein components that help guide the er signal sequences to er membrane
1.) Signal-recognition particle (SRP), present in cytosol, binds to both the ribosome and the ER signal sequence as it leaves ribosome
2.) SRP receptor, embedded in ER membrane, recognizes the SRP
describe what happens when SRP binds to ribosome that displays er signal sequence
slows protein synthesis by that ribosome until the SRP engages with SRP receptor on the ER
once bound, the SRP is released, the receptor passes ribosome to a protein translocator in ER membrane, and protein synth. continues
PP then threaded across ER membrane thru channel in translocator
-srp and srp receptor function as molecular matchmakers
–bring tg ribosomes that are synthesizing proteins with an ER signal sequence w/ protein translocators within ER membrane
structure and func of signal sequence
-directs proteins to ER (synthesized first at N terminus)
-functions to open the protein translocator
the sequence remains remains bound to translocator, while rest of PP chain is threaded thru membrane as a large loop
SS removed by transmembrane signal peptidase, which has active site facing lumenal side of ER membrane
-cleaved SS then released from protein translocator into lipid bilayer and quickly degraded
what happens when proteins made by ER-bound ribosomes are NOT released into ER lumen?
N-terminal signal sequence initiates translocation
-but transfer process stopped by additional seq. of hydrophobic AA, a stop-transfer seq., further along PP chain
protein translocater releases growing PP chain
-N-terminal SS cleaved off + stop-transfer seq. remains in bilayer where it forms an a-helical membrane-spanning segment that keeps protein IN membrane
-bc of this protein ends up as single-pass transmembrane protein inserted in membrane with defined orientation
(N-term. on lumenal side and C-term. on
cytosolic side)
once inserted into membrane, transmembrane protein will never change orientation
how can a SS be used to start protein transfer?
internal SS called start-transfer sequence is never removed from the PP
-this arrangement occurs in some transmembrane proteins where the PP chain goes back and forth across lipid bilayer
Which organelle cannot receive proteins directly from the cytosol
golgi apparatus
proteins are delivered to golgi apparatus from the er or from other components of the endomembrane system
transport vesicles
membrane vesicle that carries proteins from one intracellular compartment to another
e.g. from the ER to the golgi apparatus
vesicular transport
extends out from the er to plasma membrane, allowing proteins and other molecules to be secreted by exocytosis
reaches inward from the plasma membrane, allowing extracellular molecules to be imported by ENDOCYTOSIS
-provide routes of communication b/w interior of cell and its surroundings
secretory pathway
starts with the synthesis of proteins on the ER membrane and their entry into the ER, and it leads through the golgi apparatus
endocytic pathway
responsible for the ingestion and degradation of extracellular molecules, moves materials from plasma membrane, through endosomes to lysosomes
how does movement through the golgi apparatus occur?
occurs by vesicles that shuttle between individual parts of the apparatus and by a process of maturation, where the parts themselves move through the stack
outward secretory pathway
protein molecules are transported from the ER, through the golgi apparatus, to the plasma membrane or (via early and late endosomes) to lysosomes
how do vesicles fuse
after budding from their parent organelle, the vesicle sheds its coat, allowing its membrane to interact directly with the membrane to which it will fuse
how does a transport vesicle deliver their cargo?
once it reaches target, it has to recognize and dock with its specific organelle
then vesicle membrane can fuse with target membrane and unload vesicle’s cargo
how do transport vesicles identify their target
depends on monomeric GTPases called Rab proteins
-specific rab proteins on the surface of each type of vesicle are recognized by corresponding tethering proteins on cytosolic surface of target membrane
function of SNAREs
family of transmembrane proteins that helps with additional recognition
-once the tethering protein has captured a vesicle by grabbing hold of its Rab protein, SNAREs on the vesicle interact with complementary SNAREs on target membrane
-this firmly docks the vesicle in place
also play a role in catalyzing the membrane fusion required for a transport vesicle to deliver its cargo
-not only delivers the soluble contents of the vesicle into the interior of the target organelle or to the extracellular space, but it also adds vesicle membrane to membrane of organelle
what happens after vesicle docking?
fusion of a vesicle with its target membrane require a special signal when synaptic vesicles fuse with plasma membrane to release neurotransmitters into synaptic cleft
docking vs fusion
docking requires only that the 2 membranes come close enough for the snares protruding from the 2 lipid bilayers to interact
fusion requires a much closer approach
-water must be displaced from hydrophilic surfaces of membranes (process is energetically highly unfavourable and prevents membranes from fusing randomly)
why must all membrane fusions in cells be catalyzed only by specalized proteins
process of fusion is energetically highly unfavourable and prevents membranes from fusing randomly
specialized proteins assemble to form a fusion complex that provides the means to cross this energy barrier
for vesicle fusion, what happens when fusion is triggered?
the V-snares and t-snares wrap tightly around each other, acting like a winch that pulls the 2 lipid bilayers close together
vesicle budding is driven by which of the following?
a) assembly of a protein coat
b) binding of a cargo molecule
c) hydrolysis of GTP by dynamins
d) interactions of v- and t- SNAREs
a) assembly of a protein coat
After budding from its parent organelle, the vesicle sheds this coat, allowing its membrane to interact directly with the target membrane with which it will fuse
Botulism is a potentially fatal foodborne disease caused by the bacterium Clostridium botulinum. C. botulinum produces different toxins, several of which are proteases that cleave neuronal SNARE proteins. What normal process is blocked by cleavage and inhibition of SNARE proteins?
fusion of vesicles with target membranes
SNAREs help mediate vesicle membrane fusion. In the absence of vesicle fusion, vesicle-stored neurotransmitters cannot be released into synaptic clefts, leading to paralysis
what happens to proteins as they enter the ER?
they get chemically modified there
-disulfide bonds are formed by the oxidation of pairs of cysteine side chains, a rxn catalyzed by an enzyme that stays in ER lumen
-disulfide bonds help stabilize structure of proteins that will go thru degradative enzymes and changes in pH outside of cell
–these bonds don’t form in the cytosol bc the environ. is reducing
glycosylation
when proteins that enter the ER lumen or ER membrane are converted to glycoproteins in ER by covalent attachment of short, branched oligosaccharide side chains made up of sugars
function of oligosaccharides
protect protein from degradation, hold it in ER until properly folded, or help guide it to appropriate organelle by serving as transport signal for packing protein into appropriate transport vesicle
how do proteins travel through cisternae in the golgi network
enter by cis golgi network
1) by transport vesicles that bud from one cisterna and fuse with the next
2) by a maturation process in which the golgi cisternae migrate thru golgi stack
proteins exit from the trans golgi network in transport vesicles destined for cell surface or organelle of endomembrane system
cis vs trans golgi network
both are important for protein sorting
-proteins entering via cis: if they have an er retention signal, will be returned to er
-proteins exiting via trans: sorted according to if they’re destined for lysosomes (via endosomes) or for cell surface
constitutive exocytosis pathway
stream of vesicle buds from the trans golgi network, fuse with plasma membrane in the process of EXOCYTOSIS
this constitutive exocytosis pathway supplies the plasma membrane with newly made lipids and proteins
also carries soluble proteins to cell surface
what is secretion
when the constitutive pathway carries soluble proteins to the cell surface to be released to the outside
true or false: entry into the constitutive pathway requires a signal sequence
false
does not require ss like those that direct proteins to endosomes or back to ER
regulated exocytosis pathway
operates only in cells that are specialized for secretion
secretory vesicles
store products produced by secretory cells and are part of transmembrane system and bud off from TRANS golgi network
they wait near plasma membrane for extracellular signal that will stimulate them to fuse with plasma membrane and release their contents to the cell exterior by exocytosis
what distinguishes proteins destined for regulated secretion
a) They have a specific signal sequence that marks them for packaging into secretory vesicles
b) They bind to clathrin in order to interact directly with the proteins to be packed into secretory vesicles
c) Their surface properties allow them to form aggregates that are packed into secretory vesicles
c) Their surface properties allow them to form aggregates that are packed into secretory vesicles
Correct. Selective aggregation allows secretory proteins to be packaged into secretory vesicles at concentrations much higher than the concentration of the unaggregated protein in the Golgi lumen.
how are newly made lipids supplied to the plasma membrane?
via the constitutive pathway of exocytosis
phagocytosis vs pinocytosis
pinocytosis (cell drinking)
- involves the ingestion of fluid and molecules via small pinocytic vesicles
phagocytosis (cell eating)
-involves ingestion of large particles
structure and function of endosome
interior is kept acidic by an ATP-driven H+ (proton) pump in the endosomal membrane that pumps H+ into the endosome lumen from the cytosol
-the acidic environment helps with sorting process
cargo proteins
remain bound to receptors and share the fate of their receptors
-those that dissociate from their receptors in the endosome are doomed to destruction in lysosome
lysosome
membranous sacs of hydrolytic enzymes that carry out the controlled intracellular digestion of both extracellular materials and worn-out organelles
function of lysosome membrane
contains transporters that allow the final products of the digestion of macromolecules to be transferred to the cytosol
from there, these materials can be either exported or used by cell
also contains ATP-driven H+ pump, pumps H+ into lysosome, maintaining its contents at an acidic pH
what does it mean for the lysosome membrane to be glycosylated?
the sugars, which cover most of protein surfaces facing lysosome lumen, protect proteins from digestion by lysosome proteases
autophagy
an additional pathway that supplies materials to lysosomes, used to degrade obsolete parts of cell (cell eats itself)
involves enclosure of organelle by double membrane, creating autophagosome, which then fuses with lysosome
what happens to the final products of the digestion of macromolecules in the lysosome
they are transferred to the cytosol through transporters in lysosomal membrane
these molecules can then be reused by cell or excreted
