Section 5 - Intracellular Traffic and Energy Conversion Flashcards
How much total membrane does the ER take up?
50%
True or false: the ER is connected to the nuclear membrane
True: it extends from the nucleus into the cytosol
What are the functions of the ER?
Production of transmembrane proteins, secreted proteins, lipids, and calcium storage
What is the ER composed of?
Tubules and membranous sacs
Where is the ER the densest?
Near the nucleus
Where is the ER the least dense?
In the cytosol (away from the nucleus)
True or false: the ER in mammalian cells is the same as the ER in plant cells
False: they have very different structures
True or false: the entirety of the ER has the same function
False: different regions of the ER can be specialized for different functions
What is an example of a specific region of ER having a specialized function?
Rough ER
What is rough ER?
ER with attached ribosomes
What is smooth ER?
ER without ribosomes
What is co-translation?
When proteins are transported to the ER during translation
Is the rough ER constantly rough?
No. The ribosomes associate and dissociate from the ER, thus changing it to rough or smooth
True or false: ribosomes sit on the ER, waiting for mRNA to come
False: they are assembled in the cytosol and translocated to the ER
How does the rough ER become rough?
By the ribosome assembling in the cytosol, and then moving towards the ER
What is the function of smooth ER?
Transporting synthesized proteins / lipids to other regions of the cell (golgi)
Where is rough ER most likely to be found?
Closer to the nucleus
Why is rough ER found more commonly closer to the nucleus?
That is where mRNA is most likely to be found
What is the function of calcium in the cell?
Act as initiators for many biological functions
Why is calcium kept in the ER?
Keep cytosolic concentration low for proper function (proper cell signaling)
What is the specialized ER in muscle cells important for?
Contraction
How does the ER sequester calcium?
Through calcium binding proteins and calcium channels
What is needed on a polypeptide to direct it to the ER?
A signal sequence
Where are transmembrane proteins made?
Embedded in the ER
Where are water-soluble (secreted) proteins made?
In the ER lumen
What cleaves the signal sequence?
Signal peptidase
What does signal peptidase do?
Cleave the signal sequence off of a polypeptide
What is a translocater?
Where the growing protein in the ER is held
What does SRP stand for?
Signal recognition particle
What does the SRP do?
Move the ribosome from the cytosol to the ER
How does the SRP move a ribosome from the cytosol to the ER?
It binds to the signal sequence and an SRP receptor found on the ER membrane
What is the structure of SRP?
Proteins and RNA
True or false: the protein continues translating as it is moved from the cytosol to the ER
False: translation is halted by the SRP
Why does the SRP halt translation?
To ensure that it reaches the ER first so it can be processed correctly before continuing
What would happen if the SRP did not halt translation?
The protein would be misfolded (cassette tape)
What does an SRP do once it is bound to an SRP receptor?
It moves the polypeptide into a translocator
What are the parts of an SRP molecule?
Signal sequence binding pocket, hinge, and translational pause domain
Where is SRP most likely to be found?
Close to the nucleus
What happens to the SRP and SRP receptor after the polypeptide is in a translocator?
It gets recycled (it can be used again)
What is the structure of a ribosome in the cytosol (before translation)?
Dissociated subunits
What is the structure of the translocator?
A pore type structure
What is needed for the translocator to function properly?
A plug
What is the significance of the plug in the translocator?
Prevents the mixing of cytosol and ER lumen contents
What displaces the plug in the translocator?
The signal sequence
What happens when the plug is displaced in the translocator?
The growing polypeptide can be fed into the translocator into the ER lumen
What is the structure of the translocator in the closed position?
Hinge is closed, with a plug
What is the structure of the translocator in the open position?
The signal peptide is holding the hinge open, the plug is displaced, and the polypeptide can be fed through the pore
If a polypeptide sequence only has a start sequence at the end, what can you say about the protein?
It is a soluble (secreted) protein
For a soluble (secreted) protein, what sequence(s) does it have?
A start transfer sequence
For a multipass transmembrane protein, what sequence(s) does it have?
A start transfer sequence and a stop transfer sequence
What does a stop transfer sequence do?
Moves the polypeptide out of the translocator, and continues translation in the cytosol
True or false: the start transfer sequence can be cleaved
True: if it is at the end of a polypeptide, it can be cleaved
True or false: the stop transfer sequence can be cleaved
False: it must remain embedded in the membrane
What is the phobicity of the stop transfer sequence?
Hydrophobic
Why must the stop transfer sequence be hydrophobic?
It stays embedded within the membrane
True or false: a start transfer sequence can be found at the start or middle of the polypeptide
True: it can be in either location
True or false: a stop transfer sequence can be found at the start or middle of the polypeptide
False: it can only be in the middle of the polypeptide
True or false: the N-terminal of a polypeptide is always in the ER
False: this direction can be changed depending on the specific protein
What determines the direction of the start transfer sequence if it is in the middle of the polypeptide?
The positive and negative ends of the start transfer sequence must line up with the membrane
What side of the membrane does the positive side of the start transfer sequence line up with?
The positive side
How come the positives of the membrane and the start transfer sequence are together?
It is similar to a capacitor (like charges line up at opposite sides of the membrane)
Which leaflet of the cell membrane is more positive?
The external leaflet (compared to the internal leaflet)
For a single pass protein, where is the start sequence found?
At the beginning of the polypeptide
For a multi pass protein, where is the start sequence found?
In the middle of the polypeptide
What sequences are needed to create multi pass proteins?
Pairs of start and stop sequences
Which sequences will signal peptidase cleave?
Start signal sequences at the beginning of the polypeptide
Which sequences will signal peptidase not cleave?
Start and stop signal sequences in the middle of the polypeptide
True or false: a start sequence can be unpaired to a stop
True: it does not need a stop
True or false: a stop sequence can be unpaired to a start
False: every stop requires a start
What must the charge be between a start and stop sequence?
Negative
Why must the charge between a start and stop sequence be negative?
It needs to align with the cell membrane charge gradient
True or false: one translocator is used per polypeptide
False: multiple translocators can be used
True or false: proteins that come off of the ribosome are functional
False: they need to be processed post-translation to be functional
Where are most proteins processed after translation?
The ER
What does disulfide isomerase do?
Catalyzes the formation of the disulfide bond
Where is disulfide isomerase found?
In the ER lumen
For most loops in a transmembrane protein, are they small or large?
Small
For most tails in a transmembrane protein, are they small or large?
Large
If the loops of a transmembrane protein are large, what can you say about the loops?
They are in an organized structure (alpha helix, beta sheet, etc.)
What does oligosaccharyl transferase do?
Adds sugars to the growing polypeptide
What is the function of sugars on proteins?
Help with folding by assisting chaperone proteins
How do chaperone proteins use sugars?
If the sugar looks a certain way, then the protein should be folded correctly (on-folding pathway)
True or false: chaperones physically fold the polypeptide into the correct shape
False: they only check if it is folded correctly
What drives protein folding?
Thermodynamics
What happens if the chaperone / sugar pathway starts a perpetual loop?
It will get signaled for degradation
What pathway is used to degrade a protein?
The ubiquitin pathway
What is the purpose of the ubiquitin pathway?
It is a proteolytic pathway (break down misfolded proteins)
How can a misfolded protein signal for its own degradation?
The misfolded protein can activate a receptor to make a transcription factor, which creates more chaperones to help folding
What is the “lie” in having a misfolded protein signal for its own degradation?
Non-process mRNA was found in the cytosol (not the nucleus)
True or false: the ER synthesizes many phospholipids
True: many phospholipids are made in the ER
Where is phosphatidylcholine made?
In the ER
Where can the phospholipids in the ER be transferred to?
The cell membrane
In the ER, how are the phospholipids arranged?
Almost perfectly segregated (PC on outside, PS on inside)
Is the portion of membrane added to the cell membrane from the ER largely symmetrical or largely asymmetrical?
Largely asymmetrical
Which enzyme fixes phospholipids in the cell membrane?
Flippase
Which enzyme fixes phospholipids in the ER?
Scramblase
What is vesicular transport?
The transport of one vesicle from one compartment to another
True or false: vesicular transport can also include material
True: vesicles can deliver both membrane and material
True or false: vesicular transport is a symmetric process
False: the donor loses membrane, and the target gains membrane
What is the significance of vesicular transport being an asymmetric process?
There needs to be vesicular transport in both directions to prevent one side from losing all of its membrane
What are the functions of the golgi?
Carbohydrate synthesis, sorting and dispatching products from the ER
If a vesicle leaves the ER, what is it coated with?
COPII
If a vesicle leaves the golgi, what is it coated with?
COPI
True or false: every protein from the ER goes into the golgi
False: some proteins are ER resident and stay with the ER
True or false: only folded proteins can leave the ER
True: a chaperone signal prevents the exit of misfolded proteins
How does the ER ensure that only folded proteins can leave in vesicles?
Chaperones block the exit signal until it is properly folded and can leave the ER
What are the functions of SNARE proteins?
Allow for vesicles to fuse together
If a vesicle is coated with COPII, where is it going?
To the golgi
If a vesicle is coated with COPI, where is it going?
To the ER
What is the structure of a SNARE protein?
Has a v-SNARE and t-SNARE strands
What breaks the two SNARE strands apart?
NSF
What does NSF do?
Separates the two strands of the SNARE
When the SNARE proteins are separated by NSF, how can they reform?
By binding to SNARE strands on another vesicle
What prevents the v and t SNARES on the same vesicle from coming back together?
The NSF molecule
What are the purposes of the retrieval pathway?
To give more membrane to the ER, and to return any ER resident proteins that accidentally made it to the golgi
What must soluble proteins do to go back from the golgi to the ER?
Bind to a KDEL receptor
What is the purpose of a KDEL receptor?
Bind to soluble ER resident proteins, and bring them back into the ER through the retrieval pathway
When are the attractions between the KDEL receptor and the ER resident proteins the highest?
When they are both outside of the ER
In the ER, is the KDEL receptor bound to the ER resident protein?
No: the binding kinetics are not favorable
In the golgi, is the KDEL receptor bound to the ER resident protein?
Yes: this signals the retrieval pathway
Where does the retrieval pathway start from?
Either the golgi or vesicular tubular clusters
How is the golgi organized?
In a collection of flattened membranes
What are the flattened membranes of the golgi called?
Cisternae
What are cisternae?
Flattened membranes (pancakes) found in the golgi
True or false: the golgi is a symmetrical structure
False: it has a distinct direction
What is the cis face of the golgi?
Entry from the ER
What is the trans face of the golgi?
Exit to various location
Which face of the golgi is the entry from the ER?
The cis face
Which face of the golgi is the exit to other locations?
The trans face
What are the functions of the cisternae?
Finalize the functional form of the proteins, and get similar proteins in the same packaging
True or false: each cisternae in the golgi has a unique function
True: they each function to finalize the final protein
What are some examples of modifications done by the golgi?
Adding and removing carbohydrates, adding sulfur groups, etc.
What is the purpose of glycosylation of proteins?
Helps with folding, solubility, and the state of the protein (secreted, self molecule, etc.)
What are the two theories about transport within the golgi?
Vesicular transport, and cisternal maturation
What is vesicular transport (in terms of transport within the golgi)?
Each cisternae can bud into the next cisternae, with a retrieval pathway
What is the challenge of verifying the vesicular transport theory in golgi?
Hard to determine directional movement of vesicles
What is cisternal maturation?
The cisternae transform along the chain to perform a different function
True or false: cisternal maturation and vesicular transport are mutually exclusive
False: cisternal maturation theory needs some vesicular transport
What vesicular transport is needed in the cisternal maturation theory?
The retrieval pathway
What do the two theories about the golgi describe?
How materials move through the golgi
Why is a retrieval pathway needed for transport within the golgi?
Need to be able to move specific enzymes back into the specific cisternae to carry out their function
What are some challenges with the vesicular transport theory (in terms of transport within the golgi)?
Need a complicated mechanism (many receptors), and vesicles can skip a cisternae, thus skipping the function
What is the challenge with the cisternal maturation theory?
The enzymes must mature with the cisternae, and that vesicle transport is there
True or false: cisternal maturation can be the only mechanism of golgi transport
False: vesicles have been observed, so it can only be a part of the mechanisms
True or false: vesicular transport can be the only mechanism of golgi transport
True: however, this has not been proven yet
What is the function of the mitochondria?
Harvest energy
Why do mitochondria have large internal membrane space?
More surface area for energy creating proteins
How do mitochondria generate energy?
By using chemiosmotic coupling
What is chemiosmotic coupling?
Protons moving down their concentration gradient is coupled to the creation of ATP
Where do protons move down in their concentration gradient (in the mitochondria)?
Through ATP synthase
What are the two steps of ATP formation?
- ETC pumps protons against the concentration gradient
2. Protons move down their concentration gradient through ATP synthase to generate ATP
What energy do the pumps in chemiosmosis use?
Electrons from activated carriers
What does ETC stand for?
Electron transport chain
What does the ETC do?
Create a chain that uses electrons to pump protons across the membrane
What molecules are involved in the ETC?
Proteins and small transport molecules (NADH)
What is the input of the citric acid cycle?
Fats and carbohydrates
What is the output of the citric acid cycle?
CO2 and activated carriers
What is the purpose of the citric acid cycle?
Convert fats and carbohydrates into CO2 and activated carriers
Where does the citric acid cycle occur?
In the mitochondrial matrix
True or false: a pump in the ETC uses all the energy of the electron
False: it uses some of that energy to pump, and then passes it on
What is the final electron acceptor of the ETC?
O2
What is the product of the ETC?
H2O
Where does water come from in the ETC?
Protons and O2 being reduced
How many membranes does the mitochondria have?
2 (an inner and outer membrane)
True or false: the internal spaces of the mitochondria are the same
False: they differ in compositions and proteins
Where is the matrix located?
Within the inner mitochondrial membrane
Where is the intermembrane space located?
Between the outer and inner mitochondrial membranes
Which mitochondrial membrane is more permeable?
The outer membrane
Which mitochondrial membrane is more impermeable?
The inner membrane
Where are the protons pumped to during the ETC?
Into the intermembrane space
Where in the mitochondria is ATP made?
In the matrix
Which membrane in the mitochondria has a lot of surface area (folds)?
The inner membrane
Which proteins are found in the inner mitochondrial membrane?
The ETC proteins, and ATP synthase
True or false: the mitochondria was thought to be its own cell
True: it is thought to have originated from a symbiotic relationship with another cell
What supports the idea that mitochondria was its own cell in the past?
They have their own DNA, and the citric acid cycle is not seen anywhere else
True or false: mitochondria have their own DNA
True: this DNA is maternal
True or false: the citric acid cycle is seen in many areas of life
False: it is only seen in the mitochondria
What is the inner mitochondrial membrane composed of?
Cardiolipin
What is the structure of cardiolipin?
A double phospholipid (two phospholipids connected by isopropyl alcohol)
True or false: the cell membrane and the inner mitochondrial membrane have similar compositions
False: the cell membrane does not contain cardiolipin
True or false: activated carriers can skip pumps in the ETC (ex: go from pump 1 to pump 3)
False: they are linked in such a way so that they must go through all of the pumps
Which reaction in the ETC is associated with a lot of energy?
H2 + 1/2O2 –> H2O
How is the energy from the creation of water in the ETC used?
In a series of steps
Why is the energy from creating water broken down into a series of steps?
More useful work can be gained from this energy (can extract more energy in stages)
What is the reaction of producing electrons from activated carriers?
NADH –> NAD+ + H-; H- –> H+ + 2e-
How are activated carriers made?
Through the citric acid cycle
What is combustion?
The explosive release of energy
What is biological oxidation?
Harvesting energy through a series of redox reactions
What is the disadvantage of combustion?
Much of the energy is lost as heat and cannot be harvested
How is energy stored from the electrons in the ETC?
Pumping protons against their concentration gradient
What reaction is powered by protons moving down their concentration gradient (in the mitochondria)?
ADP + Pi –> ATP
True or false: the pumps in the ETC are all the same
False: they are all different
How many pumps are usually found within the ETC?
3
What is the structure of ATP synthase?
A stator, a rotor, and a globular head
How does ATP synthase work?
It uses a chemical gradient to drive mechanical motion
What motion does the stator go through in ATP synthase?
None (stationary)
What motion does the rotor go through in ATP synthase?
Rotation
What motion does the globular head go through in ATP synthase?
Rotation (coupled to rotor)
Where do the protons go through in ATP synthase?
Between the stator and the rotor
Where do the protons bind in ATP synthase?
The rotor section
How does the rotor of ATP synthase move?
Through the bumping of protons (due to the high gradient)
What are the subunits of the globular head in ATP synthase?
Alpha and beta
What does the rotor rotate in ATP synthase?
The globular head
What is the significance of the subunits of the globular head?
One subunit binds to ADP, and the other subunit binds to Pi
How is the bond between ADP and Pi formed in ATP synthase?
They are physically brought together due to the rotation of the rotor
True or false: ATP synthase is reversible
True: it can work in either direction
What determines the direction of ATP synthase?
The ATP:ADP ratio
What happens if ATP synthase runs in the opposite direction?
It uses ATP to pump protons across the membrane
When does ATP synthase pump protons?
When the amount of ATP in the cell is high
How is pyruvate moved into the intermembrane space?
Through the various pores
How is pyruvate moved into the matrix?
Through a coupled proton symport
How does the coupled proton / pyruvate symport work?
Protons move down their concentration gradient, which helps move pyruvate into the matrix for the citric acid cycle
True or false: the proton gradient in the mitochondria is only used for ATP synthesis
False: it is also used to transport pyruvate into the matrix
How is Pi moved into the matrix?
Through a coupled proton symport
How does the coupled proton / Pi symport work?
Protons move down their concentration gradient, which helps move Pi into the matrix for ATP synthesis
True or false: pyruvate and Pi both move into the matrix of the mitochondria through similar mechanisms
True: both use protons moving down their concentration gradients to get transported into the matrix
What is ADP influx coupled to in the mitochondria?
ATP efflux
What is ATP efflux coupled to in the mitochondria?
ADP influx
What antiport is present in the mitochondria?
The ATP/ADP antiport
True or false: transporters are found in the outer membrane of the mitochondria
False: the outer membrane is very permeable
True or false: transporters are found in the inner membrane of the mitochondria
True: they are commonly coupled to proton gradients
How come the outer membrane of the mitochondria has no transporters?
It is a fairly permeable membrane
