Week 9: Intracellular Compartments and Protein Sorting Flashcards
Section 2: Week 3
List some of the major intracellular compartments and their significance
- Mitochondrion: ATP synthesis
- Gogli apparatus: Modifies protiens & lipids
- Endoplasmic reticulum (ER) (with membrane-bound ribosomes)
- Nucleus: RNA, DNA synthesis
- Endosome: Endocytosis
- Lysosome: Digestive enzymes
- Preoxisome: Oxidative reactions
What components are “intracellular” but are NOT compartments?
- Free ribosomes
- Plasma membrane (not inside but it protects the inside)
- Cytosol
When considering the volumes of intracellular compartments, they will ____________ for different cell types
differ
The cytosol makes up ____ of the volume of a cell
half
What occurs in the cytosol?
Protein synthesis and degredation
What can be found in the cytosol?
Many metabolic pathways and cytoskeleton
True or False: There are more membranes AROUND the cell than IN it
False
What are the two types of membranes that makes up roughly half of a cells (intracellular) membranes?
Smooth ER and Rough ER
Why is rough ER considered “rough”?
Due to its membrane-bound ribsomes
What are the functions of the rough ER
synthesis of soluble proteins (i.e. secreted proteins) and transmembrane proteins for the endomembrane
What are the functions of smooth ER
phospholipid synthesis, detoxification
Why do liver hepatocytes have more smooth ER in comparison to pancreatic exocrine cells?
Liver hepatocytes have more smooth ER because of the detoxification of smooth ER
Why do pancreatic exocrine cells have more rough ER in comparison to liver hepatocyte cells?
Pancreatic exocrine cells have more rough ER because of their need to create secreted proteins like enzymes
What is the definition of an organelle?
A discrete structure or subcompartment of a eukaryotic cell that is specialized to carry out a particular function
What are examples of membrane-enclosed organelles?
- Nucleus
- ER
- Gogli apparatus
What are examples of organelles that are not membrane-bound?
- Nucleolus
- Centrosome
(which are known as biomolecular condensates)
Proteins are __________-________
nuclear; encoded
Which proteins do not get sorted? Why?
Cytosolic proteins (whose default location is the cytosol) do not get sorted because they have no sorting signal
Why do some proteins get sorted?
Some proteins get sorted because they have a sorting signal called a Signal sequence
What is a signal sequence?
A signal sequence is a specific sequence of amino acids that tells the cell where the protein should go. It is NOT added on separately as it is originally coded for by the mRNA and by the genome.
What do signal sequences specify?
They specify what location to bring the protein to, whether it be the nucleus, mitochondria, ER, peroxisomes, etc
In terms of folding, what can happen to proteins that have a signal sequence after they are synthesized but BEFORE they get sorted?
Three things can happen:
1. folded FIRST then sorted and STAYS folded
2. unfolded FIRST thens sorted
3. folded FIRST then sorted, then UNFOLDED
What is post-translational sorting?
Proteins are fully synthesized in cytosol before sorting. Proteins going to the nucleus and peroxisomes are FOLDED. Proteins going to the mitochondria and plastids are UNFOLDED.
What is co-translational sorting?
Proteins are sorted during protein synthesis. These proteins are associated with the ER.
Proteins that require transport through the nuclear pores (whether import or export) are ___________ ___________ and ________ before sorting
fully synthesized; folded
What is a nuclear localization signal?
A nuclear localization signal is a signal sequence that is bound to by a sorting receptor called the nuclear import receptor, which brings the protein to the nucleaur via nuclear pores
Proteins that are sorted to peroxisomes are ____________ ____________ and ________ before sorting
fully synthesized; folded
Proxisomes contain enzymes for ________ reactions to detoxify toxins
oxidative
What is a peroxisomal import signal?
A peroxisomal import signal is a signal sequence that is bound to by a peroxisomal import receptor, which brings the protein (enzyme in this case) to the peroxisome
How are enzymes imported into the peroxisome?
Enzymes are imported into the peroxisome through a transmembrane protein complex
Proteins that are being sorted into the mitochondria and chloroplast (plastids) are __________ __________ and ________ before sorting
fully synthesized; unfolded
Even though the mitochondria and chloroplast have their own genomes and ribosomes, most of the proteins for these organelles are ____________-__________
nuclear-encoded
Proteins imported into the mitochondria and chloroplasts are unforlded for import by association with ____ ________ proteins
hsp70 chaperone
What kind of signal sequence do proteins being sorted to the ER have?
ER signal sequence
Proteins that are being sorted to the ER are ___ ________ ___________
not fully synthesized
True or False: ER signal sequence is hydrophobic
True
What does it mean when it is said that proteins that have an ER signal sequence are associated with ER during protein synthesis in the cytosol?
It means that these proteins will begin to be synthesized in the cytosol, pause, be brought to the ER, then continue and finish being synthesized there
Why do proteins sort to the ER?
It is the entry point to the Endomembrane system
What makes up the Endomembrane system?
- ER
- Gogli apparatus
- endosomes
- lysosomes
What kinds of proteins enter the ER?
- Soluble proteins
- Transmembrane proteins
Describe the steps for the co-translational translocation of soluble proteins
- Translation starts, N-terminal ER signal sequence emerges
- Recognized by SRP, elogation arrest by SRP
- SRP-ribosome complex -> SRP receptor -> Translocon
- Translocon opens
- Protein synthesis resumes with protein transfer into ER lumen
- Signal peptidase cleaves ER signal sequence (signal sequence is hydrophobic - in lipid bilayer)
- Protein released into ER lumen
- Translocon closes
What is the destination of soluble proteins?
The lumen of an endomembrane organelle or secretion at plasma membrane
True or false: Because the ER signal sequence is located at the end of the soluble protein’s AA sequence, you usually have no Met at the end of translocation due to cleavage of the ER signal sequence
True - although it’s not the case for all
Describe the steps of the co-translational translocation of transmembrane proteins that have an N-termimus ER signal sequence that differ from soluble proteins
- Steps 1-5 are same as soluble proteins
6. Step-transfer sequence enters transolocon (internal hydrophobic segment - membrane spanning alpha-helix
7. Protein transfer stops and transmembrane domain released into lipid bilayer
8. Signal peptidase cleaves ER signal sequence
9. Protein synthesis completed
For both types of proteins, what cleaves the ER signal sequence at the end of protein synthesis?
Signal peptidase
What is the destination of transmembrane proteins?
The destination of transmembrane proteins is the membrane of an endomembrane organelle or in the plasma membrane
What are the two types of ER signal sequences and how do they differ?
- N-terminal ER signal sequences: they are a stretch of hydrophobic amino acids that lie at the N-terminus of proteins and are removed by signal peptidase
- Intenal ER signal sequences: they also serve as the start-transfer sequence, and are a stretch of hydrophobic amino acids that are within the protein and does not get removed ( it remains part of the protein as a membrane spanning alpha helix)
True or False: the hydrophobic stop-transfer sequence within an amino acid chain gets removed at the end of protein synthesis
False
Describe the steps of the co-translational translocation of transmembrane proteins that have an internal ER signal sequence that differ from soluble proteins
- translation starts, internal start-transfer sequence emerges
* Steps 2-5 from the N-terminus are the same - Stop-transfer sequence eneters translocon
- Protein transfer stops
- Start-transfer sequence and stop-transfer sequence are released into lipid bilayer (they become intenral hydrophobic segments - membrane spanning alpha helices)
- Translocon closes
- Protein synthesis completed
What components are exchanged by intracellular compartments that are part of the endomembrane system?
lipids and proteins
What happens in the secretory pathway?
Proteins and lipids that are made in the ER are delivered to other compartments such as outside the cell via exocytosis or to lysosomes via endosomes
What happens on the endocytic pathway?
Contents are moved into the cell via endocytosis
What happens on the retrieval pathway?
The retrieval of lipids, selected proteins for reuse
True or False: Proteins must stay on the same path to get to one destination
False!
What happens during exocytosis?
Vesicle contents are delivered to extracellular space and the vesicle membrane becomes part of the plasma membrane
What happens during endocytosis?
Vesicle luminal contents come from extracellular space and the plasma membrane forms vesicle membrane
True or False: During vesicular transport, there may be some flip-flopping
FALSEEEE
What is a vesicle?
A small, membrane-enclosed organelle in cytoplasm of a eukaryotic cell. It shuttles components back and forth in the endomembrane system.
What do cargo receptors on vesicles do?
Select cargo!
What is the constitutive exocytosis pathway?
- It is in all eukaryotic cells
- Continual delivery of proteins (both transmembrane and soluble) and lipids to plasma membrane
- Includes constitutive secretion of soluble proteins (e.g. collagen for ECM)
What is the regulated exocytosis pathway?
- It is regulated secretion (in specialized cells)
- Stored in specialized secretory vesicles
- Extracellular signal - vesicle fusion with PM and contents released
- E.g. pancreatic beta-cells: insulin release with increased blood glucose
Where does the ER signal sequence lie for a protein being secreated to the plasma membrane?
The N-terminus
Does a protein being secreated to the PM undergo co-translational or post-translational translocation?
Co-translational translocation
Describe the translocation required for a protein being secreted to the PM
- Protein inserted through ER membrane by a translocon protein
- ER Signal sequence cleaved and left behind in ER membrane
- Secreated protein ends up in the ER lumen
What happens to a protein being secreted to the PM after its been sorted to the ER?
The secreated protein moves via transport vesicle through the secretory pathway (ER > Golgi apparatus > Plasma membrane). Once at the PM, the vesicle membrane fuses with the PM during exocytosis which releases the protein into the extracellular space
True or False: The orientaion of a transmembrane protein being tranferred to the PM stays consistent
True
Is the ER Signal sequence for a transmembrane being transported to the PM at the N-terminal or internal?
It could be either
What happens to a transmembrane protein being transferred to the PM after its been sorted to the ER?
It moves via transport vesicles through the secretory pathway (ER > Golgi apparatus > PM). The vesicle membrane then fuses with the PM during exocytosis which allows the transmembrane protein to transfer to the PM.
How is the asymmetry of membrane proteins maintained?
It is maintained through vasicular transport
Why does each membrane protein have a specific orientation?
It is a result of membrane insertion in the ER
What happens at the Golgi apparatus?
The Golgi apparatus recieves proteins and lipids from the ER, modifies them, and then dispatches them to other destinations in the cell
What is the difference between the cis Golgi network ad the trans Golgi network in terms of what they’re facing?
The cis Golgi network faces the ER, the trans Golgi network faces away from the ER
What is the typical composition of the Golgi apparatus?
6-8 sacs (typically) but it could be 60-80
What is protein glycosylation in the ER?
Protein glycosylation is when a type of olgiosaccharide (sugar chain) is attached to many proteins
What happens with olgiosaccharides in the Golgi apparatus?
Complex oligosaccharide processing occurs in the Golgi apparatus. It happens in a multistage processing unit with different enzymes in each cisterna. There is also glycosylation modifications for proteins and lipids
What are endosomes?
They are membrane-bround organelles that contain material ingested by endocytosis
What are early endosomes?
- Endocytic vesicles fuse to early endosomes and the ingested material is then sorted (either to the lysosome or Golgi)
- Early endosomes then mature to late endosomes
What are late endosomes?
- Lysosomal proteins (hydrolases, H+ pump) continue to be delivered from trans Golgi network
- Late endosomes mature into lysosomes
What are lysosomes?
Lysosomes are membrane-bound organelles that contain hydrolytic enzymes to digest worn-out proteins, organelles and other waste
What are hydrolytic enzymes?
Hydrolytic enzymes help to digest nutrients (with the help of lysosomic enzymes)
What can happen after most things have been digested by the lysosome?
You can fuse lysosomes with endosomes (early or late) to reuse the good enzymes within the lysosomes
Lysosomes are the main cite of _____________ _________
intracellular digestion
What kind of hydrolytic enzymes do lysosomes contain?
~40 types, such as acid hydrolases (digestive enzymes that function in acidic conditions) which consist of proteases, nucleases, lipases, etc
How are lysosomes acidified? Why is it acidified?
Lysosomes are acidified by H+ pump (V-type ATPase). This happens because low pH is needed for hydrolytic enzymes.
What is done to lysosomal membrane proteins (noncytosolic face) for protection from proteases
They are glycosylated
What do transport proteins in lysosomal membrane transfer?
They transfer digested products to cytosol such as amino acids, sugars, and nucleotides
How are things outside the cell protected from acid hydrolases since they cut stuff up and can possibly escape the lysosome?
Two things: the plasma membrane and the pH outside of a cell is too high
