(bio) Unit 5 - Intracellular Compartments and Protein Sorting Flashcards
How did the evolution of nuclear and ER membranes come to be? What is it called?
- Membrane bound ribosomes and DNA come into an ancient prokaryotic cell, invagination of plasma membrane encloses genetic material.
- Endosymbiome theory.
What does protein sorting refer to?
transfer of proteins into compartments where they are needed.
Where does the synthesis of all proteins occur?
In cytosol, on free ribosomes
What are the three steps/ways to move proteins to a particular area?
- Transport through nuclear pores of the nucleus
- Transport across the membrane (of organelles)
- Transport by vesicles (to golgi body)
What are signal sequences? How do they work?
Amino acid sequence that direct proteins to particular organelles. They are removed after sorting.
Explain the nuclear pore complex
It exists in the outer nuclear membrane and the inner nuclear membrane. Consists of a nuclear basket on the inner membrane
- allows the diffusion of small (water soluble) molecules
What do imported proteins need to have attached in order to pass through the ER and into the nucleus
Nuclear protein must have nuclear localization sequence, which later will also bond to the nuclear import receptor to go into the nuclear pore. After, the nuclear import receptor detaches goes back out to deliver another protein
What is the nuclear localization signal? Why is it needed?
- amino acid sequence that ‘tags’ a protein for import into the nucleus by nuclear transport
- Needed for passage of larger proteins
What is nuclear export signal?
tags for export of large protein
Do proteins pass through the nuclear pore complex and unfold?
No, it passes without unfolding
What moves out of the nucleus?
- mature, properly processed mRNA
- ribosomal RNA (manufactured in nucleolus
What moves into the nucleus?
- histones, proteins required for transcription and DNA replication
-dNTPs, rNTPs
What does all protein transport require? And how does proteins move to become useful (ex. chloroplasts and mitochondrial proteins)?
Energy. Proteins must be moved across both outer and inner membranes at special sites where layers are in contact.
Import of Protein into Mitochondria?
- begins their synthesis on free ribosomes in cytosol
- signal sequence is attached so it can be recognized by the import receptor protein on the outer mitochondrial membrane
- these two structures migrate on the outer membrane and eventually bind to the protein translocator in inner membrane
- unfolding of protein as it enters the matrix
- the protein becomes mature as it refolds and the localization sequence cleaves off
What is the name of the process that occurs when proteins enter the ER?
serves as an entry point for endomembrane system, (golgi, lysosomes, endosomes), cell surface, secretory proteins.
How will mRNA encoding a protein will enter the ER? What structures will it contain?
It needs to have a ER signal sequence that will localize the mRNA encoding protein to the ER membrane.
A translocation signal on the membrane will attach to the ER signal sequence with its mRNA encoding protein.
The signal sequence will localize into the channel where translation of the protein will continue (into the ER)
Signal sequence will cut off once the protein is completley translated into the ER and forms its shape into a “soluble protein”
See slide 25 of unit 5
What is the purpose of the signal recognition particle (SRP)? Where is it involved?
it is attached to the ER signal sequence on the growing polypeptide chain. The entire unit binds to the SRP receptor in ER membrane, directing the ER signal sequence (which is attached to the protein) through the translocation channel and eventually into the ER lumen.
See slide 27 of unit 5
What are the two types of proteins transferred to ER?
More diagrams on lecture notes
- Water soluble proteins translocated completley across into ER lumen (pg 30)
- Prospective transmembrane proteins translocated only partially across (ex. plasma membrane, ER membrane or any organelle membrane)
AKA Single-Pass Transmembrane Proteins (pg 32)
Temporary vesicles, what are their functions?
- they allow material to leave and enter cells
- move material between endomembrane compartments
- carry soluble proteins from lumen into plasma membrane for secretion
- move membrane proteins from the membrane to be expressed on the cell surface
What are the 2 directions of vesicular transport (vesicle budding) and describe the way they travel
- Outward from ER: Golgi - other organelles - plasma membrane
- Inward: Plasma membrane - endosomes - lysosomes
What is Clatherin coated vesicle and what structures are involved?
A protein coat that helps cargo molecules from the extracellular side to enter the cytosol by creating a coated vesicle that will detach.
Some strucutres involved are adaptin, cargo receptors, dynamin, clathrin coat
see slide 39 of unit 5
How will vesicles find their correct target destinations after budding from a membrane? What do transport molecules have that can help them with this?
They must “dock” with a specific organelle. This is done by having molecular markers of both the transport vesicle and organelle interact with each other.
Transport vesicles have molecular markers that identify its cargo and origin, which can be recognized by the receptors on their target membrane.
What are molecular markers? Name three? What are they used for?
Molecular markers are found on transport vesicles to help direct them to their target destination.
Rab proteins - displayed on vesicle surface
Tethering proteins - cytosolic side of target membrane
SNARES - transmembrane proteins on vesicle (v-snare) and target membrane (t-snare) that consolidate docking and catalyze membrane fusion
refer to slide 41 of unit 5
ER processing, how are proteins covalently modified in ER? (during the secretory pathway) (2)
- With the formation of disulfide bonds (bridges) to stabilize protein shape
- Addition of sugar groups - “glycoslyation”…
- can protect protein from degradation
- help direct protein to proper organelle (transport signal)
- displaying it on cell surface allows for cell-cell recognition
How does ER glycosylation work? Why does this happen?
As growing peptide enters ER, a carbohydrate group attaches to amino groups (thats already in the ER lumen) of asaparagine (Asn) side chains via membrane-bound enzyme .
Called “N-linked glycosylation”
This occurs as a post translational modification of protein.
refer to slide 49 on unit 5
How do proteins ensure they are properly folded during secretory system?
The ER acts as a quality control centre where it’s folding can be monitored before being shipped to the golgi.
It bends in certain shapes depending on the hydrophobic residues that are exposed.
What system is established when proteins are incorrectly unfolded?
the “Unfolded Protein Response” (UPR)
- sensors for misfolded proteins exists in the ER lumen
- its sensors are activated thus activate transcription regulators and chaperone genes to increase he protein-folding capacity of the ER
- this leads to the expansion of the ER
- if this does not work the UPR triggers APOPTOSIS (cell death)
Refer to slide 53 of unit 5
Describe the golgi apparatus and its parts responsible for the secretory pathway
- consists of a series of sacs called cisternae
- organizaed into functionally distinct copartments with cis golgi network (entry, closest to ER) and trans golgi network (exit)
- cis: newly formed
- trans: breaking away
What are the functions of the golgi apparatus when new proteins arrive from the ER?
- shorten the peptide chains
- modify amino acids
- add/remove CHO groups
- glycosylation: “O-linked glycosylation” in golgi where different CHO groups are added to different AA’s
- where the most complex polysaccharides are synthesized
Constitutive vs Regulated Secretion?
Constituive secretion - happening all the time in a unregulating way
Regulated secretion - extracellular signal is involved to make secretory vesicle release cargo molecules due to high concentrations
Both are in the process of moving transport/secretory vesicles from the golgi and into the extracellular space.
Refer to slide 57 in unit 5
What is the endocytic pathway? What are the three types?
taking in substances into cell by surrounding them with membrane - membrane bound vesicle.
- Pinocytosis
- Phagocytosis
- Receptor Mediated endocytosis
What is pinocytosis? What does it engulf? Related structures? What cells do this?
A way for a substance to become a membrane bound vesicle.
“cell drinking” of solutes, macromolecules, fluid
tiny vesicles formed called endosomes
done by all eukaryotic cells - no specific and regulated
What is phagocytosis? What does it engulf? Related structures?
A way for a substance to become a membrane bound vesicle.
“cell eating” of particles, other cells, debris
large vesicles called phagosomes
done by specialized cells called macrophages
What is receptor-mediated endocytosis? What does it engulf? Related structures?
A way for a substance to become a membrane bound vesicle.
very selective concentrating mechanisms
requires specialized receptors (grouped in patches of membrane called “coated pits”
ex. clathrin coated vesicles
gathers molecules outside cell in low concentrations
The most extensive component of the endomembrane system, in terms of membrane surface area, is the …
endoplasmic reticulum
If the ER signal sequence in the gene encoding a large protein were deleted, the protein resulting would end up …
in the cytosol.
Gold nanoparticles are smaller than small proteins. If they are injected into the cytoplasm, they can later be observed in the nucleus. How is this explained?
Molecules that are that small can diffuse nonselectively through the nuclear pore complex.
Proteins encoded by the nuclear genome destined for the mitochondria enter the mitochondria by …
binding to mitochondrial import receptors, unfolding, and passing through translocator proteins in mitochondrial membranes.
In a eukaryotic cell, RNA polymerase enzymes are synthesized in the …
cytosol, by free ribosomes
While not actively engaged in translation, ribosomes …
are scattered in the cytosol with large and small subunits dissociated from each other.
Citrate synthase is an enzyme in the TCA / Krebs cycle that is encoded by the nuclear genome. It would reach its destination by …
having a mitochondrial signal sequence
The Unfolded Protein Response monitors protein folding in the ________, releasing signals into the ________ that increase the protein folding capacity of the ER.
ER lumen, cytosol
A cell in which the rate of pinocytosis exceeds the rate of constitutive secretion would …
decrease in membrane surface area.
What would be the fate of the membrane associated with a vesicle that has just secreted its cargo by exocytosis?
The vesicle membrane fuses with the plasma membrane and becomes part of it.
The carbohydrate molecules found on the extracellular surface of the plasma membranes were installed by cellular machinery…
on the luminal side of the ER and Golgi membranes.
A transmembrane protein destined for the plasma membrane protrudes from the cytosolic face of the ER membrane. On its journey to its destination, where would you expect the protein to protrude?
on the cytosolic face of the Golgi, and on the cytosolic face of the plasma membrane
What is considered the site for cellular digestion?
Lysosomes
