Intracellular Compartments and Protein Sorting 1 Flashcards
What is a nucleus?
Principal site for DNA and RNA synthesis
Contains the genome
What is a plasma membrane?
Outer boundary of cells, and a bilayer
It is a protective barrier with transporters and signaling
What is cytoplasm?
Consists of cytosol and cytoplasmic organelles
And is an intermediary metabolism
What is Endoplasmic Reticulum ER?
Ribosomes attach to the rough ER and the smooth ER has no ribosomes
It is a place for proteins synthesis, lipid synthesis, protein folding, and storage of calcium
What is the golgi apparatus?
Stacks of disc-like compartments
-post-translational changes on proteins and lipids occur here and also trafficking
What does the mitochondria do?
Makes ATP, signaling, cell differentiation and cell death.
Has an outer and inner membrane and matrix
What are lysosomes?
The digestive system of the cell: contain digestive enzymes that degrade organelles and biomolecules
What are peroxisomes?
Small vesicular compartments that contain enzymes used in oxidation reactions
what 3 topological categories does the cell divide into?
Nucleus and cytosol
Organelles in secretory and endocytic pathways
Mitochondria
How does the nucleus and cytosol communicate?
Through nuclear pore complex. Topologically they are the same and one organelle
What are organelles in secretory and endocytic pathways?
ER, Golgi, Endosomes, and lysosomes
How do organelles in secretory and endocytic pathways communicate?
Through vesicles
What allows topologically equivalent organelles to communicate with each other and with the cell exterior?
Membrane budding and fusion allows the lumen of each of these compartments to communicated
What are the types of protein trafficking?
Gated transport
Transmembrane transport
Vesicular transport
What type of protein trafficking is between the nucleus and cytosol through nuclear pore complexes?
Gated transport
Active transport and free diffusion
What is transmembrane transport?
Membrane proteins translocators directly transport specific proteins from cytosol across an organelle membrane
What is vesicular transport?
Membrane-enclosed transport intermediates that move proteins between various compartments via vesicles
What guides protein transfer/transport to various compartments?
Sorting signals
What are sorting signals?
Stretch of amino acids, typically 15-60 residues long
Where may sorting signals be localized?
On N or C terminus or within the protein sequence
What forms a signal patch?
Multiple scattered sequences in protein may form signal patch
What may remove the signal after protein reaches final destination?
Signal peptidase
Signal sequences are both necessary and sufficient for ____________
Protein targeting
What is more important than actual sequence in a sorting signal?
Physical properties of the sequence (e.g. charge, hydrophobicity)
What are signal sequences recognized by?
Complementary receptors
Describe nuclear transport?
Gated, bidirectional, and selective
What proteins are needed in nucleus?
Histones, DNA and RNA polymerases, topoisomerases, and gene regulatory proteins
Where are proteins needed in the nucleus imported from?
The cytoplasm where they are synthesized
What proteins are synthesized in the nucleus and exported to cytosol?
tRNA and mRNA molecules
What are nuclear pore complexes?
(NPCs) Perforate nuclear envelope in eukaryotes
What is the molecular mass of NPCs?
About 125 million Da
What is the NPC composed of?
30 different proteins or nucleoporins
What is the arrangement of NPCs?
Octagonal symmetry with one or more aqueous pores
How many NPCs does the nuclear envelope have?
3000-4000 NPCs
What direction does the NPCs transport molecules?
Both directions
What type of transport do NPCs do?
Passive diffusion of small molecules and facilitated transport
What is transport facilitated by in NPC?
Binding of particles to fibrils extending from NPC
What are Nuclear localization signals?
(NLS)
Sorting signals that direct molecules to nucleus
Short sequences rich in positively charged amino acids lysine and arginine
What are NLS located on? What do they form?
Many different sites on protein and form loops or patches on surface
What do NLS result in?
Selective import of proteins into nucleus
What are NLS recognized by?
Nuclear import receptors (NIRs)
What does each NIR recognize specifically?
A subset of cargo proteins
What are NIRs?
Soluble cytosolic proteins that bind to NLS on protein and to NPC proteins present on fibrils that extend into cytoplams
What do NPC proteins have? What is their purpose?
Phenylalanine glycine (FG) repeats which serve as binding sites for import receptors
How do receptors plus its cargo traverse NPC?
By binding, dissociating, and re-binding to adjacent FG repeats
What happens once the cargo passes the NPC?
It is released inside the nucleus and NIR returns to cytoplasm
What types of binding occurs with nuclear import receptors?
Direct binding with 3 different cargo proteins
and indirect binding via adaptor protein
What is nuclear export?
Works similar to import but in opposite direction. It transports cargo out of the nucleus
What does nuclear export rely on?
Nuclear export signals (NES) on molecules that need to go out of the nucleus
What receptors are needed?
Need complementary nuclear export receptors (NER)
What does NER bind to?
Cargo present in nucleus and NPC proteins
What facilitates transport during nuclear export?
Binding, dissociation and re-binding
Where is the cargo released during nuclear export?
Into cytoplasm
What drives nuclear transport in appropriate direction?
Gradient of Ran conformational states
How does the import receptor and cargo enter the nucleus?
By interacting with FG repeats on NPC proteins
What binds to complex of import receptor and cargo?
Ran-GTP
What does the binding of Ran-GTP to complex of import receptor and cargo cause?
The release of cargo
What leaves the nucleus after cargo is released in the nucleus?
Ran-GTP and import receptor
What happens to Ran-GTP in the cytoplasm?
It is hydrolyzed by Ran-GAP and the receptor is released from the Ran-GDP (hydrolyzed ran-gtp) and is ready for another cycle
Some proteins contain both ____ and _____
NLS and NES
Where do proteins with both NLS and NES shuttle back and forth?
Between nucleus and cytosol
What does the steady state localization dependent upon?
Relative rate of transport
If rate of import is greater than export, ________
It is considered nuclear, and vise versa
What can the changing rate of import/export change?
Location of protein
Gene regulatory proteins transport is _________
Stringently controlled
What is kept out of nucleus until needed?
Gene regulatory proteins
Gene regulatory protein transport is controlled by what?
By NLS and NES being turned on and off
What mechanisms are used to turn on and off the NLS and NES on gene regulatory proteins?
Phosphorylation, proteolysis, and binding to inhibitory proteins
