Intracellular Compartments and Transport

How did nuclear membranes and ER evolve

It is possible that in an ancient prokaryotic cell, the plasma membrane and its attached DNA (since DNA was typically attached to membrane) could have invaginated and formed a two layered envelope of membrane completely surrounding the DNA. The other portions of the same membrane formed the ER (to which some of the membrane-bound ribosomes)

What’s invagination

the inward folding or buckling of a surface layer of cells, tissue, or membrane to form a cavity, pouch, or tube

Main function of cytosol

contains many metabolic pathways; protein synthesis; the cytoskeleton

Main function of nucleus

contains main genome; DNA/RNA synthesis

Main function of endoplasmic reticulum

synthesis of most lipids; synthesis of proteins for distribution to many organelles/to the plasma membrane

Main function of the golgi apparatus

modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle

Main function of lysosomes

intracellular degradation

Main function of endosomes

sorting of endocytosed material

Main function of

ATP synthesis by oxidative phosphorylation

Main function of chloroplasts

ATP synthesis and carbon fixation by photosynthesis

Main function of peroxisomes

oxidative breakdown of toxic molecules

connections between nuclear envelope and ER

-nuclear envelope is in continuity with the ER

-outer nuclear membrane chemistry resembles that of ER and differs from that of inner membrane

-perinuclear space is continuous with ER lumen

-during evolution, ER prolly gave rise to golgi, peroxisomes, lysosomes, and endosomes, and it still supplies their lipids/proteins

What is the ER

a network of membrane tubules and sheets which extends through the cytoplasm

What do the polyribosomes on RER do

translate proteins of the ER, golgi, endosome, lysosome, plasma membrane, and cell exterior

What proteins that enter the ER lumen and where do they go after

soluble proteins may stay there but most move to lumen of another compartment

What proteins enter the ER membrane and where do they go after

membrane proteins may stay there but most travel to other membranes

How common is SER

uncommon in some cells but plentiful in specialized cells

In what kinds of cells is SER abundant and what does it do

-cells that produce steroid hormones (Adrenal gland): SER makes cholesterol and synthesizes steroid hormones from this

-cells that detoxify molecules (liver cells): cytochrome 450 in the ER membrane oxidizes durgs

What is SER called in muscles

sarcoplasmic reticulum (SR)

What does Calcium (Ca++) release from SR lumen cause

contraction of sarcomeres

What does SR lumen sequestration of calcium ions do

causes relaxation of sarcomeres

What the golgi compartments and in what order do vesicles from the ER move through them

cis Golgi → medial Golgi → trans Golgi

What is different about each golgi compartment

they have diff enzymes and diff functions

What happens to proteins as they pass thru the golgi

they get modified

What happens to oligosaccharides trasnferred from dolichol in the ER after leaving ER

gets phosphorylated in cis Golgi

What does trans golgi do

sorts proteins/packages them in vesicles which go to lysosomes, plasma membrane, etc.

What occurs to orientation as protein moves from ER through Golgi to membrane

the protein for export maintains its orientation

Where does vesicular traffic occur

from ER to golgi, endosomes, lysosomes; it also occurs to and from the plasma membrane (exocytosis and endocytosis)

What do nuclear pores do

transport proteins in and out of the nucleus

What does import into the eR, nuclei, mitochondria, chloroplasts, and peroxisomes use

signal sequences, not vesicles

What is the signal for each compartment

they are all specific and have their own signals

Whats normal signal sequence

specific amino acid sequences on proteins determine whther they can be imported into nucleus, mitochrondria, chloroplasts, peroxisomes, or ER (cytosolic proteins like tubulin or actin don’t have these signal sequences)

What’s relocated signal seuqence

Relocated signal sequence when ER signal sequence is removed from ER protein and attached to cytosolic protein. This stops the ER protein from entering and causes the cytosolic protein to enter the ER

What do free polyribosomes do

generate proteins of cytosol, mitochrondria, chloroplasts, and nuclei; also some peroxisomal proteins

What do polysomes on rough ER do

produce proteins for the cell’s organelles, fo rplasma membrane, and for export

What occurs at end of translation

the mRNA, the newly formed protein, and the large and small ribosome subunits all separate, and then the ribosome subunits join a common pool to be used again as free polysomes or polysomes on thee RER

How does transport across nuclear pore complexes work

large molecuels ened a nuclear localization signal which binds to a nuclear import receptor. That receptor/protein complex then binds to the fibrils which guide the import receptor/protein complex to the pore. After the complex binds to the pore proteins and enters the nucleus, Ran-GTP release the imported protein. The import receptor is then exported and dissociates from Ran-GTP

Where is energy for trnasport across nuclear pore complexes come from

GTP

How are proteins imported across nuclear pore complexes

they are folded

How does the RanGTP/GDP gradient drive nuclear trnasport in the nucleus

-high ranGTP

-ranGTP binds importin beta

-importin beta loses afffinity for importin alpha and NLS cargo-protein

importin alpha releases NLS-cargo-protein in nucleus

How does the RanGTP/GDP gradient drive nuclear trnasport in the cytoplasm

-RAnGTP-importin-beta complex exits nucleus

ranGAP (GTPase activator protein) helps hydrolyze ranGTP into RanGDP

-importin beta loses affinity to RanGDP

-importin beta is free to interact again with importin alpha and NLS-cargo-protein

How does protein import into the mitochrondria work

Nuclear-encoded mito proteins are translated on cytosolic polysomes. A protein becomes associated with chaperone proteins, which prevent the protein from folding (protecting its import competence). The import signal is recognized by an import receptor protein on the Outer mitochondrial matrix. The receptor with attached protein moves laterally to a site where the OMM and the IMM translocators are aligned. The proteins cross the two membranes and the import signal is removed by a signal peptidase

What does protein import into mitochondria require

a proton gradient across the IMM< ATP, and a chaperone protein in the matrix to enable protein folding

Whats the process of the ER signal sequence/what’s co-translational entry

The initiation of translation creates the ER signal sequence which is 30 AAs long. The signal recognition particle (SRP) recognizes the signal sequence, binds to it, and translation slows. the SRP-ribosome complex binds to the SRP receptor located on the ER membrane. The SRP is released, the protein chain inserts into a translocation channel and translation continues. The signal peptidase removes the signal sequence which enters the ER membrane and is broken down. the soluble protein enters the ER lumen and assumes its mature 3D shape.

example of post-translational entry

proteins that are translated on cytosolic polyribosomes

How does insertion of single-pass protein in ER membrane work

transmembrane proteins have additional signal, stop-transfer signal. This signal is recognized by translocation channel which discharges the protein laterally into the membrane. The signal sequence is enzymatically remoed from the N-terminus which then extends into the ER lumen

What’s the stop-transfer and start-transfer signal

both alpha helices of hydrophobic amino acids which anchors the protein into the ER membrane

How does insertion of double-pass protein in ER work

A signal-recognition particle recognizes the start-transfer sequence (the internals signal seuqence) of the protein. The SRP brings the protein to the ER and the prtoein enters the translocator channel. The protein moves laterally into ER membrane where both start-transfer and stop-transfer seuqences are in the translocator channel. Both of these seuqences are alpha helices of ydrophobic amino acids that span the membrane (NOT removed)

Are stop- and start- transfer proteins removed from the membrane

no

How can misfolded proteins happen

Excessive production of proteins may exceed the capacity of the ER

How are misfolded proteins refold

They bind to chaperone proteins which refold them

What happens to a misfolded protein that is not refolded properly

It is exported to the cytosol and destroyed in a proteasome

In unfolded protein response, what can misfolded proteins activate

transcription of genes coding for chaperones, inhibitors of protein synthesis, ER expansion, etc.

What’s KDEL signal and how do they return errant ER proteins from Golgi

ER resident proteins (proteins that aren’t translated on ER ribosomes), like chaperone proteins, have an ER retention signal (KDEL = lysine-aspartic acid-glutamic acid-leucine) at their carboxyl end, and if ER resident proteins enter the Golgi, they bind to KDEl receptors and are returned to the ER by COP vesicles

where do golgi proteins go

Signals direct proteins in the trans golgi network to the appropriate vesicle. and other signals direct veiscles to their destinations

What happens to golgi proteins in constitutive secretion

golgi products are immediately discharged (exocytosis) (ex: extracellular matrix proteins/growht factors)

What happens to golgi proteins in regulated secretion

Golgi products are stored as secretory vesicles which are thenr eleased rapidly in reponse to hormonal or neural stimuli (exocytosis)

What happens to vesicle membranes that are added to the plasma membrane

they may be internalized by endocytosis or become part of the plasma membrane (Ex: golgi vesicles transport plasma membrane proteins like ion channels)

What are SNAREs

transmembrane proteins that direct vesicles to their targets

Where do v-SNAREs occur

they occur on vesicles

Where do t-SNAREs occur

target membranes

What does specific interaction between v- and t- SNAREs ensure

ensures that vesicles reach appropriate tarfet comaprtment

How are cargo proteins delivered with SNAREs

a tethering protein binds to a Rab protein to dock the vesicle, and v-SNAREs and t-SNAREs wrap around each other; this fuses together the vesicle and target membranes and delivers the cargo protein

Whats’ forward transport

COP-coated vesicles carry mateiral from ER to cis to medial to trans golgi. Clatherin-coated vesicles exit the trans golgi

Whats backward transport

COP-coated veiscles carry material from trans to medial to cis golgi to ER

What is COP for for

coat protein

What is endocytosis

movement of cargoes to cytoplasm

What is origin and destination of clathrin-coated vesicle and what are the coat proteins involved

clathrin + adaptin 1: golgi → lysosome via endosomes

clathrin + adaptin 2: plasma membrane → endosomes

What is origin and destination of COPII- and COPI-coated vesicle and what are the coat proteins involved

COPII proteins: ER → cis golgi

COPI proteins: cis golgi → ER

What’s receptor-mediated endocytosis

Clathrin is joined by adaptin to a cargo receptor which binds to a specific cargo molecule. Clathrin moelcules assembling on the cytosolic surface shape the membrane into a coated pit. The motor molecule, dynamin, uses GTP to pinch off the coated pit to form a coated vesicle. An uncoating enzyme later removes the Clathrin forming a transport vesicle that fuses with an endosome (Note: clathrin-coated vesicles endocytose (bring in) material from the cell surface_

How are endosomes sorting stations

the low pH interior of the endosome due to ATP-driven proton pumps causes cargo molecules to dissociate from their receptors. A vesicle rich in receptor buds off to recycle recptors to the plasma membrane. Vesicles transfer cargo to lysosomes where its broken down

What can endosomes mature into

lysoosmes

Structure of lysosomes

spherical and vairable in size. contain approx 40 enzymes which break down endocytosed molecules or worn out cell components

what’s autophagy

break down endocytosed molecules or worn out cell components

optimum pH of enzymes in lyosomes + how is it maintained

5.0, maintained by proton pumps

What do lysosomes do

digest most material that enters cell by endocytosis, digest old cell components

What do lyosomal enzymes do

break down their substrates into small molecules such as amino acids, sugars, and nucleotides which then enter the cytosol via transport proteins in the lysosomal membrane.