Chapter 10

Cell bio

What does the evolutionary history of organelles dictate?

How their proteins are trafficked and where their genetic material is stored.

What is endomembrane system evolution?

The nucleus, endoplasmic reticulum (ER), and Golgi apparatus evolved through the infolding of the plasma membrane

What is endosymbiosis?

Mitochondria and chloroplasts evolved via endosymbiosis, where an ancestral prokaryote was endocytosed by another cell

What is the trafficking distinction?

Because they originated from endosymbiotic events, mitochondria and chloroplasts are not part of the endomembrane system; consequently, their proteins are not trafficked via the endomembrane pathway

What are organelle derived genes?

These are transcribed and translated directly within the organelle itself.

What are nuclear derived genes?

These are translated in the cytosol and must be translocated across the organelle membranes to reach their destination.

What is the function of POLG protein?

Encodes for mitochondrial DNA polymerase

What are chaperone proteins?

specialized cellular molecules that assist in the proper folding, unfolding, assembly, and disassembly of other proteins without becoming part of their final structures

What are the roles of chaperone proteins?

Assisting in folding, preventing aggregation (proteins stick together (clump) to form soluble or insoluble clusters) of misfolded proteins, transporting, targeting specific proteins for degradation, and functioning in stress responses

What is the TOM complex (Translocase of outer mitochondrial membrane)?

The initial entry point for most mitochondrial proteins

What is the TIM complex (Translocase of inner mitochondrial membrane)?

Facilitates movement across the inner membrane 30.

What is the mechanism of transport when the destination is the outer membrane?

Inserted into TOM, threaded through the membrane, and released into the membrane

What is the mechanism of transport when the destination is the intermembrane space?

Pass through a channel in TOM; chaperones help thread the unfolded proteins; proteins may stay in the space or proceed to the inner membrane

What is the mechanism of transport when the destination is the inner membrane space?

Pass through both TOM and TIM complexes, then are released into the membrane

What is the mechanism of transport when the destination is the mitochondrial matrix?

Pass through both TOM and TIM; once in the matrix, the proteins are folded

What is the TOC complex (Translocase of outer chloroplast membrane)

Inserts proteins into the outer membrane or transports them to the intermembrane space

What is the TIC complex (Translocase of inner chloroplast membrane)

Inserts proteins into the inner membrane or transports them to the stroma

What are peroxisomes?

Organelles found in all eukaryotic cells that play vital roles in detoxification and lipid metabolism

How many pathways do peroxisomes utilize?

Two distinct pathways for protein delivery

When is the cytosolic pathway used?

Used for proteins containing a Peroxisome-targeting signal (PTS). The PTS is recognized by a specific targeting protein called Pex5.

When is the endomembrane pathway used?

Used for proteins that follow the traditional secretory route: ER —> Golgi —> vesicle fusion to peroxisome

What is protein trafficking?

The process by which proteins are transported to their final functional destinations within a cell. Because proteins function in diverse locations, the cell must employ specific mechanisms to ensure they reach the correct site.

What are some of the protein destinations?

Nucleus, cytosol, organelles (e.g., mitochondria, chloroplasts, peroxisomes), extracellular space, and membranes

Most proteins begin their life cycle being synthesized on ribosomes located in the cytosol. What are the two expectations?

Endoplasmic Reticulum (ER) Targeting: Some ribosomes move to the ER after the initiation of protein synthesis in the cytosol. Organelle-Specific Synthesis: Certain mitochondrial and chloroplast proteins are synthesized by ribosomes located specifically within those organelles.

What is cytosolic trafficking?

The movement of proteins through the cytosol to reach specific destinations.

What are key destinations for proteins undergoing cytosolic trafficking?

The cytosol, the Nucleus (Proteins enter through the Nuclear Pore Complex (NPC)), mitochondria (Proteins cross organelle membranes via translocation channels), chloroplasts (Like mitochondria, these require translocation through membranes), and peroxisomes (Proteins are translocated across the peroxisomal membrane)

What is a signal sequence?

The "address" that directs a protein to its destination. A specific sequence of amino acids written into the primary structure of certain proteins that targets them to a final organelle destination.

Where are signal sequences located?

These are usually located on the N-terminus (the first part of the protein exposed during translation, as proteins are translated from the N-terminus to the C-terminus)

What are the characteristics of signal sequence?

The function of the signal sequence is driven by both its amino acid composition and its hydrophobicity 7. Hydrophobic sequences: Typically target proteins to the ER. Positively charged sequences: Typically target proteins to the nucleus

When are signal sequences not required?

They are not required for proteins that are destined to remain in the cytoplasm

What do signal sequences need to be a valid targeting mechanism?

Necessary: Without the signal sequence, a protein cannot reach its final destination. Sufficient: Nothing other than the signal sequence is required to ensure the protein reaches its correct destination.

What is the nuclear pore complex (NPC)?

It is a large protein complex embedded in the nuclear envelope, which is composed of two membranes. Proteins destined for the nucleus enter through the (NPC).

Proteins destined for mitochondria or chloroplasts must cross organelle membranes via protein translocation channels in which mechanical sequence?

1. Unfolding: The protein must unfold to fit through the narrow channel. 2. Snaking: The unfolded polypeptide is "snaked" through the channel. 3. Refolding: Once on the other side of the membrane, the protein refolds into its functional shape.

How does peroxisomal transport work?

Translocated across the peroxisomal membrane, though the exact mechanism of this process is not yet fully understood

What does the NPC serve as?

The primary gatekeeper for the nucleus, regulating the movement of molecules between the cytosol and the nucleoplasm

What is the structure and organization of the NPC?

Enormous structure with a diameter exceeding 100 nm. Its organization is described latitudinally, moving from the cytoplasm toward the nucleoplasm

What does the cytosolic side of the NPC contain?

Contains cytoplasmic filaments that serve to guide proteins to and from the pore

What happens in the central channel of the NPC?

The actual pore through which transport occurs. It is surrounded by a central ring embedded in the nuclear envelope.

What are the three distinct parts of the central ring surrounding the central channel of the NPC?

Cytoplasmic ring, spoke ring (he narrowest part of the structure, which defines the diameter of the pore), and the nucleoplasmic ring

What does the nucleoplasmic side of the NPC contain?

The nuclear basket, which guides proteins to and from the pore.

How does movement through the NPC occur?

Simple Diffusion - allows for the passage of small molecules, ions, small proteins, water, certain mRNAs, and rRNA. Signal-Based Transport - required for medium to large cargo proteins and large nucleic acids 16. This method relies on specific signal sequences and carrier (shuttle) proteins.

How do you facilitate signal-based transport?

Proteins utilize specific amino acid sequences that interact with shuttle proteins

What are the signal sequences used for singal based transport?

Nuclear Localization Signal (NLS) - an amino acid sequence that targets a protein (or a protein bound to another protein) for import into the nucleus. Nuclear Export Signal (NES) - an amino acid sequence that targets a protein (or a protein bound to another protein) for export out of the nucleus

What are shuttle proteins?

They carry the cargo across the NPC and return to their original side after releasing the cargo

What are G-proteins?

GTP-binding proteins that act as "timed switches" to regulate transport

What are the three functions of G-proteins?

Activation: G-proteins are activated by the binding of GTP. Deactivation: G-proteins are deactivated by GTP hydrolysis. Timer Function: Because G-proteins are GTPases, they will eventually hydrolyze their bound GTP, "flipping the switch" from an active to an inactive state.

What is the function of the regulatory protein GEF (Guanine nucleotide exchange factors)?

Accelerates the release of GDP so GTP can bind, moving the G-protein to an active state

What is the function of the regulatory protein GAP (GTPase-activating proteins)?

Accelerates GTP hydrolysis, returning the G-protein to an inactive state

What is the function of the regulatory protein GDI (Guanine nucleotide dissociation inhibitors)?

Prevents the release of GDP, which prevents GTP from binding

What is Ran?

A specific G-protein essential for driving the directionality of both nuclear import and export

What is the sequence of the nuclear import process?

1. Binding: The NLS of a cargo protein binds to the shuttle protein Importin. 2. Translocation: The cargo-bound Importin binds to a conserved sequence known as an FG repeat on the cytoplasmic filaments of the NPC to move into the nucleus. 3. Cargo Release: Inside the nucleoplasm, Ran-GTP binds to the Importin, which causes the cargo protein to be released. 4. Recycling (Resetting): The Ran-GTP-Importin complex moves back to the cytosol. GAP binds to Ran, triggering GTP hydrolysis. This causes Ran-GDP to dissociate from the Importin. The Importin is now free to shuttle more proteins. Ran-GDP returns to the nucleus, where a GEF replaces the GDP with a new GTP, restarting the cycle 20.

What is the sequence of the nuclear export process?

1. Binding: A cargo protein in the nucleus binds to the shuttle protein Exportin via its NES. 2. Complex Formation: Unlike import, Ran-GTP must bind to the cargo-exporting complex within the nucleus before export can occur. 3. Translocation: The ternary complex (Ran-GTP-cargo-exportin) is transported from the nucleoplasmic side of the NPC to the cytosolic side. 4. Dissociation: In the cytosol, GAP binds to Ran, causing it to hydrolyze GTP into GDP and inorganic phosphate (Pi). This causes the entire complex to dissociate, releasing the cargo into the cytosol. 5. Recycling: Ran-GDP diffuses back into the nucleus. GEF exchanges the GDP for a new GTP on Ran. The Exportin also diffuses back into the nucleoplasm to begin a new cycle.