Chapter 15 Notes: Intracellular Compartments and Transport

Intracellular Compartments and Transport

• Cells are filled with organelles that perform different functions.
• Proteins need to be transported within a cell to reach their designated compartments.
• Cells have compartments.
• A signal sequence (signal peptide) determines the destination of proteins.

Translocation for Different Compartments

• Nuclei
• Mitochondria
• Endoplasmic Reticulum (ER)
• Membrane-bound proteins

Other Transport Mechanisms involving Membranes

• Golgi Apparatus
• Vesicles: Clathrin-coated and COP-coated
• Membrane protein modification
• Chaperones
• Endocytosis and Exocytosis
• Lysosomes

Protein Transport Overview

• After being synthesized, proteins must be transported to the compartments where they are needed.
• Proteins are transported to their designated compartments after synthesis.

Protein Structure Review

• Complete functional proteins are long polypeptides in 3D structures, achieved after folding into their tertiary structure.
• Polypeptides are synthesized by connecting amino acids together, from the NH2 group (N-terminus) to the COOH group (C-terminus).
• Proteins are translated from mRNA, which is transcribed from DNA.

Signal Sequence (Signal Peptide)

• The N-terminal (front) section of a polypeptide often determines its destination; this section is the signal sequence or signal peptide.
• The signal peptide sequence tells the cell where to send the protein, acting like a tag.
• The N-terminus often contains a signal sequence (or signal peptide).
• This short section (about 10 amino acids) indicates the protein's destination, guiding the protein translocation process.
• The signal peptide is not part of the functional protein and is cleaved off after the protein has been transported to its destination.

Nuclear Protein Import

• Nucleus proteins are synthesized in the cytosol and then transported into the nucleus through nuclear pores.
• Nuclear pores are complex structures allowing nuclear proteins to enter and mature mRNA to exit, while preventing incompletely spliced messenger RNA from exiting or unwanted substances from entering.

Nuclear Protein Transport Mechanism

• Nuclear proteins have a special signal sequence recognized and bound by a “nuclear transport receptor.”
• The bound complex is transported through the nuclear pore.
• This process requires energy input from GTP hydrolysis.
• After entering the nucleus, the nuclear receptor dissociates and exits back to the cytosol to transport the next protein.
• A receptor is always involved in transport to an organelle.

Protein Transport to Mitochondria

• The signal sequence is recognized and bound by a receptor protein associated with a translocator.
• The protein-translocator complex diffuses to a contact site, where two channels align, allowing the new protein to enter.
• The signal sequence is cleaved off after translocation is complete.

Protein Biosynthesis in the Cytosol and ER

• Cytosolic proteins are translated in the cytosol.
• The same ribosomal components can be used to make ER ribosomes.
• ER proteins are translated on the surface of the ER.

Soluble Protein Transport to ER

• When a soluble protein is synthesized, the signal sequence on the N-terminus is made first.
• The signal sequence is recognized by the signal recognition particle (SRP), which directs the peptide-ribosome complex to the SRP receptor on the ER membrane.
• Then, the SRP releases the peptide-ribosome complex to a translocation channel.
• The newly made peptide enters the ER through the translocation channel and is folded into the correct conformation.
• The signal sequence is cleaved off by signal peptidase.
• After entering, the protein is folded into its correct conformation.

Protein Transport to ER (Membrane-Bound Proteins)

• For membrane-bound proteins with an internal transmembrane domain:
  • The signal sequence is cleaved off by signal peptidase as usual.
  • When the transmembrane domain (a special sequence) goes through the translocation channel, the channel discharges the domain to the membrane, where it remains bound.

Chaperones

• Misfolded proteins (resulting from denaturation) are refolded by chaperones (proteins responsible for repair) before exiting the ER.
• After repair, a vesicle budding process transports the correctly folded protein to its destination.

Golgi Apparatus and Protein Translocation

• After transport to the ER, proteins are transported to the Golgi Apparatus via budding and fusion of vesicles.
• Membrane-bound proteins remain bound in the membrane at this stage.

Vesicle Budding (Clathrin-Coated)

1. Cargoes are bound by cargo receptors (which recognize transport signals), and this complex is then bound by adaptin.
2. Adaptin is then bound by the clathrin coat, forming a vesicle.
3. Dynamin clips the vesicle off.
4. Once completed, the coating is removed, and the naked vesicle is released.

Exocytosis through Secretory Vesicles

• Constitutive secretion releases newly made proteins constantly.
• Regulated secretion waits for a signal to release newly made proteins.

Endocytosis

• Pinocytosis: the ingestion of fluid (including small particles), a way of obtaining food.
• Phagocytosis: the ingestion of large particles/cells, performed by specialized phagocytic cells.
• During phagocytosis, target particles/cells must bind and activate surface receptors, requiring specific recognition.
• Once activated, phagocytes extend sheet-like pseudopods to engulf the target cell/particle.