Cell Biology: Intracellular Organization and Protein Sorting

Intracellular Organization and Protein Sorting

• Eukaryotic cells have distinct intracellular compartments, including the nucleus, cytoplasm, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, mitochondria, and peroxisomes.
• The nucleus contains the genome, while the cytoplasm consists of cytosol and cytoplasmic organelles suspended in it.
• The cytosol makes up over half the cell's volume and is the main site of protein synthesis and degradation.

Protein Traffic and Sorting

• Proteins can move between compartments in different ways, depending on their amino acid sequence and sorting signals.
• Proteins without sorting signals remain in the cytosol as permanent residents.
• There are four fundamentally different ways a protein is moved from one compartment to another:
  • Protein translocation: transmembrane protein translocators transport specific proteins from the cytosol into a topologically distinct space.
  • Gated transport: proteins and RNA molecules move between the cytosol and the nucleus through nuclear pore complexes.
  • Vesicular transport: membrane-enclosed transport intermediates ferry proteins from one compartment to another.
  • Engulfment: double membrane sheets wrap around portions of the cytoplasm, including fragments of organelles, to enclose a separate compartment.

Endoplasmic Reticulum (ER)

• The ER has a central role in the biosynthesis of lipids and proteins, and stores intracellular Ca2+ that is mobilized in many cell signaling responses.
• The ER membrane is the site of production of many transmembrane proteins and lipids of the cell's organelles.
• Almost all proteins that will be secreted to the cell exterior or destined for the lumen of the ER, Golgi apparatus, or lysosomes are initially delivered to the ER lumen.
• The ER is structurally and functionally diverse, with functional specialization leading to dramatic changes in the proportional abundance of different parts of the ER.

ER Specialization

• Rough ER has a characteristic rough appearance due to the abundance of ribosomes bound to its surface, and is dedicated to the biosynthesis of proteins.
• Smooth ER lacks ribosomes and is dedicated to other ER functions such as the biosynthesis and metabolism of lipids.
• Transitional ER is a type of smooth ER found in all cells, from which transport vesicles carrying newly synthesized proteins and lipids bud off for transport to the Golgi apparatus.
• ER can be specialized in regions that make intimate contacts with other organelles, such as mitochondria, plastids, endosomes, and the plasma membrane.

Signal Sequences and Protein Sorting

• Signal sequences are discovered in secreted water-soluble proteins that are first translocated across the ER membrane.
• The signal hypothesis proposes that the mRNA for the secretory protein codes for a protein that is bigger than the protein that is eventually secreted.
• The extra polypeptide is a signal sequence that directs the secreted protein to the ER membrane, where it is cleaved off by a signal peptidase before the polypeptide chain has been completed.

Signal-Recognition Particle (SRP) and ER Signal Sequence

• The ER signal sequence is guided to the ER membrane by the signal-recognition particle (SRP), which binds to the signal sequence, and an SRP receptor in the ER membrane.
• SRP is a large complex that consists of six different polypeptide chains bound to a single RNA molecule.
• SRP wraps along the large ribosomal subunit, positioning the signal sequence–binding pocket near the ribosomal tunnel through which newly made polypeptides emerge.
• SRP engages a signal sequence as it emerges from the ribosome, slowing down translation and allowing the ribosome to bind to the ER membrane before completion of the polypeptide chain.
• SRP exposes a binding site for an SRP receptor, bringing the SRP–ribosome complex to an unoccupied protein translocator in the ER membrane.