Cell Biology Chapter 12

Intracellular Organization and Protein Sorting

• Eukaryotic cells have various intracellular compartments, including the nucleus, cytoplasm, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, mitochondria, chloroplasts, and peroxisomes.
• The nucleus contains the genome, while the cytosol constitutes more than half of the cell's volume and is the main site of protein synthesis and degradation.
• The ER performs most of the cell's intermediary metabolism, and its membrane encloses a labyrinthine space.

Protein Sorting

• Nearly all proteins, except those inside mitochondria and plastids, begin their synthesis on ribosomes in the cytosol.
• The final location of each protein depends on its amino acid sequence, which can contain one or more sorting signals that direct its delivery to different parts of the cell.
• Proteins that do not have any sorting signals remain in the cytosol as permanent residents.

Protein Trafficking

• There are four fundamentally different ways a protein is moved from one compartment to another:
  • Protein translocation: direct transport of specific proteins from the cytosol into a topologically distinct space.
  • Gated transport: movement of proteins and RNA molecules between the cytosol and the nucleus through nuclear pore complexes.
  • Vesicular transport: ferrying proteins from one compartment to another through membrane-enclosed transport intermediates.
  • Engulfment: wrapping of double membrane sheets around portions of the cytoplasm to form an autophagosome.

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, including the ER itself, Golgi apparatus, lysosomes, endosomes, secretory vesicles, peroxisomes, and the plasma membrane.
• The ER is structurally and functionally diverse, with different types of ER membrane in different types of cells, including rough ER and smooth ER.

Rough ER

• The rough ER is characterized by the abundance of ribosomes bound to its surface, and is involved in the synthesis of secreted proteins.
• Cells specialized to secrete vast amounts of protein are packed with an abundance of rough ER.

Smooth ER

• The smooth ER lacks ribosomes and is dedicated to other ER functions, such as lipid biosynthesis and metabolism.
• A type of smooth ER found in all cells is called transitional ER, from which transport vesicles carrying newly synthesized proteins and lipids bud off for transport to the Golgi apparatus.

ER Function

• The ER can sequester Ca2+ from the cytosol, and its release into the cytosol from the ER, and its subsequent reuptake, occur in many rapid responses to extracellular signals.
• The ER can be specialized in regions that make intimate contacts with other organelles, such as mitochondria, plastids, endosomes, and the plasma membrane.
• These organelle contact sites are enriched for proteins involved in the communication or transport of key metabolites between the juxtaposed membranes.

Signal Sequences

• 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, and is cleaved off by a signal peptidase in the ER membrane before the polypeptide chain has been completed.

Signal-Recognition Particle (SRP)

• The ER signal sequence is guided to the ER membrane by at least two components: a signal-recognition particle (SRP) and an SRP receptor in the ER membrane.
• SRP binds to the signal sequence, and the SRP receptor directs the signal sequence to the ER membrane.

Post-Translational Translocation

• Post-translational translocation: proteins are completely synthesized in the cytosol as precursors before they are imported into the ER.
• Precursor proteins do not fold after their initial synthesis in the cytosol, and interact with other cytosolic proteins that prevent precursor folding or aggregation before they engage the Sec61 translocator.

Co-Translational Translocation

• The signal peptide of a precursor directly engages the Sec61 translocator to open the channel.
• Accessory proteins called Sec62 and Sec63 associate with the Sec61 translocator and position an hsp70-like chaperone protein (BiP) adjacent to the lumenal opening of the translocation channel.
• BiP binds tightly to an imported protein chain as it emerges from the Sec61 translocator in the ER lumen, preventing the protein chain from sliding backwards, and favoring more of the chain to emerge into the lumen where it can bind another molecule of BiP.