Intracellular Compartments and Protein Transport Study Notes

CHAPTER 15: Intracellular Compartments and Protein Transport

How Do Cells Control the Chaos?

• Cells maintain organization through compartmentalization, using membrane-enclosed organelles to separate various biochemical processes.

Eukaryotic Cells: Basic Membrane-Enclosed Organelles

• Overview of Eukaryotic Cells:

  • Contain a basic set of membrane-enclosed organelles that compartmentalize cellular functions to manage metabolic chaos effectively.

• Major Organelles:

  • Nucleus: Stores genetic information

  • Mitochondrion: Site of ATP production and energy metabolism

  • Endoplasmic Reticulum (ER): Synthesis of proteins and lipids

  • Golgi apparatus: Modifies and packages proteins and lipids

  • Lysosome: Degradation of cellular waste

  • Peroxisome: Breakdown of fatty acids and detoxification of harmful hydrogen peroxide

  • Endosome: Involved in sorting endocytosed material

  • Cytosol: Site of many metabolic pathways and protein synthesis

Table 15–1: Main Functions of Membrane-Enclosed Organelles

• Compartment | Main Function

  • Cytosol: Contains metabolic pathways, protein synthesis, and cytoskeleton formation.

  • Nucleus: Houses the genome and is involved in DNA/RNA synthesis.

  • Endoplasmic Reticulum (ER): Synthesizes most lipids and proteins for distribution.

  • Golgi Apparatus: Modifies, sorts, and packages proteins for secretion or delivery.

  • Lysosomes: Responsible for intracellular degradation.

  • Endosomes: Sorts endocytosed materials.

  • Mitochondria: ATP synthesis via oxidative phosphorylation.

  • Chloroplasts (plant cells only): ATP synthesis and carbon fixation via photosynthesis.

  • Peroxisomes: Oxidative breakdown of toxic molecules.

Table 15–2: Relative Volumes and Numbers of Major Membrane-Enclosed Organelles in a Liver Cell (Hepatocyte)

• Intracellular Compartment | Percentage of Total Cell Volume | Approximate Number per Cell

  • Cytosol: 54% | 1

  • Mitochondria: 22% | 1700

  • Endoplasmic Reticulum: 12% | 1

  • Nucleus: 6% | 1

  • Golgi Apparatus: 3% | 1

  • Peroxisomes: 1% | 400

  • Lysosomes: 1% | 300

  • Endosomes: 1% | 200

Evolution of Membrane-Enclosed Organelles

• Membrane-enclosed organelles are thought to have originated as cells evolved to larger sizes.

  • Key Processes:

  • Ancestral archaeon engulfs aerobic bacterium, leading to the formation of eukaryotic cells.

  • Endosymbiotic theory suggesting engulfed bacteria evolved into mitochondria.

  • Internal membranes surrounded archaeal DNA and evolved into more complex organelles.

Protein Sorting Mechanisms

• Proteins are imported into membrane-enclosed organelles via three main mechanisms:

  1. Transport through Nuclear Pores: Proteins enter the nucleus through large complexes in the nuclear envelope.

  2. Transport Across Membranes: Involves translocation through organelle membranes (e.g. mitochondria, ER).

  3. Transport by Vesicles: Involves vesicles that bud from one membrane and fuse with another.

Signal Sequences

• Short amino acid sequences (15-60 amino acids) direct proteins to their targets.

  • Often removed post-delivery, but can be manipulated for experimental localization studies.

Proteins Entering the Nucleus

• Proteins destined for the nucleus enter via nuclear pores comprised of nuclear pore complexes that regulate passage based on size and properties of the molecule.

Nuclear Pore Complex Structure

• Composed of approximately 30-400 different proteins forming a gate-like structure.

  • Disordered segments within the pores act as selective barriers, allowing small molecules to pass freely while blocking larger entities.

Nuclear Import Process

1. Recognition: Nuclear import receptors interact with nuclear localization signals (NLS) on prospective nuclear proteins.

2. Transport: Receptors guide proteins to the nuclear pore, where they engage with the nucleoporin proteins to facilitate entry into the nucleus.

3. Release: Upon entering the nucleus, the import receptor releases the nuclear protein and is recycled back to the cytosol through the nuclear pore.

GTP Hydrolysis Energy Requirement

• The process of nuclear transport relies on the energy from GTP hydrolysis via the action of RAN protein.

  • RAN exists in two forms:

  • RAN-GTP: High concentration in the nucleus.

  • RAN-GDP: High concentration in cytosol.

  • RAN-GAP and RAN-GEF are crucial for maintaining the balance between these forms to facilitate import and export processes.

Mitochondrial Protein Import

• Mitochondrial proteins are imported in an unfolded state via specific signaling sequences recognized by receptors on the outer membrane, followed by lateral diffusion to the inner membrane for translocation into the matrix, where the signal peptide is cleaved. Chaperones and ATP play essential roles in assisting this process.

Endoplasmic Reticulum (ER) Dynamics

• The ER is a highly dynamic membrane network that serves as a site for protein synthesis and initial folding processes.

• Proteins enter the ER while still co-translationally synthesized by ribosomes.

  • Types of Proteins:

  • Water-soluble proteins: Fully translocated across the membrane.

  • Transmembrane proteins: Partially translocated and embedded into the membrane.

Mechanism of Protein Entry into the ER

1. Signal Recognition Particle (SRP): Binds to the ER signal sequence as translation occurs, slowing protein synthesis.

2. SRP Complex: This complex then directs the ribosome to the ER membrane.

3. Translocation: Protein synthesis resumes as the peptide is transferred across the membrane via a translocator, which opens in response to the ER signal.

4. Signal Peptide Cleavage: Signal peptides are cleaved by signal peptidases after successful translocation.

Transmembrane Protein Import

• Single-pass and multi-pass transmembrane proteins employ start and stop transfer sequences for integration into the membrane.

Vesicular Transport Between Organelles

• Intracellular transport of proteins and lipids occurs through vesicles that bud and fuse with various organelles.

• The endomembrane system consists of the ER, Golgi apparatus, lysosomes, endosomes, and peroxisomes, facilitating the movement of proteins and lipids within the cell.

Vesicle Budding and Docking Mechanisms

• Coat Proteins: Such as clathrin, COPII, and COPI facilitate vesicle budding with cargo selection facilitated by adaptors.

• Docking Mechanisms: Rabs, tethers, and SNARE proteins play critical roles in ensuring accurate vesicle targeting and fusion with the appropriate membrane.

Protein Modification in the ER

• Many proteins undergo glycosylation in the ER, aiding in proper folding, protection from degradation, and signaling for transport to downstream organelles.

Understanding the Secretory Pathway

• Vesicles exiting the ER travel to the Golgi apparatus, where they are modified and sorted before being dispatched to their final destinations.

• Distinction between constitutive (ongoing and unregulated) and regulated (specialized secretion) pathways is essential in the secretory process.

Lysosomal Function

• Lysosomes degrade various cellular components through acid hydrolases, forming from the fusion of late endosomes with pre-existing lysosomes to manage cellular waste.

Studying the Secretory Pathway

• Various experimental methods, including temperature-sensitive mutant yeast and GFP tagging, allow scientists to visualize transport pathways and protein localization.

Endocytosis Processes

• Phagocytosis: Ingestion of large particles (cell eating) facilitated by specialized cells like macrophages.

• Pinocytosis: Ingestion of small vesicles (cell drinking) practiced by almost all cell types.

• Receptor-Mediated Endocytosis: A specialized process for importing extracellular molecules, exemplified by the uptake of LDL.

Application of Endocytosis in Virus Entry

• Certain viruses exploit receptor-mediated endocytosis mechanisms to enter host cells, illustrating the importance of these cellular pathways in both health and disease.