Chapter 12: The Endomembrane System and Protein Sorting

Chapter 12: The Endomembrane System and Protein Sorting

Introduction

  • Understanding the endomembrane system is crucial for appreciating eukaryotic cells.

  • This system includes intercellular membranes and the compartmentalization of cell functions.

  • Lipid and protein movement between organelles is referred to as trafficking and is tightly regulated.

Components of the Endomembrane System

  • Key Organelles:

    • Endoplasmic Reticulum (ER): Site for protein synthesis, processing, and sorting.

    • Golgi Complex: Processes and sorts lipids and proteins received from the ER.

    • Endosomes: Carry and sort materials brought into the cell.

    • Lysosomes: Digest ingested material and unneeded cellular components.

Structure of the Endoplasmic Reticulum
12.1 The Endoplasmic Reticulum

  • Structure:

    • Continuous network of flattened sacs, tubules, and vesicles throughout eukaryotic cytoplasm.

    • Membranes form structures called ER cisternae (singular: ER cisterna); the enclosed space is known as the ER lumen.

Functions of the ER

  • Main Functions:

    • Biosynthesis of proteins for:

    • Plasma membrane incorporation.

    • Organelles of the endomembrane system.

    • Export outside the cell.

    • Lipid synthesis.

Two Types of Endoplasmic Reticulum

  • Rough Endoplasmic Reticulum (RER):

    • Characterized by ribosomes on the cytosolic side.

    • Transitional Elements (TEs): Role in forming transition vesicles that shuttle proteins and lipids to the Golgi complex.

  • Smooth Endoplasmic Reticulum (SER):

    • Lacks ribosomes; involved in processing and storage of non-protein molecules.

Distinguishing RER and SER

  • Rough ER:

    • Large, flattened sheets.

  • Smooth ER:

    • Tubular structures; transitional elements resemble the smooth ER but connect RER and Golgi.

  • Continuity: Lumenal spaces of RER and SER are continuous.

Variations in ER

  • Presence of RER or SER varies in eukaryotic cells:

    • Cells synthesizing secretory proteins have prominent RER.

    • Cells producing steroid hormones feature extensive SER networks.

Proteins in the Rough ER
12.2 Rough ER and Protein Biosynthesis

  • Biosynthesis Function:

    • Ribosomes synthesize membrane-bound and soluble proteins for the endomembrane system.

  • Cotranslational Insertion:

    • Newly made proteins inserted into the ER during synthesis through a pore complex.

Additional Functions of Rough ER

  • Initial steps of glycoprotein carbohydrate addition.

  • Protein folding and assembly of multimeric proteins.

  • Removal and degradation of misfolded proteins (quality control).

Role of Quality Control in Rough ER

  • Misfolded, incorrectly assembled proteins are sent out for degradation in cytosolic proteasomes.

Smooth ER Functions
12.3 Smooth ER Functions

  • Primarily processes/stores non-protein molecules.

  • Main Functions include:

    • Drug Detoxification:

    • Hydroxylation increases solubility for easier excretion, catalyzed by cytochrome P-450 family (monooxygenases).

    • Carbohydrate Metabolism:

    • Smooth ER in liver cells with glucose-6-phosphatase breaks down glycogen.

    • Calcium Storage:

    • Specialized sarcoplasmic reticulum in muscle cells stores calcium by pumping CA2+ ions into ER.

    • Steroid Biosynthesis:

    • Smooth ER in some cells synthesizes cholesterol and steroid hormones.

Drug Detoxification Mechanism

  • The smooth ER detoxifies drugs by adding hydroxyl groups (-\text{OH}) to them, making them more polar and soluble in water. This process, called hydroxylation, is catalyzed by enzymes of the cytochrome P-450 family (monooxygenases).

  • Hydroxylation reaction:

    • R H + N A D(P)H + O2 \longrightarrow R O H + H2 O + N A D(P)^+

    • In this reaction, RH represents a drug molecule, and it is converted to ROH (a hydroxylated drug) using oxygen (O_2) and a reducing agent (NAD(P)H). This increases its solubility, allowing for easier excretion from the body.

  • Repeated exposure to certain drugs leads to an increase in smooth ER membrane and its associated detoxifying enzymes (ER proliferation). This enhanced detoxification capacity means higher drug doses are required to achieve the same effect, leading to drug tolerance.

Calcium and Muscle Contraction

  • Calcium ions stored in the ER are crucial for muscle contractions.

  • Calcium-binding proteins are abundant in the ER lumen.

Lipids and Membrane Biosynthesis
Membrane Formation

  • ER is the source of membrane lipids, excluding some cases like chloroplasts and peroxisomes.

  • Membrane phospholipids synthesized from fatty acids in the cytoplasm and transferred to the ER membrane.

12.4 Lipid Transfer and Asymmetry

  • Phospholipid translocators (flippases) assist in translocating phospholipids, establishing membrane asymmetry.

  • Phospholipid exchange proteins facilitate transfer between ER and other organelles.

Golgi Apparatus Structure and Function
12.5 Golgi Apparatus Overview

  • Functionally linked to the ER, processing glycoproteins and lipids.

  • Comprised of a series of membrane-bounded cisternae organized in stacks.

  • Transport Vesicles:

    • Numerous vesicles surround Golgi to carry materials from the ER and to other cell destinations.

Golgi Structure Details

  • Each Golgi stack consists of distinct compartments:

    • Cis Face: Faces ER (cis-Golgi network).

    • Trans Face: Faces plasma membrane (trans-Golgi network).

    • Medial cisternae are involved in protein processing.

Golgi Protein and Lipid Movement

  • Two models forecasting lipid and protein flow are the stationary cisternae model and cisternal maturation model.

Transport Mechanisms

  • Anterograde transport moves materials toward the plasma membrane.

  • Retrograde transport returns vesicles to the ER.

Protein Processing in ER and Golgi
12.6 Protein Processing Overview

  • Includes:

    • Protein folding, quality control, and glycosylation.

Glycosylation Process

  • N-Linked Glycosylation involves adding oligosaccharides to asparagine residues.

  • O-Linked Glycosylation involves adding oligosaccharides to serine, threonine, or tyrosine residues.

Protein Folding and Chaperones

  • Molecular chaperones assist in protein folding.

  • B i P (an Hsp70 chaperone) binds polypeptides to prevent aggregation.

Quality Control Systems

  • Unfolded Protein Response (UPR): Detects misfolded proteins using sensor molecules.

  • ER-Associated Degradation (ERAD): Exports misfolded proteins for cytosolic degradation.

Protein Trafficking and Sorting
12.7 Protein Trafficking Overview

  • Proteins synthesized in rough ER must reach various destinations.

  • Each protein has specific tags targeting them to transport vesicles.

Protein Transport Pathways

  1. Cytosolic Destination Pathway:

    • Synthesized by free ribosomes and released upon completion.

    • Posttranslational import occurs when specific signals guide proteins to organelles.

  2. Endomembrane/Export Pathway:

    • Ribosomes attach to ER, allowing cotranslational import as proteins are synthesized.

Intracellular Sorting Involves Multiple Steps

  • Anterograde trafficking moves proteins through the cytoplasm toward the Golgi and plasma membrane.

  • Retrograde trafficking returns specific proteins to earlier compartments for recycling.

Exocytosis and Endocytosis
12.8 Material Transport Across Plasma Membrane

  • Exocytosis: Release of contents from secretory vesicles outside the cell.

  • Endocytosis: Internalization of materials from the extracellular environment.

Exocytosis Mechanism

  1. Vesicle movement to the cell surface.

  2. Membrane fusion with the plasma membrane.

  3. Contents discharge and become part of the plasma membrane.

Endocytosis Mechanism

  • Involves membrane folding inward to form a vesicle containing ingested substances.

  • Results in early endosomes evolving into late endosomes and lysosomes.

Phagocytosis

  • Engulfing of large particles or microorganisms is essential for defense in some immune cells.

Receptor-Mediated Endocytosis

  • Cells acquire specific substances by binding ligands to receptors on their surface.

  • Process involves recruitment of proteins like clathrin and dynamin for vesicle formation.

Clathrin-Coated Vesicles

  • Coat proteins such as clathrin and adaptor proteins facilitate vesicle formation and sorting.

Significance of Lysosomes in Cellular Digestion
12.9 Lysosomal Functions

  • Store digestive enzymes and are essential for intracellular digestion, processing both external and internal materials.

  • Autophagic lysosomes recycle cellular components.

  • Heterophagic lysosomes digest external materials inserted through endocytosis.

Lysosomal Development

  • Derived from endosomes, lysosomes ensure safe enzymatic degradation occurs within an isolated acidic environment.

Implications of Lysosomal Dysfunction

  • Absence of lysosomal enzymes leads to accumulation diseases, indicating potential treatment avenues such as enzyme replacement therapy and gene therapy.

Peroxisomes
12.10 Functions of Peroxisomes in Metabolism

  • Integral for metabolizing hydrogen peroxide and other reactive species while assisting in fatty acid oxidation and nitrogen compound processing.

Peroxisomal Structure

  • Bounded by single membranes, possess compartmentalized enzymes crucial for specific metabolic reactions.

Biogenesis of Peroxisomes

  • New peroxisomes arise from existing ones or from vesicles supplied by the ER.

Disorders Related to Peroxisomes

  • Certain genetic defects lead to impaired peroxisomal functions, causing a range of diseases related to metabolic dysfunction.

Conclusion

  • The endomembrane system, including the ER, Golgi apparatus, lysosomes, and peroxisomes, plays a critical role