AE

Functional Organization of the Cell

Phospholipid Bilayers and Membrane Biochemistry

  • Major topics cover phospholipid bilayers, membrane biochemistry, membrane proteins (structure, synthesis, trafficking), organelle membranes (nucleus, mitochondria, lysosomes), cytoskeleton organization, ER/Golgi roles in synthesis and trafficking, exocytosis/endocytosis mechanisms, and polarized epithelial tissue organization.
  • Goal: understand how membrane structure sustains cellular homeostasis and enables selective transport, signaling, and organization within cells.

Structure of Individual Phospholipids and membranes as phospholipid bilayers

  • Phospholipids are amphipathic molecules with a hydrophilic head and hydrophobic tails that drive bilayer formation in aqueous environments.
  • Common phospholipid exemplified: Phosphatidylethanolamine (PE) with ethanolamine headgroup.
  • General bilayer formation:
    • Polar head groups orient toward water (hydrophilic surface).
    • Hydrophobic tails orient away from water, forming a hydrophobic core.
  • Monolayer concept: when a single leaflet is exposed to water, head groups face water while tails face inward.
  • Bilayer concept: two leaflets align with hydrophilic heads outward and hydrophobic tails inward, forming a stable barrier.

Major types of lipids in membranes

  • Phospholipids, sphingolipids, cholesterol are major membrane components.
  • Headgroup charge affects electrostatic surface charge of membranes (important for interactions with ions, proteins, and other molecules).
  • Composition contributes to membrane fluidity, thickness, curvature, and microdomain (lipid raft) formation.

Mobility and asymmetry of phospholipids

  • Phospholipids and cholesterol diffuse laterally within each leaflet.
  • The plasma membrane is asymmetric: different lipids populate the outer vs inner leaflets.
    • Example: Phosphatidylcholine (PC) is enriched in the outer (extracellular) leaflet.
    • Phosphatidylserine (PS) is enriched in the inner (cytosolic) leaflet.
  • Asymmetry is crucial for signaling (e.g., PS exposure in apoptosis) and protein targeting.

Structure, Function, and Synthesis of Membrane Proteins

  • Membrane proteins are categorized by location: peripheral (extrinsic) vs integral (intrinsic) membrane proteins.
  • Integral membrane proteins include four major structural subtypes (not all enumerated here) and span the membrane.
  • Five major functions of membrane proteins:
    • Receptors
    • Adhesion proteins (two types)
    • Transport proteins
    • Enzymes
  • Synthesis of membrane proteins occurs in the endoplasmic reticulum (ER).
  • Maturation and trafficking of membrane proteins occur in the Golgi apparatus.

Peripheral versus Integral Membrane Proteins

  • Peripheral proteins are noncovalently associated with integral membrane proteins and are located on either side of the membrane (extracellular space or cytosol).
  • Integral proteins typically have membrane-spanning domains; many are alpha-helical (about ~20 amino acids per span) and some have multiple transmembrane segments.
  • Some proteins are anchored to membranes via covalent attachments:
    • Linked to membrane phospholipids via an oligosaccharide (glycophosphatidylinositol, GPI) anchor
    • Linked directly to fatty acids or prenyl groups
  • Transmembrane-spanning domains are usually alpha-helices; beta-sheets can appear in some proteins (beta-barrel proteins).

Two Functions of Plasma Membrane Proteins: Receptors and Adhesion Molecules

  • Receptors detect extracellular signals and initiate intracellular responses.
  • Adhesion proteins support cell–cell and cell–matrix interactions; two subtypes:
    • Bind to extracellular matrix (ECM)
    • Bind to adjacent cells (cell–cell adhesion via adhesion proteins)

Another major function: Transport of ions, metabolites, and cellular wastes

  • Three subtypes of transport proteins:
    • Channels: provide aqueous pores for passive diffusion driven by gradients
    • Carriers: undergo conformational changes to transport specific substrates (facilitated diffusion or secondary active transport)
    • ATP-driven ion pumps: use energy from ATP to move ions against gradients

Interaction with the submembrane cytoskeleton

  • Membrane proteins interact with the underlying cytoskeleton to regulate mobility, localization, and stability of proteins within the membrane.

Organization and Special Functions of Membranes in Nucleus, Mitochondria, and Lysosomes

  • Nucleus and mitochondria have double membrane bilayers.
  • Nuclear pores enable bidirectional transport between the nucleus and cytosol; essential for RNA export and protein import.
  • Mitochondria generate and maintain a large proton gradient (inside is more basic) essential for ATP synthesis via oxidative phosphorylation.
  • Lysosomes maintain an acidic interior via a proton gradient to degrade proteins and other macromolecules.

Organization of the Membranes that Comprise the Nucleus vs Mitochondria

  • Animal cell components: smooth ER, rough ER, Golgi, lysosomes, endosomes, peroxisomes, transport vesicles; cytosolic vs organelle locations.
  • Nucleus: outer nuclear membrane, inner nuclear membrane, nuclear pore complexes, nucleolus, chromatin, nuclear lamina.
  • Mitochondrion: outer membrane, inner membrane, intermembrane space, matrix space; ribosomes may associate with outer surface; transporter subunits.
  • Central protein complexes include transporters, scaffolds, and ring subunits for nuclear pores and other channels.

Subunits and Components of the Cytoskeleton

  • Intermediate filaments: diameter 8{-}10 ext{ nm}; tetramer of two coiled dimers.
  • Microtubules: diameter 25 ext{ nm}; composed of heterodimers of b1-tubulin and b2-tubulin forming long protofilaments (each protofilament ~5 nm in diameter along the filament axis).
  • Thin (actin) filaments: diameter 5{-}8 ext{ nm}; globular actin (G-actin) polymerizes to form fibrous actin (F-actin) in a double helix.
  • Thick filaments: diameter 10 ext{ nm}; assemblies of myosin molecules.
  • Overall, these components constitute the cytoskeleton that provides structure, tracks for motor proteins, and mechanical properties to cells.

Structure and Function of Microtubules

  • Tubulin (alpha and beta) forms dimers that assemble into protofilaments, which stack to form the hollow microtubule cylinder (~25 nm diameter).
  • Major motor proteins: kinesin and dynein, which move along microtubules to transport cargo, generate forces, and contribute to organelle positioning and intracellular transport.

Synthesis of Actin-based Thin Filaments

  • G-actin bound to ATP polymerizes to form F-actin under appropriate conditions.
  • Activation and assembly proceed from G-actin dimers to nuclei, then to stable actin oligomers and finally mature F-actin filaments.
  • Treadmilling describes addition of actin monomers at the barbed (+) end and disassembly at the pointed (−) end, enabling dynamic remodeling of the cytoskeleton.
  • ATP-bound G-actin incorporation drives polymerization; hydrolysis to ADP-actin regulates filament stability and turnover.

Structure of Myosin-based Thick Filaments and Myosin as a Molecular Motor

  • Thick filaments comprise assemblies of myosin molecules.
  • Myosin interacts with actin filaments to generate contractile force in muscle and produce movements in non-muscle cells.
  • Cyclic interactions between actin and myosin drive contraction and movement in various cell types.

Actin-Myosin Interaction in Non-Muscle Motility (e.g., microvilli movement in intestinal brush border)

  • Example of actin–myosin driven motility: movement of microvilli in the brush border of intestinal epithelial cells.
  • Structural components involved:
    • Dense plaque material at the terminal web
    • Actin filaments in microvilli connected by crosslinkers (e.g., fimbrin, villin)
    • Myosin I motors link to the terminal web (via fodrin/spectrin) and regulate movement and stability
  • This system illustrates how cytoskeletal networks drive dynamic changes in specialized cellular surfaces.

Synthesis, Processing, and Trafficking of Membrane and Secreted Proteins in the Rough Endoplasmic Reticulum (ER)

  • Key components:
    • Interaction of ribosomes and ER membranes
    • Signal sequences on nascent polypeptides
    • Signal recognition particle (SRP) and SRP receptor
    • Translocon complex through which nascent chains pass into/through the ER membrane
    • Stop-transfer sequences which halt translocation of certain segments
  • Functions in the ER:
    • Co-translational insertion of membrane proteins
    • Initial post-translational modifications and protein folding
    • Quality control and quality assurance for proper folding
  • Exit from the ER to the Golgi: packaged into vesicles for trafficking

Interaction of Ribosomes and the Endoplasmic Reticulum Membrane

  • Ribosomes engage with ER membranes to initiate synthesis of secreted and membrane-embedded proteins.
  • Recognition and targeting of nascent polypeptides rely on signal sequences and SRP/SRP receptor interactions.

Synthesis of Integral Membrane Proteins with Membrane-Spanning Alpha Helices

  • A single membrane-spanning segment with a cytosolic C-terminus involves:
    • Signal sequence guiding insertion into ER
    • Translocon channel to move nascent chain into the lumen
    • Stop-transfer sequence that terminates translocation
  • Importance: precise topology ensures correct orientation of functional domains relative to cytosol and ER lumen.

Processing Enzymes in the ER and Glycosylation/GPI Anchors

  • The ER contains processing enzymes that modify and ensure proper folding of nascent proteins.
  • Some membrane proteins acquire glycosylation sites; others receive GPI anchors for membrane tethering.
  • These modifications influence protein stability, trafficking, and interactions.

Trafficking of Membrane and Secreted Proteins to the Plasma Membrane

  • Step 1: ER-to-Golgi transport via membrane carrier vesicles.
  • Step 2: Golgi processing and post-translational modifications (glycosylation, sorting signals).
  • Step 3: Golgi-to-plasma membrane transport via carrier vesicles.
  • Step 4a: Constitutive exocytosis/secretion (continuous, unregulated release).
  • Step 4b: Regulated exocytosis/secretion (secretory vesicles release contents in response to signals).

Constitutive vs Regulated Secretion and Exocytosis

  • Constitutive secretory pathway: continuous, unregulated shipment of newly synthesized proteins to the plasma membrane or extracellular space.
  • Regulated secretory pathway: secretory proteins stored in secretory (secretory) vesicles and released in response to hormonal or neuronal signals.
  • Visualized via a rough ER, transitional zone (cis), Golgi apparatus, and medial/trans regions culminating in regulated vesicle fusion.

Molecular Mechanisms for Formation of Secretory Vesicles and Fusion

  • Critical roles for:
    • Clathrin (coat protein for vesicle formation)
    • SNARE proteins (drive membrane fusion specificity)
    • SNAP proteins (assist SNARE function)
    • Rab-family GTPases (regulate vesicle targeting and docking)

Post-translational Glycosylation of Membrane and Secreted Proteins

  • Remodeling of N-linked sugars as proteins traverse the Golgi network (cis to trans):
    • cis-Golgi network
    • Medial Golgi
    • Trans-Golgi network
  • Glycosylation types include:
    • Proteoglycans and glycosaminoglycans (GAGs)
    • N-linked glycosylation remodeling
    • O-linked glycosylation
  • GPI anchors attach certain proteins to the plasma membrane; sugars involved include N-acetylglucosamine, mannose, galactose, glucose, xylosylation, sialic acid.
  • Transport through Golgi involves cis, medial, and trans cisternae with processing enzymes localizing to respective compartments.
  • Secretory granules carry processed proteins toward the plasma membrane or lysosome/

Trafficking of Membranes to Other Organelles

  • Step 1: ER-to-Golgi transport via vesicles.
  • Step 2: Golgi modifications and sorting.
  • Step 3: Golgi-to-destination organelle via vesicles with organelle-specific SNAREs/SNAPs/Rabs and receptor ligands.
  • Step 4: Immediate fusion with the target organelle’s membrane; specialized recognition ensures delivery to the right organelle.
  • This trafficking parallels the ER-to-Golgi-to-PM route but uses organelle-specific trafficking machinery.

Lysosome Targeting: Mannose-6-Phosphate (M6P) Pathway

  • M6P modification on hydrolases and other lysosomal proteins targets them to lysosomes via M6P receptors.
  • M6P receptors recognize M6P tags and guide cargo to lysosomes, ensuring proper degradation capacity within lysosomal compartments.
  • Example: targeted trafficking of membrane vesicles and specific proteins to lysosomes relies on M6P sorting signals.

Endocytosis: Fluid-Phase vs Receptor-Mediated

  • Fluid-phase endocytosis (bulk-phase): nonspecific uptake of extracellular fluid and solutes.
  • Receptor-mediated endocytosis: specific uptake of ligands bound to receptors, often via clathrin-coated pits.
  • Common players in endocytosis include clathrin and Rab GTPases, analogous to exocytosis machinery but oriented toward inward trafficking.

The Special Structural Requirements of Epithelial Tissues

  • Epithelial cells form barriers and specialized transepithelial transport systems.
  • Two distinct plasma membrane domains per cell: apical membrane (facing lumen/external environment) and basolateral membrane (facing extracellular fluid/blood).
  • Polarized trafficking ensures correct delivery of membrane and secreted proteins to the apical vs basolateral surfaces.
  • Barrier function is maintained by specialized intercellular junctions: tight junctions, adhering junctions, and gap junctions.

Epithelial Cell Junctional Complexes

  • Tight junctions (claudins) create a seal to prevent paracellular diffusion and help establish polarity.
  • Adhering junctions (cadherins) provide strong cell–cell adhesion and link to the actin cytoskeleton via plaques.
  • Gap junctions (connexons) enable direct cytoplasmic communication between adjacent cells.
  • Structural arrangement often includes groove–ridge geometry, basal microvilli, and a basement membrane supporting polarity and transport.

Connections to Foundational Principles and Real-World Relevance

  • Membrane asymmetry and selective permeability underlie cellular homeostasis, signaling, and nutrient uptake.
  • Trafficking and organelle identity are critical for properly localized enzymes, receptors, and transporters, impacting metabolism and physiology.
  • Cytoskeletal networks not only provide structure but also serve as tracks for motor proteins, enabling vesicle trafficking, organelle positioning, and cell motility.
  • Epithelial polarity is essential for organ function (e.g., intestine, kidney) and for maintaining barriers against pathogens and toxins.
  • Dysregulation of membrane trafficking, glycosylation, or junctional complexes can contribute to disease processes (e.g., lysosomal storage disorders, cystic fibrosis, inflammatory diseases).

Key Terms and Concepts to Remember

  • Phospholipid bilayer; amphipathic lipids; membrane asymmetry (outer leaflet vs inner leaflet).
  • Integral vs peripheral membrane proteins; transmembrane domains; signal sequences; SRP pathway; translocon; stop-transfer sequences; GPI anchors.
  • Membrane protein functions: receptors, adhesion proteins, transporters, enzymes.
  • Cytoskeletal components: intermediate filaments, microtubules, actin filaments, myosin thick filaments; diameters: 8{-}10 ext{ nm}, 25 ext{ nm}, 5{-}8 ext{ nm}, 10 ext{ nm} respectively.
  • Microtubule motors: kinesin and dynein.
  • Actin dynamics: G-actin; F-actin; treadmilling; ATP-bound vs ADP-actin states.
  • Vesicle trafficking: ER-to-Golgi; Golgi processing; vesicle-mediated export; constitutive vs regulated secretion.
  • Secretory vesicle formation and fusion: clathrin, SNAREs, SNAPs, Rab GTPases.
  • Glycosylation and GPI anchors; N-linked and O-linked glycosylation; N-linked remodeling in Golgi; M6P tagging for lysosome targeting.
  • Endocytosis: fluid-phase vs receptor-mediated; clathrin and Rab GTPases involvement.
  • Epithelial polarity and junctions: tight (claudins), adherens (cadherins), gap (connexins).