🧪 Lysosomes + Vacuoles + Cytoskeleton

Vesicle Targeting Pathways

• Trans-Golgi → Endosomes

• Trans-Golgi → Lysosomes

• Plasma Membrane (PM) → Endosomes

Clathrin and Adaptor Proteins (AP)

• AP/Clathrin-coated vesicles move from TGN to other vesicles (e.g. lysosomes, endosomes, plant vacuoles)

• AP/Clathrin-coated vesicles also help form endocytic vesicles to transport vesicles from plasma membrane to endosomes or lysosomes

• Summary: Depending on what the vesicles are coated with, they are sent to different areas

Clathrin AP (Adaptor Proteins) vs. COPs (Coat Protein Complexes)

• Clathrin is a protein involved in forming vesicles, especially during endocytosis (from plasma membrane to endosomes or lysosomes)

  • It coats vesicles/endosomes to ensure proper trafficking and sorting of cargo

• COP (COPI and COPII) proteins are involved in vesicle formation and cargo selection within Golgi apparatus and endoplasmic reticulum (ER)

• Both coat proteins to help direct them to different areas

  • Clathrin coats are geometric, and usually for endosomes

  • COPI and COPII are used for Golgi-related transport (retrograde and anterograde)

Virus Entry and Clathrin's Role

• Some viruses exploit clathrin-mediated endoxytosis to enter host cells

• Virus Entry Mechanism

  • Endocytosis: Most viruses enter host cells via clathrin-mediated endocytosis

  • Virus binds to cell surface receptors, triggering clathrin-coated vesicle formation

  • Vesicle forms, internalizes virus into cell, and moves towards early endosomes

  • Once inside endosome, acidification triggers the virus to uncoat and release its genetic material

• Clathrin's Role

  • Clathrin stabilizes budding process of vesicle

  • Clathrin-coated vesicles facilitate internalization of viruses into host cell

  • The virus interacts with receptor proteins on the membrane, which then recruit clathrin to form the vesicle

  • After vesicle formation, dynamin helps pinch off vesicle from membrane

• Outcome

  • Virus reaches early endosome, uncoats, and releases its genome to begin replication within the host

  • Clathrin plays key role in initial internalization process

Lysosome Functions

1. Autophagy - Normal breakdown of unnecessary/dysfunctional organelles/components

2. Degradation of internalized material

   a) Recycling of PM components

   b) Pathogen destruction (only occurs in phagocytic cells)

Autophagy

• Normal disassembly of unnecessary or dysfunctional cellular components

• Involves organelle turnover

Autophagosome Formation

• Isolation membrane from ER engulfs target organelles

• Forms an autophagosome

Autolysosome Formation

• Lysosome fuses with autophagosome to form autolysosome

• Content of autolysosome is enzymatically digested and released (via exocytosis)

Autophagy Process

• Autophagosome formation → Lysosome recruitment → Autolysosome → Digestion and release

Role in Cell Homeostasis

• Plays important role in maintaining cell homeostasis

• Degrades intracellular components and provides degradation products for recycling

• Dysfunction of autophagy implicated in neurodegenerative diseases, tumorigenesis, and other conditions

Degradation of Internalized Material

1. Recycling

   • Plasma membrane components like receptors and extracellular material are recycled

2. Phagocytosis (in phagocytic cells)

   • Pathogen (e.g., bacteria) is internalized by phagocytic cells

   • Pathogen-containing vesicle fuses with lysosome

   • Hydrolytic enzymes in lysosome degrade and kill pathogen

   • Debris is released outside the cell via exocytosis

Plant Vacuole Structure

• Fluid-filled, membrane-bound

• Can occupy ~90% of cell volume

• Surrounded by tonoplast (vacuolar membrane, - - - -)

• Tonoplast contains active transport systems for ion and molecule movement

  • Helps in dark reactions

Vacuole Functions

1. Intracellular digestion

   • Similar to lysosomes

   • Slightly acidic pH (~5.0)

   • Contains acid hydrolases

2. Mechanical support & turgor pressure

   • Provides rigidity to plant

   • Supports soft tissues

   • Helps stretch cell wall during growth

3. Storage

   • Stores solutes, macromolecules, amino acids, sugars

   • Stores toxic compounds and pigments (e.g. anthocyanin)

4. Other roles

   • Regulation of cytoplasmic pH

   • Sequestration of toxic ions

   • Regulation of turgor pressure

   • CO₂ storage as malate

Cytoskeleton

• Dynamic network of interconnected filaments and tubes

• Extends through cytosol and some organelles in eukaryotes

Functions

1. Structural support

2. Spatial organization within cell

3. Intracellular transport

4. Contractility and motility

Components

• Microtubules

• Microfilaments

• Intermediate filaments

Functions of the Cytoskeleton

Vesicle transport

• Centrosome releases tubules to form cytoskeleton

• Cytoskeleton forms tracks for motor proteins like kinesin and dynein

• Vesicles move along microtubules to reach specific destinations (e.g. Golgi, plasma membrane)

Extension of neurites (Axons/Dendrites)

• Actin filaments and microtubules support growth of neurites (axons or dendrites)

• Important for forming neural connections during development

Cell division

• Microtubules form mitotic spindles to separate chromosomes

• Actin filaments form contractile ring for cytokinesis (splitting cytoplasm)

Cilium or flagellum

• Made of microtubule-based structures

• Dynein arms slide microtubules to produce bending movement

• Used for motility (e.g. sperm flagellum) or fluid movement across cell surfaces (e.g. respiratory tract)

• Shortening of tubules allows for movement

Components of Cytoskeleton

1. Microfilaments

   • 7-9 nm

   • Double helix of actin (protein) monomers

2. Intermediate filaments

   • 10 nm

   • Strong fiber made up of various kinds of proteins

3. Microtubules

   • 25 nm

   • Hollow tube made up of alpha- and beta-tubulin (called dimers when they combine, also protein)

Microtubules (MT)

• Largest cytoskeletal element (25 nm diameter)

• Polymer of two tubulin monomers: α-tubulin and β-tubulin

• Form hollow tubes made of repeating α-β dimers

Types of Microtubules

1. Axonemal MT

   • Highly organized and stable

   • Found in motile structures like cilia and flagella

   • Involved in cell movement

2. Cytoplasmic MT

   • Loosely organized, very dynamic

   • Found in cytosol

   • Involved in vesicle transport, cell shape, spindle formation during division

Microtubule Structure

• Made of α/β-tubulin heterodimers

• Heterodimers form long protofilaments

• 13 protofilaments align in parallel

• Form a hollow cylindrical polymer

• Cylinder gives rigidity and polarity to microtubule structure

• Heterodimers aligned in same direction (head to tail) → creates structural polarity

• Microtubules have a fast-growing + end and slow-growing - end

• Polarity is important for MT growth and direction of transport along MT

Microtubule Assembly and Disassembly

• Dynamic instability → MTs rapidly grow and shrink

  • Half-life of most MTs in vivo is just minutes

• Shrinkage at + end can happen quickly → Called catastrophe

• MT formation is regulated

• Microtubule-organizing center (MTOC) = Main site of MT assembly

Microtubule-Associated Proteins (MAPs)

• Bind to microtubules (MTs)

• Modulate MT assembly and function

• Mediate interactions with vesicles, organelles, other structures

• Can stabilize MTs or stimulate their assembly

• Tau is primarily found in axons

• MAP2 is primarily found in dendrites

Classes of Microtubule-Associated Proteins (MAPs)

1. Non-Motor MAPs

• Control MT organization in cytosol

• Example: Tau protein in neurons

• Defective Tau → neurofibrillary tangles → linked to Alzheimer’s disease

2. Motor MAPs

• Two main types: Kinesin and dynein

• Use ATP to generate force

• Move material along MTs

• Generate sliding force between MTs

Summary

Exocytosis

• Secretory vesicles deliver contents outside cell

• Path: ER → vesicles → Golgi → vesicles → PM

Endocytosis

• Vesicles bring contents into cell

• Path: Vesicles (endosomes) → Lysosomes

Autophagy

• Lysosomes recycle "used" organelles

Phagocytosis

• Capture and destruction of pathogens (e.g. bacteria)

Vacuoles

• Plant organelles that store compounds and provide structural support via turgor pressure

Cytoskeleton

• Main structural components: Microtubules, Intermediate filaments, and Microfilaments

Microtubules (MT)

• Polymers of α and β tubulin

• Provide structural support and intracellular tracks (in animals)