The Cell — Chapter Notes (Junqueira's Basic Histology, 17th Ed.)

Overview

Chapter 2: The Cytoplasm

Cell Differentiation

A. The Plasma Membrane

• Phospholipid bilayer: hydrophilic heads face outward; hydrophobic fatty-acid tails face inward
• Integral proteins: embedded within the lipid bilayer, often spanning the membrane multiple times ("multipass proteins"); extracted only with detergents
• Peripheral proteins: bound to cytoplasmic surface; extracted with salt solutions
• Glycocalyx: oligosaccharide chains (from glycolipids and glycoproteins) projecting from the external surface — important for cell recognition, adhesion, and antigenicity
• Many membrane proteins are mobile laterally (fluid mosaic model); tight junctions restrict this in epithelial cells

• Phagocytosis: large particles engulfed by pseudopods → phagosome → fused with lysosome → phagolysosome
• Pinocytosis: small fluid droplets engulfed in tiny vesicles
• Receptor-mediated endocytosis: ligand binds receptor → coated pit (lined with clathrin) → coated vesicle → early endosome → late endosome → lysosome
• Multivesicular bodies: endosomal compartments containing intraluminal vesicles; may release contents outside the cell as exosomes (50–150 nm), a form of cell-to-cell communication

• A cytoplasmic vesicle fuses with the plasma membrane and releases contents extracellularly
• Triggered by a transient rise in cytosolic Ca²⁺
• Two pathways:
  • Constitutive secretion: continuous release (e.g., collagen from fibroblasts)
  • Regulated secretion: in response to signals (e.g., digestive enzymes from pancreas)

1. Channel-linked receptors — open ion channels upon ligand binding
2. Catalytic receptors — ligand binding activates an enzyme domain (e.g., receptor tyrosine kinases)
3. G-protein-coupled receptors (GPCRs) — activate second messengers (cAMP, Ca²⁺, IP₃)

B. Cytoplasmic Organelles

1. Ribosomes

• Composed of rRNA + proteins; two subunits: 60S (large) + 40S (small) = 80S ribosome
• Free polyribosomes: synthesize proteins destined for the cytoplasm (cytoskeletal proteins, enzymes)
• Membrane-bound ribosomes (on RER): synthesize proteins for secretion, lysosomes, or membranes
• Protein targeting to the RER depends on a signal peptide (15–40 hydrophobic amino acids) recognized by a signal-recognition particle (SRP)

2. Endoplasmic Reticulum (ER)

• Cisternae studded with ribosomes; highly basophilic
• Functions: protein synthesis for secretion, membrane integration, and lysosomal storage
• ERAD (ER-associated degradation): defective proteins retro-translocated to cytoplasm, ubiquitinated, and degraded by proteasomes
• Well-developed in secretory cells (pancreatic acini, plasma cells, fibroblasts)

• Lacks ribosomes; tubular network
• Functions: lipid and steroid hormone synthesis; drug/toxin detoxification (liver); Ca²⁺ storage and release (muscle — called sarcoplasmic reticulum)
• Abundant in: steroid-secreting cells (adrenal cortex, Leydig cells), liver hepatocytes, muscle

3. Golgi Apparatus

• Stack of flattened membrane-bound cisternae (saccules); polarized:
  • Cis face (entry side): receives vesicles from RER (COPII-coated)
  • Trans face (exit side): vesicles leave toward destinations
• Functions:
  • Post-translational modification (glycosylation, phosphorylation, sulfation)
  • Sorting and packaging of proteins into vesicles
  • Destination tags direct vesicles: to lysosomes, plasma membrane, or secretory granules
• Clathrin-coated vesicles go to late endosomes/lysosomes
• COPI-coated vesicles return to RER (retrograde)

4. Secretory Granules

• Membrane-bound vesicles containing concentrated secretory products
• Undergo regulated exocytosis upon appropriate stimulation
• Prominent in: zymogen granules of pancreatic acini, secretory granules of mucous cells

5. Lysosomes

• Membrane-bound organelles (0.5–1 μm) containing ~50 hydrolytic enzymes (acid hydrolases)
• Maintain acidic pH (~5) via H⁺-ATPase
• Primary lysosomes: newly formed, not yet active
• Secondary lysosomes: fused with endocytic/phagocytic vesicles; active digestion
• Autophagy: lysosome digests dysfunctional organelles surrounded by autophagosomal membrane
• Residual bodies: indigestible remnants; accumulate as lipofuscin (age pigment)

Medical application: Lysosomal storage diseases (e.g., Gaucher, Tay-Sachs) result from deficiency of specific acid hydrolases.

6. Proteasomes

• Cylindrical structures of 4 stacked rings (each with 7 proteins including proteases)
• Capped by regulatory particles that recognize ubiquitin-tagged proteins
• Degrade misfolded, denatured, or short-lived proteins
• Released peptides may serve in antigen presentation (MHC class I pathway)

Medical application: Proteasome failure → protein aggregates → neurodegeneration (Alzheimer, Huntington diseases).

7. Mitochondria

• Size: 0.5–1 μm diameter; up to 10× longer in length; highly dynamic (fuse, divide, move along microtubules)
• Number correlates with cell's energy demand (many in cardiac muscle, kidney tubules; few in low-metabolism cells)
• Two membranes:
  • Outer membrane: porous (porins); small molecules pass freely
  • Inner membrane: impermeable; forms cristae (folds that increase surface area); contains electron-transport chain and ATP synthase
• Matrix: enclosed by inner membrane; contains enzymes for:
  • β-oxidation of fatty acids
  • Krebs (citric acid) cycle
  • Mitochondrial DNA (mtDNA), own ribosomes
• Energy yield: mitochondrial oxidative phosphorylation produces 15× more ATP than cytoplasmic glycolysis
• Apoptosis: stressed mitochondria release cytochrome c → triggers caspase cascade → programmed cell death

Medical application: Mutations in mtDNA cause MERRF (myoclonic epilepsy with ragged-red fibers) due to defective lysine-tRNA.

8. Peroxisomes

• Small spherical organelles (~0.5 μm); contain oxidative enzymes
• Perform β-oxidation of very long chain fatty acids (complements mitochondrial oxidation)
• Contain catalase — breaks down H₂O₂ produced by oxidative reactions
• Detoxification in liver
• Formed by budding from pre-existing peroxisomes

C. The Cytoskeleton

1. Microtubules (25 nm diameter)

• Hollow tubes; walls of 13 protofilaments of α/β-tubulin heterodimers
• Dynamic instability: rapid polymerization at plus (+) end, depolymerization at minus (-) end
• Organize from MTOCs (microtubule-organizing centers) — usually the centrosome (pair of centrioles)
• Functions:
  • Maintain cell shape
  • Intracellular transport tracks — motor proteins kinesin (toward +) and dynein (toward –)
  • Form mitotic spindle during cell division
  • Form core of cilia and flagella — 9+2 axoneme arrangement; dynein arms power movement
• Drugs: colchicine and vinca alkaloids depolymerize microtubules; taxol stabilizes them (anti-cancer)

2. Microfilaments / Actin Filaments (5–7 nm diameter)

• Two-stranded helix of globular actin (G-actin) monomers forming filamentous actin (F-actin)
• Treadmilling: G-actin added at (+) end, removed at (–) end — even at steady state
• Concentrated in cell cortex (beneath plasma membrane)
• Arp2/3 complex produces branched actin networks important for endocytosis
• Actin-binding proteins: profilin (promotes assembly), cofilin (promotes disassembly), formin, filamin (cross-linking)
• Motor: myosin proteins move along actin; myosin II forms contractile rings for cytokinesis
• Functions:
  • Cell locomotion (lamellipodia, stress fibers)
  • Cytokinesis (contractile ring constriction)
  • Endocytosis
  • Cytoplasmic streaming

3. Intermediate Filaments (8–10 nm diameter)

• Most stable cytoskeletal component; do not undergo dynamic assembly/disassembly
• Provide mechanical strength to cells
• Cell-type specific:

  Protein	Cell type
  Keratins (acidic + basic)	Epithelial cells
  Vimentin	Mesenchymal cells (fibroblasts, endothelium)
  Desmin	Muscle cells
  GFAP	Glial (astrocytes)
  Neurofilament proteins	Neurons
  Nuclear lamins	All nuclei (under inner nuclear membrane)

Intermediate filaments are diagnostically important — immunohistochemistry for specific IF proteins identifies tumor cell origin.

D. Inclusions

• Not metabolically active — primarily storage structures
• Types:
  • Lipid droplets: energy store; not membrane-bound
  • Glycogen granules: glucose polymer; abundant in liver and muscle (PAS-positive)
  • Pigment granules: melanin (produced by melanocytes), lipofuscin (age pigment in post-mitotic cells)
  • Residual bodies: indigestible lysosomal remnants

Chapter 3: The Cell Nucleus

Components of the Nucleus

1. Nuclear Envelope

• Two concentric membranes separated by a perinuclear space (30–50 nm)
• Outer nuclear membrane: continuous with RER; bears ribosomes
• Inner nuclear membrane: associated with nuclear lamina (meshwork of lamin proteins)
• Nuclear lamina: intermediate filament network (A-type lamins: A, C; B-type lamins: B1, B2); provides structural support and anchors chromatin

Medical application: Mutations in lamin A → progeria (premature aging — laminopathies). Laminopathies selectively affect some tissues despite ubiquitous expression.

2. Nuclear Pore Complexes (NPCs)

• Large (~125 MDa) protein complexes spanning both nuclear membranes
• ~3,000–4,000 pores per nucleus
• Composed of ~30 different nucleoporins arranged with 8-fold symmetry
• Functions as a selective, bidirectional gate:
  • Export: mature mRNA, rRNA, tRNA, ribosomal subunits → cytoplasm
  • Import: proteins needed for nuclear function (transcription factors, histones, polymerases) ← cytoplasm
• Small molecules (<40 kDa) diffuse freely; large molecules require nuclear localization signals (NLS) and energy (GTP)

3. Chromatin

• DNA + associated proteins (mainly histones)
• Nucleosome: basic unit — 147 bp of DNA wrapped ~1.65× around an octamer of histones (H2A, H2B, H3, H4 × 2); H1 histone linker seals the DNA at entry/exit
• Two forms:

  Form	Appearance (H&E)	Activity
  Euchromatin	Light-staining, dispersed	Transcriptionally active
  Heterochromatin	Dark-staining, condensed	Transcriptionally silent

• Peripheral heterochromatin lines the inner nuclear membrane
• Barr body: one inactivated X chromosome in female cells — visible as a dark chromatin mass (sex chromatin) at the nuclear periphery

4. Nucleolus

• Non-membranous, highly basophilic structure visible by light microscopy
• Present only in cells actively synthesizing proteins (prominent nucleoli = active protein synthesis)
• Functions: site of rRNA transcription, processing, and ribosomal subunit assembly
• Ultrastructural regions:

  Region	Contents
  Fibrillar centers (FC)	rRNA genes (nucleolar organizers) undergoing transcription
  Dense fibrillar component (F)	New rRNA transcripts being processed
  Granular component (G)	Assembling ribosomal subunits

• Newly assembled large (60S) and small (40S) subunits exit through nuclear pores

Large, prominent nucleoli → high protein synthesis → feature of cancer cells (used in pathological assessment)

The Cell Cycle

• Cells may exit to G₀ (quiescent state) from G₁
• Checkpoints: G₁/S checkpoint (restriction point — most critical; regulated by cyclin D, CDK4/6, Rb protein), G₂/M checkpoint, spindle assembly checkpoint
• Dysregulation of checkpoints → cancer

Mitosis (stages)

1. Prophase: chromatin condenses; mitotic spindle begins to form; nuclear envelope breaks down (prometaphase)
2. Metaphase: chromosomes align at metaphase plate; spindle fibers attach to kinetochores
3. Anaphase: sister chromatids separate to opposite poles
4. Telophase: nuclear envelope reforms around each chromosome set
5. Cytokinesis: contractile ring of actin/myosin II constricts → two daughter cells

Meiosis

• Two successive divisions (Meiosis I and II) producing four haploid daughter cells
• Meiosis I = reductional division (homologous chromosomes separate)
• Meiosis II = equational division (sister chromatids separate)
• Crossing-over during prophase I → genetic recombination

Apoptosis (Programmed Cell Death)

• Regulated, energy-dependent process eliminating unwanted or damaged cells — essential in development, immune regulation, and tumor suppression
• Morphology: cell shrinkage, chromatin condensation, nuclear fragmentation, membrane blebbing → apoptotic bodies (phagocytosed without inflammation)
• Two pathways:
  1. Intrinsic (mitochondrial): stress → mitochondria release cytochrome c → forms apoptosome with Apaf-1 + caspase-9 → activates effector caspases (3, 6, 7)
  2. Extrinsic (death receptor): FasL binds Fas (CD95) or TNF binds TNFR → activates caspase-8 → effector caspases
• Bcl-2 family regulates the intrinsic pathway (pro-apoptotic: Bax, Bak; anti-apoptotic: Bcl-2, Bcl-xL)
• Distinguished from necrosis (passive, inflammatory cell death)

Key Summary Points