Unit 1: Cellular Organization; Cytoskeleton and Function of Intracellular Organelles

Cells are the fundamental units of life, ranging from ~1 µm bacteria to ~100 µm eukaryotic cells, all built from the same chemical logic and bounded by a lipid membrane. This unit establishes what all cells share, the chemistry from which they are built, and the compartmentalized architecture of the eukaryotic cell.

• Universal principle: Every cell arises from a pre-existing cell, stores information in DNA, expresses it via RNA into protein, and is enclosed by a phospholipid membrane.
• Two lineages: Prokaryotes (no membrane-bound nucleus; bacteria, archaea) vs. eukaryotes (compartmentalized organelles; ~1000× larger volume).
• Convention used below: "Compartmentalization" = spatial separation of incompatible reactions into membrane-bound organelles, each with a distinct lumenal environment.

II. Universal Features and Chemical Organization of Cells

What every cell holds in common and the molecules it is made of.

A. Universal features of cells

Certain properties are shared by every living cell regardless of lineage.

• Genetic continuity: DNA as hereditary material, replicated semi-conservatively before division.
• Common expression machinery: Ribosomes (70S in prokaryotes, 80S in eukaryotes) translate mRNA using a near-universal genetic code (64 codons, 20 amino acids).
• Bounding membrane: A phospholipid bilayer separates cytoplasm from environment and maintains ion gradients (e.g. high K⁺, low Na⁺ inside).
• Energy currency: ATP hydrolysis (ATP → ADP + Pᵢ, ΔG°′ ≈ −30.5 kJ/mol) powers biosynthesis and transport in all cells.

B. Cell chemistry and biosynthesis — chemical organization of cells

The cell is built from a small set of carbon-based building blocks assembled into macromolecules.

• Elemental basis: ~99% of mass is C, H, N, O, P, S; water forms ~70% of cell weight and is the universal solvent.
• Four macromolecule classes:
  • Proteins: polymers of 20 amino acids linked by peptide bonds; fold into functional 3-D shapes (enzymes, structure, transport).
  • Nucleic acids: nucleotide polymers (sugar + phosphate + base); DNA stores, RNA transfers information.
  • Polysaccharides: glucose polymers (e.g. glycogen, cellulose) for storage and structure.
  • Lipids: fatty acids and glycerol; hydrophobic, form membranes and store energy.
• Biosynthesis by condensation: Monomers join by removing water (dehydration); breakdown is by hydrolysis.
• Metabolic coupling: Catabolism (breakdown, releasing energy) is coupled to anabolism (synthesis, consuming ATP and NADPH).

III. Internal Organization — Cell Membranes and Compartmentalization

The bilayer as barrier and the logic of dividing the eukaryotic cell into compartments.

A. Structure of cell membranes

Membranes are self-assembling lipid bilayers studded with proteins, described by the fluid-mosaic model (Singer & Nicolson, 1972).

• Lipid bilayer: Amphipathic phospholipids orient hydrophilic heads outward, hydrophobic tails inward; ~5 nm thick.
• Membrane proteins: Integral (transmembrane, e.g. transporters, channels) and peripheral (surface-bound); carry out transport, signalling, catalysis.
• Fluidity: Lateral diffusion of lipids is rapid; cholesterol modulates fluidity by packing between phospholipids.
• Asymmetry: Inner and outer leaflets differ in lipid and carbohydrate composition; glycolipids and glycoproteins face the exterior.
• Selective permeability: Small nonpolar molecules (O₂, CO₂) cross freely; ions and large polar molecules require transporters.

B. Concepts related to compartmentalization in eukaryotic cells

Internal membranes create distinct chemical environments, enabling specialization.

• Purpose: Segregates incompatible processes (e.g. hydrolytic digestion in lysosomes vs. synthesis in the cytosol).
• Endomembrane system: ER, Golgi, lysosomes, endosomes and plasma membrane function as an interconnected trafficking network via vesicles.
• Lumen specificity: Each compartment maintains its own pH and ion content (e.g. lysosome pH ~4.5, cytosol pH ~7.2).
• Surface-to-volume advantage: Internal membranes vastly increase reactive surface area within the cell.

IV. Structure and Organization of the Cytoskeleton

The internal protein scaffold that shapes, supports and moves the cell.

A. Structure and organization of cytoskeleton

The cytoskeleton is a dynamic three-filament network spanning the cytoplasm.

• Microfilaments (actin): ~7 nm diameter; helical polymers of globular actin; concentrated at the cell cortex; control shape and surface movement.
• Intermediate filaments: ~10 nm; ropelike, made of tissue-specific proteins (keratin, vimentin, lamins); provide tensile mechanical strength.
• Microtubules: ~25 nm hollow tubes of α/β-tubulin dimers; radiate from the centrosome; act as tracks for transport and form the mitotic spindle.
• Dynamic assembly: Filaments continuously polymerize/depolymerize; microtubules show "dynamic instability" (GTP-cap driven growth and catastrophe).
• Organizing centres: Centrosome nucleates microtubules; focal adhesions and desmosomes anchor filaments to membranes.

V. The Nucleus

The information-control centre.

A. Nucleus

The nucleus houses and protects the genome and directs gene expression.

• Nuclear envelope: Double membrane continuous with the ER, perforated by nuclear pores that gate RNA/protein traffic.
• Chromatin: DNA wound around histone octamers (nucleosomes); condenses into chromosomes during division.
• Nucleolus: Site of rRNA synthesis and ribosome subunit assembly.
• Nuclear lamina: Intermediate-filament (lamin) mesh giving structural support beneath the envelope.

VI. Mitochondria and Plastids

The energy-transducing organelles of double-membrane, endosymbiotic origin.

A. Mitochondria

Mitochondria generate most cellular ATP via aerobic respiration.

• Double membrane: Smooth outer membrane; inner membrane folded into cristae bearing the electron-transport chain and ATP synthase.
• Matrix: Contains citric-acid-cycle enzymes, mitochondrial DNA and 70S ribosomes.
• Function: Oxidative phosphorylation couples the proton gradient across the inner membrane to ATP synthesis.

B. Plastids

Plastids are plant/algal organelles for synthesis and storage.

• Types: Chloroplasts (photosynthesis), chromoplasts (pigment storage), leucoplasts/amyloplasts (starch storage).
• Common origin: Interconvertible, developing from proplastids; carry their own DNA (endosymbiotic origin).

C. Chloroplast

The chloroplast conducts photosynthesis, converting light to chemical energy.

• Triple-membrane organization: Outer and inner envelope plus internal thylakoid membranes stacked into grana.
• Stroma: Site of the Calvin cycle fixing CO₂ into sugar; holds chloroplast DNA and ribosomes.
• Light reactions: Occur on thylakoids, producing ATP and NADPH used by the stroma.

VII. The Endomembrane System

The connected network of synthesis, modification and degradation.

A. Endoplasmic reticulum

The ER is a membrane network for protein and lipid synthesis.

• Rough ER: Ribosome-studded; synthesizes and folds secretory and membrane proteins into its lumen.
• Smooth ER: No ribosomes; makes lipids, stores Ca²⁺, detoxifies drugs (liver).

B. Golgi bodies

The Golgi apparatus modifies, sorts and dispatches ER products.

• Cisternal stacks: Flattened sacs with a cis face (receiving from ER) and trans face (shipping out).
• Function: Glycosylation and sorting of proteins/lipids into vesicles bound for lysosomes, membrane or secretion.

C. Lysosomes

Lysosomes are the cell's digestive compartments.

• Contents: ~40 acid hydrolases active at pH ~4.5, maintained by membrane proton pumps.
• Function: Degrade macromolecules from endocytosis, phagocytosis and autophagy; recycle components.

D. Peroxisomes

Peroxisomes carry out oxidative reactions isolated from the cytosol.

• Enzymes: Oxidases generate H₂O₂; catalase then breaks it down (2 H₂O₂ → 2 H₂O + O₂).
• Function: β-oxidation of long-chain fatty acids and detoxification reactions.

E. Vacuoles

Vacuoles are storage and homeostatic compartments, prominent in plants.

• Central vacuole: Occupies most plant cell volume; maintains turgor pressure via the tonoplast membrane.
• Function: Stores water, ions, pigments and waste; contributes to cell enlargement.

VIII. The Cell Wall

The rigid extracellular boundary of plant, fungal and bacterial cells.

A. Cell wall

The cell wall provides mechanical protection and defines cell shape.

• Composition: Cellulose in plants, chitin in fungi, peptidoglycan in bacteria.
• Layers: Primary wall (thin, flexible during growth) and secondary wall (thick, rigid, laid down after growth).
• Function: Resists turgor pressure, prevents lysis, and mediates cell-to-cell connections (plasmodesmata).

IX. Structure & Function of Cytoskeleton and its Role in Motility

How the filament systems generate movement.

A. Structure & function of cytoskeleton and its role in motility

Motility arises from motor proteins moving along, or the assembly of, cytoskeletal filaments.

• Actin-based movement:
  • Muscle contraction: Myosin heads walk along actin, powered by ATP (sliding-filament model).
  • Cell crawling: Actin polymerization at the leading edge pushes out lamellipodia and filopodia.
• Microtubule-based movement:
  • Intracellular transport: Kinesin moves cargo toward the plus end; dynein toward the minus end.
  • Cilia and flagella: A 9+2 axoneme of microtubule doublets bends as dynein arms slide adjacent doublets, driving beating.
• Chromosome movement: Spindle microtubules pull sister chromatids apart in mitosis.
• Energy dependence: All motor activity consumes ATP (or GTP for microtubule dynamics), converting chemical energy into directed force.