Cell Structure and Organization Notes

Historical Context: Cells were first observed by Robert Hooke in $1665$ . The Cell Theory was later proposed by Mathias Schleiden ( $1838$ ) and Theodor Schwann ( $1839$ ).
Principles of Cell Theory: - All organisms are composed of one or more cells. - Cells are the smallest living units. - Cells arise only from the division of pre-existing cells.
Size Constraints: Cell size is limited by the surface-area-to-volume ratio to ensure efficient diffusion. Factors affecting diffusion rate include surface area, temperature, concentration gradient, and distance.
Microscopy and Resolution: - Resolution is the minimum distance required to distinguish two points as separate. - Human Eye: $100\,\mu m$ . - Light Microscope: Use visible light; resolves to $200\,nm$ . - Electron Microscope: Use electron beams; resolves to $0.2\,nm$ . Includes Transmission (TEM) and Scanning (SEM).

General Characteristics: Simplest organisms belonging to domains Archaea and Bacteria. They lack a membrane-bound nucleus and contain DNA in a nucleoid region.
Bacterial Components: - Cell Wall: Composed of peptidoglycan; protects the cell and maintains shape. - Bacterial Microcompartments (BMCs): Protein-shelled compartments ( $40$ to $400\,nm$ ) used for metabolic isolation and storage. - Flagella: Used for locomotion via rotary motion.
Archaea: Cell walls lack peptidoglycan. Membrane lipids contain saturated hydrocarbons attached to glycerol at both ends, often forming a monolayer.

Compartmentalization: Achieved through membrane-bound organelles and a cytoskeleton.
Nucleus: Repository of genetic information. Features include the nucleolus (rRNA synthesis), a double-membrane nuclear envelope, and nuclear pores.
Ribosomes: Complexes of ribosomal RNA (rRNA) and protein; site of protein synthesis in all cell types.
Endoplasmic Reticulum (ER): - Rough ER (RER): Studded with ribosomes; synthesizes proteins for secretion or membranes. - Smooth ER (SER): Few ribosomes; involved in lipid synthesis, storage, and detoxification.
Golgi Apparatus: Flattened stacks of membranes (cis and trans faces) that package and distribute molecules.
Lysosomes: Digestive vesicles containing enzymes to break down macromolecules or old organelles.
Peroxisomes: Contain enzymes for fatty acid oxidation; utilize catalase to neutralize hydrogen peroxide.

Mitochondria: Found in all eukaryotic cells; site of oxidative metabolism. Features an outer membrane, intermembrane space, inner membrane (cristae), and matrix. They possess their own DNA.
Chloroplasts: Found in plants and some eukaryotes; site of photosynthesis. Contain chlorophyll, thylakoids (organized in grana), and their own DNA.
Endosymbiosis Theory: Proposes that mitochondria and chloroplasts originated from a symbiotic relationship between a precursor eukaryotic cell and engulfed prokaryotes.

Cytoskeleton Components: - Microfilaments (Actin): Facilitate cellular movements like crawling or pinching. - Microtubules: Dimers of $\alpha$ - and $\beta$ -tubulin; largest fibers; facilitate internal transport. - Intermediate Filaments: Stable structures providing mechanical support.
Centrosomes: Microtubule-organizing centers containing centrioles (found in animals and most protists).
Cell Movement: Eukaryotic flagella and cilia exhibit a $9 + 2$ arrangement of microtubules.
Extracellular Matrix (ECM): Found in animal cells; consists of glycoproteins like collagen and elastin. Integrins link the ECM to the cytoskeleton.
Cell Walls: Cellulose in plants and protists; chitin in fungi.

Surface Markers: Glycolipids and MHC proteins allow for cell identification and immune recognition.
Junction Types: - Adhesive Junctions: Mechanically attach cytoskeletons (e.g., desmosomes). - Septate/Tight Junctions: Create leak-proof sheets of cells. - Communicating Junctions: Allow chemical or electrical signals to pass between cells. Includes gap junctions in animals and plasmodesmata in plants.