Assemblies of molecules, cells, and groups of cells

Shorter and more unsaturated tails pack loosely → more fluid; longer, saturated tails pack tightly → less fluid. Cholesterol is a fluidity buffer: at high temperature it restrains phospholipid movement (less fluid), and at low temperature it wedges between tails to prevent tight packing (more fluid, prevents freezing). The membrane is also asymmetric — the two leaflets carry different lipids, and carbohydrate chains (glyco-lipids/-proteins) sit only on the extracellular face, where they serve in cell recognition.

Integral proteins have hydrophobic regions that match the bilayer core and can only be removed by disrupting the membrane (e.g., detergent); peripheral proteins associate loosely with surfaces or with integral proteins. Functional roles: transport (channels, pumps, carriers), enzymatic activity, cell-cell recognition (glycoproteins), attachment to the cytoskeleton/matrix, and signal transduction. Classic receptor types — G-protein-coupled receptors and receptor tyrosine kinases — convert an outside signal into an intracellular cascade without the signal molecule ever entering the cell.

• GPCR cascade — a 7-transmembrane receptor coupled to a G protein (αβγ). Ligand binding makes the Gα subunit swap GDP for GTP and dissociate; Gα-GTP activates an effector — classically adenylate cyclase, which makes the second messenger cAMP, which activates protein kinase A (PKA). The signal shuts off when Gα's built-in GTPase hydrolyzes GTP back to GDP. One cascade amplifies a few signal molecules into a large response — the mechanism behind most peptide hormones (see peptide vs. steroid hormones).
• Receptor tyrosine kinase (RTK) — ligand binding makes two receptors dimerize and cross-phosphorylate each other's tyrosines, creating docking sites that launch growth and differentiation pathways (e.g., insulin, growth factors).

Simple diffusion needs no protein and works for O₂, CO₂, and small lipophilic molecules. Facilitated diffusion is still passive but uses a protein: channels form a pore (often gated by voltage or ligand; e.g., aquaporins for water), and carriers bind the solute and change shape (e.g., GLUT transporters for glucose). Because carriers are limited in number, facilitated diffusion saturates at high solute concentration — a kinetics curve that looks like Michaelis–Menten, a favorite passage hook.

Water moves to dilute the more concentrated solution. Define everything relative to the cell: a hypotonic environment has less solute than the cytoplasm, so water rushes in (animal cells lyse; plant cells become turgid); a hypertonic environment has more solute, so water leaves and the cell shrinks (crenation); an isotonic environment is balanced, with no net movement. Solute concentration sets osmotic pressure — the pressure needed to stop osmosis — a colligative property that depends on the number of dissolved particles, not their identity.

The Na⁺/K⁺-ATPase pumps 3 Na⁺ out and 2 K⁺ in per ATP, against both gradients. This does two jobs: it maintains the ion gradients underlying the resting membrane potential (more on this in 3A), and the steep inward Na⁺ gradient it builds becomes a battery. Secondary active transport (cotransport) taps that battery: as Na⁺ flows back in down its gradient, it drags another solute along — the same direction is symport (e.g., the Na⁺/glucose cotransporter in the gut), the opposite direction is antiport. Secondary transport uses no ATP itself, but depends on the primary pump that built the gradient.

Phagocytosis engulfs large solids (immune cells eating bacteria); pinocytosis takes in extracellular fluid nonspecifically; receptor-mediated endocytosis uses surface receptors to concentrate a specific cargo (e.g., LDL) into coated pits. Exocytosis fuses a vesicle with the plasma membrane to dump contents outside — how cells secrete hormones, neurotransmitters, and digestive enzymes, and how new membrane is added.

The nuclear envelope is continuous with the rough ER, and nuclear pores let mRNA exit and proteins enter. Inside, DNA wraps around histones as chromatin. The dense nucleolus is where rRNA is transcribed and ribosomal subunits are assembled before export to the cytoplasm. Keeping transcription (nucleus) physically separate from translation (cytoplasm) is a defining eukaryotic trait — and the reason eukaryotes can process mRNA before translating it.

A secreted protein's journey is a classic ordered process: ribosome on the rough ER → protein threaded into the ER lumen and folded/glycosylated → vesicle buds off to the Golgi → Golgi modifies (trims sugars, adds tags) and sorts → vesicle to the plasma membrane for exocytosis. Smooth ER has no ribosomes and instead synthesizes phospholipids and steroids, stores Ca²⁺ (prominent in muscle), and detoxifies drugs in the liver.

The matrix holds the citric acid cycle and pyruvate oxidation; the inner membrane holds the electron transport chain and ATP synthase, and its cristae maximize surface area. Mitochondria carry their own circular DNA and ribosomes, self-replicate, and are maternally inherited — evidence for the endosymbiotic theory that they descend from engulfed aerobic bacteria. (See the machinery in detail under oxidative phosphorylation.)

Lysosomes digest material delivered by endocytosis/phagocytosis and recycle the cell's own components (autophagy); their enzymes work best at the low pH the lysosome maintains. Peroxisomes carry out β-oxidation of very-long-chain fatty acids and other oxidations that generate H₂O₂, then use catalase to convert that peroxide to water and oxygen before it can damage the cell.

• Microfilaments — polymers of actin, the thinnest; responsible for muscle contraction (with myosin), cell motility, and the cleavage furrow that splits a dividing animal cell.
• Intermediate filaments — a diverse middle-sized group (keratin, vimentin, lamins); the most stable, they provide tensile strength and anchor organelles.
• Microtubules — hollow tubes of α/β-tubulin, the thickest; form the tracks along which kinesin (toward the +/periphery) and dynein (toward the −/center) walk cargo, and build the mitotic spindle and cilia/flagella.

A motile cilium/flagellum has the 9+2 axoneme — nine doublet microtubules around a central pair — and bends when dynein arms slide the doublets. Centrioles and the basal bodies of cilia have the 9+0 pattern (nine triplets, no center). Centrioles sit in the centrosome, the cell's main microtubule-organizing center, which nucleates the spindle during division.

• Tight junctions — fuse adjacent membranes into a continuous barrier, preventing molecules from slipping between cells (e.g., the gut lining and the blood-brain barrier force material to go through cells, not around them).
• Desmosomes — "spot welds" linked to intermediate filaments that give tissues mechanical strength in stretchy tissue like skin and heart muscle.
• Gap junctions — protein channels (connexons) that directly couple cytoplasms, allowing electrical/chemical coupling (e.g., synchronized contraction of cardiac muscle).

Recognize the three families by what they bind. Cadherins are calcium-dependent and mediate cell-to-cell adhesion — they're the proteins underlying adherens junctions and the desmosomes from tight junctions, desmosomes & gap junctions. Integrins anchor cells to the extracellular matrix (binding fibronectin, laminin, collagen) and transmit signals bidirectionally across the membrane, a role that matters in immune-cell adhesion and migration. Selectins bind carbohydrate ligands on the surface of other cells and are the weak, transient grip that lets leukocytes roll along the blood-vessel wall before firmly adhering.

Epithelial cells pack tightly, joined by tight junctions and desmosomes, and rest on a basement membrane that separates them from underlying connective tissue. Classified by shape (squamous, cuboidal, columnar) and layers (simple = one, stratified = many). It is avascular — nourished by diffusion from below — and continually renews.

Unlike epithelium, connective tissue is defined by its matrix, not its cells — the matrix's composition sets the tissue's properties (the calcified matrix of bone, the firm matrix of cartilage, the fluid matrix of blood). Fibroblasts secrete the collagen and elastin fibers that give the tissue its strength and stretch.