Biology Foundations – Chapters 1 to 5 Vocabulary

Learning Objectives

• Describe characteristics of living organisms
• Explain hierarchical organization of living systems (cell → biosphere)
• Understand & apply scientific method; differentiate deductive vs. inductive reasoning
• Explain Darwin’s theory of evolution by natural selection and supporting evidence
• Recognize biology’s five core concepts (chem.–phys. laws, structure–function, energy–matter, information flow, evolution)
• Describe atomic structure, chemical bonding, and periodic trends
• Explain water’s structure, hydrogen bonding, and resulting properties
• Define acids, bases, buffers; use pH = -\log[H^+]
• Identify functional groups; distinguish isomers
• Describe structure–function of carbohydrates, lipids, proteins, nucleic acids
• Explain protein structural levels & chaperone-assisted folding
• State cell theory, compare prokaryotic vs. eukaryotic cells, plant vs. animal
• Identify organelles, cytoskeleton, extracellular structures & cell junctions
• Explain membrane fluid mosaic model, transport mechanisms (passive, active, bulk)

Visual Overview & Unifying Themes

• Biology intersects natural sciences (chemistry, physics); life obeys chemical & physical laws
• Core unifying concepts: hierarchy, structure→function, energy transformations, information transactions, evolution
• All living systems exhibit shared characteristics but enormous diversity explained by common descent + evolutionary change

Properties of Life

• Composed of cells
• Complex & ordered
• Respond to environment
• Grow & reproduce
• Obtain & use energy (metabolism)
• Maintain homeostasis (internal balance)
• Exhibit evolutionary adaptation

Hierarchical Organization of Living Systems

1. Cellular level: atoms → molecules → macromolecules → organelles → cells (basic unit of life)
2. Organismal level: tissues → organs → organ systems → organism
3. Populational level: population → species → community → ecosystem → biosphere

• Emergent properties: new functions arise at higher levels (e.g., consciousness not present in single neuron)

Nature of Science & Scientific Method

• Goal: increasingly accurate understanding via observation & reasoning
• Deductive reasoning: general → specific (e.g., All wasps sting → this wasp stings)
• Inductive reasoning: specific → general (all observed dogs have hair → all dogs have hair)
• Scientific method steps: Observation → Hypothesis → Prediction → Experiment → Results → Conclusion (iterative)
• Hypothesis: testable, falsifiable explanation; theories: interconnected concepts supported by vast evidence (may be modified)
• Use reductionism & modeling but recognize limitations; emergent properties can be lost when reducing

Darwin & Evolution by Natural Selection

• Voyage on HMS Beagle; observations: extant resemble extinct (glyptodont ↔ armadillo), geographic variation (finches), population limits (inspired by Malthus)
• Four postulates:
  1. More offspring produced than survive
  2. Heritable variation exists
  3. Variants differ in reproductive success (fitness)
  4. Advantageous traits transmitted, changing population
• Predictions: transitional fossils, genetic mechanism, homologous structures, etc.

Evidence Supporting Evolution

1. Fossil record & transitional forms (Archaeopteryx, whale lineage: Pakicetus → Ambulocetus → Rodhocetus)
2. Earth’s age ≈ 4.5 \text{ Ga} allows time for change
3. Comparative anatomy: homologous limbs vs. analogous wings; vestigial organs
4. Mechanism of inheritance (Mendel → DNA)
5. Molecular evidence: phylogenetic trees from nucleotide/protein sequences
6. Comparative embryology (gill slits, tails)
7. Observed evolution (peppered moth melanism graph 1959–1995)

• Quote: “Nothing in Biology Makes Sense Except in the Light of Evolution” — Dobzhansky (1973)

Chemistry of Life: Atoms & Elements

• Atom = protons (+), neutrons (0), electrons (–) in orbitals/energy levels (K, L, M…)
• Atomic number = # protons; atomic mass ≈ protons + neutrons (daltons)
• Isotopes: same Z, different neutrons (C-12, C-13, C-14)
• Ions: cation (+), anion (–); oxidation–reduction (electron transfer)
• Periodic table groups elements by valence; octet rule drives reactions; noble gases inert (full shells)
• 12 biologically abundant elements: C, H, O, N, P, S, Na, K, Ca, Mg, Fe, Cl

Chemical Bonds & Reactions

• Covalent (sharing e⁻): single, double, triple; non-polar (equal), polar (unequal; electronegativity O> N> C> H)
• Ionic: attraction of opposite charges (Na⁺ + Cl⁻ → NaCl)
• Hydrogen bonds: weak, between polar molecules (esp. water)
• van der Waals, hydrophobic interactions
• Chemical reaction rate influenced by T°, [reactants/products], catalysts
• Photosynthesis equation: 6CO2 + 6H2O \rightleftharpoons C6H{12}O6 + 6O2 (reversible)

Water: Structure & Properties

• Polar covalent O–H; bent 104.5^\circ; forms extensive H-bond lattice
• Cohesion (water–water) → surface tension; Adhesion (water–polar) → capillary action
• High specific heat & high heat of vaporization buffer temperatures & enable evaporative cooling
• Ice less dense (H-bonds space molecules) → aquatic life survives winter
• Universal solvent for polar/ionic compounds; organizes non-polar molecules (hydrophobic effect)
• Autoionization: H_2O \leftrightarrow H^+ + OH^-

Acids, Bases, Buffers

• pH = -\log[H^+]; acid: [H^+] \uparrow, base: [H^+] \downarrow
• Change of 2 pH units = 10^2 = 100-fold [H⁺] change
• Buffers (e.g., carbonic acid H2CO3 / HCO_3^-) resist pH change by reversible H^+ release/uptake

Organic Molecules & Functional Groups

• Carbon: up to 4 covalent bonds; forms chains, rings, double bonds
• Hydrocarbons = C–H non-polar (energy-rich); functional groups add polarity/reactivity
  • Hydroxyl –OH (alcohols)
  • Carbonyl C=O (aldehydes/ketones)
  • Carboxyl –COOH (acids)
  • Amino –NH₂ (bases)
  • Sulfhydryl –SH (disulfide bridges)
  • Phosphate –PO₄²⁻ (energy transfer)
  • Methyl –CH₃ (non-polar tag)
• Isomers: structural (different C skeleton), stereoisomers (same bonds, spatial diff.; enantiomers L/D)
• Macromolecules built by dehydration synthesis (release H2O); broken by hydrolysis (add H2O)

Carbohydrates

• Empirical formula (CH2O)n; C–H bonds store energy
• Monosaccharides: 3C glyceraldehyde, 5C ribose/deoxyribose, 6C glucose, fructose, galactose (ring forms; α/β stereoisomers)
• Disaccharides (sucrose, lactose, maltose) for transport/storage
• Polysaccharides:
  • Energy storage: starch (plants, α-1,4 & α-1,6 branches), glycogen (animals, highly branched)
  • Structural: cellulose (β-1,4 glucose, indigestible), chitin (N-acetylglucosamine, exoskeleton)

Nucleic Acids

• Nucleotide = 5-C sugar + phosphate + nitrogenous base (purines A/G; pyrimidines C/T/U)
• Phosphodiester bond links 5′-phosphate to 3′-OH (sugar-phosphate backbone)
• DNA: deoxyribose; double helix; antiparallel; complementary base pairing (A=T, C≡G); genetic storage
• RNA: ribose; single-stranded; U replaces T; roles—mRNA (info), rRNA (ribosome), tRNA (transport), ribozymes
• ATP: adenine + ribose + 3 Pi; \gamma-Pi hydrolysis releases \approx 7.3 kcal/mol; universal energy currency
• NAD⁺, FAD: electron carriers (redox coenzymes)

Proteins

• Amino acid: central C (α-carbon) + H + amino (NH₂) + carboxyl (COOH) + R group; peptide bond (dehydration between COOH & NH₂)
• R groups categories: non-polar (Leu), polar uncharged (Ser), charged (Glu, Lys), aromatic (Phe), special (Pro, Cys –SH, Gly)
• Structural hierarchy:
  1. Primary = AA sequence
  2. Secondary = \alpha-helix & \beta-sheet (H-bonds in backbone)
  3. Tertiary = 3-D folding via H-bond, ionic, hydrophobic, disulfide bridges
  4. Quaternary = multiple polypeptides (subunits) assemble
• Domains = independently folded units; motifs = recurring substructures (β-α-β)
• Chaperones assist folding; misfolding → diseases (e.g., prions)
• Denaturation: loss of structure/function by pH, T°, salt; may be reversible (renaturation experiment with ribonuclease)
• Functions (Table 3.2): catalysis (enzymes), defense (antibodies), transport (hemoglobin), support (collagen), motion (myosin), regulation (hormones), storage (ferritin)

Lipids

• Hydrophobic due to non-polar C–H; insoluble; cluster via hydrophobic effect
• Fatty acid = carboxyl + hydrocarbon tail; saturated (no C=C, solid), unsaturated (≥1 C=C cis, liquid)
• Triglyceride = glycerol + 3 FA; long-term energy storage (2× energy of carbs)
• Phospholipid = glycerol + 2 FA + phosphate + polar head (e.g., choline); amphipathic → bilayers, micelles; basis of membranes
• Steroids: four fused rings; cholesterol (membrane fluidity), hormones (estrogen)
• Terpenes (carotene), prostaglandins (5-C rings, signaling)

Cell Theory & Cell Size

• All organisms composed of cells; cell = basic unit; cells arise from pre-existing cells (continuity)
• Diffusion limits size; surface area (SA) ∝ r^2, volume (V) ∝ r^3; SA:V ratio decreases with size
• Microscopy: light (~200\,nm); TEM (~0.2\,nm); SEM for surfaces

Prokaryotic Cells

• Domains Bacteria & Archaea
• Features: no true nucleus (nucleoid DNA circle), ribosomes, plasma membrane, cell wall (peptidoglycan in bacteria; polysaccharide/ protein in archaea), sometimes capsule, flagella (rotary), internal membrane folds (photosynthetic), magnetosomes

Eukaryotic Cells & Organelles

• Compartmentalization via endomembrane system; DNA in membrane-bound nucleus (double envelope with pores; nuclear lamina)
• Ribosomes: rRNA + protein; free or bound to RER
• Endoplasmic reticulum:
  • RER: ribosomes; synthesize proteins/glycoproteins for secretion/membranes
  • SER: lipid synthesis, detox, Ca²⁺ storage
• Golgi apparatus: cis → trans stacks; modify, sort, package into vesicles
• Lysosomes: hydrolytic enzymes; recycle; Tay-Sachs = hexosaminidase defect
• Peroxisomes: oxidative metabolism, H₂O₂ detox
• Vacuoles: central (plants, storage, turgor), contractile, storage (protists, fungi)
• Mitochondria: outer & inner membrane (cristae), matrix; own circular DNA; oxidative phosphorylation; diseases (MELAS, LHON)
• Chloroplasts: outer membrane + thylakoid grana; stroma; own DNA; photosynthesis
• Endosymbiont theory: mitochondria & chloroplasts derived from engulfed bacteria

Cytoskeleton & Cellular Movement

• Microfilaments (actin): cell shape, motility, cleavage furrow, cytoplasmic streaming
• Microtubules (α/β-tubulin): organize organelles, tracks for kinesin/dynein, mitotic spindle, cilia/flagella (9+2)
• Intermediate filaments (keratin, vimentin): mechanical strength
• Centrosome = MTOC with centrioles (animals); basal bodies anchor cilia/flagella
• Motor proteins + ATP produce movement (myosin–actin; dynein–microtubule)

Extracellular Structures & Cell Junctions

• Plant cell wall: cellulose; plasmodesmata (cytoplasmic channels)
• Animal extracellular matrix (ECM): collagen, elastin, fibronectin; integrins link ECM to cytoskeleton
• Identity markers: glycolipids (ABO), MHC glycoproteins (self vs. non-self)
• Junctions:
  • Adhesive (desmosomes – cadherins + IFs; adherens – actin)
  • Tight/septate (claudins) – seal epithelia
  • Communicating: gap junctions (connexons, 1.5 nm pores) & plasmodesmata

Membrane Structure – Fluid Mosaic Model

• Phospholipid bilayer + proteins + cholesterol; dynamic
• Four components: phospholipids, transmembrane proteins, interior protein network, cell-surface markers
• Lipid bilayer forms spontaneously (hydrophobic effect); fluidity ↑ with unsaturated tails, temp; cholesterol buffers
• Transmembrane domains = hydrophobic α-helices or β-barrels; peripheral proteins anchored by lipids

Membrane Transport Mechanisms

Passive Transport

• Simple diffusion: non-polar molecules down gradient
• Facilitated diffusion: via proteins
  • Channel proteins: ion channels (selective) & gated (ligand-, voltage-, mechano-)
  • Carrier proteins: bind–flip; exhibit saturation kinetics
• Osmosis: water diffusion; tonicity (hyper-, iso-, hypotonic); osmotic pressure = force to stop osmosis
• Aquaporins accelerate water flow

Active Transport (requires energy)

• Uniporter (one solute), symporter (co-transport same direction), antiporter (opposite)
• Na⁺/K⁺ ATPase: 3 Na⁺ out / 2 K⁺ in per ATP \rightarrow ADP + P_i (maintains gradients, membrane potential)
• Coupled (secondary) transport: uses ion gradient; e.g., Na⁺-glucose symport brings glucose against gradient
• Active transport cannot occur via open channels because it needs directional conformational changes & energy coupling

Bulk Transport

• Endocytosis: phagocytosis (solid), pinocytosis (fluid), receptor-mediated (clathrin-coated pits; LDL uptake)
• Exocytosis: vesicle fusion releases hormones, neurotransmitters, ECM proteins