BIOLOGY LECTURE NOTES – TAXONOMY, SCIENTIFIC METHOD & CHEMICAL FOUNDATIONS

Prokaryotes vs. Eukaryotes, Nuclei & Nucleoids

• Eukaryotes
  • Possess a membrane-bound nucleus
  • DNA → transcription → mRNA occurs inside nucleus; mRNA exits to cytoplasm
• Prokaryotes (Bacteria & Archaea)
  • No true nucleus; DNA localized in a nucleoid region (non-membranous)
  • Historically distinguished from eukaryotes visually; reliance exclusively on morphology can be misleading
  • Molecular comparison of DNA nucleotide sequences provides more accurate relatedness metrics

Modern Taxonomic Hierarchy

• Taxon = any named group of organisms
• Domains (most inclusive): Bacteria, Archaea, Eukarya
  • Bacteria ≈ older lineage; Eukaryotes thought to share a more recent common ancestor with Archaea
• Hierarchy mnemonic: “King Philip Came Over For Great Spaghetti”
  • Kingdom → Phylum → Class → Order → Family → Genus → Species
• Binomial nomenclature (Linnaeus)
  • Two-part Latinized name: Genus species (e.g., Homo sapiens)
  • Formatting rules: both italicized; Genus capitalized, species lowercase
• Why Latin? Dead language → vocabulary no longer evolves; ensures global continuity & high descriptive precision

Scientific Inquiry & Hypothesis Testing

• Process
  1. Ask a question about a natural system
  2. Formulate a testable hypothesis
  3. Derive predictions
  4. Collect empirical data (observational or experimental)
  5. Evaluate whether data supports or refutes hypothesis
• Key ideas
  • No such thing as “scientific proof”; only accumulation of evidence
  • Null hypothesis (H₀): default statement of no effect/relationship
  • Scientists assume they are wrong first, then gather data to reject H₀ in favor of an alternative hypothesis (H₁)
  • Observational studies can precede formal hypothesis testing ("tyranny of hypothesis testers" anecdote)

Case Study 1: Why Do Giraffes Have Long Necks?

• Food-competition hypothesis
  • Predictions:
  1. Neck length variable & heritable
  2. Long-neck individuals access food unavailable to shorter individuals
  3. Giraffes feed predominantly at canopy heights
• Field data
  • Majority of feeding occurs at shoulder height → Prediction 3 falsified
  • Long neck imposes physiological cost: large heart, high blood pressure needed
• Alternative (sexual-selection) hypothesis
  • Long necks confer advantage in intraspecific “necking” combat → winners get more matings → trait frequency rises
  • Demonstrates necessity of revisiting hypotheses upon contradictory data

Case Study 2: “Pedometer” Navigation in Desert Ants

• Question: How do Saharan desert ants return to nest in a straight line after foraging meanders?
• Pedometer hypothesis: Ants maintain internal step count × stride length to compute distance
  • Null: Stride parameters irrelevant to homing accuracy
• Experimental manipulation (3 groups, n=75 each)
  1. Stumps – legs surgically shortened (short stride)
  2. Control – normal legs
  3. Stilts – bristles glued to legs (long stride)
• Results (run 1)
  • Stilts overshot nest; stumps undershot; controls accurate (box-and-whisker plots visualized)
• Results (run 2)
  • After one learning trip with altered legs, ants re-calibrated and homed correctly → dynamic stride integration
• Ethical aside: Insects tolerate limb alteration better than vertebrates; still prompts moral reflection

Fundamental Chemistry for Biology

Atom Structure & Terminology

• Nucleus (chem): protons (+) + neutrons (0); electrons (–) occupy orbitals
• Typical bio-relevant elements: H, C, N, O, P, S, Cl
• Atomic number = # protons; Mass number = protons + neutrons (units: Daltons)
• Spatial metaphor: if atom = stadium, nucleus ≈ peach at center → vast electron cloud spacing

Isotopes & Radioactivity

• Isotope: same element, different neutron count → different mass
  • Example carbon isotopes: ^{12}\text C,\ ^{13}\text C,\ ^{14}\text C
• Atomic weight: weighted avg of natural isotopes
• Radioactive isotopes: unstable; emit radiation during decay; valuable in medical tracing & research

Electron Shells & Orbitals

• Orbitals grouped into shells (1, 2, 3 …) by distance from nucleus
  • Shell 1: 1 orbital → up to 2 e⁻
  • Shell 2: 4 orbitals → up to 8 e⁻
• Valence shell = outermost; chemical behavior dictated by # unpaired valence electrons

Electronegativity (EN)

• Tendency to attract shared electrons
• Biological trend (low → high EN): \text{P} < \text{S} \approx \text C < \text N < \text O
• Highly electronegative atoms (O, N) are more reactive

Bond Types Continuum

1. Non-polar covalent – equal e⁻ sharing; no charge separation
   • Example: \text{H}2,\ \text{C–H} in methane \text{CH}4
2. Polar covalent – unequal sharing; partial charges \delta^{+}/\delta^{-}
   • Water: \text H_2\text O bent geometry (~104.5°), O (δ−) attracts e⁻; H (δ+) repelled → molecular polarity
   • Ammonia \text{NH}_3 similar concept
3. Ionic – complete e⁻ transfer → ions
   • Sodium loses 1 e⁻ → \text{Na}^+ (cation)
   • Chlorine gains 1 e⁻ → \text{Cl}^- (anion)
   • Electrostatic attraction produces crystalline salt (NaCl)
   • Important ionic vocabulary:
     • Cation: net + (electron loss)
     • Anion: net – (electron gain)

Water: Central Biological Solvent

• Formed via polar covalent bonds; bent shape gives rise to:
  • Cohesion/adhesion (H-bond networks)
  • High specific heat & heat of vaporization
  • Solid state (ice) less dense than liquid
• “Meat-sacks full of water” analogy → life depends on these emergent properties

Key Numerical / Symbolic References

• \text{CH}4, \text{NH}3, \text{H}_2\text O – representative molecules along bonding continuum
• n=75 ants per treatment in pedometer study
• Angle in water ≈ 104.5^{\circ} (commonly approximated “~90°” in lecture)

Ethical, Philosophical & Practical Notes

• Language precision critical; Latin binomials italicized to visually segregate scientific names
• “Scientific proof” ≠ evidence-based science; term valid only in mathematics
• Observational data foundational; premature hypothesis tyranny cautioned
• Experimental manipulation of animals (e.g., ant leg surgery) provokes ethical reflection but yields mechanistic insight

Connections & Real-World Relevance

• Prokaryote taxonomy underpins microbiology, medicine, evolutionary biology
• Hypothesis—and null-hypothesis—logic parallels legal burden-of-proof frameworks
• Giraffe neck research informs sexual selection theory; examples like peacock tails, antlers
• Ant navigation principles inspire robotic path-integration algorithms
• Understanding electronegativity & bond types essential for biochemistry, pharmacology, environmental science

Study Tips & Reminders

• Always check valence electrons to predict bonding behavior
• Memorize electronegativity trend C < N < O; oxygen = “electron hog”
• Differentiate bond types with phone-sharing analogy (equal vs. unequal vs. phone seizure)
• When writing Genus species, italicize!
• For null vs. alternative hypotheses: think courtroom—assume innocence (null) until evidence proves otherwise