Chemical Context of Life & Molecular Diversity Lecture

Overview: Chemistry as the Basis of Life

• Life’s “support systems” (water cycles, temperature regulation, nutrient flows) are fundamentally chemical; climate-driven changes (e.g., melting sea ice) alter these systems and, in turn, ecological relationships (phytoplankton blooms vs. black guillemot decline).

• Water is the only common substance that exists naturally as solid, liquid, and gas on Earth; its chemistry underlies this rarity and the habitability of the planet.

• Biology is inherently interdisciplinary: every biological structure or process can be reduced to chemical interactions—or emergent properties arising from them.

Concept 2.1 Matter, Elements & Compounds

• Matter = takes up space + has mass; appears as rocks, oils, gases, organisms.

• Element = substance that can’t be broken down chemically (92 naturally occurring: O, C, H, N, …).

• Compound = 2+ elements combined in fixed ratio, exhibiting emergent properties (Na ⟶ poisonous metal, Cl₂ ⟶ deadly gas, NaCl ⟶ edible salt).

• Essential elements: ≈20–25% of natural elements; humans need 25, plants 17; top four (O, C, H, N) ≈ 96 % of body mass.

• Trace elements (<0.01 %): Fe (universal), I (vertebrate thyroid; deficiency → goiter). Ethical/health angle: iodized salt as a public-health intervention.

• Evolutionary tolerance: sunflower hyper-accumulates heavy metals → used in phytoremediation (post-Katrina), illustrating natural selection for “toxic” soils.

Concept 2.2 Atoms, Isotopes & Energy Levels

• Atom = smallest unit retaining element’s properties; composed of protons (+) & neutrons (0) in nucleus, electrons (–) in cloud.

• Dalton (amu) ≈ 1.7 \times 10^{-24}\,g = mass of 1 p⁺ or n⁰.

• Atomic number (Z) = # protons = # e⁻ in neutral atom.

• Mass number (A) = p⁺ + n⁰; \text{n}^0=A-Z.

• Isotopes: same Z, different n⁰ ⇒ different mass; e.g., {^{12}C},{^{13}C}\text{ (stable)}, {^{14}C}\text{ (radioactive)}.

  • Radioactive isotopes decay → emit particles/energy; applications: fossil dating, metabolic tracers, PET scan (↑ metabolic regions mark tumors).

• Electron shells/energy levels: discrete; 1st shell ≤2 e⁻, 2nd ≤8, 3rd ≤18 …

• Potential energy increases with distance from nucleus; electrons can “jump” shells by absorbing/losing quanta (photosynthesis first step).

• Valence shell (outer) determines chemical behavior; atoms with full shells = inert (He, Ne, Ar).

Concept 2.3 Chemical Bonding & Molecular Shape

• Covalent bonds = shared e⁻ pair; single vs. double bonds.

  • Non-polar: equal EN (H₂, O₂); polar: unequal EN (H₂O).

• Ionic bonds = attraction between cation & anion after e⁻ transfer (Na⁺ + Cl⁻ → NaCl crystal lattice). Strength environment-dependent (strong dry, weak aqueous).

• Hydrogen bonds = attraction between δ⁺ H and δ⁻ O/N; fragile but collectively strong (water, DNA, proteins).

• van der Waals interactions = transient dipoles (gecko adhesion).

• Molecular shape (determined by orbitals & weak bonds) → specificity: morphine mimics endorphin by matching receptor shape; black-box principle: “lock & key.”

Concept 2.4 Chemical Reactions & Equilibrium

• Chemical reaction = making/breaking bonds; reactants → products; atoms conserved.

  • Example: 2H2 + O2 \rightarrow 2H_2O.

  • Photosynthesis: 6CO2 + 6H2O + \text{light} \rightarrow C6H{12}O6 + 6O2 (life’s primary energy input).

• Chemical equilibrium: forward rate = reverse rate; concentrations stabilize (not necessarily equal).

Concept 2.5 Water’s Life-Supporting Properties

Hydrogen-Bond Network

• Each H₂O forms up to 4 H-bonds → dynamic lattice.

1 Cohesion & Adhesion

• Cohesion → surface tension (water strider walks on pond); adhesion to cell walls + transpiration pull lifts sap >100 m.

2 Temperature Moderation

• Specific heat C=1\,\text{cal g}^{-1}\,^{\circ}!\text{C}^{-1}; water resists T change → coastal climate buffering, human thermoregulation.

• Heat of vaporization ≈ 580\,cal\,g^{-1} → evaporative cooling (sweat, transpiration).

3 Expansion Upon Freezing

• Ice < density than liquid (H-bonds lock into lattice) → floating ice insulates aquatic life; climate change threat: shrinking Arctic ice impacts polar bears, guillemots.

4 Versatile Solvent

• Hydration shell surrounds ions/polar molecules (NaCl → Na⁺/Cl⁻); even large proteins dissolve if surface is polar.

• Hydrophilic vs. hydrophobic substances (oil, membrane lipids).

Acid–Base Chemistry

• Auto-ionization: 2H2O \rightleftharpoons H3O^+ + OH^- ⇒ [H^+][OH^-]=10^{-14} (25 °C).

• pH scale: \text{pH} = -\log[H^+] (acid <7, base >7); a change of 1 pH unit = ×10 [H⁺].

• Buffers: weak acid/base pairs (carbonic acid – bicarbonate) stabilize blood at pH 7.4.

• Ocean acidification: $CO2 + H2O \rightarrow H2CO3 \rightarrow H^+ + HCO3^-; H^+ + CO3^{2-} \rightarrow HCO_3^- ⇒ ↓ carbonate → coral calcification ↓40 % (reef threat).

Concept 3.1 Carbon — Molecular Diversity Architect

• Valence 4 → tetrahedral geometry (methane), planar when C=C (ethylene).

• Skeleton variation: length, branching, double-bond position, rings (benzene).

• Hydrocarbons: energy-rich, hydrophobic (fats, fossil fuels).

• Isomers: structural, cis-trans (geometric), enantiomers (pharmacology—ibuprofen, thalidomide; street “crank” vs. decongestant).

• Functional groups (Figure 3.6):

  • Hydroxyl (–OH) alcohols

  • Carbonyl (>C=O) aldehyde/ketone

  • Carboxyl (–COOH) acids

  • Amino (–NH₂) bases

  • Sulfhydryl (–SH) thiols (disulfide bridges)

  • Phosphate (–OPO₃²⁻) energy (ATP)

  • Methyl (–CH₃) epigenetic tag, non-reactive.

• ATP: adenosine + 3 phosphates; hydrolysis ATP + H2O \rightarrow ADP + Pi + \text{energy} (~7 kcal/mol).

Concept 3.2 Polymers & Monomers

• Dehydration reaction links monomers (loss H₂O); hydrolysis reverses.

• 40–50 common monomers → huge polymer diversity (analogous to 26 letters → millions of words).

Concept 3.3 Carbohydrates

Monosaccharides

• General formula CnH{2n}On; glucose C6H{12}O6; aldose vs. ketose; ring formation (α vs. β).

Disaccharides

• Glycosidic linkage (1→4 or 1→2, etc.); sucrose = glucose+fructose; lactose intolerance = lactase deficiency.

Polysaccharides

• Storage: starch (plants: amylose α-1→4, amylopectin α-1→6 branch); glycogen (animals, highly branched).

• Structural: cellulose (β-1→4, unbranched microfibrils; “insoluble fiber”); chitin (N-acetylglucosamine, exoskeleton, fungal walls).

Concept 3.4 Lipids

Fats (Triacylglycerols)

• Glycerol + 3 fatty acids via ester linkage.

• Saturated (no C=C, solid, animal lard) vs. unsaturated (cis C=C, kinks, oils). Hydrogenation → trans fats (health risk).

• Energy density: >2× polysaccharides; adipose tissue cushions, insulates.

Phospholipids

• Glycerol + 2 fatty acids + phosphate (+ choline/others); amphipathic → self-assemble bilayer (membranes).

Steroids

• Four fused rings; cholesterol (membranes, precursor hormones); estrogen/testosterone differ by functional groups.

Concept 3.5 Proteins

Functions

• Enzymatic, defensive, storage, transport, hormonal, receptor, contractile/motor, structural (keratin, collagen).

Amino Acids

• 20 standard; side-chain categories: non-polar, polar, acidic (–), basic (+).

Structure Levels

1. Primary = amino acid sequence.

2. Secondary = α-helix, β-sheet (H-bonds backbone).

3. Tertiary = 3-D fold; interactions among side chains (hydrophobic, ionic, H-bond, disulfide).

4. Quaternary = multiple subunits (hemoglobin α₂β₂, collagen triple helix).

• Denaturation (pH, salt, heat, solvents) disrupts weak bonds → loss of function; some proteins renature.

• Misfolding diseases: Alzheimer’s, Parkinson’s, mad cow, sickle-cell (E→V in β-globin causes aggregation; see Figure 3.23).

• Chaperonins assist folding; structure determination: X-ray crystallography, NMR, cryo-EM.

Concept 3.6 Nucleic Acids & Gene Expression

Nucleotide Structure

• Base (pyrimidine: C,T,U; purine: A,G) + pentose (ribose/deoxyribose) + phosphate.

• Phosphodiester linkage joins 5'-phosphate to 3'-OH → sugar-phosphate backbone (antiparallel strands).

DNA vs. RNA

• DNA: deoxyribose, bases A,T,C,G; double helix, antiparallel, complementary base pairing (A=T, G≡C).

• RNA: ribose, bases A,U,C,G; usually single-stranded; folds via internal pairing (tRNA L-shape).

• Gene expression: DNA \xrightarrow{\text{transcription}} mRNA \xrightarrow{\text{translation}} \text{polypeptide} (ribosome).

Concept 3.7 Genomics & Proteomics

• DNA sequencing revolution: cost per million bases ↓ from >\$5000 (2001) to <\$0.02; Human Genome Project spurred bioinformatics.

• Genomics analyzes entire genomes; proteomics entire sets of proteins; applications: evolutionary relationships, personalized medicine, forensic ecology, cancer therapy, microbial ecology.

• Evolutionary insights: molecular “tape measure”; human vs. chimp genome 95–98 % identical; β-globin sequence similarity mirrors phylogeny (humans≈gorilla > frog).

Problem-Solving & Ethical Extensions

• Detecting seafood fraud by DNA barcoding (coho vs. Atlantic salmon).

• Ocean acidification’s socio-ecological cost: coral reef collapse affects coastal economies, biodiversity ethics.

• Trans fats led to FDA regulation; illustrates intersection of chemistry, policy, and public health.

Key Equations & Values (Quick Reference)

• Photosynthesis: 6CO2 + 6H2O + \text{light} \rightarrow C6H{12}O6 + 6O2

• pH definition: \text{pH} = -\log_{10}[H^+]

• Water constant (25 °C): [H^+][OH^-] = 10^{-14}

• ATP hydrolysis: ATP + H2O \rightarrow ADP + Pi + \text{energy}

• Specific heat of water: 1\,\text{cal g}^{-1}\,^\circ!\text{C}^{-1}

Exam Tips

• Always link molecular structure to function (e.g., why does ice float? → lattice expands).

• For pH questions, remember “every pH unit is ×10”; going from pH 9 → 4 increases [H⁺] by 10^{5}$$.

• When drawing carbon skeletons, count valence: C forms 4 bonds; each line end/corner = C.

• Be able to identify functional groups in unfamiliar molecules.

• Practice translating a DNA sequence (5'→3') to mRNA (complement) to amino acid sequence using codon chart.

• Relate macromolecule properties to dietary/health contexts (fiber, saturated vs. trans fat, lactose intolerance).