Unit A1–A2: Water, Nucleic Acids, Cell Origins & Structure — Detailed Study Notes

A1.1 Water — Unity & Diversity of Molecules

• Guiding questions
– What physical & chemical properties of water make it essential for life?
– What are the challenges & opportunities of water as a habitat?

A1.1.1 Water as the medium for life

• First cells arose in aqueous environments → water is still the setting for most biochemical reactions.
• Inside organisms, cytoplasm, blood, xylem sap, phloem sap, interstitial fluid, etc. are all water-based.
• Key idea: Life is “wet chemistry”; without water, metabolism would halt.

A1.1.2 Molecular polarity & hydrogen bonding

• O–H bonds in water are polar due to unequal electron sharing (O more electronegative).
• Dipole leads to inter-molecular hydrogen bonds (H-bonds).
• Notation to show polarity
– δ– on O, δ+ on each H.
– Dotted line (···) between δ+H and δ–O of adjacent molecules.
• Each molecule can form up to 4 H-bonds → explains many emergent properties.

A1.1.3 Cohesion & surface tension

• Cohesion = attraction between like molecules; in water, caused by H-bonds.
• Consequences
– Transport under tension in xylem (transpirational pull).
– Surface tension allows insects (e.g., water striders) to inhabit water surface.

A1.1.4 Adhesion to polar/charged surfaces

• Water sticks to cellulose (plant cell walls), soil particles, glass, etc.
• Capillary action: drives water up narrow tubes, soil pores, cell wall microfibrils.

A1.1.5 Solvent properties

• “Universal solvent” for hydrophilic solutes: ions, sugars, aa, nucleotides.
• Most enzymes catalyse reactions in aqueous phase.
• Hydrophobic molecules (lipids) retain distinct functions precisely because they do NOT dissolve → basis of membranes.

A1.1.6 Physical properties relevant to aquatic animals

• Buoyancy: density of water ≈ 1 g cm^{-3} → supports body mass; permits giant sizes (whales).
• Viscosity: ~50 × greater than air → creates drag; promotes streamlined shapes (black-throated loon).
• Thermal conductivity: higher than air → heat loss rapid; mammals like ringed seal have blubber insulation.
• Specific heat capacity c=4.18\,\text{kJ kg}^{-1}\,°\text{C}^{-1} → water buffers temperature fluctuations; stabilises climates & body temps.
• Comparison to air
– Air less dense, low viscosity, poor conductor, low heat capacity → different adaptive pressures for terrestrial taxa.

A1.1.7 (Additional HL) Origin & retention of Earth’s water

• Hypothesis: Delivered by asteroids (carbonaceous chondrites).
• Retention factors
– Earth’s gravity prevented escape of \text{H}_2\text{O} vapor.
– Surface temperatures dropped below 100 °\text{C} → water condensed.

A1.1.8 (Additional HL) Search for extraterrestrial life

• “Goldilocks zone” = orbital radius where liquid water can exist.
• Detection of water (ice, vapor, hydrated minerals) is a primary biosignature target in astrobiology.

• Linking questions
– How do intermolecular forces influence biology?
– Which processes are surface-dependent (e.g., gas exchange, enzymatic catalysis at membranes)?

A1.2 Nucleic Acids — Unity & Diversity of Molecules

• Guiding questions
– How does nucleic-acid structure store heredity?
– How does DNA enable accurate replication?

A1.2.1 DNA as universal genetic material

• All living organisms use DNA; some viruses use RNA but are “non-living”.

A1.2.2 Components of a nucleotide

• Phosphate (circle), pentose sugar (pentagon), nitrogenous base (rectangle).
• Pentose
– DNA: 2-deoxyribose
– RNA: ribose

A1.2.3 Sugar–phosphate backbone

• Covalent phosphodiester bonds create a continuous chain → chemical stability.

A1.2.4 Nitrogenous bases

• Purines: adenine (A), guanine (G).
• Pyrimidines: cytosine (C), thymine (T), uracil (U).

A1.2.5 RNA polymerization

• Condensation reaction: nucleotide + nucleotide → \text{RNA}n + \text{H}2\text{O}.
• Students should draw single-stranded RNA chains showing 5'→3' orientation.

A1.2.6 DNA double helix & complementary base pairing

• Two antiparallel strands (5'→3' opposite 3'→5').
• H-bonds: A–T (2 bonds), G–C (3 bonds) assure complementarity.
• Helical twist ensures uniform diameter.

A1.2.7 DNA vs RNA

• Strands: DNA double; RNA single.
• Sugar: deoxyribose vs ribose (note 2′-OH absent in DNA).
• Base: T in DNA, U in RNA.
• Structural sketches distinguish ribose (OH at C2') & deoxyribose (H at C2').

A1.2.8 Role of complementary base pairing

• Replication: each strand serves as template (semiconservative).
• Expression: transcription uses base pairing; translation uses codon–anticodon pairing.

A1.2.9 Limitless information capacity

• Any length & any sequence possible → astronomical number of permutations =4^n for length n.
• Compact storage: 1 g of DNA could in theory store \approx 215\,\text{PB} of data.

A1.2.10 Universal genetic code

• Same codons specify same amino acids across all life → evidence for common ancestry.

A1.2.11 (Additional HL) Directionality

• Phosphodiester linkage joins 3'-OH to 5'-phosphate → enzymes like DNA polymerase synthesize 5'→3'.

A1.2.12 (Additional HL) Purine–pyrimidine pairing stabilizes helix

• A–T and C–G pairs have equal length → constant helix width.

A1.2.13 (Additional HL) Nucleosome structure

• ~146 bp DNA wraps 1.65 turns around histone octamer (2×H2A, H2B, H3, H4).
• Linker DNA + H1 histone compacts chromatin; visualize via molecular software.

A1.2.14 (Additional HL) Hershey–Chase experiment

• Used ^{32}\text{P}-labeled DNA & ^{35}\text{S}-labeled protein in bacteriophage.
• Only ^{32}\text{P} entered E. coli → DNA is genetic material.
• Illustrates how novel tech (radioisotopes) drives discovery (NOS).

A1.2.15 (Additional HL) Chargaff’s rules & falsification

• Observed [A]\approx[T] & [G]\approx[C] varied across species → disproved tetranucleotide model.
• Example of “certainty of falsification” vs “problem of induction” (NOS).

• Linking questions
– Why might RNA have preceded DNA? (Catalytic, self-replicating).
– How does polymerization create emergent properties (information storage, catalysis)?

A2.1 Origins of Cells — Additional HL Only

• Guiding questions
– What hypotheses explain life’s origin?
– What intermediates bridge non-living to living?

A2.1.1 Early Earth conditions & abiotic synthesis

• No O2 → no ozone; high CO2, CH_4; high UV; high temperatures.
• These conditions allowed spontaneous synthesis of organic molecules (e.g., amino acids).

A2.1.2 Cells as smallest self-sustaining units

• Define living vs non-living; viruses lack metabolism, cannot reproduce without host.

A2.1.3 Difficulty of spontaneous cell origin

• Cells need catalysis, self-replication, self-assembly, compartmentalization.
• Currently only arise from pre-existing cells → “all cells from cells”.
• NOS: Some hypotheses hard to test (ancient conditions not reproducible).

A2.1.4 Miller–Urey experiment

• Simulated lightning + reducing atmosphere → produced amino acids within days.
• Evaluate limitations (modern atmosphere differs; yields racemic mixtures).

A2.1.5 Spontaneous vesicle formation

• Fatty acids self-assemble into bilayer vesicles (protocells) → create internal milieu distinct from environment.

A2.1.6 RNA world hypothesis

• RNA can self-replicate & act as ribozyme (e.g., peptidyl transferase in ribosome).

A2.1.7 Evidence for LUCA

• Universal genetic code, conserved gene families (ribosomal RNA).
• Alternative early lineages likely went extinct due to competition with LUCA descendants.

A2.1.8 Dating first life & LUCA

• Isotope ratios, stromatolite fossils, molecular clocks → life by \approx 3.5–4.0\,\text{Ga}.

A2.1.9 Hydrothermal vent origin

• Ancient vent precipitates hold microfossils; chemiosmotic gradients favorable for metabolism.
• Modern genomic data show enzymes adapted to high temperature & metal-rich environments.

• Linking questions
– Why is heredity essential? (Allows natural selection).
– What features are needed for evolution by natural selection? (Variation, inheritance, differential survival).

A2.2 Cell Structure — Unity & Diversity of Cells

• Guiding questions
– What features are universal vs variable across cells?
– How does microscopy reveal structure?

A2.2.1 Cell theory

• All organisms composed of cells; cells are basic units; cells arise from pre-existing cells.
• Deductive reasoning: any novel organism will consist of ≥1 cell.

A2.2.2 Microscopy skills (application)

• Prepare wet mounts, stain, calibrate eyepiece graticule, focus, measure, create scale bars, photography.

A2.2.3 Advances in microscopy

• Electron microscopy (TEM, SEM) → higher resolution (≈0.1 nm).
• Freeze-fracture, cryo-EM, fluorescent stains, immunofluorescence for protein localization.

A2.2.4 Universal cell structures

• Genetic material (DNA), aqueous cytoplasm, plasma membrane (lipid bilayer).
• Rationale: membranes create internal chem environment; DNA stores info; water enables reactions.

A2.2.5 Prokaryote cell structure (Gram-positive eubacteria)

• Cell wall (thick peptidoglycan), plasma membrane, cytoplasm, nucleoid with naked circular DNA, 70S ribosomes.
• Variation exists (e.g., mycoplasmas lack wall) but not examinable.

A2.2.6 Eukaryote cell structure

• Plasma membrane; compartmentalized cytoplasm; 80S ribosomes.
• Nucleus (double membrane, pores, DNA + histones).
• Organelles: mitochondria, ER (rough & smooth), Golgi, vesicles/vacuoles, lysosomes.
• Cytoskeleton: microtubules, microfilaments.

A2.2.7 Life processes in unicellular organisms

• Homeostasis, metabolism, nutrition, movement, excretion, growth, responsiveness, reproduction.

A2.2.8 Differences among animal, plant, fungal cells

• Cell wall: present in plants (cellulose) & fungi (chitin), absent in animals.
• Vacuoles: large central sap vacuole in plants; small in animals; variable in fungi.
• Plastids: chloroplasts (& chromoplasts, leucoplasts) in plants.
• Centrioles/cilia/flagella: typically animal; rare in plants.

A2.2.9 Atypical eukaryotic structures

• Multinucleate cells: aseptate fungal hyphae, skeletal muscle fibers.
• Enucleate cells: mammalian red blood cells.
• Sieve tube elements: enucleate but alive via companion cells.

A2.2.10 Identification in micrographs (skills)

• Determine prokaryote vs plant vs animal.
• Locate organelles in EMs: nucleoid, cell wall, nucleus, mitochondrion, chloroplast, vacuole, Golgi, RER, SER, chromosomes, ribosomes, plasma membrane, microvilli.

A2.2.11 Drawing & annotation from EMs (skills)

• Ability to draw nucleus, mitochondria, chloroplasts, vacuole, Golgi, RER, SER with labels & functions.

• NOS notes
– Instrumental measurement = quantitative observation.