IB^® Biology HL/SL

In each H–O bond, the oxygen is more electronegative than hydrogen and pulls the shared electrons toward itself. This creates a partial negative charge ($\delta^-$) on oxygen and a partial positive charge ($\delta^+$) on each hydrogen. The resulting DIPOLE is the source of every special property water has.

Because of the dipole, the $\delta^+$ hydrogen of one water molecule attracts the $\delta^-$ oxygen of an adjacent molecule. Each individual hydrogen bond is weak (~10% the strength of a covalent bond) but collectively they are strong because each water molecule can form up to four simultaneous bonds. Hydrogen bonds break and reform millions of times per second in liquid water, freeze into a fixed lattice in ice, and break completely on evaporation.

Water molecules stick to each other (cohesion). At the surface this creates a "skin" of high surface tension: small organisms (water striders, mosquito larvae) walk on it. In plants, cohesion lets a continuous column of water be pulled up the xylem under tension by transpiration (the COHESION-TENSION THEORY). Without cohesion, the column would break and water transport would fail.

Water molecules are also attracted to polar surfaces (cellulose cell walls, soil particles, glass). Adhesion gives capillary action: water rises in narrow tubes against gravity. In soils, adhesion holds water films around particles, making it available to root hairs.

Water has an unusually HIGH SPECIFIC HEAT CAPACITY (~4,200 J kg⁻¹ K⁻¹). Heating water requires breaking hydrogen bonds before kinetic energy can rise, so water resists temperature change. This buffers aquatic habitats against rapid temperature swings and gives organisms (which are mostly water) thermal stability. The HIGH HEAT OF VAPORISATION (~2,260 kJ kg⁻¹) means evaporation removes a lot of heat per gram: the basis of evaporative cooling in sweating, panting, and transpiration.

Polar water molecules surround polar and ionic solutes (sugars, amino acids, salts), forming a HYDRATION SHELL that dissolves them. This makes water the universal solvent of metabolism: virtually every reaction in a cell occurs in aqueous solution. Hydrophobic (non-polar) molecules like lipids do not dissolve and instead aggregate to minimise contact with water: the basis of membrane self-assembly.

Water reaches maximum density at 4 °C, not at 0 °C. Ice is less dense than liquid water because hydrogen bonds in the crystal lattice space molecules apart. Consequence: lakes freeze from the top. The ice insulates water below from sub-zero air, allowing aquatic organisms to overwinter.

Earth's water likely came from a mix of sources: partly from volatile-rich asteroids and comets that struck the early Earth (the D/H isotope ratios of carbonaceous asteroids match terrestrial water reasonably well; those of most comets measured do not), and partly from OUTGASSING of water vapour from Earth's molten interior, which condensed once the surface cooled. The relative contribution of each remains debated. Earth retains water because its gravity is sufficient and its surface temperature stays in the narrow range where water is liquid: the GOLDILOCKS ZONE ("habitable zone") around a star. The search for extraterrestrial life follows water: Mars, Europa (Jupiter), Enceladus (Saturn) all show evidence of past or present liquid water.

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides. They are the only molecules in life that store inheritable information as a sequence of monomers. Their universality (the same four bases and the same genetic code in essentially all known life) is the strongest single piece of evidence for common ancestry (LUCA: the Last Universal Common Ancestor).

Each nucleotide has three parts:

• A PENTOSE SUGAR: deoxyribose in DNA, ribose in RNA. Ribose has an OH on the 2' carbon; deoxyribose has only H. The extra OH makes RNA more reactive (and less stable).
• A PHOSPHATE GROUP attached to the 5' carbon of the sugar.
• A NITROGENOUS BASE attached to the 1' carbon. Bases are either PURINES (adenine, guanine: two-ring) or PYRIMIDINES (thymine, cytosine, uracil: single-ring).

Nucleotides are linked end-to-end by PHOSPHODIESTER BONDS between the 3'-OH of one sugar and the 5'-phosphate of the next, forming the SUGAR-PHOSPHATE BACKBONE.

DNA is DOUBLE-STRANDED. Two polynucleotide strands wind around a common axis to form a right-handed double helix (Watson and Crick, 1953). The two strands are ANTIPARALLEL: one runs 5' → 3', the other 3' → 5'. Bases project inward and pair with bases on the opposite strand by HYDROGEN BONDS.

Adenine always pairs with thymine via 2 hydrogen bonds; guanine always pairs with cytosine via 3 hydrogen bonds. Each base pair has the same width (~2 nm), giving the helix uniform diameter. CHARGAFF'S RULES ([A] = [T], [G] = [C]) are a direct consequence, and were one of the key clues that let Watson and Crick crack the structure. Note: in RNA, uracil replaces thymine, so A–U pairs.

• Strands: DNA double-stranded, RNA usually single-stranded.
• Sugar: deoxyribose vs ribose.
• Bases: T (DNA) vs U (RNA); A, G, C in both.
• Stability: DNA stable (suited to long-term storage); RNA short-lived (suited to transient messages).
• Function: DNA is the genome; RNA includes mRNA (carries genetic message), tRNA (delivers amino acids), and rRNA (catalytic core of ribosomes).

(Hershey–Chase, A1.2.14, and Chargaff's data, A1.2.15, are HL only; Avery and Watson–Crick are background.)

• AVERY, McCARTY & MacLEOD (1944): extended Griffith's transformation experiment. Showed that destroying DNA (with DNase) abolished bacterial transformation; destroying protein or RNA did not. Conclusion: DNA carries the inheritable trait.
• HERSHEY & CHASE (1952, HL): used bacteriophages with either ³⁵S-labelled protein or ³²P-labelled DNA. Only the radioactive DNA entered infected bacteria. Conclusion: DNA, not protein, is the molecule that directs phage reproduction. It was widely influential in persuading biologists that genes are made of DNA.
• WATSON & CRICK (1953): proposed the double-helix structure that immediately suggested how DNA could be REPLICATED (each strand templates a new complementary strand). Built on ROSALIND FRANKLIN'S X-ray diffraction images (Photo 51, showing the helix's spacing and dimensions) and CHARGAFF'S base-ratio data (HL).

The eukaryotic genome (~2 m of DNA in a human cell) must fit into a nucleus only ~6 µm across. The first level of compaction is the NUCLEOSOME: ~147 base pairs of DNA wrap ~1.65 turns around a core of 8 histone proteins (an octamer of H2A, H2B, H3, H4: two copies each). A linker histone (H1) seals the DNA where it enters and exits. Nucleosomes pack into 30-nm fibres, then loops, then chromatids. Histone modifications (acetylation, methylation) influence whether DNA is accessible for transcription: central to gene regulation.

PCR (POLYMERASE CHAIN REACTION) amplifies a target DNA sequence in vitro by repeatedly cycling

1. DENATURATION at ~95 °C: H-bonds between strands break. 2. ANNEALING at ~55 °C: short oligonucleotide PRIMERS bind to specific sequences flanking the target. 3. EXTENSION at ~72 °C: heat-stable Taq polymerase extends from primers using free dNTPs. Each cycle doubles the target → after 30 cycles, ~10⁹ copies. GEL ELECTROPHORESIS then separates DNA fragments by size: DNA is loaded into wells in a porous agarose gel, and an electric field pulls the negatively charged fragments through the gel: smaller fragments travel faster and end up further from the wells. Together, PCR + gel underpin DNA profiling, paternity testing, forensic identification, and pathogen detection.