A Unity and Diversity

• First cells originated in water, where oceans shielded early life from UV radiation • Water remains the medium for most life processes and forms much of cell mass

• O-H covalent bonds and water's V-shape make molecules polar • Hydrogen bonds form between water molecules, not within a molecule • Hydrogen bonding explains many unusual water properties

• Hydrogen bonding creates cohesion and surface tension • Cohesion prevents xylem water columns breaking under tension • Surface tension supports droplets and surface-skating insects

• Water adheres to polar or charged surfaces • Adhesion supports capillary action in soil channels and cellulose cell walls • Cohesion is the stronger force in xylem transport; adhesion helps refill vessels

• Water dissolves ions and polar molecules by hydration and hydrogen bonding • Aqueous solution enables diffusion, transport, enzyme activity, and metabolism • Non-polar molecules are hydrophobic; O₂ and N₂ have low solubility in water

• Specific heat capacity stabilizes aquatic temperatures and body temperature • Thermal conductivity, buoyancy, and viscosity shape aquatic adaptations • Compare black-throated loon and ringed seal adaptations for diving, insulation, and movement

• Asteroid delivery is the syllabus hypothesis for Earth's water origin • Carbonaceous chondrites and Vesta meteorites provide isotope evidence • Gravity and cooler temperatures allowed water vapour to condense and be retained

• Liquid water guides searches for extraterrestrial life • Goldilocks zones mark where surface liquid water could exist • Transit spectroscopy can detect water signatures in exoplanet atmospheres

• DNA is the genetic material of all living organisms • DNA occurs in chromosomes and also in mitochondria and chloroplasts • Some viruses use RNA, but viruses are not considered living organisms

• A nucleotide contains a phosphate group, pentose sugar, and nitrogenous base • DNA nucleotides use deoxyribose; RNA nucleotides use ribose • Bases include purines A/G and pyrimidines C/T/U

• Condensation reactions link nucleotides by sugar-phosphate bonds • The sugar-phosphate backbone is a continuous covalent chain • Bases project from the backbone and carry sequence information

• Genetic information lies in the order of nitrogenous bases • DNA uses A, T, G, C; RNA uses A, U, G, C • Triplet codons specify amino acids in protein synthesis

• RNA is a single-stranded polynucleotide formed by condensation • RNA contains ribose and the bases A, U, G, and C • mRNA, tRNA, and rRNA have different roles in protein synthesis

• DNA has two antiparallel polynucleotide strands in a double helix • Complementary bases pair by hydrogen bonding: A-T and G-C • Draw bases attached to sugars, not phosphates

• DNA is usually double-stranded; RNA is usually single-stranded • DNA uses deoxyribose and thymine; RNA uses ribose and uracil • RNA molecules are usually much shorter than DNA molecules

• A pairs with T in DNA and U in RNA; C pairs with G • Complementary base pairing enables accurate DNA replication • It also enables transcription and translation in gene expression

• DNA can vary in length and in base sequence • Genome size and gene number vary widely between organisms • Base-sequence diversity gives DNA enormous information-storage capacity

• The 64 codons have nearly the same meanings across life • Conserved genes for transcription, translation, and ribosomes support common ancestry • Synonymous mutations can preserve amino acid sequences

• 3'-5' phosphodiester bonds create 5' and 3' strand ends • DNA strands are antiparallel: one 5' to 3', the other 3' to 5' • RNA is synthesized and translated in the 5' to 3' direction

• Purine-pyrimidine pairing keeps DNA helix width constant • A-T and C-G pairs have equal length and fit the model • Hydrogen bonding between complementary bases stabilizes DNA

• DNA wraps nearly twice around an octamer of histone proteins • H1 histone binds linker DNA to the histone core • Nucleosomes package DNA and allow regulated access to genes

• Hershey-Chase used bacteriophages labelled with ³²P in DNA or ³⁵S in protein • ³²P-labelled DNA entered E. coli and appeared in new viruses • Results showed DNA, not protein, carries genetic information

• Chargaff found purines equal pyrimidines across DNA samples • A = T and G = C supported complementary base pairing • These data falsified the tetranucleotide hypothesis

• Early Earth had volcanic gases, high CO₂, methane, water vapour, and little free oxygen • Lack of ozone allowed intense UV radiation at Earth's surface • Prebiotic chemistry may have formed amino acids, bases, sugars, fatty acids, and nucleotides

• Cells are self-sustaining units with membranes, genetic material, and metabolism • Life requires heredity, variation, compartmentalization, and Darwinian evolution • Viruses contain genetic material but lack independent cellular metabolism

• First cells had to arise from non-living materials by self-assembly • Required steps include organic synthesis, polymerization, self-replication, and membranes • Competing hypotheses include protocell-first, gene-first, and metabolism-first models

• Miller-Urey produced amino acids from methane, ammonia, hydrogen, and water vapour • Later experiments used different gases and energy sources, including UV and ionizing radiation • Results support abiotic synthesis of amino acids, fatty acids, sugars, bases, and simple polymers

• Amphipathic fatty acids can spontaneously form monolayers, bilayers, and vesicles • Microspheres could enclose polymers and monomers, creating internal chemistry • Fatty acids likely preceded more complex phospholipid membranes

• RNA can store genetic information and fold into catalytic ribozymes • RNA world hypothesis proposes RNA acted before DNA and protein enzymes • Evidence includes ribosomal RNA catalysis, RNA primers, and ribose forming under prebiotic conditions

• LUCA links the abiotic phase of Earth history to all later cellular life • Universal genetic code, shared biochemistry, and conserved genes support common ancestry • Genomic studies found shared gene families likely inherited from LUCA

• Fossils and surrounding rocks can be dated by radiometric methods • Molecular clocks use DNA or protein changes to estimate divergence times • LUCA may have existed around 4 billion years ago

• Nuvvuagittuq haematite tubes provide fossil evidence from ancient hydrothermal vents • Conserved genes suggest LUCA was anaerobic, CO₂-fixing, H₂-dependent, N₂-fixing, and thermophilic • Hydrothermal vents supplied hydrogen, carbon dioxide, iron, heat, and chemosynthetic energy

• Cells are the basic structural and functional units of living organisms • Cells carry out essential life processes and are usually microscopic

• Use light microscopes to prepare mounts, stain specimens, and observe cells • Measure cells with eyepiece graticules and stage micrometers • Calculate magnification, actual size, and scale bars

• Resolution, not only magnification, determines visible detail • TEM reveals internal ultrastructure; SEM reveals surface detail • Cryogenic EM, fluorescence, and immunofluorescence reveal molecules and specific structures

• All cells have a plasma membrane, cytoplasm, DNA, and ribosomes • These structures control exchange, support metabolism, store information, and make proteins

• Prokaryotes lack a nucleus and membrane-bound organelles • Structure includes cell wall, plasma membrane, cytoplasm, 70S ribosomes, naked circular DNA, and plasmids • E. coli, Bacillus, and Staphylococcus are bacterial examples

• Eukaryotes have a nucleus, 80S ribosomes, cytoskeleton, and compartmentalized cytoplasm • Organelles include mitochondria, ER, Golgi apparatus, vesicles, lysosomes, and vacuoles • Plant cells may include chloroplasts, large vacuoles, and cellulose cell walls

• Unicellular organisms carry out all life processes in one cell • Examples include Amoeba, Chlamydomonas, and Escherichia coli • Processes include nutrition, metabolism, response, excretion, homeostasis, growth, and reproduction

• Animal, fungal, and plant cells differ in cell walls, vacuoles, and storage structures • Plant cells have cellulose walls, chloroplasts, and large permanent vacuoles • Animal cells may have centrioles, cilia, flagella, lysosomes, and temporary vacuoles

• Atypical cells show limits of simple cell theory • Examples include multinucleate fungal hyphae and striated muscle fibres • Red blood cells and phloem sieve tubes lack nuclei at maturity

• Identify prokaryotic, plant, and animal cells in light and electron micrographs • Recognize organelles such as nucleus, mitochondria, chloroplasts, ER, Golgi, vacuoles, and ribosomes • Use visible structures, scale, and tissue context as evidence

• Draw clear biological diagrams from electron micrographs without shading • Label visible organelles and include magnification or scale information • Annotate structures with functions where required

• Larger prokaryotic cells engulfed smaller prokaryotes that became mitochondria or chloroplasts • Evidence includes binary fission, circular naked DNA, 70S ribosomes, double membranes, and similar size • Chloroplast DNA links to cyanobacteria; mitochondrial DNA links to alphaproteobacteria/Rickettsiales

• Differentiation produces specialized cells, tissues, and organs in multicellular organisms • Cells share the same genome but express different genes • Proteome differences reflect cell specialization

• Multicellularity evolved repeatedly in fungi, algae, plants, and animals • Required features include cell adhesion, communication, and differentiation • Advantages include larger body size and cell specialization

• Viruses are non-cellular obligate parasites with fixed small size • Viral genome is either DNA or RNA, surrounded by a protein capsid • Viruses lack cytoplasm, ribosomes, and most metabolic enzymes

• Viral genomes may be DNA or RNA, single- or double-stranded, linear, circular, or segmented • Capsids may be helical, polyhedral, conical, or complex • Viruses may be enveloped or non-enveloped; examples include TMV, HIV, coronavirus, and lambda phage

• Lambda phage attaches to E. coli and injects double-stranded DNA • Viral DNA remains separate, host DNA is degraded, and host machinery makes viral parts • New phages assemble and are released by lysis of the host cell

• Lambda phage DNA integrates into the E. coli chromosome as a prophage • The prophage replicates with the host genome during binary fission • Stress can induce prophage excision and entry into the lytic cycle

• Viruses are likely polyphyletic, with several independent origins • Hypotheses include virus-first, escaped genes/progressive, and regressive/reduction models • Shared obligate parasitism may reflect convergent evolution

• Viral evolution is driven by mutation, recombination, large population size, and short life cycles • RNA viruses often mutate rapidly because replication lacks proofreading • Influenza antigenic drift/shift and HIV reverse transcriptase errors affect vaccines and treatments

A3.1.1Variation as defining feature of life

• Variation occurs between individuals within every species • Continuous variation often results from polygenes and environmental effects • Darwin's observations of variation supported natural selection

A3.1.2Species as groups with shared traits

• Species can be grouped by shared morphology and structural traits • Morphological species concept is useful in fieldwork, fossils, and many plants • Sexual dimorphism and within-species variation can make morphology difficult

A3.1.3Binomial system

• Binomial nomenclature gives each species a universal two-part Latin name • Genus is capitalized; species is lowercase; both are italicized or underlined • Species in the same genus share similar traits

A3.1.4Biological species concept

• Biological species concept defines species by interbreeding and fertile offspring • It emphasizes gene flow between members of the same species • Limits include extinct organisms, asexual species, and cases with gene flow between distinct forms

A3.1.5Difficulties in distinguishing species

• Speciation is gradual as isolated populations diverge • Populations may still be theoretically able to interbreed but cannot meet • Species boundaries can therefore be partly arbitrary

A3.1.6Diversity in chromosome numbers

• Chromosome number is usually constant within a species but varies between species • Diploid chromosome numbers are even because chromosomes occur in homologous pairs • Examples include fruit fly 8, rice 24, human 46, chimpanzee 48, and dog 78

A3.1.7Karyotyping and karyograms

• Karyotypes show chromosome number and structure in a cell • Karyograms arrange chromosomes by length, banding pattern, and centromere position • Human chromosome 2 supports fusion from two ancestral ape chromosomes

A3.1.8Unity and diversity of genomes within species

• A genome is all genetic information in an organism • Members of a species share most of their genome but differ at variants • SNPs are common single-base differences used as biological markers

A3.1.9Diversity of eukaryote genomes

• Eukaryote genomes vary in size and base sequence • Between-species variation is much larger than within-species variation • Not all DNA codes for proteins

A3.1.10Comparison of genome sizes

• Genome size is the DNA amount in one chromosome set • Larger genome size does not necessarily mean greater organism complexity • Polyploidy can greatly increase genome size, especially in plants

A3.1.11Whole genome sequencing

• Whole genome sequencing began at scale with the Human Genome Project • Current uses include evolutionary relationships, gene discovery, and pathogen research • Future uses include personalized medicine, diagnosis, disease prevention, and vaccine targets

A3.1.12(HL)—Difficulties with biological species concept

• Biological species concept does not apply well to asexual organisms • Bacteria gain diversity by mutation and horizontal gene transfer • Transformation, plasmids, and recombination blur bacterial species boundaries

A3.1.13(HL)—Chromosome number as shared trait

• Diploid and haploid chromosome numbers are usually constant within a species • Meiosis conserves chromosome number across generations • Different chromosome numbers can prevent fertile hybrids, as in mules

A3.1.14(HL)—Dichotomous key development

• Dichotomous keys identify organisms through paired yes/no choices • Construct keys from observable features arranged in a character matrix • Local plant or animal species can be used to build and test keys

A3.1.15(HL)—Environmental DNA barcodes

• DNA barcoding identifies species using short sequences from selected genes • eDNA from habitats can be amplified by PCR and compared with databases • Barcoding is rapid and useful for damaged, partial, or hard-to-identify specimens

• Classification organizes biodiversity into groups with shared characteristics • Universal taxonomy supports communication, comparison, and further study • Classification helps reveal functional, structural, and evolutionary relationships

• Traditional hierarchy uses kingdom, phylum, class, order, family, genus, and species • Fixed ranks can be arbitrary and may not match evolutionary divergence • Morphological similarity can reflect convergence rather than common ancestry

• Evolutionary classification aims to match phylogeny • Natural groups are monophyletic and include an ancestor plus all descendants • DNA and protein evidence can correct misleading morphology

• A clade is a group evolved from a common ancestor • Clades are identified using shared derived characteristics, or synapomorphies • Evidence may be anatomical, behavioural, genetic, or protein sequence data

• Sequence differences accumulate after clades diverge • Molecular clocks estimate divergence time from DNA or amino acid differences • Rates must be calibrated and can vary between genes or lineages

• Cladograms can be built by aligning DNA, RNA, or protein sequences • Computer analysis infers trees that best explain sequence similarities • Parsimony favours the tree requiring the fewest evolutionary changes

• Nodes represent common ancestors or speciation events • Branch points show order of divergence, not simply end-position similarity • Roots, terminal branches, ingroups, outgroups, and sister groups support interpretation

• Cladistics tests whether traditional taxa match evolutionary relationships • Figwort family reclassification used conserved chloroplast gene sequences • Some morphological similarities were falsified as convergence

• rRNA sequence evidence separated prokaryotes into eubacteria and archaea • Three domains are Archaea, Eubacteria, and Eukarya • Domains differ in rRNA, chromosomes, histones, introns, cell walls, and membrane lipids

• Evolution is cumulative change in heritable characteristics of a population • Acquired characteristics are not inherited in the Darwinian sense

• Universal DNA, genetic code, ATP use, and core metabolism support common ancestry • DNA, RNA, and protein sequence differences indicate relatedness and divergence

• Selective breeding shows traits can change rapidly under selection • Examples include pigeons, domesticated animals, Brassica crops, wheat, and maize

• Homologous structures share ancestry even when functions differ • Vertebrate pentadactyl limbs support divergent evolution and adaptive radiation

• Analogous structures have similar functions but different evolutionary origins • Similar selection pressures can produce convergence, such as bat and insect wings

• Speciation forms new species by splitting a pre-existing species • Isolated gene pools diverge through selection, mutation, and genetic drift

• Reproductive isolation reduces gene flow so populations can diverge • Geographic separation and different selection pressures can drive speciation • Chimpanzees and bonobos illustrate river-linked isolation and divergence

• Allopatric speciation involves geographic isolation • Sympatric speciation occurs without spatial separation • Temporal, behavioural, or intrinsic isolation can separate sympatric populations

• Adaptive radiation produces many related species from one ancestor • Divergence into different niches reduces competition • Darwin's finches illustrate beak adaptation to different feeding niches

• Prezygotic barriers include habitat, temporal, and behavioural isolation • Postzygotic barriers include inviable or infertile hybrids, such as mules

• Polyploidy can cause abrupt reproductive isolation in plants • Autopolyploidy and allopolyploidy can create fertile new lineages • Hybridization in Persicaria illustrates plant speciation by chromosome change

• Biodiversity is the variety of life in its forms, levels, and combinations • It includes ecosystem, species, and genetic diversity • Species diversity depends on richness and evenness; Simpson's reciprocal index compares communities

• About 9 million species are estimated, with many still undescribed • Fossils and radiometric dating give incomplete evidence of past biodiversity • Current species diversity may be higher than in the past, but fossil gaps make this uncertain

• Human activity is driving a sixth mass extinction • Hunting, habitat change, and resource use caused extinctions such as North Island giant moa • Caribbean monk seal loss shows how removing a top predator can alter food webs

• Ecosystem loss is mainly caused by anthropogenic disturbance and habitat conversion • Mixed dipterocarp forests in Borneo are lost through logging and oil palm plantations • Great Barrier Reef loss is linked to climate, pollution, fishing, and other human pressures

• IPBES reports and repeated biodiversity surveys provide evidence of crisis • Richness, evenness, and Simpson's reciprocal index can compare disturbed and undisturbed habitats • Peer-reviewed studies and citizen science both contribute data, with reliability checks needed

• Human population growth increases demand for food, housing, energy, and land • Major drivers include overexploitation, urbanization, deforestation, agriculture, mining, and pollution • Invasive species such as lionfish and water hyacinth can outcompete or disrupt native species

• Conservation needs multiple approaches because species and threats differ • In situ conservation uses protected areas, reserve design, corridors, active management, and rewilding • Ex situ conservation uses zoos, captive breeding, botanic gardens, seed banks, and tissue banks

• EDGE prioritizes evolutionarily distinct and globally endangered species • It combines phylogenetic uniqueness with IUCN extinction risk • The goal is to prevent disproportionate loss of evolutionary history