D Continuity and Change

• Produces exact DNA copies before cell division • Maintains genetic continuity for reproduction, growth, and tissue replacement

• Each new DNA molecule has one original strand and one new strand • Complementary base pairing gives accurate copying; Meselson-Stahl isotope evidence supports the model

• Helicase unwinds DNA and breaks hydrogen bonds between strands • DNA polymerase joins complementary nucleotides to build new strands

• PCR amplifies selected DNA using primers, temperature cycles, and Taq polymerase • Gel electrophoresis separates DNA fragments by size and charge

• PCR and gel electrophoresis support DNA profiling • Applications include forensic identification and paternity testing

• DNA strands have 5' and 3' ends • DNA polymerase adds nucleotides to the 3' end, so new DNA forms 5' to 3'

• Leading strand synthesis is continuous; lagging strand synthesis is discontinuous • Lagging strand forms Okazaki fragments using repeated RNA primers

• Prokaryotic model: primase, DNA polymerase III, DNA polymerase I, and ligase • Primase starts, polymerases extend/replace primers, and ligase joins fragments

• DNA polymerase III removes mismatched nucleotides from the 3' end • Proofreading improves copying accuracy and reduces mutations

• Transcription makes mRNA as a mobile copy of gene information • RNA polymerase synthesizes RNA complementary to the DNA template strand

• Free RNA nucleotides align by complementary base pairing and hydrogen bonding • DNA adenine pairs with RNA uracil, while cytosine pairs with guanine

• DNA template strands are transcribed without altering the base sequence • Sugar-phosphate backbone and base pairing preserve genetic information

• Transcription is the first stage of gene expression • Cells regulate which genes are transcribed according to tissue, stage, and signals

• Translation decodes mRNA at ribosomes to synthesize polypeptides • mRNA codon order determines amino acid sequence

• mRNA provides codons; tRNA carries activated amino acids with anticodons • Ribosomes hold mRNA and tRNAs so peptide bonds can form

• tRNA anticodons pair with complementary mRNA codons by hydrogen bonding • Specific tRNA-amino acid attachment helps ensure correct amino acid addition

• The genetic code is triplet, degenerate, and almost universal • Codons specify amino acids, a start signal, or stop signals

• Genetic code tables use mRNA codons, not DNA triplets • Convert template DNA to mRNA first, then read codons 5' to 3'

• Ribosomes move along mRNA one codon at a time from start to stop • Peptide bonds join amino acids; multiple ribosomes can form a polysome

• Mutations can change codons and therefore amino acid sequence • Changed primary structure may alter folding and function, such as sickle-cell haemoglobin

• RNA polymerase reads template DNA 3' to 5' and synthesizes RNA 5' to 3' • Ribosomes translate mRNA codons in the 5' to 3' direction

• Promoters mark transcription start regions and orientation • Transcription factors help RNA polymerase bind and initiate in eukaryotes

• Non-coding DNA does not code for polypeptide amino acid sequences • Includes introns, regulatory sequences, telomeres, rRNA genes, and tRNA genes

• Eukaryotic pre-mRNA is modified before export and translation • Processing adds a 5' cap and poly-A tail and removes introns by splicing

• Alternative splicing joins different exon combinations from one pre-mRNA • One gene can produce multiple protein variants in different cells or stages

• Translation initiation assembles ribosomal subunits at the start codon AUG • Initiator tRNA enters the P site; A, P, and E sites organize tRNA movement

• Newly made polypeptides may be folded, cleaved, or chemically modified • Preproinsulin processing to active insulin is a key example

• Proteasomes degrade tagged, damaged, or unneeded proteins • Amino acid recycling supports new protein synthesis and proteome quality control

• Gene mutations are changes in the base sequence of DNA • Main types are substitution, insertion, deletion, and duplication

• Base substitutions can create SNPs and change codons • Degeneracy can make substitutions silent, missense, or nonsense

• Insertions or deletions not in multiples of three cause frameshifts • Frameshifts alter downstream codons and often disrupt protein function

• Mutations can arise from replication errors, repair errors, or chromosome damage • Mutagens include chemicals, ionizing radiation, and ultraviolet radiation

• Mutations occur randomly with respect to organism need or advantage • Mutation rate varies with DNA sequence, gene expression, repair, and mutagen exposure

• Germ-line mutations can be inherited by offspring • Somatic mutations affect only descendant body cells and can contribute to cancer

• Mutation is the original source of new alleles and genetic variation • Many mutations are neutral or harmful, but variation supplies material for natural selection

• Gene knockout makes a specific gene non-functional to investigate phenotype • Model organisms such as mice, Drosophila, zebrafish, and Arabidopsis support KO libraries

• Guide RNA directs Cas9 to a complementary DNA target sequence • Cas9 cutting enables deletion, replacement, insertion, or gene disruption

• Conserved sequences remain similar across species or long evolutionary times • Conservation suggests essential function, lower mutation rate, or strong purifying selection

• All cells arise from pre-existing parent cells by cell division • Division produces daughter cells for growth, replacement, repair, or reproduction

• Cytokinesis splits cytoplasm after nuclear division • Animal cells use a contractile ring; plant cells form a vesicle-derived cell plate

• Equal cytokinesis gives daughter cells similar amounts of cytoplasm • Unequal cytokinesis occurs in oogenesis and yeast budding

• Mitosis maintains chromosome number for growth, repair, and asexual reproduction • Meiosis halves chromosome number for gametes and generates genetic diversity

• DNA replication in interphase produces chromosomes with sister chromatids • Sister chromatids remain joined at centromeres until separation

• Mitosis and meiosis both condense chromatin into movable chromosomes • Histones, nucleosomes, spindle microtubules, and motor proteins organize movement

• Prophase condenses chromosomes; metaphase aligns them at the equator • Anaphase separates chromatids; telophase reforms nuclei, producing identical nuclei

• Mitosis phases are identified in diagrams, micrographs, and root-tip squashes • Chromosome condensation, equator alignment, separation, and nuclear membranes are cues

• Meiosis has two nuclear divisions after one round of DNA replication • Homologous chromosomes separate in meiosis I, producing haploid nuclei

• Non-disjunction is failed separation of homologues or sister chromatids in meiosis • Down syndrome usually results from trisomy 21 after non-disjunction

• Crossing over at chiasmata exchanges DNA between non-sister chromatids • Random orientation of bivalents and fertilization create new allele combinations

• Cell proliferation increases cell number by repeated mitosis • Examples include plant meristems, early embryos, skin replacement, and wound healing

• The cell cycle includes interphase, mitosis, and cytokinesis • Interphase has G1 growth, S-phase DNA replication, and G2 preparation

• Interphase is metabolically active, not a resting state • Cells synthesize proteins, replicate DNA, grow cytoplasm, and increase organelles

• Cyclin concentrations rise and fall to activate cyclin-dependent kinases • CDK-cyclin complexes such as MPF control checkpoints and mitosis entry

• Proto-oncogene activation and tumour suppressor loss disrupt checkpoints • Accumulated mutations can cause uncontrolled proliferation and cancer

• Benign tumours grow locally; malignant tumours invade neighbouring tissues • Metastasis spreads cancer cells to form secondary tumours

• Gene expression uses DNA information to affect phenotype through proteins • Main stages are transcription, translation, and protein function

• Transcription factors bind specific DNA sequences to regulate transcription • Promoters, enhancers, activators, and repressors alter RNA polymerase activity

• mRNA degradation controls how long translation can continue • Poly-A tail shortening and nucleases help remove mRNA after use

• Epigenesis develops differentiation patterns from an undifferentiated zygote • Epigenetic changes alter gene activity without changing DNA base sequence

• Genome is all genetic information; transcriptome is expressed mRNA set • Proteome is the dynamic protein set produced by cell type, time, and environment

• Promoter DNA methylation usually represses downstream transcription • Histone methylation or acetylation changes chromatin access and gene expression

• Epigenetic inheritance passes gene-expression changes without DNA sequence change • Persistent DNA methylation or histone tags can survive cell division or gamete formation

• Diet, oxygen, light, drugs, temperature, mutagens, and pollution can alter expression • Air pollution can modify DNA and histone methylation linked to lung disease

• Most epigenetic tags are reset during human egg and sperm development • Retained imprints can silence one parental allele and affect offspring phenotypes

• Monozygotic twins share a genome, helping test genetic versus environmental effects • Epigenetic differences can accumulate with age and different environments

• Hormones regulate eukaryotic expression through receptors and transcription factors • Lac and trp operons show inducible and repressible gene control in bacteria

D2.3.1Solvation with water

• Water forms hydration shells around ions and polar solutes • Hydrogen bonding and charge attraction reduce free water movement

D2.3.2Water movement

• Water moves by osmosis across partially permeable membranes • It moves from hypotonic/lower solute solutions toward hypertonic/higher solute solutions

D2.3.3Osmosis into/out of cells

• Osmosis direction depends on internal and external solute concentration • Isotonic conditions have dynamic water movement but no net osmosis

D2.3.4Changes in plant tissue

• Plant tissue changes mass or length when placed in sucrose solutions • Percentage change graphs estimate isotonic/osmotic concentration

D2.3.5Effects on cells without wall

• Animal cells can lyse in hypotonic solutions and crenate in hypertonic solutions • Freshwater protists use contractile vacuoles to expel excess water

D2.3.6Effects on cells with wall

• Plant cells become turgid in hypotonic solutions as vacuoles swell • Hypertonic solutions cause flaccidity and plasmolysis from water loss

D2.3.7Medical applications

• Isotonic saline prevents harmful water gain or loss in body cells • IV fluids and transplant organ baths must match tissue osmotic concentration

D2.3.8(HL)—Water potential

• Water potential is potential energy of water per unit volume, measured in kPa • Pure water at standard conditions has water potential of 0 kPa

D2.3.9(HL)—Movement from higher to lower potential

• Water moves from higher water potential to lower water potential • Solutes lower water potential by restricting water molecule movement

D2.3.10(HL)—Solute and pressure potential

• Water potential equals solute potential plus pressure potential • Solute potential is zero or negative; pressure potential is often positive in walled cells

D2.3.11(HL)—Water potential in plant tissue

• Water entering plant cells increases pressure potential and dilutes solutes • Water leaving plant cells lowers pressure potential and makes solute potential more negative

• Asexual reproduction uses mitosis without gametes or fertilization, producing clones • Sexual reproduction uses meiosis and fertilization to generate genetic variation

• Meiosis produces haploid gametes and prevents chromosome doubling each generation • Random fertilization fuses gametes to form unique diploid zygotes

• Male gametes are small, numerous, and usually motile • Female gametes are larger, fewer, and contain resources for early development

• Male structures include testes, epididymis, sperm duct, glands, urethra, and penis • Female structures include ovaries, oviducts, uterus, endometrium, cervix, vagina, and vulva

• FSH, LH, oestradiol, and progesterone coordinate ovarian and uterine cycles • Follicle growth, ovulation, corpus luteum, endometrium build-up, and menstruation are linked

• Fertilization occurs in the oviduct after sperm reaches the egg • Sperm and egg nuclei fuse so paternal and maternal chromosomes form the zygote genome

• IVF uses hormones to stimulate superovulation and control egg maturation • Eggs are collected, fertilized outside the body, and embryos transferred to the uterus

• Flowering plants produce male gametes in pollen and female gametes in ovules • Pollination, pollen-tube growth, and fertilization produce embryos inside seeds

• Insect-pollinated flowers often have petals, scent, nectar, sticky pollen, and sticky stigma • Floral structures position pollinators to transfer pollen from anther to stigma

• Cross-pollination increases variation by transferring pollen between different plants • Mechanisms include dioecy, self-incompatibility, and different maturation times

• Self-incompatibility prevents pollen from fertilizing ovules of the same plant • Recognition systems block self-pollen growth and reduce inbreeding

• Seed dispersal reduces competition with parent plants and spreads offspring • Germination uses water uptake, enzyme activation, and food reserve mobilization

• GnRH from the hypothalamus stimulates pituitary FSH and LH release • Oestradiol and testosterone drive primary and secondary sexual development

• Spermatogenesis produces four sperm by equal divisions and differentiation • Oogenesis produces one ovum and polar bodies by unequal cytokinesis

• Acrosome enzymes allow sperm penetration of the zona pellucida • Cortical granule release changes the zona pellucida to block polyspermy

• Cleavage divisions form a morula and then a blastocyst with inner cell mass • The blastocyst implants in the endometrium and begins placental development

• Early embryo/placenta secretes hCG to maintain the corpus luteum • Pregnancy tests use monoclonal antibodies to detect hCG in urine

• Placental villi provide large surface area for exchange without mixing blood • The placenta transfers gases, nutrients, wastes, antibodies, and hormones

• Progesterone and oestradiol maintain endometrium and inhibit further ovulation • Oxytocin and prostaglandins create positive feedback during childbirth contractions

• HRT replaces declining oestradiol/progesterone after menopause to reduce symptoms • Evaluate benefits against risks including coronary heart disease and other side effects

• Haploid gametes fuse during fertilization to form a diploid zygote • Diploid organisms usually carry two alleles for each autosomal gene

• Genetic crosses track parental, F1, and F2 generations using Punnett grids • Flowering plant crosses control pollen transfer to study inheritance ratios

• Genotype is the allele combination inherited for a gene or genes • Homozygous genotypes have matching alleles; heterozygous genotypes have different alleles

• Phenotype is the observable characteristic or trait • Phenotype can be determined by genotype, environment, and their interaction

• Dominant alleles are expressed in heterozygotes • Recessive alleles are expressed when no dominant allele masks them

• Phenotypic plasticity is environment-driven phenotype change without genotype change • It depends on altered gene expression and can be adaptive

• PKU is an autosomal recessive disorder affecting phenylalanine metabolism • Low-phenylalanine diet and newborn screening reduce harmful effects

• SNPs are single-base differences that can create different alleles • Populations can have multiple alleles, but diploid individuals carry at most two

• ABO blood group is controlled by IA, IB, and i alleles • IA and IB are codominant; i is recessive, producing four blood phenotypes

• Codominance expresses both heterozygous alleles, as in AB blood type • Incomplete dominance gives an intermediate heterozygote phenotype

• Human chromosomal sex is usually determined by XX or XY chromosome combination • The SRY/TDF region on the Y chromosome directs testis development

• Haemophilia is an X-linked recessive blood-clotting disorder • Carrier females and affected males are represented with X-linked allele notation

• Pedigree charts show family inheritance across generations • Patterns help infer autosomal dominant, autosomal recessive, or sex-linked inheritance

• Continuous variation often results from polygenic inheritance plus environment • Human skin colour, height, and body mass show many intermediate phenotypes

• Box-and-whisker plots summarize non-normal continuous data • They show median, quartiles, interquartile range, maximum/minimum, and outliers

• Alleles segregate as homologous chromosomes separate during meiosis • Unlinked genes assort independently through random bivalent orientation

• Dihybrid crosses track inheritance of two genes simultaneously • Unlinked autosomal genes can produce 9:3:3:1 F2 or 1:1:1:1 test-cross ratios

• Genome databases identify human gene loci and polypeptide products • Genes on different chromosomes are unlinked; close loci on one chromosome can be linked

• Linked autosomal genes are on the same non-sex chromosome • Linked genes tend to be inherited together unless crossing over occurs between loci

• Recombinants have allele combinations different from parental chromosomes • Crossing over between linked genes produces fewer recombinants than parental types

• Chi-squared tests whether observed genetic data fit expected ratios • Use observed/expected values, degrees of freedom, and p = 0.05 significance

• Homeostasis maintains a stable internal environment within narrow limits • Variables include body temperature, blood pH, glucose, gases, ions, and osmotic concentration

• Negative feedback detects deviation from a set point and reverses it • Receptors, coordinators, effectors, and feedback loops restore normal conditions

• Beta cells secrete insulin when blood glucose rises • Alpha cells secrete glucagon when blood glucose falls, affecting liver and muscle stores

• Type 1 diabetes results from autoimmune destruction of pancreatic beta cells • Type 2 diabetes involves insulin-receptor/response failure and is linked to lifestyle risk factors

• Thermoregulation uses negative feedback to maintain core temperature near 37 °C • Thermoreceptors signal the hypothalamus, which coordinates skin, muscles, liver, and hormones

• Cooling uses vasodilation, sweating, and hairs lying flat • Warming uses vasoconstriction, reduced sweating, shivering, metabolic heat, and brown fat

• Kidneys regulate blood composition by excretion and osmoregulation • Nephrons remove urea and adjust water and ion concentrations in urine

• Glomerular blood pressure drives ultrafiltration into Bowman's capsule • The proximal convoluted tubule selectively reabsorbs glucose, amino acids, ions, and water

• Ascending limb pumps Na⁺/Cl⁻ and is impermeable to water • Descending limb loses water, creating a medulla gradient for water conservation

• Hypothalamus osmoreceptors control posterior pituitary ADH release • ADH inserts aquaporins in collecting ducts, increasing water reabsorption and concentrated urine

• Vasoconstriction and vasodilation redistribute blood according to activity • Exercise and epinephrine increase skeletal muscle flow and reduce gut or renal flow

• Natural selection is the mechanism driving evolutionary change • It acts on heritable variation and can produce adaptation, speciation, and biodiversity

• Mutation creates new alleles, especially when germ-line mutations are inherited • Meiosis and random fertilization create new combinations of existing alleles

• Overproduction of offspring leads to high mortality in limited environments • Competition for food, space, mates, and other resources promotes selection

• Abiotic factors can act as density-independent selection pressures • Temperature, drought, light, salinity, and pH can favour different variants

• Individuals vary in adaptation, survival, and reproductive success • Fitness means passing alleles to offspring in a particular environment

• Natural selection causes evolution only if traits are heritable • Acquired characteristics are not inherited through DNA base sequences

• Sexual selection favours traits that increase mate choice or mating competition success • Displays, ornaments, and behaviours such as birds-of-paradise plumage can be selected

• Selection can be modelled by experimentally controlling selection pressures • Endler's guppy experiments test predation pressure, colour pattern, and mating success

• A gene pool contains all genes and alleles in an interbreeding population • Evolution can be measured as changes in allele frequencies over generations

• Allele frequency is the proportion of a specific allele in the gene pool • Geographically isolated populations can diverge in allele frequencies

• Natural selection increases alleles linked to higher survival or reproduction • Neo-Darwinism combines Mendelian genetics, mutation, recombination, and Darwinian selection

• Directional selection favours one extreme phenotype • Stabilizing favours intermediate phenotypes; disruptive favours both extremes

• Hardy-Weinberg equations calculate allele and genotype frequencies in equilibrium • Use p + q = 1 and p² + 2pq + q² = 1 for two alleles

• Equilibrium requires large population, random mating, no selection, mutation, migration, or drift • Deviations from expected frequencies indicate evolutionary forces acting

• Artificial selection deliberately chooses parents with desired heritable traits • Crop, livestock, and pet breeding show directed change; resistance can arise unintentionally

• Some ecosystems remain stable over long timescales despite local fluctuations • Ancient forests, deserts, and long-lived communities provide evidence of stability

• Stability requires energy input, nutrient cycling, biodiversity, and genetic diversity • Abiotic conditions must remain within tolerance ranges for key species

• Amazon deforestation reduces transpiration, rainfall recycling, and regional cooling • Loss of forest can push rainforest toward savanna-like tipping points

• Mesocosms model ecosystem stability under controlled experimental conditions • Closed bottle systems restrict matter exchange but allow light energy input

• Keystone species have disproportionate effects on community structure • Removal can trigger trophic cascades and ecosystem instability

• Sustainable harvesting removes biomass at or below replacement rate • Managed plant harvests and marine fish stocks require monitoring population recovery

• Agricultural sustainability depends on soil conservation, nutrient balance, and biodiversity • Erosion, leaching, fertilizers, agrochemicals, irrigation, and carbon footprint are key factors

• Eutrophication follows nitrate and phosphate enrichment of water • Algal blooms, decomposition, high biochemical oxygen demand, and hypoxia harm aquatic life

• Biomagnification increases toxin concentration at higher trophic levels • DDT and mercury show how top predators receive the highest doses

• Macroplastics and microplastics persist, fragment, and move through marine ecosystems • Effects include entanglement, ingestion, toxin transport, and food-web impacts

• Rewilding restores natural processes, trophic interactions, and habitat connectivity • Keystone species reintroductions can restart trophic cascades and reduce intensive management

• Ecological succession is community change over time after new habitat or disturbance • Abiotic modification and species interactions drive replacement of pioneer species

• Primary succession begins on bare surfaces without soil • Soil depth, biomass, diversity, food-web complexity, and nutrient cycling increase

• Cyclical succession repeats predictable community changes in the same area • It reflects recurring disturbance or species interactions rather than one fixed endpoint

• Climax communities are relatively stable communities shaped by local conditions • Grazing, burning, mowing, or drainage can arrest succession before climax

• Human activities increase atmospheric CO₂, methane, and other greenhouse gases • Fossil fuels, cement, agriculture, deforestation, and land-use change are major sources

• Positive feedback amplifies warming after an initial climate change • Examples include ice-albedo loss, permafrost methane, ocean CO₂ release, and wildfire feedback

• Boreal forests can shift from carbon sinks to carbon sources • Warming, drought, reduced snowfall, browning, insects, and fire increase tipping-point risk

• Melting landfast ice and sea ice alters breeding, feeding, and resting habitat • Emperor penguins and walruses illustrate species dependent on ice timing and extent

• Ocean warming strengthens stratification and can reduce nutrient upwelling • Reduced upwelling lowers phytoplankton productivity and food supply

• Species ranges can shift poleward, upslope, or contract as climate zones move • Montane birds and North American tree species show changing distribution limits

• Warming causes coral bleaching by disrupting coral-zooxanthellae mutualism • Ocean acidification suppresses calcification, threatening reef biodiversity and collapse

• Carbon sequestration captures and stores atmospheric carbon dioxide • Afforestation, agroforestry, forest regeneration, and peatland rewetting increase carbon stores

• Phenology studies timing of seasonal biological events • Events include flowering, budburst, migration, nesting, breeding, and insect emergence

• Climate change can desynchronize interacting species that rely on matched timing • Arctic plant-reindeer migration and great tit-caterpillar peaks are key examples

• Warmer temperatures can shorten insect development and add generations per year • Spruce bark beetles can shift from one to two annual attack periods

• Climate change alters selection pressures and can shift phenotype frequencies • Finnish tawny owl colour change links milder winters, snow cover, and survival