A Level Biology (A2) key facts

Energy and respiration

Energy

• ATP + water → ADP + phosphate (P_i), releasing energy in one step; ADP + P_i → ATP during respiration and photosynthesis
• ATP is made in two ways: substrate-linked reactions (in glycolysis and the Krebs cycle) and chemiosmosis (in membranes of mitochondria and chloroplasts)
• Energy value per gram: lipid (about 39 kJ) > protein (about 17 kJ) > carbohydrate (about 16 kJ)
• Lipids have more hydrogen atoms per gram, so they give more reduced NAD and more ATP is made by chemiosmosis
• RQ = molecules of carbon dioxide produced ÷ molecules of oxygen taken in
• Typical RQ values: carbohydrate 1.0, protein about 0.9, lipid about 0.7; a value above 1.0 suggests some anaerobic respiration
• In a respirometer, potassium hydroxide solution absorbs carbon dioxide, so the movement of the liquid shows the volume of oxygen taken in

Respiration

• Glycolysis: glucose (6C) is phosphorylated to fructose 1,6-bisphosphate, which splits into 2 triose phosphate (3C), then oxidised to 2 pyruvate (3C); net gain 2 ATP and 2 reduced NAD
• Link reaction: pyruvate (3C) loses carbon dioxide and hydrogen to form an acetyl group (2C); coenzyme A carries the acetyl group into the Krebs cycle
• Krebs cycle: acetyl (2C) + oxaloacetate (4C) → citrate (6C); each turn gives 2 CO₂, 3 reduced NAD, 1 reduced FAD and 1 ATP
• Decarboxylation removes carbon dioxide; dehydrogenation removes hydrogen, which reduces NAD or FAD
• Lactate fermentation (mammals): pyruvate + reduced NAD → lactate + NAD. Ethanol fermentation (yeast): pyruvate → ethanal + CO₂, then ethanal + reduced NAD → ethanol + NAD
• Rice in flooded fields: aerenchyma in the roots carries oxygen down, root cells use ethanol fermentation, and stems grow faster to keep leaves above the water
• DCPIP and methylene blue turn from blue to colourless when reduced; rate of respiration is proportional to 1 ÷ time taken

Photosynthesis

Photosynthesis as an energy transfer process

• Cyclic photophosphorylation: photosystem I only; makes ATP only
• Non-cyclic photophosphorylation: photosystems I and II; makes ATP, reduced NADP and oxygen
• Photolysis at photosystem II, by the oxygen-evolving complex: 2H₂O → 4H⁺ + 4e⁻ + O₂
• Electrons passing along the electron transport chain release energy that moves protons into the thylakoid space; protons return to the stroma through ATP synthase, making ATP
• Calvin cycle: CO₂ + RuBP (5C) → 2 GP (3C), catalysed by rubisco; GP is reduced to TP using reduced NADP and ATP; RuBP is regenerated from TP using ATP
• Absorption spectrum: how much light a pigment absorbs at each wavelength. Action spectrum: the rate of photosynthesis at each wavelength
• R_f = distance moved by pigment ÷ distance moved by solvent front

Investigation of limiting factors

• Light supplies the energy to make ATP and reduced NADP in the light-dependent stage; low light limits the supply of both to the Calvin cycle
• Carbon dioxide is the substrate for rubisco; a low concentration limits the fixation of carbon in the Calvin cycle
• Temperature affects the enzymes of the Calvin cycle; it has little effect when light is limiting, and above about 40 °C enzymes begin to denature
• DCPIP and methylene blue accept electrons from the light-dependent stage and turn from blue to colourless; rate is proportional to 1 ÷ time taken
• Light intensity is proportional to 1 ÷ d², where d is the distance from the lamp
• Sodium hydrogencarbonate in the water supplies carbon dioxide to an aquatic plant
• Rate of photosynthesis = volume of gas collected ÷ time; volume in a capillary tube = π × r² × length of bubble

Homeostasis

Homeostasis in mammals

• Urea is made in the liver by deamination: the amino group of an excess amino acid is removed, forms ammonia, and this is converted to urea
• Ultrafiltration: high blood pressure in the glomerulus (afferent arteriole wider than efferent) forces water and small solutes into the Bowman's capsule; the basement membrane holds back blood cells and large proteins
• Selective reabsorption in the proximal convoluted tubule: all glucose and amino acids, most water and ions; glucose enters by cotransport with Na⁺; the cells have microvilli and many mitochondria
• Low water potential of blood → osmoreceptors in the hypothalamus → ADH released from the posterior pituitary → more aquaporins in collecting duct membranes → more water reabsorbed → small volume of concentrated urine
• Insulin (from β cells): more GLUT4 proteins in muscle cell membranes and glucose → glycogen in liver and muscle cells, so blood glucose falls
• Glucagon (from α cells) on liver cells: receptor → G-protein → adenylyl cyclase → cyclic AMP (second messenger) → protein kinase A → enzyme cascade → glycogen broken down to glucose
• Test strip: glucose oxidase turns glucose into gluconic acid and hydrogen peroxide; peroxidase uses the hydrogen peroxide to make the chromogen coloured. A biosensor gives an electric current and a number instead

Homeostasis in plants

• Stomata tend to open in light and when carbon dioxide in the leaf is low; they tend to close in darkness, high carbon dioxide, low humidity, high temperature and water stress
• Opening: proton pumps use ATP to move H⁺ out of guard cells → K⁺ channels open and K⁺ enters → water potential falls → water enters by osmosis → cells turgid → stoma opens
• Guard cell walls are thicker on the side next to the pore, and cellulose microfibrils are arranged in hoops, so a turgid cell gets longer and curves
• Guard cells have chloroplasts and many mitochondria; other cells of the lower epidermis have no chloroplasts
• ABA binds to receptors on guard cell membranes → Ca²⁺ enters the cytoplasm as a second messenger → K⁺ leaves → water potential rises → water leaves by osmosis → cells flaccid → stoma closes
• The daily rhythm continues for some days in constant light or constant dark, so it is controlled from inside the plant

Control and coordination

Control and coordination in mammals

• Resting potential (about −70 mV): the sodium–potassium pump uses ATP to move 3 Na⁺ out and 2 K⁺ in, and the membrane is more permeable to K⁺, which diffuses out
• Action potential: voltage-gated Na⁺ channels open and Na⁺ diffuses in (depolarisation); then they close, voltage-gated K⁺ channels open and K⁺ diffuses out (repolarisation)
• An action potential happens only if the threshold is reached, and it is always the same size; a stronger stimulus gives a higher frequency of impulses
• Refractory period: no new action potential can start, so impulses stay separate, travel one way and have a maximum frequency (1 ÷ refractory period)
• Myelin insulates the axon, so action potentials occur only at nodes of Ranvier and the impulse jumps from node to node (saltatory conduction)
• Cholinergic synapse: impulse arrives → Ca²⁺ enters the presynaptic knob → vesicles release acetylcholine → it binds to receptors, Na⁺ channels open in the postsynaptic membrane → acetylcholinesterase breaks it down
• Muscle: impulse passes down T-tubules → sarcoplasmic reticulum releases Ca²⁺ → Ca²⁺ binds to troponin → tropomyosin moves off the binding sites on actin → myosin heads attach and pull; ATP is needed for the heads to detach and reset

Control and coordination in plants

• Venus fly trap: bending a sensory hair opens ion channels in cells at its base → receptor potential → action potentials spread across the lobes
• The trap closes only if hairs are stimulated twice within a short time (two hairs, or one hair twice); this avoids wasting energy on rain or debris
• Closure: rapid movement of ions and water changes the turgor of cells in the lobes, which flip from convex to concave
• Auxin: stimulates proton pumps to move H⁺ into the cell wall → the low pH activates expansins → links between cellulose microfibrils loosen → water enters by osmosis and turgor stretches the wall
• Barley germination: seed absorbs water → embryo makes gibberellin → gibberellin diffuses to the aleurone layer → aleurone cells make amylase
• Amylase hydrolyses starch in the endosperm to maltose, which is turned into glucose for respiration and growth of the embryo

Inheritance

Passage of information from parents to offspring

• Homologous chromosomes: same size, same centromere position and the same genes at the same loci, but they may carry different alleles
• Prophase I: homologous chromosomes pair to form bivalents and crossing over occurs. Metaphase I: bivalents line up on the equator. Anaphase I: whole chromosomes (each with two chromatids) move to opposite poles
• Metaphase II: single chromosomes line up on the equator. Anaphase II: centromeres divide and sister chromatids separate. Result: four haploid cells
• Crossing over: non-sister chromatids of a bivalent exchange sections at chiasmata, giving new combinations of alleles
• Random orientation (independent assortment) of bivalents at metaphase I gives 2ⁿ chromosome combinations, where n is the haploid number
• Animal cells have centrioles and divide by the cell surface membrane pinching in; flowering plant cells have no centrioles and form a new cell wall

The roles of genes in determining the phenotype

• Monohybrid ratios: heterozygote × heterozygote gives 3 : 1 (1 : 2 : 1 with codominance); a test cross (× homozygous recessive) of a heterozygote gives 1 : 1
• Dihybrid ratios for unlinked genes: double heterozygote × double heterozygote gives 9 : 3 : 3 : 1; its test cross gives 1 : 1 : 1 : 1
• Sex linkage: the gene is on the X chromosome, so a male has only one allele and shows it; a father passes his X to all his daughters and to none of his sons
• Autosomal linkage: genes on the same chromosome are inherited together, so a test cross gives many parental types and few recombinants (from crossing over)
• Epistasis: one gene affects the expression of another gene at a different locus, which changes the 9 : 3 : 3 : 1 ratio
• χ² = Σ (O − E)² ÷ E; degrees of freedom = number of classes − 1; if χ² is less than the critical value at p = 0.05, the difference is not significant
• TYR → tyrosinase (none: albinism); HBB → β-globin (sickle cell anaemia); F8 → factor VIII (haemophilia, sex-linked); HTT → huntingtin (Huntington's disease, dominant); Le → enzyme that makes active gibberellin (tall pea plants)

Gene control

• Inducible enzyme: made only when its substrate is present (β-galactosidase with lactose).
• Repressible enzyme: made all the time until its end-product builds up and switches synthesis off.
• lac operon order: promoter, operator, then the structural genes lacZ (β-galactosidase), lacY (lactose permease) and lacA.
• The regulatory gene lacI codes for the repressor, which binds to the operator and stops RNA polymerase transcribing the genes.
• Lactose binds to the repressor and changes its shape, so it leaves the operator and the genes are transcribed.
• Transcription factors are proteins that bind to DNA and increase or decrease the rate of transcription.
• Gibberellin causes DELLA proteins to be broken down; the freed transcription factor then switches on genes such as the one for amylase.

Selection and evolution

Variation

• Phenotype = genotype + effect of the environment.
• Discontinuous: distinct categories, one or few genes, alleles with large effects, shown on a bar chart.
• Continuous: a range of values, many genes (polygenes) with small additive effects, shown on a histogram.
• t = (x̄₁ − x̄₂) ÷ √(s₁²/n₁ + s₂²/n₂), where x̄ is a mean, s a standard deviation and n a sample size.
• Degrees of freedom = n₁ + n₂ − 2.
• Null hypothesis: there is no significant difference between the two means.
• If t is greater than the critical value at p = 0.05, reject the null hypothesis: the difference is significant.

Natural and artificial selection

• Stabilising selection favours the mean; directional favours one extreme; disruptive favours both extremes.
• Founder effect: a few individuals start a new population that carries only some of the original alleles.
• Bottleneck effect: a population falls to very low numbers, alleles are lost, and genetic diversity stays low after recovery.
• Antibiotic resistance: a chance mutation gives resistance, the antibiotic kills the others, and the resistant bacteria survive and multiply.
• Hardy–Weinberg: p + q = 1 for alleles and p² + 2pq + q² = 1 for genotypes (q² = homozygous recessive, 2pq = heterozygous).
• Hardy–Weinberg applies only if the population is large, mating is random, and there is no selection, mutation or migration.
• Maize: inbred lines are homozygous and uniform but weak; crossing two inbred lines gives vigorous, uniform F1 hybrids.

Evolution

• Gene pool: all the alleles of all the genes in a population.
• Evolution: a change in the allele frequencies of a gene pool over many generations, leading to new species.
• Mutation is the original source of new alleles.
• Allopatric speciation: populations are separated by a geographical barrier such as a sea, river or mountain range.
• Sympatric speciation: populations live in the same area but are separated by ecology (food, habitat, breeding time) or by behaviour (courtship, song).
• Fewer base differences in the same gene = a more recent common ancestor.
• Speciation is complete when the two groups cannot interbreed to produce fertile offspring.

Classification, biodiversity and conservation

Classification

• Biological species: organisms that can interbreed to produce fertile offspring. Morphological: same structural features. Ecological: same niche.
• Hierarchy: domain, kingdom, phylum, class, order, family, genus, species.
• Bacteria: peptidoglycan cell walls and ester-linked, unbranched membrane lipids. Archaea: no peptidoglycan and ether-linked, branched lipids. Their rRNA base sequences differ.
• Protoctista: eukaryotes, mostly single-celled, that do not fit the other three kingdoms.
• Fungi: cell walls of chitin, no chlorophyll, heterotrophic, absorb digested food.
• Plantae: multicellular, cellulose cell walls, autotrophic by photosynthesis. Animalia: multicellular, heterotrophic, no cell walls.
• Viruses are classified by nucleic acid: DNA or RNA, single stranded or double stranded.

Biodiversity

• Line transect: record what touches the line. Belt transect: place quadrats along the line.
• Lincoln index: population N = (n₁ × n₂) ÷ m₂, where n₁ = number marked and released, n₂ = number in second sample, m₂ = marked animals in second sample.
• Simpson's index of diversity: D = 1 − Σ(n/N)², where n = number of one species and N = total number of individuals of all species.
• D near 1 means high diversity; D near 0 means low diversity, with one or a few species dominating.
• Spearman's rank correlation: r_s = 1 − (6 × ΣD²) ÷ (n³ − n); use it for ranked data or data that are not normally distributed.
• Pearson's linear correlation: use it for two sets of continuous, normally distributed data with a linear relationship.
• A correlation coefficient runs from −1 to +1; a correlation does not prove cause and effect.

Conservation

• Conserved areas protect the whole ecosystem and keep the species in its natural habitat.
• Zoos: captive breeding that avoids inbreeding, research, education and release to the wild.
• Seed banks: seeds are dried and kept cold so they stay alive for many years. Frozen zoos: gametes, embryos and tissue are stored in liquid nitrogen.
• IVF: eggs are fertilised by sperm in a dish outside the body.
• Embryo transfer: embryos are placed in surrogate mothers, often of a related common species, so one rare female can have many young.
• Invasive alien species have no natural predators or diseases in the new area; they out-compete, eat or infect native species.
• IUCN assesses the extinction risk of species and publishes the Red List. CITES controls international trade in endangered species and their products.

Genetic technology

Principles of genetic technology

• Restriction endonucleases cut DNA at specific base sequences, often leaving sticky ends; cut the gene and the plasmid with the same enzyme.
• DNA ligase joins the sugar-phosphate backbones by forming phosphodiester bonds.
• Reverse transcriptase makes single-stranded cDNA from mRNA; DNA polymerase then makes the second strand.
• A promoter is where RNA polymerase binds; without one that the host recognises, the gene is not transcribed.
• PCR cycle: denature at about 95 °C, anneal primers at about 55–65 °C, extend with Taq polymerase at about 72 °C. The amount of DNA doubles each cycle.
• Taq polymerase is heat stable, so it is not denatured at 95 °C.
• Gel electrophoresis: DNA is negative (phosphate groups) and moves to the anode; shorter fragments move further.

Genetic technology applied to medicine

• Recombinant insulin treats diabetes; factor VIII treats haemophilia; ADA treats one form of SCID.
• BRCA1 and BRCA2: mutant alleles raise the risk of breast cancer; a carrier can choose extra checks or preventive surgery.
• Huntington's disease is caused by a dominant allele and appears in middle age; a test allows a person to plan ahead.
• Cystic fibrosis is recessive; screening finds carriers, and two carriers have a 1 in 4 chance of an affected child each time.
• SCID gene therapy: stem cells are taken from the patient, given a working ADA gene by a vector, and returned.
• Eye disease: the vector carrying the normal allele is injected into the retina, which is easy to reach.
• Somatic gene therapy changes body cells only, so it is not inherited; germ-line therapy would be passed to later generations.

Genetically modified organisms in agriculture

• GM salmon: a growth hormone gene with a promoter from another fish, active all year, so growth hormone is made continuously.
• GM salmon are kept as sterile females in tanks on land so the gene cannot reach wild salmon.
• Herbicide-resistant soybean: the field can be sprayed with glyphosate; the weeds die, there is less competition and the yield rises.
• Bt cotton has a gene from the bacterium Bacillus thuringiensis for a protein toxic to insect larvae, so less insecticide is sprayed.
• Environmental concerns: pollen may carry genes to wild relatives; pests and weeds may evolve resistance; fewer weeds means less food for wildlife.
• Social and economic concerns: seed is patented and costly and must often be bought each year; people want labelling and a choice.
• Benefits: more food from the same area of land, so less natural habitat needs to be cleared.