Biological organization, inheritance, regulation and ecosystems
Cells, biomolecules, heredity and metabolism
Module 1: Cell Biology - Ultrastructure, Membranes and Cell Division
Cell biology links organelle structure with function, membrane exchange and cell division. This chapter reviews shared foundations and interprets supplied water-potential data. It does not assert a target paper structure or marking scheme.
Organelles: structure fits function
Prokaryotic cells lack a membrane-bound nucleus. Bacteria commonly have a nucleoid, 70S ribosomes and a peptidoglycan wall, but wall-less bacteria exist; archaeal walls do not contain peptidoglycan. Plasmids and flagella occur in some cells, not all. Eukaryotes compartmentalise functions: nucleus with chromatin and nucleolus; mitochondria with inner membrane and matrix; chloroplasts with thylakoids and stroma in photosynthetic cells; rough and smooth ER; Golgi apparatus and ribosomes. A typical plant cell additionally has a cellulose wall and a large vacuole. A structure should be identified by its actual features rather than assuming every member has every listed organelle.
Membranes and transport
The fluid mosaic model describes a lipid bilayer with proteins and, in suitable cells, sterols, glycoproteins and glycolipids. Cholesterol is characteristic of many animal membranes; sterol composition differs among organisms. Simple diffusion moves suitable molecules down a chemical gradient. Osmosis is net water movement down water potential across a selectively permeable membrane. Facilitated diffusion uses proteins without direct ATP hydrolysis; carrier-mediated flux can saturate. Primary active transport can use ATP directly, while secondary transport uses an electrochemical gradient maintained by another energy-dependent process. The mammalian sodium-potassium pump moves three sodium ions out and two potassium ions in per ATP in its ordinary cycle. Sodium-coupled glucose uptake illustrates secondary transport. Vesicular transport uses energy. Surface area, diffusion distance, gradients and permeability together influence exchange.
Mitosis and the cell cycle
Interphase: G1 growth, S DNA replication, G2 organelle replication. Prophase - chromosomes condense, spindle forms, nuclear envelope breaks down. Metaphase: spindle microtubules attach through kinetochores at centromeric regions and chromosomes align at the equator. Anaphase - centromeres divide and sister chromatids move to opposite poles. Telophase - nuclei reform and chromosomes decondense. Cytokinesis is by cleavage furrow in animals, cell plate in plants. Mitosis maintains genetic constancy for growth, repair and asexual reproduction.
Worked example
A plant cell has solute potential -1200 kPa and pressure potential +400 kPa, giving water potential -800 kPa. In an external solution at -900 kPa, initial net water movement is out because -800 is higher than -900. As water leaves, pressure and solute concentration can change. The initial comparison does not prove complete plasmolysis: a new equilibrium may retain positive pressure. Distinguish a direction predicted by initial potentials from a final cellular condition that requires further information.
Traps that cost marks
Common errors include adding potentials with inconsistent signs, describing osmosis without comparing water potentials, and confusing centromeres with centrioles. Mitosis normally preserves the starting chromosome complement; it does not automatically turn every cell into a haploid or diploid product. DNA replication precedes chromosome separation. Specify whether an active transport step uses ATP directly or a pre-existing electrochemical gradient.
Module 2: Biomolecules - Water, Carbohydrates, Lipids, Proteins and Enzymes
Biochemistry relates water, carbohydrates, lipids and proteins to biological functions. Interpret structure, chemical bonds and supplied observations. This is shared conceptual practice rather than a claim about an official module or paper.
Water
Water is dipolar, so it forms hydrogen bonds: high specific heat capacity and high latent heat of vaporisation (thermal stability, cooling by sweating), cohesion and surface tension (xylem transport), a good solvent for ions and polar molecules, and ice floating because it is less dense than liquid water.
Carbohydrates and lipids
Monosaccharides (trioses to hexoses; α- and β-glucose differ only in the position of the –OH on carbon 1) join by condensation, forming glycosidic bonds, to give disaccharides (maltose, sucrose, lactose) and polysaccharides. Starch (amylose helix plus branched amylopectin) stores energy in plants, glycogen is more branched for animals, cellulose is unbranched β-1,4 chains held by hydrogen bonds into microfibrils for strength. Reducing sugars (all monosaccharides, maltose, lactose) reduce Benedict's solution; sucrose is non-reducing. Triglycerides form by condensation of glycerol with three fatty acids into ester bonds; saturated chains pack tightly, cis-unsaturated chains commonly kink and reduce close packing; trans configurations behave differently. Phospholipids are amphipathic and build bilayers.
Proteins and enzymes
Amino acids join through peptide bonds. Protein primary structure is sequence; secondary alpha-helices and beta-sheets involve backbone hydrogen bonding; tertiary structure depends on several interactions and quaternary structure joins subunits. Fibrous and globular describe broad structural patterns rather than universally separate functions. Most enzymes are proteins, while some RNA molecules also catalyze reactions. Catalysts lower an activation barrier without changing the reaction equilibrium. Rate depends on temperature, substrate, enzyme amount and assay conditions. High temperature can destabilize a protein; pH can change protonation and binding without necessarily causing unfolding. Denaturation usually disrupts the folded state rather than cleaving every peptide bond. In a simple reversible competitive model apparent Km increases while Vmax is unchanged. In a pure noncompetitive model Vmax decreases while Km is unchanged. Those kinetic patterns do not uniquely identify an atomic binding pocket. Cofactors can support catalytic activity.
Worked example
A supplied food-test dataset reports no reducing-sugar signal from sucrose before hydrolysis and a positive signal afterward, with suitable positive and negative controls. Hydrolysis can release glucose and fructose, explaining the changed observation. Interpret the recorded chemistry rather than treating this paragraph as an operating procedure. Appropriate assay conditions and controls matter: a negative result can reflect a failed assay as well as absence of the target compound.
Traps that cost marks
Avoid calling every polysaccharide reducing, confusing alpha- and beta-glucose linkages, or treating enzymes as organisms that are killed. A declining measured rate can reflect substrate depletion, pH effects, inhibition or instability; inspect the supplied conditions before assigning a cause. A typical glycerophospholipid has two fatty-acid tails and a phosphate-containing head, unlike a triacylglycerol with three fatty acids.
Module 3: Genetics - DNA, Gene Expression, Meiosis and Inheritance
Genetics traces the storage, replication and expression of information, chromosome behavior and inheritance probabilities. Use explicit organism, ploidy and dominance assumptions. Shared practice does not establish a current official module or paper format.
DNA structure and replication
Nucleotides: deoxyribose, phosphate, and a base - purines adenine and guanine, pyrimidines thymine and cytosine. Nucleotides link 3′–5′ by phosphodiester bonds into two antiparallel strands; A pairs with T by two hydrogen bonds, G with C by three. Replication is semi-conservative: helicase unwinds, each strand acts as a template, DNA polymerase adds nucleotides 5′→3′, the leading strand is continuous while the lagging strand forms Okazaki fragments joined by ligase. Meselson–Stahl's density-gradient experiment supports this.
Gene expression
The code is a triplet, degenerate, non-overlapping and (nearly) universal, with AUG the usual start and UAA/UAG/UGA stop codons in the standard code; alternative initiation and code exceptions exist. Transcription: RNA polymerase makes mRNA from the template strand; eukaryotic mRNA is spliced to remove introns. Translation: mRNA binds a ribosome, tRNA anticodons pair with codons, peptide bonds form between amino acids, and the polypeptide is released at a stop codon.
Meiosis and inheritance
Meiosis I separates homologous chromosomes and meiosis II separates sister chromatids. A standard diploid-cell model gives four haploid products, though not all become equivalent functional gametes. Crossing over and independent assortment can create variation. An Aa by Aa cross gives a 3:1 phenotype expectation only with complete dominance and suitable viability assumptions. Aa by aa gives a 1:1 expectation; AA by aa does not. Codominance and multiple alleles require different genotype-to-phenotype rules. In a conventional XY model, an X-linked locus can be hemizygous in males; sex-determination systems differ among organisms. A 9:3:3:1 expectation requires an AaBb by AaBb cross, independent assortment, complete dominance at both loci and the stated viability model. Nearby linked loci often yield excess parental combinations in an informative test cross.
Worked example
A supplied informative fly test cross gives 41 grey-normal, 39 ebony-vestigial, 10 grey-vestigial and 9 ebony-normal offspring. Under the stated parental-phase and viability assumptions, the parental total is 80 and recombinant total 19, suggesting linkage rather than a 1:1:1:1 model. The observed recombinant frequency is 19/99, about 19.2 percent. Treating this percentage as a map distance is a short-interval approximation; undetected multiple crossovers can make actual genetic distance larger. The observation estimates a frequency, not a universally exact physical distance or an assumption-free genetic map.
Traps that cost marks
Confusing the template strand with the coding strand. Saying DNA polymerase works 3′→5′. Giving genotype ratios where gamete or phenotype ratios are asked. Using a test cross with anything other than a homozygous recessive. Assuming independent assortment for linked genes. Forgetting that crossing over occurs in prophase I, not anaphase.
Metabolismo celular: catabolismo y anabolismo, respiración, fotosíntesis, enzimas
Esta revisión relaciona rutas metabólicas, compartimentos celulares, transferencia de electrones y modelos enzimáticos. Los balances se interpretan con los supuestos indicados, sin atribuir un número fijo universal de ATP ni una estructura oficial de examen.
Enzimas
Las enzimas reducen la barrera de activación. Vmax depende de la cantidad de enzima en el modelo; Km es un parámetro cinético y no equivale universalmente a una constante de afinidad. En el modelo competitivo reversible sencillo aumenta Km aparente sin cambiar Vmax. En el modelo no competitivo puro disminuye Vmax sin cambiar Km. Un patrón cinético no demuestra por sí solo una localización de unión; la regulación alostérica puede producir varios patrones. También existen modificación covalente y retroinhibición.
Catabolismo
Glucólisis en el citosol: glucosa → 2 piruvato, 2 ATP netos y 2 NADH. El piruvato se descarboxila a acetil-CoA (2 NADH). Ciclo de Krebs: dos vueltas por glucosa, con 6 NADH, 2 FADH₂, 2 ATP y CO₂. Cadena respiratoria en la membrana interna y quimiosmosis: el gradiente de protones mueve la ATP sintasa y el aceptor final es el O₂, que forma agua. Algunos modelos modernos aproximan 2,5 ATP por NADH y 1,5 por FADH2 en condiciones eucariotas determinadas. El rendimiento real depende del acoplamiento, las lanzaderas y otros costes; los valores 3 y 2 pertenecen a una contabilidad histórica y no son universales.
Anabolismo
Fotosíntesis: fase luminosa en tilacoides, con fotólisis del agua (origen del O₂), transporte de electrones por los fotosistemas II y I y fotofosforilación, que producen ATP y NADPH. Fase oscura o ciclo de Calvin en el estroma: fijación por la RuBisCO, reducción y regeneración de la ribulosa-1,5-bifosfato, consumiendo ATP y NADPH. Quimiosíntesis: bacterias que oxidan compuestos inorgánicos para reducir CO₂.
Ejemplo resuelto
Un conjunto de datos suministrado presenta la misma Vmax y una Km aparente diez veces mayor con inhibidor. En el modelo reversible sencillo es compatible con competencia y predice que aumentar sustrato reduce el efecto. No demuestra que el inhibidor ocupe un bolsillo atómico idéntico. Una Vmax menor podría corresponder a inhibición mixta u otros cambios, no solo a no competitiva pura. La falta de recuperación después de un lavado tampoco prueba por sí sola irreversibilidad: deben considerarse el tiempo, la eliminación incompleta y la estabilidad de la enzima.
Errores que cuestan puntos
Colocar la glucólisis en la mitocondria, olvidar que el O₂ liberado procede del agua y no del CO₂, confundir el ciclo de Calvin con el de Krebs, contar ATP brutos en vez de netos en la glucólisis y creer que la fermentación produce ATP en grandes cantidades (la reducción fermentativa regenera NAD+ y permite continuar la glucólisis, donde se obtiene ATP por fosforilación a nivel de sustrato).
Physiology, immunity, ecology and evolution
Organismal Structure and Function (Anatomy and Physiology)
Physiology
Items test how organ systems maintain internal stability, how exchange surfaces are built, and how structure at each level serves function.
Homeostasis and control
Negative feedback reverses a deviation: a sensor detects change, an integrating center compares it with a set point, and an effector counters it (insulin lowers glucose; sweating lowers temperature). Positive feedback amplifies a change and must terminate (oxytocin in labor, clotting cascade). Levels of organization run from cells to tissues (epithelial, connective, muscle, nervous) to organs to systems.
Systems
- Circulation: mammals have a four-chambered heart and double circulation; arteries carry blood away from the heart, and pulmonary arteries carry deoxygenated blood.
- Gas exchange: alveoli and gill lamellae maximize surface area and minimize diffusion distance; countercurrent flow in fish gills maintains a gradient along the whole lamella.
- Digestion: enzymes act at specific pH (pepsin acid; pancreatic amylase and lipase alkaline); villi and microvilli increase absorptive area.
- Excretion: the nephron filters at the glomerulus, reabsorbs glucose, water, and ions, and secretes wastes; the loop of Henle builds a concentration gradient.
- Nervous and endocrine: fast neuronal action potentials involve sodium and potassium channel currents; the sodium-potassium pump maintains gradients over time rather than directly causing rapid repolarization; hormones act on target cells bearing receptors.
- Plants: xylem moves water and minerals upward under transpiration pull (cohesion–tension); phloem translocates sugars by pressure flow; guard cells open stomata when turgid.
Worked example
After a carbohydrate-rich meal, blood glucose rises. Pancreatic beta cells detect it and secrete insulin; insulin promotes glucose uptake in responsive muscle and adipose tissue, promotes glycogen storage and suppresses hepatic glucose production, so glucose falls toward the set point. When glucose drops below the set point, alpha cells release glucagon, triggering glycogen breakdown and gluconeogenesis in the liver. Both arms are negative feedback: the response opposes the original deviation. In diabetes mellitus, insulin secretion and/or action is impaired and hyperglycemia can result; this model is not a clinical diagnosis.
Traps
Labeling a loop positive because the outcome is "good"; forgetting that pulmonary arteries carry deoxygenated blood; confusing xylem and phloem direction; assuming diffusion suffices in large animals; mixing the roles of the loop of Henle and the collecting duct; assuming all hormones are lipid-soluble.
Microbiología, inmunología y biotecnología: virus, bacterias, respuesta inmunitaria, aplicaciones biotecnológicas
Esta revisión relaciona estructura microbiana, defensa inmunitaria y métodos de análisis de ADN. Se interpretan modelos celulares y datos suministrados; no se ofrecen diagnósticos, dosis, decisiones de tratamiento ni normas sanitarias extranjeras.
Virus y bacterias
Los virus son entidades acelulares con genoma de ADN o ARN, cápside y, en algunos casos, envuelta. Los ciclos lítico y lisogénico describen determinados bacteriófagos, no todos los virus. Los retrovirus utilizan transcripción inversa y pueden integrar ADN viral. Muchas bacterias poseen pared de peptidoglicano, pero existen bacterias sin pared; plásmidos, flagelos y endosporas no son universales. La estructura de una bacteria concreta debe leerse en los datos. Conjugación, transformación y transducción son mecanismos distintos de transferencia genética horizontal.
Inmunidad
Innata: barreras, pH, complemento, fagocitos, células NK e inflamación; reconoce patrones mediante receptores y no utiliza la memoria clonal clásica de linfocitos B y T; la inmunidad entrenada evita reducirla a una ausencia absoluta de memoria. Adaptativa: linfocitos B → células plasmáticas → anticuerpos (IgG, IgM, IgA, IgE, IgD); los linfocitos T auxiliares CD4 reconocen antígeno en MHC II y activan a B y a CD8; los T citotóxicos CD8 destruyen células infectadas presentadas por MHC I. Selección clonal, memoria y respuesta secundaria más rápida y con mayor título, sobre todo de IgG.
Biotecnología
Las enzimas de restricción reconocen secuencias determinadas y pueden producir extremos cohesivos o romos; no todas las enzimas reconocen el mismo tipo de secuencia. Las ligasas unen enlaces del esqueleto del ADN. Los vectores permiten estudiar secuencias introducidas en sistemas adecuados. PCR, electroforesis y secuenciación responden preguntas diferentes: amplificación de una región, comparación de fragmentos y orden de bases. En una comparación convencional de ADN lineal en el mismo gel, los fragmentos pequeños suelen migrar más lejos; la conformación y el sistema importan. Una banda no demuestra por sí sola identidad de secuencia ni expresión funcional. La ingeniería genética requiere comprobar tanto el cambio previsto como su efecto en el modelo estudiado.
Ejemplo resuelto
Partimos de una sola molécula de ADN y aplicamos PCR. En el modelo ideal de duplicación perfecta, tras 5 ciclos el número sería 2^5 = 32 y tras 20 ciclos aproximadamente 1,05 millones. El razonamiento es multiplicativo porque cada ciclo duplica cada molécula, hasta que la fase exponencial se satura al agotarse cebadores o dNTP. Si la muestra inicial tuviera 10 moléculas, tras 5 ciclos habría 320 copias.
Errores que cuestan puntos
Afirmar que los antibióticos matan virus, olvidar que los virus solo se replican dentro de una célula, tratar IgM e IgG como un diagnóstico binario de fase: una respuesta secundaria sistémica suele mostrar aumento de anticuerpos de alta afinidad, pero el isotipo depende del contexto y creer que los linfocitos T producen anticuerpos.
Ecology and Environmental Science
Ecology
This domain tests population dynamics, species interactions, energy and nutrient flow, succession, and human effects on ecosystems.
Populations and communities
- Exponential growth (r) is unlimited; logistic growth adds carrying capacity K, producing an S-curve with density-dependent limits (food, disease, space). Density-independent factors include weather and fire.
- Survivorship curves: Type I (late loss, humans), Type II (constant, birds), Type III (early loss, many fish and plants).
- Interactions: competition (competitive exclusion; resource partitioning allows coexistence), predation (including keystone effects), mutualism (+/+), commensalism (+/0), parasitism (+/−).
- Age structure informs growth potential: a broad base can indicate many future reproductive individuals, but survival, fertility and migration determine actual change.
Ecosystems
Energy flows one way and is lost as heat; a simplified example may assume 10 percent transfer, but actual efficiencies and food-web lengths vary. Gross primary productivity minus respiration equals net primary productivity. Biogeochemical cycles: carbon (photosynthesis, respiration, combustion, dissolution), nitrogen (fixation, nitrification, assimilation, denitrification - atmospheric N₂ is unusable to most organisms), phosphorus (mainly sedimentary, without a major atmospheric reservoir in the standard school model, and sometimes limiting). Primary succession begins on bare substrate (lichens, mosses); secondary succession follows disturbance with soil intact.
Worked example
A lake is sampled by mark–recapture: 50 fish are captured, marked, released, and mixed. A second sample of 120 contains 15 marked fish. Estimated population N = (marked in first sample × total in second sample) ÷ marked in second sample = (50 × 120) ÷ 15 = 400. The estimate assumes a closed population, no mark loss or mortality, thorough mixing, and equal catchability; if marked fish become trap-shy, the estimate is biased upward.
Traps
Confusing exponential with logistic growth; calling a density-dependent factor density-independent; reversing the 10% rule (energy is lost, not gained); assuming nitrogen gas is directly usable; mixing up primary and secondary succession; forgetting that habitat loss and invasive species, not pollution alone, are leading causes of biodiversity decline; treating a population estimate as a census.
Evolutionary Biology and Diversity of Life
Evolution
Items test the mechanisms that change allele frequencies, the evidence for common descent, speciation, and how organisms are classified and related.
Mechanisms of evolution
- Natural selection acts on heritable phenotypic variation that affects fitness; it is not goal-directed and does not create new variation.
- Mutation is the ultimate source of new alleles. Gene flow and genetic drift (bottleneck, founder effect) also change frequencies; drift is strongest in small populations and is random with respect to fitness.
- Directional, stabilizing, and disruptive selection shift, narrow, or split a trait distribution.
- Hardy–Weinberg equilibrium (p² + 2pq + q² = 1) holds only with no mutation, no migration, random mating, infinite population size, and no selection - a null model, not a description of most real populations.
- Speciation: allopatric speciation can follow geographic isolation; sympatric speciation can occur via polyploidy or habitat/behavioral divergence. Prezygotic barriers (temporal, habitat, behavioral, mechanical, gametic) prevent fertilization; postzygotic barriers (hybrid inviability, hybrid sterility) act afterward.
Evidence and classification
Homologous structures share ancestry (forelimb bones); analogous structures share function only (bird and insect wings) and indicate convergence. Fossils, biogeography, embryology, and molecular sequence comparisons support common descent. Cladistics groups organisms by shared derived characters (synapomorphies); monophyletic groups contain an ancestor and all its descendants. A common three-domain teaching model distinguishes Bacteria, Archaea and Eukarya; mitochondria and chloroplasts descend from endosymbiotic bacteria.
Worked example
In a supplied two-allele autosomal model with complete recessivity and penetrance, 16% show the recessive phenotype. Assuming Hardy-Weinberg equilibrium, aa = q² = 0.16, so q = 0.4 and p = 1 − 0.4 = 0.6. Heterozygote frequency is 2pq = 2(0.6)(0.4) = 0.48, and homozygous dominants are p² = 0.36; the three sum to 1.00. Note the reasoning step: the recessive phenotype frequency equals q² only when the trait is recessive and the population is in equilibrium.
Traps
Equating dominant with frequent; assuming a population at Hardy–Weinberg is evolving; confusing allele frequency with genotype frequency; calling drift "selection"; treating analogous structures as evidence of close relatedness; applying reproductive isolation as a universal species definition even to asexual organisms, rather than recognizing the limits of the biological species concept; using a phenotype frequency as q without squaring it.