OBQ cheat sheet

Central dogma: DNA → RNA → protein; transcription uses RNA polymerase, translation uses ribosomes, tRNAs, and aminoacyl-tRNA synthetases.

Membrane transport: simple diffusion follows concentration gradient; facilitated diffusion uses channels/carriers; active transport requires ATP (e.g., Na+/K+ ATPase moves 3 Na+ out, 2 K+ in).

Cell cycle checkpoints: G1/S (size, nutrients, DNA damage), G2/M (DNA replication complete, damage), spindle assembly checkpoint (chromosome attachment).

Apoptosis pathways: intrinsic (mitochondrial cytochrome c release, caspase-9) vs extrinsic (death receptors, caspase-8); both converge on caspase-3.

Enzyme kinetics: Michaelis-Menten v = Vmax[S]/(Km+[S]); Km is substrate at half Vmax; Lineweaver-Burk plot y-intercept = 1/Vmax, x-intercept = -1/Km.

Signal transduction: G-protein coupled receptors activate adenylyl cyclase → cAMP → PKA; receptor tyrosine kinases autophosphorylate and recruit SH2-domain proteins.

Cytoskeleton: microfilaments (actin, 7 nm) for shape/motility; intermediate filaments (10 nm) for mechanical strength; microtubules (25 nm) for transport and spindle.

DNA replication is semiconservative, bidirectional from origins; leading strand continuous, lagging strand discontinuous (Okazaki fragments); DNA polymerase requires primer.

Mendelian ratios: monohybrid F2 3:1; dihybrid F2 9:3:3:1 if genes assort independently; testcross reveals genotype.

Hardy-Weinberg equilibrium: p + q = 1; p² + 2pq + q² = 1; assumptions: no mutation, no migration, no selection, infinite population, random mating.

Linkage: recombination frequency (RF) = (number recombinant offspring / total offspring) × 100%; 1% RF = 1 centimorgan (cM); RF < 50% indicates linkage.

Pedigree analysis: autosomal recessive traits skip generations, affect both sexes equally; autosomal dominant appear every generation; X-linked recessive mostly males, no male-to-male transmission.

Mutations: transitions (purine↔purine, pyrimidine↔pyrimidine) vs transversions; frameshift indels not multiple of 3 alter reading frame; nonsense creates stop codon.

Genomic techniques: PCR amplifies DNA exponentially (2^n after n cycles); Sanger sequencing uses dideoxynucleotides; next-generation sequencing uses massively parallel clonal amplification.

Population genetics: allele frequency change under selection Δp = pqs / (1 - qs) for recessive lethal; genetic drift stronger in small populations; Fst measures population differentiation (0-1).

Epistasis modifies Mendelian ratios (e.g., 9:3:4 recessive epistasis, 12:3:1 dominant epistasis); pleiotropy = one gene affects multiple traits.

Gibbs free energy: ΔG = ΔH - TΔS; spontaneous if ΔG < 0; ΔG°' = -RT ln Keq; coupled reactions share intermediates.

Glycolysis net: glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 pyruvate + 2 NADH + 2 ATP + 2 H2O; occurs in cytosol; key regulated enzyme phosphofructokinase-1.

Citric acid cycle per acetyl-CoA: 3 NADH, 1 FADH2, 1 GTP, 2 CO2; occurs in mitochondrial matrix; rate-limiting enzyme isocitrate dehydrogenase.

Oxidative phosphorylation: electron transport chain pumps H+ (complexes I, III, IV); ATP synthase uses proton-motive force; ~2.5 ATP per NADH, ~1.5 ATP per FADH2.

Enzyme inhibition: competitive increases apparent Km, Vmax unchanged; noncompetitive decreases Vmax, Km unchanged; uncompetitive decreases both.

Protein structure: primary (sequence), secondary (α-helix, β-sheet via H-bonds), tertiary (3D folding, disulfide bonds), quaternary (subunit assembly).

Lipid metabolism: β-oxidation yields 1 FADH2, 1 NADH, 1 acetyl-CoA per cycle; fatty acid synthesis uses acetyl-CoA carboxylase (rate-limiting) and NADPH.

pH and buffers: Henderson-Hasselbalch pH = pKa + log([A-]/[HA]); buffer effective within ±1 pH unit of pKa; bicarbonate buffer system in blood.

Animal tissue types: epithelial (covering/lining), connective (support/binding), muscle (contraction: skeletal, cardiac, smooth), nervous (signal transmission).

Mammalian circulation: double circulation; left ventricle → aorta → systemic → vena cava → right atrium → right ventricle → pulmonary artery → lungs → pulmonary vein → left atrium.

Gas exchange: Fick's law (rate ∝ surface area × concentration gradient / thickness); countercurrent exchange in fish gills maximizes O2 uptake.

Osmoregulation: freshwater fish excrete dilute urine, actively uptake ions; marine bony fish drink seawater, excrete concentrated ions via gills; elasmobranchs retain urea.

Plant transport: xylem (water/minerals, transpiration pull, cohesion-tension), phloem (sugars, pressure-flow from source to sink).

Hormonal regulation: insulin lowers blood glucose (uptake/storage); glucagon raises it; negative feedback maintains homeostasis; hypothalamus-pituitary axis controls many endocrine glands.

Nervous system: resting potential ~-70 mV (Na+/K+ pump, K+ leak); action potential depolarization (Na+ in), repolarization (K+ out); threshold must be reached.

Immune responses: innate (barriers, phagocytes, inflammation, complement) vs adaptive (B cells → antibodies, T cells → cell-mediated); memory cells provide faster secondary response.

Population growth: exponential dN/dt = rN; logistic dN/dt = rN(1 - N/K); K = carrying capacity; r = intrinsic growth rate.

Hardy-Weinberg (evolution null model): allele frequencies constant without evolutionary forces; deviations indicate selection, drift, migration, mutation, or nonrandom mating.

Natural selection modes: directional (shifts mean), stabilizing (reduces variance), disruptive (increases variance, may lead to speciation).

Species interactions: competition (-/-), predation/herbivory (+/-), mutualism (+/+), commensalism (+/0), parasitism (+/-); competitive exclusion principle.

Trophic levels: 10% rule (energy transfer efficiency ~10%); biomass pyramids can invert in aquatic systems; keystone species have disproportionate impact.

Speciation: allopatric (geographic isolation), sympatric (polyploidy, habitat differentiation, sexual selection); prezygotic vs postzygotic barriers.

Evolutionary mechanisms: mutation (source of variation), genetic drift (random, stronger in small populations, founder effect, bottleneck), gene flow (migration), natural selection (nonrandom).

Life history strategies: r-selected (many offspring, little parental care, early maturity) vs K-selected (few offspring, high parental care, late maturity).

Descriptive statistics: mean = Σx/n; median = middle value; standard deviation s = √[Σ(x - x̄)²/(n-1)]; standard error SE = s/√n.

Probability: P(A or B) = P(A) + P(B) - P(A and B); P(A and B) = P(A) × P(B|A); binomial P(k) = C(n,k) p^k (1-p)^(n-k).

Hypothesis testing: null (H0) vs alternative (H1); p-value = probability of data (or more extreme) given H0; reject H0 if p < α; Type I error (false positive) = α; Type II error (false negative) = β; power = 1 - β.

Statistical tests: t-test compares means (two groups); ANOVA compares ≥3 means; chi-square goodness-of-fit or independence for categorical data; regression fits relationship.

Correlation coefficient r ranges -1 to +1; r² = proportion of variance explained; correlation does not imply causation.

Chi-square statistic: χ² = Σ[(O - E)²/E]; degrees of freedom = (rows - 1)(columns - 1) for independence, or categories - 1 for goodness-of-fit.

Graph interpretation: linear scale vs logarithmic (log y shows exponential growth as straight line); error bars may represent SD, SE, or 95% CI; specify which.

Experimental design: control group, randomization, replication, blinding; confounding variables distort results; sample size affects power and precision.

Controls: negative control (no treatment, establishes baseline), positive control (known effect, verifies assay works); both needed to validate results.

Replication and randomization reduce random error and bias; sample size determined by power analysis (desired power typically 0.8, α = 0.05).

Spectrophotometry: Beer-Lambert law A = εcl; absorbance proportional to concentration; use blank to zero; measure at λmax for maximum sensitivity.

Chromatography: separates by differential affinity; size-exclusion (size), ion-exchange (charge), affinity (specific binding), reverse-phase (hydrophobicity).

Electrophoresis: agarose for DNA/RNA (size separation), SDS-PAGE for proteins (denatured, separates by mass); Western blot transfers to membrane and detects with antibodies.

Microscopy: resolution = 0.61λ/NA; fluorescence uses excitation/emission filters; confocal improves optical sectioning; electron microscopy (TEM/SEM) higher resolution.

PCR/qPCR: denaturation (~95°C), annealing (~55-65°C), extension (~72°C); qPCR quantifies fluorescence (Ct value inversely related to template amount).

Cell culture: aseptic technique, appropriate medium (pH, nutrients, serum), incubation at 37°C/5% CO2; contamination detected by turbidity, pH change, microscopy.