https://teddyrookbook.com/biology/advanced-biology/Recent content in Advanced Biology (AP and College) on Teddy Rook Bookhttps://teddyrookbook.com/img/share.jpghttps://teddyrookbook.com/img/share.jpgHugoenhttps://teddyrookbook.com/biology/advanced-biology/error-bars/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/error-bars/The standard error of a mean is SE = s/√n. Error bars of ±2 SE give roughly a 95% confidence interval; when such bars for two groups do not overlap, the difference is likely real. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/null-hypothesis/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/null-hypothesis/The null hypothesis says there is no effect or no difference; the alternative says there is. A test asks how likely data this extreme would be if the null were true. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/chi-square/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/chi-square/χ² = Σ (observed − expected)² / expected. Compare it with the critical value for (categories − 1) degrees of freedom at p = 0.05: larger means reject the expected ratio. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/protein-structure/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/protein-structure/Primary structure is the amino acid sequence; secondary is α-helices and β-sheets held by backbone hydrogen bonds; tertiary is the overall fold from R-group interactions; quaternary is several chains together. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/amino-acid-properties/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/amino-acid-properties/Amino acids differ only in their R groups: nonpolar, polar, acidic (negative) or basic (positive). Where each kind sits, inside the fold or on the surface, sets how a protein folds. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/nucleic-acid-direction/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/nucleic-acid-direction/Each strand has a 5′ end (phosphate) and a 3′ end (hydroxyl). The two strands of DNA run antiparallel, and nucleotides are always added to the 3′ end. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/surface-volume/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/surface-volume/For a cube of side s, surface area is 6s² and volume s³, so SA:V = 6/s. Cells stay small, flatten, or fold their membranes to keep SA:V high enough for exchange. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/water-potential/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/water-potential/Water moves from higher to lower water potential: Ψ = Ψs + Ψp. Solute potential is Ψs = −iCRT (R = 0.0831 L·bar/(mol·K)); adding solute makes Ψ more negative. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/membrane-potential/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/membrane-potential/Pumps and channels make an uneven spread of ions: the sodium-potassium pump moves 3 Na⁺ out and 2 K⁺ in per ATP, and K⁺ leaks out, leaving the inside negative (about −70 mV in a resting neuron). Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/compartmentalization/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/compartmentalization/Membranes divide eukaryotic cells into compartments with different conditions, so incompatible reactions can run at once: lysosome enzymes work at pH 5 inside, while the cytoplasm stays near pH 7. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/free-energy/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/free-energy/Reactions with ΔG < 0 (exergonic) release free energy and can happen on their own; ΔG > 0 (endergonic) need an input. Cells couple endergonic steps to ATP hydrolysis so the total ΔG is negative. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/enzyme-kinetics/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/enzyme-kinetics/Rate rises with substrate concentration and levels off when the enzymes are saturated (Vmax). Doubling the enzyme doubles Vmax; temperature and pH move the curve. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/enzyme-inhibition/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/enzyme-inhibition/A competitive inhibitor blocks the active site, and enough substrate outcompetes it. A noncompetitive (allosteric) inhibitor binds elsewhere and changes the enzyme's shape, lowering Vmax no matter how much substrate. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/light-reactions/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/light-reactions/In the thylakoids, photosystem II splits water (releasing O₂) and passes electrons down a chain that pumps H⁺; photosystem I re-energizes them to make NADPH; ATP synthase makes ATP as H⁺ flows back out. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/calvin-cycle/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/calvin-cycle/In the stroma, the enzyme rubisco fixes CO₂ onto RuBP; ATP and NADPH reduce the products to G3P. Three CO₂ give one G3P for the cell, using 9 ATP and 6 NADPH. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/c4-cam/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/c4-cam/When stomata close in hot, dry weather, rubisco fixes O₂ instead of CO₂ (photorespiration). C4 plants like corn separate fixation in space; CAM plants like cactuses separate it in time, taking in CO₂ at night. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/glycolysis-krebs/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/glycolysis-krebs/Glycolysis splits glucose into 2 pyruvate (net 2 ATP, 2 NADH). Pyruvate oxidation and the Krebs cycle release the carbons as CO₂ and load electrons onto NADH and FADH₂. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/oxidative-phosphorylation/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/oxidative-phosphorylation/NADH and FADH₂ give electrons to the chain in the inner mitochondrial membrane; it pumps H⁺ into the intermembrane space. H⁺ flowing back through ATP synthase makes most of the ATP; O₂ takes the spent electrons and forms water. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/signaling-types/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/signaling-types/Cells signal by direct contact (gap junctions, surface molecules), locally (paracrine signals and synapses), or over long distances (hormones carried in the blood). Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/signal-transduction/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/signal-transduction/A ligand binds a receptor (on the surface, or inside for steroid hormones); a relay of proteins, often kinases adding phosphates and second messengers like cAMP, passes and amplifies the signal; the cell responds. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/signal-amplification/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/signal-amplification/Each activated enzyme in a cascade activates many of the next, so one ligand can trigger millions of product molecules. A mutated receptor or relay protein can block a response or switch it on for good. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/feedback-ap/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/feedback-ap/Negative feedback holds a variable near a set point (blood glucose, body temperature); positive feedback drives a change to completion (blood clotting, fruit ripening with ethylene). Disrupting either shows in the data. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/cell-cycle-regulation/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/cell-cycle-regulation/Cyclins rise and fall through the cycle and switch on cyclin-dependent kinases (CDKs) that push the cell past checkpoints. Proteins like p53 halt the cycle when DNA is damaged and can trigger apoptosis. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/linked-genes/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/linked-genes/Genes close together on one chromosome tend to be inherited together. A dihybrid test cross then gives mostly parental types and a few recombinants made by crossing over. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/gene-maps/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/gene-maps/Recombination frequency = recombinant offspring ÷ total offspring. 1% equals one map unit; genes far apart recombine more, so frequencies give the order of genes on a chromosome. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/nondisjunction/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/nondisjunction/If a pair of homologs (meiosis I) or sister chromatids (meiosis II) fails to separate, some cells made get an extra chromosome (n + 1) and others are missing one (n − 1). Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/non-nuclear-inheritance/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/non-nuclear-inheritance/Mitochondria and chloroplasts carry their own genes. They are usually passed down from one parent only, most often the mother, so these traits do not show Mendelian ratios. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/environment-phenotype/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/environment-phenotype/The same genotype can show different phenotypes in different conditions: hydrangea flower color follows soil pH, and Himalayan rabbits grow dark fur where their body is cooler. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/replication-details/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/replication-details/Helicase opens the fork, primase lays an RNA primer, DNA polymerase extends 5′ to 3′: the leading strand continuously, the lagging strand in Okazaki fragments that ligase joins. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/rna-processing/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/rna-processing/RNA polymerase binds a promoter and builds RNA 5′ to 3′. In eukaryotes the pre-mRNA gets a 5′ cap and a poly-A tail, and introns are spliced out; alternative splicing makes several proteins from one gene. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/translation-details/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/translation-details/The small ribosomal subunit finds the start codon; tRNAs enter the A site, the peptide moves from the P site, and empty tRNAs leave from the E site. A release factor ends the chain at a stop codon. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/operons/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/operons/In bacteria, the lac operon is inducible: lactose inactivates the repressor, so genes are on only when lactose is present. The trp operon is repressible: tryptophan activates the repressor and shuts the genes off. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/eukaryotic-regulation/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/eukaryotic-regulation/Transcription factors bind promoters and enhancers; packing matters too: acetylating histones opens chromatin (more expression), methylating DNA usually closes it. These epigenetic marks can pass to daughter cells. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/differentiation/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/differentiation/Different cell types switch on different sets of genes using different transcription factors, which is why a muscle cell and a nerve cell with the same genome make different proteins. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/mutation-effects/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/mutation-effects/Read a mutation's effect from the codon table: silent, missense, nonsense or frameshift. Its effect on the organism depends on where it falls and on the environment, and mutations are the raw material of variation. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/gel-sizing/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/gel-sizing/Distance moved is roughly linear in the logarithm of fragment size, so read an unknown band against the ladder: between the 1,000 and 500 base-pair bands means between those sizes. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/transformation-sequencing/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/transformation-sequencing/In bacterial transformation, cells take up a plasmid; an antibiotic-resistance gene lets only transformed cells grow on selective plates. Sequencing reads the order of bases, as in reading fragments by their ends. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/hardy-weinberg-problems/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/hardy-weinberg-problems/From one known frequency find the rest: q² from the recessive phenotype, q = √q², p = 1 − q, carriers = 2pq. Compare observed genotypes with expected ones to test for equilibrium. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/genetic-drift/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/genetic-drift/Drift is a random change in allele frequency, strongest in small populations. A bottleneck (most die by chance) or a founder effect (a few start a new population) can change frequencies sharply. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/molecular-clock/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/molecular-clock/If differences in a gene build up at a roughly steady rate, the number of differences estimates how long ago two lineages split, once the rate is calibrated with fossils. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/trees-from-data/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/trees-from-data/Build a tree from a table of traits or sequence differences: the pair with the fewest differences shares the most recent ancestor. Parsimony picks the tree that needs the fewest changes. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/speciation-patterns/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/speciation-patterns/Speciation may be gradual or come in bursts after long stable periods (punctuated equilibrium). Adaptive radiation fills open niches quickly, often after mass extinctions; extinction is part of life's history. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/origin-of-life/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/origin-of-life/Earth formed about 4.5 billion years ago, and fossil microbes date back about 3.5 billion years. Experiments show simple organic molecules form under early-Earth conditions; how the first cells arose is still an open question, with hypotheses such as an "RNA world". Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/behavior-responses/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/behavior-responses/Organisms respond to cues: plants by tropisms and photoperiod, animals by kinesis (changing speed) and taxis (moving toward or away), and by signals such as alarm calls and the honeybee's waggle dance. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/energy-budgets/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/energy-budgets/Endotherms spend much of their energy keeping warm, so they need more food per gram than ectotherms; smaller endotherms have higher metabolic rates per gram. Net intake goes to growth and offspring. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/productivity/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/productivity/Gross primary productivity (GPP) is all the energy producers capture; net primary productivity NPP = GPP − R (respiration). Ecologists measure it with oxygen or carbon changes in light and dark bottles. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/population-equations/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/population-equations/Exponential growth: dN/dt = rN. Logistic growth: dN/dt = rN(K − N)/K, which slows growth as N nears K. Calculate rates at a given N and read the S-curve. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/diversity-index/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/diversity-index/Simpson's diversity index D = 1 − Σ(n/N)² runs from 0 (one species) toward 1 (many even species). It rewards both richness and evenness. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/community-structure/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/community-structure/Communities are shaped from the top down (predators) and the bottom up (nutrients). Keystone species, ecosystem engineers like beavers, and invasive species can restructure them. Advanced Biology (AP and College) · Biology Ladderhttps://teddyrookbook.com/biology/advanced-biology/ecosystem-disruptions/Mon, 01 Jan 0001 00:00:00 +0000https://teddyrookbook.com/biology/advanced-biology/ecosystem-disruptions/Invasive species, habitat loss, pollution, disease and changes in climate can change populations fast. A population with more genetic variation is more likely to have individuals that survive a change. Advanced Biology (AP and College) · Biology Ladder