United Grade 11 AP Biology

Chapters: 8

1. Chemistry of Life

Structure of Water and Hydrogen Bonding · Elements of Life · Introduction to Macromolecules · Carbohydrates · Lipids · Nucleic Acids · Proteins

Biomolecules – A cell is mostly water, plus four big families of carbon compounds: proteins, carbohydrates, lipids and nucleic acids. Grinding tissue in acid separates small molecules (acid-soluble pool) from big ones – proteins, polysaccharides and nucleic acids (acid-insoluble pool). Proteins are chains of amino acids folded into four levels of structure. Polysaccharides are chains of sugars; lipids are fatty acids on glycerol; nucleic acids are chains of nucleotides. Enzymes are protein catalysts that bind a substrate at the active site, lower the activation energy, and are affected by temperature, pH, substrate level and inhibitors.

2. Cells

Cell Structure and Function · Cell Size · Plasma Membrane · Membrane Permeability · Membrane Transport · Facilitated Diffusion · Tonicity and Osmoregulation · Mechanisms of Transport · Cell Compartmentalization · Origins of Cell Compartmentalization

Cell: The Unit of Life – Every living thing is made of cells, and every new cell comes from an old cell. Prokaryotic cells (bacteria) have no nuclear envelope and no membrane-bound organelles; eukaryotic cells have a true nucleus and many organelles. The membrane is a fluid mosaic of lipids and proteins; plants add a cellulose wall. ER, Golgi, lysosomes and vacuoles form the endomembrane system. Mitochondria and plastids make energy and food, ribosomes make proteins, the cytoskeleton, cilia, flagella and centrioles give shape and movement, and the nucleus holds the DNA.
Cell Size, Compartments and Energy: Why Cells Are Built the Way They Are – Cells are small because a cell's surface (its membrane) must exchange materials for its whole volume, and as a cell grows its volume rises faster than its surface: the surface area to volume (SA:V) ratio falls. Eukaryotic cells solve this with membrane-bound compartments that split jobs and add membrane area. Mitochondria and chloroplasts came from bacteria swallowed long ago (endosymbiosis). Their folded inner membranes, cristae and thylakoids, give a large area for making ATP and capturing light.
Membrane Transport: How Things Get In and Out of a Cell – The cell membrane is a thin double layer of fat-like molecules with proteins in it. It lets some substances through and stops others (selectively permeable). Diffusion moves particles from high to low concentration with no energy. Facilitated diffusion does the same through protein channels. Osmosis is the diffusion of water through a partially permeable membrane. Active transport uses ATP and a protein pump to move particles from low to high concentration. Very large things enter and leave in bubbles (endocytosis and exocytosis).

3. Cellular Energetics

Enzymes · Environmental Impacts on Enzyme Function · Cellular Energy · Photosynthesis · Cellular Respiration

Biomolecules – A cell is mostly water, plus four big families of carbon compounds: proteins, carbohydrates, lipids and nucleic acids. Grinding tissue in acid separates small molecules (acid-soluble pool) from big ones – proteins, polysaccharides and nucleic acids (acid-insoluble pool). Proteins are chains of amino acids folded into four levels of structure. Polysaccharides are chains of sugars; lipids are fatty acids on glycerol; nucleic acids are chains of nucleotides. Enzymes are protein catalysts that bind a substrate at the active site, lower the activation energy, and are affected by temperature, pH, substrate level and inhibitors.
Cell Size, Compartments and Energy: Why Cells Are Built the Way They Are – Cells are small because a cell's surface (its membrane) must exchange materials for its whole volume, and as a cell grows its volume rises faster than its surface: the surface area to volume (SA:V) ratio falls. Eukaryotic cells solve this with membrane-bound compartments that split jobs and add membrane area. Mitochondria and chloroplasts came from bacteria swallowed long ago (endosymbiosis). Their folded inner membranes, cristae and thylakoids, give a large area for making ATP and capturing light.
Photosynthesis in Higher Plants – Green plants make sugar from carbon dioxide and water using light. It happens in chloroplasts. The light reaction in the thylakoids splits water, gives out oxygen and makes ATP and NADPH. The Calvin cycle in the stroma uses that ATP and NADPH to fix CO₂ into sugar. C₄ plants add a CO₂ pump that stops the wasteful photorespiration. The slowest factor, such as light, CO₂ or temperature, sets the rate.
Respiration in Plants – Respiration breaks food like glucose to release energy stored as ATP. Plants take in O₂ through stomata and lenticels. Glycolysis in the cytoplasm splits glucose into two pyruvates. Without O₂, pyruvate is fermented to ethanol or lactic acid. With O₂, pyruvate enters the mitochondrion, runs the Krebs cycle, and the electron transport system uses O₂ to make most of the ATP: up to 38 per glucose. The same path also builds molecules (amphibolic). RQ = CO₂ given out ÷ O₂ taken in.

4. Cell Communication and Cell Cycle

Cell Communication · Introduction to Signal Transduction · Signal Transduction Pathways · Feedback · Cell Cycle · Regulation of Cell Cycle

Cell Signaling: How Cells Talk to Each Other – Cells send messages using signal molecules (ligands). A signal works in three stages: reception (the ligand binds a matching receptor), transduction (a relay chain of proteins, often with second messengers like cAMP, passes and amplifies the message) and response (the cell switches a gene on, opens a channel or changes an enzyme). Feedback controls the result: negative feedback brings a value back to normal, positive feedback pushes it further.
Cell Cycle and Cell Division – A cell grows, copies its DNA and splits in a fixed order called the cell cycle: interphase (G1, S, G2) and M phase. In S phase the DNA doubles (2C → 4C) but the chromosome number stays the same. Mitosis (prophase, metaphase, anaphase, telophase) and cytokinesis give two cells identical to the parent – it is an equational division used for growth and repair. Meiosis has two divisions; in meiosis I homologous chromosomes pair, cross over and separate, halving the chromosome number (2n → n). It makes four haploid cells for gametes and creates variation.

5. Heredity

Meiosis · Meiosis and Genetic Diversity · Mendelian Genetics · Non-Mendelian Genetics · Environmental Effects on Phenotype

Cell Cycle and Cell Division – A cell grows, copies its DNA and splits in a fixed order called the cell cycle: interphase (G1, S, G2) and M phase. In S phase the DNA doubles (2C → 4C) but the chromosome number stays the same. Mitosis (prophase, metaphase, anaphase, telophase) and cytokinesis give two cells identical to the parent – it is an equational division used for growth and repair. Meiosis has two divisions; in meiosis I homologous chromosomes pair, cross over and separate, halving the chromosome number (2n → n). It makes four haploid cells for gametes and creates variation.
Principles of Inheritance and Variation – Genes come in pairs (alleles). Each parent passes one allele of each pair to the child. Mendel showed dominance (3 : 1), segregation and independent assortment (9 : 3 : 3 : 1). Real life has twists: incomplete dominance (1 : 2 : 1), co-dominance (AB blood), multiple alleles, pleiotropy (one gene, many effects) and polygenic traits (many genes, one trait). Genes sit on chromosomes, so genes on the same chromosome are linked and are separated only by crossing over. Sex chromosomes decide sex (XX-XY in humans, ZW in birds, haplo-diploid in honeybees) and carry sex-linked genes (haemophilia, colour blindness). Mistakes in genes cause Mendelian disorders (thalassemia, sickle-cell) and mistakes in chromosome number cause Down, Turner and Klinefelter syndromes.
Ecosystems in Depth: Biomes, Nutrient Cycles and Disruption – Biomes are large regions with similar climate and life. On land, temperature and rainfall decide the biome; in water, salt, depth, light and flow decide the zones. Matter cycles through ecosystems: nitrogen moves between air, soil, organisms and back through fixation, nitrification, assimilation, ammonification and denitrification; phosphorus cycles slowly between rock, soil, water, organisms and sediment with no gas stage. Decomposers recycle matter with oxygen (aerobic) or without it (anaerobic). Human actions such as fertiliser runoff, habitat loss, invasive species and climate change disrupt these systems; ecosystems respond with resistance and resilience.

6. Gene Expression and Regulation

DNA and RNA Structure · DNA Replication · Transcription and RNA Processing · Translation · Regulation of Gene Expression · Gene Expression and Cell Specialization · Mutations · Biotechnology

Molecular Basis of Inheritance – DNA is the genetic material in most living things (some viruses use RNA). It is a double helix: two antiparallel strands of nucleotides, A pairs with T by 2 hydrogen bonds and G with C by 3. Long DNA is packed on histones into nucleosomes and then chromatin. DNA copies itself semi-conservatively (Meselson–Stahl). The central dogma says DNA → RNA → protein. Transcription makes RNA from one strand; in eukaryotes the hnRNA is capped, tailed and spliced. The genetic code is a triplet, has 64 codons (61 for amino acids, 3 stops), starts with AUG, is nearly universal and degenerate. Ribosomes translate mRNA into protein with tRNA adaptors. Genes are switched on and off; the lac operon is the classic example. The Human and Rice Genome Projects read whole genomes, and DNA fingerprinting uses repeat DNA (VNTRs) to identify people.
Protein Synthesis: From Gene to Protein – A gene is a stretch of DNA that holds the recipe for one protein. In transcription, the cell copies the gene into messenger RNA (mRNA) inside the nucleus; U replaces T. The mRNA goes to a ribosome in the cytoplasm. In translation, the ribosome reads the mRNA three bases at a time (a codon). Each codon matches one amino acid, carried in by a transfer RNA (tRNA). The amino acids join into a chain that folds into a protein. A change in the DNA (a mutation) can change the protein.
Principles of Inheritance and Variation – Genes come in pairs (alleles). Each parent passes one allele of each pair to the child. Mendel showed dominance (3 : 1), segregation and independent assortment (9 : 3 : 3 : 1). Real life has twists: incomplete dominance (1 : 2 : 1), co-dominance (AB blood), multiple alleles, pleiotropy (one gene, many effects) and polygenic traits (many genes, one trait). Genes sit on chromosomes, so genes on the same chromosome are linked and are separated only by crossing over. Sex chromosomes decide sex (XX-XY in humans, ZW in birds, haplo-diploid in honeybees) and carry sex-linked genes (haemophilia, colour blindness). Mistakes in genes cause Mendelian disorders (thalassemia, sickle-cell) and mistakes in chromosome number cause Down, Turner and Klinefelter syndromes.
Biotechnology: Principles and Processes (Recombinant DNA Technology) – Genetic engineering means changing the genes of a living thing on purpose. We cut the gene we want with restriction enzymes (molecular scissors), paste it into a carrier DNA called a vector using DNA ligase (molecular glue), put it into a host cell, pick out the cells that took it, and grow them in big tanks (bioreactors) to collect the product. PCR makes millions of copies of a gene, and gel electrophoresis sorts DNA pieces by size.

7. Natural Selection

Introduction to Natural Selection · Natural Selection · Artificial Selection · Population Genetics · Hardy-Weinberg Equilibrium · Evidence of Evolution · Common Ancestry · Continuing Evolution · Phylogeny · Speciation · Variations in Populations · Origins of Life on Earth

Evolution: Origin of Life, Mechanisms and Human Evolution – Life began on the early Earth from simple chemicals: Oparin and Haldane proposed it and Miller made amino acids in a flask. Evidence of evolution comes from fossils, homologous and analogous organs, embryos, molecules and changes we can watch (industrial melanism, drug resistance). Darwin explained it by natural selection acting on variation in populations; the modern synthetic theory adds genes: mutation, recombination, gene flow, genetic drift and natural selection change allele frequencies. If none of these act, frequencies stay constant: Hardy–Weinberg, p² + 2pq + q² = 1. Selection can be stabilising, directional or disruptive. One ancestor spreading into many habitats gives adaptive radiation (Darwin’s finches, Australian marsupials). Humans evolved from Dryopithecus-like apes through Australopithecus, Homo habilis, Homo erectus and Neanderthals to Homo sapiens.
Population Genetics: Gene Pools, Hardy–Weinberg and New Species – Population genetics studies how allele frequencies change in a population. The gene pool is all alleles of all individuals. For one gene with alleles A and a, p + q = 1. If a population is large, mates randomly, and has no migration, mutation or selection, the Hardy–Weinberg principle says frequencies stay the same and genotypes are p² (AA) + 2pq (Aa) + q² (aa) = 1. Any change from this means evolution is happening, caused by genetic drift (bottleneck, founder effect), gene flow, mutation, natural selection or non-random mating. A species, in the biological species concept, is a group whose members can interbreed: a shared gene pool. New species form when gene pools are cut off by reproductive isolation: allopatric (geographic barrier) or sympatric (same area, e.g. polyploidy, habitat or behaviour). One ancestor can split into many forms (adaptive radiation, divergence), while unrelated groups can evolve similar shapes (convergence).
Population Ecology: r and K Species, Survivorship and Human Populations – Species follow different life plans. r-selected species have many small young and give no care; K-selected species have few big young and care for them. Survivorship curves show who dies when (Type I late, Type II steady, Type III early). Generalists use many resources; specialists need one. For humans, age pyramids, the total fertility rate (replacement about 2.1) and the four stages of the demographic transition explain how populations grow, level off or shrink.

8. Ecology

Responses to the Environment · Energy Flow Through Ecosystems · Population Ecology · Effect of Density on Populations · Community Ecology · Biodiversity · Disruptions in Ecosystems

Ecosystems in Depth: Biomes, Nutrient Cycles and Disruption – Biomes are large regions with similar climate and life. On land, temperature and rainfall decide the biome; in water, salt, depth, light and flow decide the zones. Matter cycles through ecosystems: nitrogen moves between air, soil, organisms and back through fixation, nitrification, assimilation, ammonification and denitrification; phosphorus cycles slowly between rock, soil, water, organisms and sediment with no gas stage. Decomposers recycle matter with oxygen (aerobic) or without it (anaerobic). Human actions such as fertiliser runoff, habitat loss, invasive species and climate change disrupt these systems; ecosystems respond with resistance and resilience.
Ecosystem: Structure, Productivity, Energy Flow and Pyramids – An ecosystem is a working unit of nature where living things (biotic) and non-living things (abiotic) interact. Plants make food at a rate called productivity: gross (GPP) minus respiration gives net (NPP = GPP − R). Dead matter is broken down in five steps: fragmentation, leaching, catabolism, humification and mineralisation. Energy enters as sunlight, flows one way through trophic levels and only about 10% passes on each time. Ecological pyramids of number, biomass and energy show this; number and biomass pyramids can be inverted, but the energy pyramid is always upright.
Organisms and Populations: Growth and Interactions – A population is a group of the same species living in one area at one time. It has features that a single organism does not have: density, birth rate, death rate, sex ratio and age structure. N grows by births and immigration and shrinks by deaths and emigration. With unlimited food it grows fast (J-curve, dN/dt = rN); with limited food it slows and stops at the carrying capacity K (S-curve, dN/dt = rN(1 − N/K)). Different species affect each other: mutualism (+/+), competition (−/−), predation and parasitism (+/−), commensalism (+/0) and amensalism (−/0).
Biodiversity and its Conservation – Biodiversity is the variety of life at three levels: genetic, species and ecological. It is highest near the equator and grows with area (log S = log C + Z log A). Every species matters, like rivets on a plane. We are losing species fast because of the 'evil quartet': habitat loss and fragmentation, over-exploitation, alien species invasions and co-extinction. The IUCN Red List (Red Data Book) ranks species from Least Concern to Extinct. We protect life in situ (hotspots, national parks, sanctuaries, biosphere reserves, sacred groves, Ramsar wetlands) and ex situ (zoos, botanical gardens, seed and gene banks).