Biology curriculum

Living things share a set of traits: they are organized, respond to their surroundings, reproduce, grow and develop, regulate their internal conditions, and take in and use energy. No single trait settles the question; a crystal grows and a fire uses energy, but neither has the whole set.

Life is organized in levels: atoms, molecules, organelles, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems and the biosphere. Each level has properties its parts lack, so ask which level a question is really about before you answer it.

Science moves from observation to a hypothesis, a testable prediction, an experiment and a conclusion. A hypothesis must be falsifiable: some possible result has to be able to show it wrong. A claim that fits every outcome explains nothing.

In a controlled experiment you change one independent variable and measure the dependent variable, keeping everything else the same. A control group shows what happens without the change, and replication shows the result was not luck. A confound, a second difference between groups, ruins the conclusion.

In science, a theory is a broad explanation supported by a large body of evidence, such as the theory of evolution or cell theory. It is not a guess. A theory is refined as new evidence arrives, and saying something is only a theory misreads the word.

Every species has a two-part scientific name, its genus and species, written in italics with only the genus capitalized, as in Homo sapiens. Species are grouped into ever broader ranks, from genus up through family, order, class, phylum and kingdom to domain.

An atom has protons and neutrons in its nucleus and electrons around it. The atomic number counts protons, and the mass number counts protons plus neutrons. Isotopes of an element differ in neutron number; radioactive ones serve as tracers in experiments and as clocks for dating.

Electrons occupy shells around the nucleus, and the outermost, the valence shell, decides how an atom bonds. Atoms tend to bond until their valence shell is full, so carbon, with four valence electrons, forms four bonds.

Covalent bonds share electrons and are the strongest bonds in biological molecules; they are polar when the sharing is unequal. Ionic bonds come from attraction between opposite charges. Hydrogen bonds and van der Waals attractions are much weaker, but in large numbers they hold DNA strands together and shape proteins.

Hydrogen bonds between water molecules explain most of water's unusual behavior: molecules cling to each other (cohesion) and to surfaces (adhesion), giving surface tension. Water also absorbs a lot of heat before warming and a lot more to evaporate, which steadies temperatures and makes sweating cool you.

Water's polarity lets it surround ions and polar molecules with shells of water molecules, so they dissolve; these substances are hydrophilic. Nonpolar substances, such as oils, are hydrophobic and do not dissolve. Ice is less dense than liquid water, so it floats and insulates the water below.

The pH scale is logarithmic: each step is a tenfold change in hydrogen ion concentration. Acids lower pH and bases raise it. A buffer is a weak acid with its partner base that soaks up added acid or base, which keeps the pH of cells and body fluids nearly constant.

Carbon forms four covalent bonds and links to other carbons, building chains, branches and rings. Isomers have the same formula but different arrangements: structural isomers differ in bonding order, geometric isomers in arrangement around a double bond, and enantiomers are mirror images.

Functional groups give a molecule its chemical character. Hydroxyl groups make molecules polar, carboxyl groups make them acidic, amino groups make them basic, and phosphate groups carry negative charge and energy. Sulfhydryl groups can form links that stabilize proteins, and methyl groups can tag DNA.

Cells build large molecules by linking smaller ones, removing a water molecule at each new bond: dehydration synthesis. They break them apart by adding water back: hydrolysis. Digestion is hydrolysis on a large scale.

Monosaccharides, such as glucose and fructose, are single sugar units. Two joined by a glycosidic bond form a disaccharide, such as sucrose or lactose. Sugars with an aldehyde group are aldoses, and those with a ketone group are ketoses.

Starch, glycogen and cellulose are all long chains of glucose, but the links differ. Plants store energy as starch and animals as glycogen, while cellulose's linkage makes strong fibers for plant cell walls that most animals cannot digest. Chitin, a related polymer, builds insect exoskeletons and fungal walls.

Fats and oils are triglycerides, glycerol joined to three fatty acids. Saturated fatty acids have no double bonds and pack tightly, so they are solid at room temperature. Unsaturated fatty acids have double bonds that kink the chain, so they are liquid. Trans fats have straightened double bonds that pack like saturated ones.

A phospholipid has a water-loving head and two water-avoiding tails, so in water phospholipids line up into a double layer, the basis of every cell membrane. Steroids, such as cholesterol and many hormones, are built on four fused carbon rings.

Each amino acid has a central carbon bonded to an amino group, a carboxyl group and a side chain, the R group, which distinguishes the 20 amino acids. Peptide bonds link them into chains with a direction, from the amino end to the carboxyl end.

A protein's primary structure is its amino acid sequence. Hydrogen bonds fold the chain into helices and sheets, its secondary structure. The whole chain then folds into a three-dimensional tertiary shape, and several chains can assemble into a quaternary structure. Heat or extreme pH can denature it, destroying the shape and the function.

Nucleotides have a sugar, a phosphate and a nitrogen base. DNA uses the sugar deoxyribose and the bases adenine, thymine, guanine and cytosine, and is usually double-stranded. RNA uses ribose, has uracil in place of thymine, and is usually single-stranded. Purines have two rings and pyrimidines one.

Cell theory states that all living things are made of cells, that the cell is the basic unit of life, and that new cells come only from existing cells. It grew from microscope observations of plant and animal tissue.

As a cell grows, its volume rises faster than its surface area. Since everything the cell takes in or gets rid of must cross that surface, a large cell would struggle to supply its interior. That limit keeps most cells small, and folded membranes help larger ones cope.

Prokaryotic cells, bacteria and archaea, have no nucleus; their DNA sits in a region called the nucleoid, and they are usually small. Eukaryotic cells keep their DNA in a nucleus and have membrane-bound organelles, and they are usually much larger.

The nucleus stores the cell's DNA behind a double membrane with pores that control traffic. Ribosomes build proteins. Free ribosomes in the cytoplasm make proteins used there, while ribosomes on the rough endoplasmic reticulum make proteins destined for membranes or export.

The endomembrane system processes and ships proteins and lipids. The rough endoplasmic reticulum makes proteins, the smooth endoplasmic reticulum makes lipids, and the Golgi apparatus modifies, sorts and packages them into vesicles. Lysosomes break down worn-out parts and food particles.

Mitochondria carry out cellular respiration, and chloroplasts carry out photosynthesis. Both have their own DNA and ribosomes and divide on their own, which supports the idea that they began as bacteria living inside an ancestral cell, the endosymbiotic theory.

The cytoskeleton is a network of protein fibers that gives a cell its shape and lets it move. Microfilaments drive movement and division, intermediate filaments bear tension, and microtubules guide transport and form the spindle. Cilia and flagella move cells using microtubules.

Plant cells have cellulose walls, and fungi have walls of chitin. Animal cells sit in an extracellular matrix of proteins such as collagen. Junctions connect neighbors: tight junctions seal, anchoring junctions bind, and gap junctions in animals and plasmodesmata in plants pass small molecules between cells.

The fluid mosaic model describes a membrane as a phospholipid bilayer with proteins embedded in it. It is fluid because the lipids and many proteins drift sideways within the layer, and a mosaic because many different proteins are scattered through it.

Membranes become more fluid when warm and stiffer when cold. Unsaturated fatty acids, with kinked tails, keep a membrane fluid. Cholesterol buffers both ways: it restrains movement when warm and prevents tight packing when cold.

Integral proteins span or sit within the membrane, while peripheral proteins attach to its surface. Membrane proteins transport substances, act as enzymes, receive signals, identify the cell to others, and anchor the membrane to the cytoskeleton.

Passive transport moves substances down their concentration gradient without using energy. Small nonpolar molecules diffuse straight through the bilayer. Ions and polar molecules need help from channel or carrier proteins, which is facilitated diffusion.

Osmosis is the diffusion of water across a membrane toward the side with more dissolved solute. In a hypotonic solution, an animal cell swells; in a hypertonic one, it shrinks; in an isotonic one, it holds steady. Plant cells resist bursting because their walls push back, giving turgor.

Active transport moves substances against their concentration gradient, which costs energy. Pumps such as the sodium-potassium pump spend ATP directly. Secondary active transport uses the gradient those pumps build to carry another substance along.

Large particles cross in vesicles. In endocytosis the membrane folds inward to take material in: phagocytosis engulfs particles, pinocytosis takes in fluid, and receptor-mediated endocytosis takes in specific molecules. In exocytosis, vesicles fuse with the membrane to release their contents.

Energy cannot be created or destroyed, only converted, and every conversion loses some as heat, raising disorder. That is why living things need a steady input of energy to stay organized: they must keep replacing what each conversion loses.

An exergonic reaction releases free energy and can proceed on its own. An endergonic reaction absorbs free energy and needs an energy input. Releasing free energy says nothing about speed; many exergonic reactions are very slow without an enzyme.

Catabolic pathways break large molecules down and release energy, while anabolic pathways build large molecules and use energy. Cells couple the two, so energy released by one drives the other.

ATP stores energy in bonds between its phosphate groups. Breaking off a phosphate releases energy, and transferring that phosphate to another molecule, phosphorylation, powers an otherwise uphill reaction. ATP is then rebuilt from ADP using energy from food.

Every reaction must climb an energy barrier, the activation energy, before it proceeds, even if it releases energy overall. That barrier is why sugar does not burst into flame on the table.

Enzymes speed reactions by lowering their activation energy; they do not change whether a reaction releases or absorbs energy. The substrate fits the enzyme's active site, which shifts shape slightly to grip it, an induced fit. The enzyme is not used up.

A competitive inhibitor occupies the active site itself; a noncompetitive one attaches at another spot and distorts the enzyme's shape. Many enzymes need helpers, cofactors or organic coenzymes. In feedback inhibition, a pathway's end product shuts down an early enzyme, so the cell makes only what it needs.

Cellular respiration is a series of redox reactions: glucose is oxidized, losing electrons, and oxygen is reduced at the end. The carriers NAD+ and FAD pick up electrons along the way, becoming NADH and FADH₂, and deliver them to the electron transport chain.

Glycolysis splits one glucose into two pyruvate molecules in the cytoplasm, without needing oxygen. It spends two ATP early on and makes four later, for a net gain of two ATP, plus two NADH.

Each pyruvate enters the mitochondrion and is converted to acetyl-CoA, releasing one carbon dioxide and reducing NAD+ to NADH. This step links glycolysis to the citric acid cycle.

In the citric acid cycle, each acetyl-CoA is fully oxidized, releasing two carbon dioxide molecules and loading NADH and FADH₂ with electrons, with a little ATP made directly. Because each glucose gives two acetyl-CoA, the cycle turns twice per glucose.

Proteins in the inner mitochondrial membrane pass electrons from NADH and FADH₂ down a chain to oxygen, which combines with hydrogen to form water. As electrons move, the chain pumps protons across the membrane, building up a concentration gradient.

Protons flow back across the membrane through ATP synthase, which uses that flow to make ATP; this is chemiosmosis. It produces most of the ATP from glucose. The exact total is given as a range because the yield per NADH and transport costs vary.

Without oxygen, cells can still run glycolysis if they regenerate NAD+. Fermentation does that: muscle cells convert pyruvate to lactate, and yeast convert it to ethanol and carbon dioxide. Fermentation yields only the two ATP from glycolysis.

Cells can burn fats and proteins as well as sugar. Fats are broken into units that enter as acetyl-CoA, and amino acids, after their nitrogen is removed, enter at several points in glycolysis and the citric acid cycle.

Autotrophs, such as plants, make their own food from carbon dioxide and water using light; heterotrophs eat other organisms. The overall photosynthesis equation is roughly the reverse of cellular respiration: carbon dioxide and water become sugar and oxygen.

Inside a chloroplast, stacks of membrane discs called thylakoids sit in a fluid called the stroma. Chlorophyll a and b absorb mostly red and blue light and reflect green, which is why leaves look green. Accessory pigments widen the range of light the plant can use.

Light is captured by two photosystems in the thylakoid membrane. Photosystem II acts first and photosystem I second; they are numbered in the order they were discovered, not the order they work.

The light reactions in the thylakoids use light energy to split water, releasing oxygen. Electrons pass along a transport chain, producing ATP and NADPH, which carry energy to the next stage.

In the Calvin cycle in the stroma, the enzyme RuBisCO fixes carbon dioxide onto a five-carbon sugar. ATP and NADPH then reduce the products to a three-carbon sugar, and most of it is recycled to regenerate the starting molecule.

RuBisCO sometimes grabs oxygen instead of carbon dioxide, wasting energy in photorespiration, especially when it is hot and dry. C4 plants fix carbon in one cell type and run the Calvin cycle in another; CAM plants open their stomata at night and fix carbon then.

Cells signal over different distances. Paracrine signals act on nearby cells, endocrine signals travel through the blood to distant targets, autocrine signals act on the cell that released them, and some signals pass directly between touching cells.

Most signal molecules cannot cross the membrane, so they bind receptors on the cell surface: G-protein-coupled receptors, ion channels or enzyme-linked receptors. Small nonpolar signals, such as steroid hormones, pass through the membrane and bind receptors inside the cell.

When a receptor is activated, it starts a cascade inside the cell, often a chain of enzymes adding phosphate groups to one another. Each step activates many molecules, so a single signal molecule can trigger a large response.

Second messengers are small molecules that spread a signal inside the cell. Cyclic AMP, calcium ions and inositol phosphates relay and amplify the message from the receptor to its targets.

A signal ends in a response, such as turning genes on or activating enzymes. Every signal must also be switched off, by breaking down the signal or resetting the receptor and relay molecules, or the cell would respond indefinitely.

Apoptosis is programmed cell death: the cell dismantles itself in an orderly way and is cleaned up without spilling its contents. Necrosis, death from injury, is messy and causes inflammation. Apoptosis shapes development and removes damaged cells.

The cell cycle runs through G1, a growth phase; S, when DNA is copied; G2, a second growth phase; and M, mitosis and division. Cells that stop dividing enter a resting state called G0. Most of a cycle is spent in interphase, the three phases before M.

DNA is wrapped into chromatin and, before division, condenses into chromosomes. After copying, each chromosome has two identical sister chromatids joined at a centromere, where kinetochores attach to spindle fibers. Homologous chromosomes are matching pairs, one from each parent.

In prophase the chromosomes condense; in prometaphase the nuclear envelope breaks down and spindle fibers attach; in metaphase the chromosomes line up in the middle; in anaphase the sister chromatids separate; and in telophase new nuclei form at each end.

The spindle is built of microtubules that grow from centrosomes at opposite poles. Kinetochore microtubules attach to chromosomes and pull the sister chromatids apart, while other microtubules push the poles away from each other.

Cytokinesis divides the cytoplasm after mitosis. In animal cells a ring of protein filaments pinches the cell in two, forming a cleavage furrow. In plant cells, which have rigid walls, a new cell plate forms between the two nuclei.

Checkpoints in G1, G2 and M stop the cycle if DNA is damaged or chromosomes are not properly attached. Proteins called cyclins rise and fall during the cycle and switch on cyclin-dependent kinases, which drive the cell from one phase to the next.

Cancer is uncontrolled cell division. Proto-oncogenes normally promote division; mutated into oncogenes, they push it too hard. Tumor suppressor genes, such as the one for p53, normally stop the cycle to repair damage; when they fail, damaged cells keep dividing.

A diploid cell has two sets of chromosomes, one from each parent, arranged in homologous pairs. A haploid cell, such as an egg or sperm, has one set. Gametes must be haploid so that fertilization restores the diploid number instead of doubling it every generation.

In meiosis I, homologous chromosomes pair up and then separate into two cells, halving the chromosome number. That is the reductional division, and it is what makes meiosis different from mitosis.

In meiosis II, the sister chromatids of each chromosome separate, much as in mitosis. Starting from one diploid cell, meiosis ends with four haploid cells.

During meiosis I, homologous chromosomes pair closely and exchange segments at crossover points called chiasmata. This crossing over produces chromatids that carry new combinations of the parents' alleles.

At metaphase I, each homologous pair lines up independently of the others, so a gamete can receive either chromosome of each pair. With n pairs, that alone allows 2^n combinations; for humans, with 23 pairs, about 8 million.

Mitosis makes two cells genetically identical to the parent, with the same chromosome number, for growth and repair. Meiosis makes four genetically different cells with half the chromosome number, and it happens only in the cells that produce gametes.

Nondisjunction is a failure of chromosomes to separate properly. It produces gametes with an extra or missing chromosome, aneuploidy. A missing chromosome is monosomy and an extra one is trisomy, as in Down syndrome, an extra chromosome 21.

Mendel bred pea plants that were true-breeding, consistently producing the same trait. Crossing them showed that traits do not blend but reappear unchanged in later generations, in predictable ratios.

A gene is a stretch of DNA for a trait, and alleles are its different versions. Having two identical alleles is homozygous, and two different ones is heterozygous. The genotype is the alleles you carry; the phenotype is the trait you show.

Each parent passes on only one of its two alleles for a gene, chosen at random. Crossing two heterozygotes gives offspring in a 3:1 ratio of dominant to recessive phenotype and a 1:2:1 ratio of genotypes.

Genes on different chromosomes are inherited independently. Crossing two individuals heterozygous for two such genes gives four phenotypes in a 9:3:3:1 ratio.

Use the product rule for independent events (multiply) and the sum rule for alternative outcomes (add). To find whether an individual showing a dominant trait is homozygous or heterozygous, cross it with a homozygous recessive: any recessive offspring reveal that it is heterozygous.

Not every trait shows simple dominance. In incomplete dominance the heterozygote is intermediate; in codominance both alleles show, as in AB blood type. Many genes have more than two alleles, and some alleles are lethal when inherited from both parents.

In epistasis, one gene masks or changes the effect of another. In pleiotropy, one gene affects several traits at once, which is why a single mutation can show up in many parts of the body.

A pedigree charts a trait through a family. A recessive trait can skip generations; a dominant one appears in every generation it passes through, and an X-linked recessive trait shows up mostly in males. Polygenic traits, such as height, vary continuously because many genes and the environment contribute.

Sutton and Boveri noticed that chromosomes behave in meiosis just as Mendel's factors must: they pair, separate and assort independently. That match established that genes are carried on chromosomes.

In humans and many animals, XX individuals are female and XY are male. Other systems exist: in birds, females are ZW and males ZZ; in bees, males develop from unfertilized eggs; and in some reptiles, the incubation temperature decides sex.

Genes on the X chromosome are X-linked. A male has only one X, so a single recessive allele on it shows in his phenotype. That is why X-linked recessive conditions, such as color blindness, are far more common in males.

In female mammals, one X chromosome in each cell is randomly shut down early in development, condensing into a Barr body. Different cells silence different X chromosomes, so a female can show patches of different traits, as in a calico cat.

Genes close together on one chromosome tend to be inherited together. Crossing over can separate them, more often the farther apart they are, so recombination frequency measures distance: 1 percent is one map unit. Genes far apart recombine about half the time and look unlinked.

Aneuploidy is having an extra or missing chromosome, which is usually harmful. Polyploidy is having extra whole sets of chromosomes; it is common and often harmless in plants, but rarely survivable in animals.

Chromosomes can lose a segment (deletion), repeat one (duplication), flip one (inversion), or swap segments with another chromosome (translocation). Their effects depend on which genes are lost, doubled or disrupted.

Griffith showed that something from dead bacteria could transform living ones. Avery, MacLeod and McCarty showed that the transforming substance was DNA, and Hershey and Chase showed that viruses inject DNA, not protein, into the cells they infect.

DNA is a double helix of two antiparallel strands, with bases paired across the middle: adenine with thymine and guanine with cytosine. That pairing explains Chargaff's observation that a DNA sample has equal amounts of A and T, and of G and C.

DNA wraps around histone proteins to form nucleosomes, like beads on a string. Those coil into thicker fibers and loops, and before division they condense into the compact chromosomes visible under a microscope.

When DNA copies itself, each new double helix keeps one original strand and one new strand; it is semiconservative. Meselson and Stahl showed this by tracking heavy and light nitrogen through rounds of replication.

Helicase unwinds the helix, single-strand binding proteins hold the strands apart, and topoisomerase relieves the twisting ahead. Primase lays down a short RNA primer, DNA polymerase adds nucleotides, and ligase seals the gaps.

DNA polymerase builds only in one direction, 5' to 3'. One strand, the leading strand, is made continuously; the other, the lagging strand, is made in short Okazaki fragments that are later joined. Chromosome ends shorten with each copy, and telomerase can rebuild them.

DNA polymerase proofreads as it copies, and repair systems fix remaining errors. A point mutation changes one base and can be silent, missense (a different amino acid) or nonsense (an early stop). Adding or removing bases can cause a frameshift, which garbles everything downstream.

Genetic information flows from DNA to RNA in transcription and from RNA to protein in translation. Some viruses run part of it backward, using reverse transcriptase to copy RNA into DNA.

Transcription copies a gene's DNA into RNA. RNA polymerase binds a promoter, reads the template strand and builds a matching RNA strand, then stops at a termination signal.

In eukaryotes, the first RNA copy is processed before it leaves the nucleus: a cap is added to the front, a tail of adenines to the end, and noncoding introns are spliced out. Splicing the same RNA in different ways lets one gene make several proteins.

Messenger RNA carries the gene's instructions to the ribosome, transfer RNA brings matching amino acids, and ribosomal RNA forms the core of the ribosome. Other small RNAs help regulate which genes are active.

The genetic code reads RNA in three-base codons, each specifying an amino acid or a stop signal. Several codons can code for the same amino acid. AUG starts translation, and almost all organisms use the same code.

A ribosome reads messenger RNA codon by codon. Transfer RNAs carrying amino acids enter at the A site, the growing chain sits at the P site, and empty tRNAs leave from the E site. A stop codon brings a release factor that frees the finished protein.

In prokaryotes, ribosomes can start translating an RNA while it is still being transcribed, and one RNA can carry several genes. In eukaryotes, transcription happens in the nucleus and translation in the cytoplasm, with RNA processing in between.

Nearly every cell in your body has the same DNA. Cells differ because they switch different genes on and off, which is what makes a nerve cell different from a muscle cell.

The lac operon controls the genes bacteria use to digest lactose. Normally a repressor blocks them. When lactose is present, it inactivates the repressor and the genes turn on, and they work hardest when glucose, the preferred sugar, is scarce.

The trp operon makes the amino acid tryptophan. When tryptophan is plentiful, it activates a repressor that shuts the genes off, so the product of the pathway switches the pathway down.

How tightly DNA is packed affects whether genes can be read. Adding acetyl groups to histones loosens packing and makes genes accessible, while adding methyl groups to DNA usually silences genes.

Transcription factors are proteins that bind DNA and help or hinder RNA polymerase at a gene's promoter. Activators bound at distant enhancers can reach the promoter because the DNA loops around, which boosts transcription.

After transcription, cells still control gene output: by splicing RNA in different ways, by controlling how long an RNA lasts and whether it leaves the nucleus, and by controlling when translation starts.

Small RNAs, microRNAs and siRNAs, can silence genes by blocking or destroying matching messenger RNA. Epigenetic changes, such as DNA methylation, alter gene activity without changing the DNA sequence, and some, as in genomic imprinting, pass to offspring.

Restriction enzymes cut DNA at specific short sequences, leaving matching ends. A gene cut out this way can be joined into a plasmid, a small circle of DNA, with the enzyme ligase, then put into bacteria, which copy it as they divide.

Gel electrophoresis separates DNA fragments by size. DNA is negatively charged, so in an electric field it moves toward the positive end, and smaller fragments travel farther through the gel.

The polymerase chain reaction copies a chosen piece of DNA. Each cycle heats the DNA to separate the strands, cools it so primers attach, then lets DNA polymerase extend them. Each cycle doubles the amount, so copies multiply exponentially.

Sequencing reads the order of bases in DNA. The chain-termination method used modified nucleotides that stop copying at each base. Newer methods read millions of fragments at once, making whole genomes far cheaper and faster to sequence.

DNA profiling compares regions where short sequences repeat a variable number of times. The number of repeats differs between people, so a set of such regions gives a pattern useful for forensic identification and for testing who is related to whom.

Genetic engineering moves genes between organisms. Bacteria engineered with the human insulin gene produce insulin for treatment, genetically modified crops carry traits such as pest resistance, and gene therapy aims to treat disease by delivering working genes.

Genomics studies whole genomes, comparing them across species, and proteomics studies all of an organism's proteins. CRISPR lets scientists cut DNA at a chosen spot and edit genes precisely, which raises ethical questions, especially about changes that could be inherited.

Darwin and Wallace independently proposed that species change over time through natural selection: individuals with traits better suited to their environment survive and reproduce more, so those traits become more common. Darwin called the result descent with modification.

Natural selection needs three things: variation in a trait, inheritance of that trait, and differences in survival or reproduction linked to it. If any one is missing, selection cannot change the population.

Fossils show organisms changing over time, including transitional forms, and deeper rock layers generally hold older fossils. Radiometric dating gives their ages. The distribution of species, such as unique species on islands, also reflects their evolutionary history.

Homologous structures, such as the bones of a human arm and a bat wing, share an origin from a common ancestor even when their uses differ. Analogous structures, such as bird and insect wings, do similar jobs but evolved separately. Vestigial structures are reduced remnants of features that once had a use.

All living things share the same genetic code and many similar genes, pointing to common ancestry. The more closely related two species are, the more similar their DNA. Steady rates of change in some genes act as molecular clocks for estimating when lineages split.

Evolution can be watched directly. Bacteria become resistant to antibiotics and insects to pesticides within years, and breeders have reshaped crops and animals by artificial selection.

Individuals do not evolve; populations do, over generations. Natural selection does not respond to need; it acts on variation that already exists. And calling evolution just a theory misreads the word, since a scientific theory is a well-supported explanation.

Evolution is measured in populations, as changes in how common each allele is. The gene pool is all the alleles in a population, and evolution is a change in their frequencies from one generation to the next.

Hardy–Weinberg equilibrium describes a population that is not evolving: p² + 2pq + q² = 1, with p and q the frequencies of two alleles. It holds only with no mutation, random mating, no selection, a very large population and no migration. A population that departs from it is evolving.

Genetic drift is random change in allele frequencies, strongest in small populations. A bottleneck, when a population shrinks sharply, and a founder effect, when a few individuals start a new population, can shift allele frequencies by chance alone.

Gene flow, the movement of alleles between populations through migration, makes populations more alike. Mutation is the only source of entirely new alleles, although it changes frequencies only slowly.

Stabilizing selection favors average traits, directional selection favors one extreme, and disruptive selection favors both extremes over the middle. Sexual selection favors traits that win mates, which is why costly ornaments such as a peacock's tail can persist.

The biological species concept defines a species as a group that can interbreed and produce fertile offspring. Barriers before fertilization, such as different mating seasons or behaviors, and barriers after it, such as sterile hybrids, keep species apart.

Allopatric speciation happens when a physical barrier separates populations, which then diverge. Sympatric speciation happens without separation, often in plants through polyploidy, which can create a new species in one generation.

A phylogenetic tree shows relationships through common ancestors. Each branch point is an ancestor, and sister taxa share the most recent one. Read relatedness from the branch points, not from how close two names sit at the tips; branches can rotate without changing the tree.

Classification groups species into nested ranks: domain, kingdom, phylum, class, order, family, genus and species. The groupings change as new evidence, especially from DNA, reveals how organisms are actually related.

Life is divided into three domains: Bacteria, Archaea and Eukarya. Comparisons of ribosomal RNA showed that archaea, though they look like bacteria, are a separate lineage, in some ways closer to eukaryotes.

A monophyletic group, or clade, includes an ancestor and all its descendants. A paraphyletic group leaves some descendants out, and a polyphyletic group lumps together organisms without their common ancestor. Clades are defined by shared derived traits, not ancient ones they all inherited.

Parsimony prefers the tree that needs the fewest evolutionary changes to explain the data. Molecular clocks use the rate at which DNA changes to estimate how long ago two lineages split.

Experiments show that simple organic molecules can form without life. The RNA world idea proposes that early life relied on RNA, which can both store information and catalyze reactions. Horizontal gene transfer between microbes, and the endosymbiotic origin of organelles, also shaped early life.

A virus is genetic material, DNA or RNA, inside a protein coat called a capsid, sometimes wrapped in a lipid envelope. It has no metabolism of its own and can reproduce only inside a host cell, which is why viruses are not counted as cells.

In the lytic cycle a virus takes over its host, makes many copies and bursts the cell. In the lysogenic cycle its DNA joins the host's DNA and is copied quietly along with it until it switches to lytic. Retroviruses carry an enzyme, reverse transcriptase, that turns their RNA genome into DNA inside the host.

Antibiotics target structures bacteria have, such as their cell walls, which viruses lack, so antibiotics do not treat viral infections. Antiviral drugs must block a step specific to the virus without harming the host's cells, and vaccines prepare the immune system in advance.

Many new human viruses spill over from animal reservoirs. Influenza changes gradually through small mutations, antigenic drift, and occasionally abruptly when strains swap whole gene segments, antigenic shift. Epidemiology tracks where and how a new virus spreads.

A typical bacterium has a cell wall, often a sticky capsule, hairlike pili for attaching, and flagella for moving. Its DNA sits in the nucleoid, and many bacteria carry extra small DNA circles called plasmids.

Bacteria and archaea both lack nuclei but differ in chemistry: their membrane lipids are built differently, and archaea lack the peptidoglycan found in bacterial cell walls. Many archaea live in extreme places, such as hot springs and very salty water.

Microbes run essential cycles: some fix nitrogen from the air into forms plants can use, and others decompose dead material and return nutrients. Many live in communities called biofilms, and the human body carries a large community of microbes, its microbiome.

Protists are mostly single-celled eukaryotes that are not plants, animals or fungi. Some make food by photosynthesis, some eat other organisms and some absorb nutrients. They move with flagella, cilia or extensions of their cell.

Fungi grow as threads called hyphae, which form a network called a mycelium, and their cell walls contain chitin. They reproduce with spores. Fungi decompose dead matter, partner with plant roots as mycorrhizae, join algae in lichens, and some cause disease.

Plants have three tissue systems: dermal tissue covers them, vascular tissue moves water and food, and ground tissue fills the rest. These are arranged differently in roots, stems and leaves; a leaf, for instance, has layers built for capturing light and exchanging gases.

Apical meristems at the tips of roots and shoots make plants longer, which is primary growth. Lateral meristems make stems and roots thicker, which is secondary growth; in woody plants, each year's new wood forms a growth ring.

Water rises through xylem mainly because it evaporates from leaves, transpiration, and the water column below is pulled up by cohesion. Guard cells open and close stomata, balancing water loss against taking in carbon dioxide.

Phloem carries sugars from sources, where they are made or stored, to sinks, where they are used or stored. Loading sugar at the source draws in water and raises pressure, which pushes the sap toward the sink.

Soil forms layers, called horizons, from the surface down. Plants need macronutrients such as nitrogen, phosphorus and potassium in large amounts and micronutrients in small amounts, and a shortage shows as specific symptoms. Some plants host nitrogen-fixing bacteria in root nodules.

Plant hormones control growth: auxin drives cell elongation, gibberellins promote stem growth and germination, cytokinins promote cell division, abscisic acid helps plants handle drought, and ethylene ripens fruit. Plants bend toward light and grow in response to gravity, and many flower by day length.

A flower has sepals, petals, stamens that make pollen and a pistil that holds the ovules. Pollinators, wind or water carry pollen to the pistil. In flowering plants, one sperm fertilizes the egg and another joins two other nuclei to form the seed's food store; this is double fertilization.

A seed holds an embryo and stored food inside a protective coat, and fruits help disperse seeds. Many seeds stay dormant until conditions suit germination. Plants can also reproduce without seeds, from cuttings, runners or bulbs.

Animals differ in symmetry, radial or bilateral, in the number of embryonic tissue layers, and in whether they have a body cavity. Their bodies are built from four tissue types: epithelial, connective, muscle and nervous tissue.

Homeostasis keeps internal conditions near a set point. Most control uses negative feedback, which counteracts a change, as when sweating cools you when you overheat. Positive feedback amplifies a change and is rare, as in childbirth.

Endotherms, such as birds and mammals, generate their own body heat; ectotherms rely mostly on their surroundings. Heat moves between an animal and its environment by conduction, convection, radiation and evaporation, and animals adjust each route to control their temperature.

Simple animals have a digestive sac with one opening; most have a complete tract with a mouth and an anus. Enzymes break food down in stages along the tract, and the small intestine's folds and villi give it a large surface for absorbing nutrients. Ruminants use microbes to ferment plant fiber.

Skeletons may be fluid-filled, external or internal, and bones and muscles work together as levers. Muscles contract when myosin filaments pull actin filaments past them, a process triggered by calcium and powered by ATP; this is the sliding-filament model.

Animals exchange gases across moist surfaces: skin, gills, insect tracheae or lungs. Fish gills use countercurrent flow, with blood moving opposite to water, which keeps oxygen diffusing into the blood along the whole length of the gill.

Oxygen moves from high partial pressure in the lungs to low partial pressure in tissues. Hemoglobin picks up oxygen in the lungs and releases it in tissues, and it lets go more readily where carbon dioxide and acidity are high, the Bohr effect. Most carbon dioxide travels in the blood as bicarbonate.

Blood is plasma carrying three kinds of cells and cell fragments. Red blood cells carry oxygen, white blood cells defend against infection, and platelets help form clots. Three jobs, three different components.

In an open circulatory system, as in insects, fluid bathes the organs directly. In a closed system, blood stays in vessels. Fish have two-chambered hearts, amphibians three, and birds and mammals four, which keeps oxygen-rich and oxygen-poor blood fully separate.

The heart beats in a cycle of contraction and relaxation, set by a natural pacemaker. Arteries have thick, elastic walls to carry high-pressure blood from the heart, capillaries are thin for exchange, and veins carry blood back at low pressure, with valves to stop backflow.

Animals need carbohydrates, fats, proteins, vitamins, minerals and water. A nutrient is essential when the body cannot make enough of it and must get it from food. Water and fiber are counted as nutrients even though they supply no usable energy.

Vitamins are organic compounds needed in small amounts, many acting as coenzymes. Fat-soluble vitamins, A, D, E and K, can be stored in the body, while water-soluble ones, the B vitamins and C, are mostly not stored. Minerals are inorganic elements, such as calcium for bones and iron for hemoglobin.

Specific deficiencies cause specific diseases: lack of vitamin C causes scurvy, lack of vitamin D causes rickets, lack of iron causes anemia, lack of iodine causes goiter, and lack of vitamin A causes night blindness. Severe shortages of protein and energy cause kwashiorkor and marasmus.

Fat is the most energy-dense of the three macronutrients, carrying far more energy per gram than carbohydrate or protein. Basal metabolic rate is the energy the body uses at rest, and activity raises daily needs above it. Energy taken in beyond what is used is stored, mostly as fat.

Sponges filter food from water and have no true tissues. Cnidarians, such as jellyfish and corals, have radial symmetry and stinging cells. Many cnidarians alternate between an attached polyp form and a free-swimming medusa form.

Flatworms have a gut with only one opening and no body cavity. Roundworms have a complete gut and a fluid-filled cavity. Annelids, such as earthworms, have a complete gut, a true body cavity and a body divided into repeated segments.

Mollusks have a soft body with a mantle, a muscular foot and, in many, a rasping tongue called a radula. Snails are gastropods, clams are bivalves, and octopuses and squid are cephalopods, with the largest brains of any invertebrates.

Arthropods have a hard exoskeleton containing chitin and jointed legs. To grow they must shed the exoskeleton, molting. Insects, spiders and crustaceans belong here, and the phylum contains the majority of described animal species.

Echinoderms, such as sea stars, move with a water vascular system and have radial symmetry as adults. Chordates share four features at some stage of life: a notochord, a nerve cord along the back, openings in the throat called pharyngeal slits, and a tail past the anus.

Fishes include jawless fishes such as lampreys, cartilaginous fishes such as sharks, and bony fishes. They breathe with gills and are mostly ectothermic.

Amphibians have moist skin that can lose water and must usually return to water to breed. Reptiles have dry scaly skin and lay amniotic eggs with protective membranes, which let them reproduce away from water.

Birds have feathers and are endothermic. Mammals have hair and feed their young with milk from mammary glands. Monotremes lay eggs, marsupials give birth to tiny young that develop in a pouch, and placental mammals nourish their young through a placenta.

A neuron receives signals on its dendrites and cell body and sends them along its axon to its terminals. A myelin sheath around many axons speeds conduction. Glial cells support neurons, providing nutrients, insulation and protection.

A resting neuron is more negative inside than outside. The sodium-potassium pump keeps sodium high outside and potassium high inside, and potassium leaking out through open channels makes the inside negative.

When a stimulus pushes a neuron past threshold, sodium channels open and the inside turns positive; then potassium channels open and restore the negative charge. An action potential is all-or-none, a refractory period keeps it moving one way, and on myelinated axons it jumps between gaps called nodes of Ranvier.

At a synapse, an arriving signal makes vesicles release neurotransmitter into the gap. It binds receptors on the next cell, either exciting or inhibiting it, and the effects of many inputs add up. The neurotransmitter is then broken down or taken back up so the signal ends.

The central nervous system is the brain and spinal cord; the peripheral nervous system is the nerves beyond them. The somatic division controls voluntary movement, and the autonomic division controls internal organs, with sympathetic fight-or-flight and parasympathetic rest-and-digest branches. A reflex arc can act without the brain.

The cerebrum handles thought, sensation and voluntary movement; the cerebellum coordinates movement and balance; and the brainstem controls breathing, heart rate and other basic functions. The limbic system is involved in emotion and memory.

Sensory receptors convert stimuli into nerve signals, transduction. Photoreceptors in the retina respond to light and hair cells in the inner ear respond to sound vibrations. Many receptors adapt, responding less to a constant stimulus.

Hormones travel in the blood to distant targets, so their effects are slower and longer-lasting than nerve signals. Steroid hormones pass through the cell membrane and act inside the cell, while peptide hormones bind receptors on the cell surface.

The hypothalamus controls the pituitary gland, which in turn directs other glands. The thyroid sets metabolic rate, the parathyroids control blood calcium, the adrenal glands respond to stress, the pancreas controls blood sugar with insulin and glucagon, and the gonads make sex hormones.

Innate defenses act quickly against any invader: skin and mucous membranes block entry, phagocytes engulf microbes, inflammation brings blood and immune cells to an injury, fever slows pathogens, and complement proteins help destroy them.

Adaptive immunity targets specific invaders and remembers them. When a lymphocyte recognizes an antigen, it multiplies, clonal selection. B cells make antibodies that tag invaders in body fluids, while T cells kill infected cells, and memory cells give a faster response next time.

An antibody is a Y-shaped protein whose variable regions bind one specific antigen, while its constant region decides how it acts. Cells display fragments of proteins on MHC molecules, which lets immune cells tell the body's own cells from infected or foreign ones.

Active immunity comes from your own response to infection or a vaccine; passive immunity comes from receiving antibodies, as a baby does from its mother. When enough people are immune, herd immunity protects others. Allergies are overreactions, autoimmunity is an attack on the body's own tissue, and immunodeficiency is a weakened defense.

Animals must get rid of nitrogen waste: ammonia needs a lot of water to remove, urea less, and uric acid least. In the kidney, each nephron filters blood, reabsorbs useful substances and water, and secretes extra waste into the urine.

Some animals reproduce asexually, by budding or splitting. Sexual reproduction uses fertilization, which may happen outside the body, as in many fish, or inside it. Sperm are made continually in large numbers, while eggs develop in cycles controlled by hormones.

After fertilization, the egg blocks other sperm from entering. It divides rapidly, cleavage, into a hollow ball called a blastula. In gastrulation the cells rearrange into germ layers, and each layer gives rise to particular tissues and organs.

Development is guided by chemical signals. Morphogens form gradients that tell cells their position, cells influence their neighbors' fate through induction, and homeotic genes set the identity of each body region.

Temperature and rainfall largely decide which land biome develops, from tundra to tropical rainforest. In water, light, temperature, salinity and nutrients set the limits, distinguishing freshwater, estuarine and ocean zones.

With unlimited resources a population grows exponentially, faster and faster. Real populations level off at the carrying capacity, the largest population the environment can support, following a logistic curve. Survivorship curves show when in life individuals tend to die.

Density-dependent factors, such as competition and disease, hit harder as a population grows. Density-independent factors, such as a drought or a freeze, strike regardless of size. Species also trade off traits such as many small offspring against few well-cared-for ones.

Age-structure diagrams show whether a population will grow, with a wide base of young people, or shrink. The demographic transition describes how death rates and then birth rates fall as countries develop. An ecological footprint estimates the resources a population uses.

Species compete for resources, eat one another as predators or herbivores, or live together in symbiosis: mutualism benefits both, commensalism benefits one without affecting the other, and parasitism benefits one at the other's expense. These interactions drive defenses and mimicry.

A species' fundamental niche is everything it could use; its realized niche is what it actually uses in the presence of competitors. Two species cannot share exactly the same niche indefinitely, competitive exclusion, so species often divide resources.

A keystone species, such as a top predator, has an effect far larger than its numbers suggest, and removing it can trigger a trophic cascade. Succession is the gradual change of a community: primary succession starts on bare ground, secondary succession after a disturbance leaves soil behind.

Energy enters ecosystems through producers and passes up food chains to consumers. Only a small share of the energy at one trophic level passes to the next, because most is used or lost as heat, which is why food chains are short and biomass pyramids narrow toward the top.

Carbon, nitrogen, phosphorus and water cycle between living things and the environment. Carbon moves through photosynthesis, respiration and burning; nitrogen depends on bacteria to be fixed into usable forms; phosphorus cycles mainly through rocks and soil; water cycles by evaporation, transpiration and precipitation.

Fertilizer runoff overloads water with nutrients, feeding algae whose decay creates low-oxygen dead zones. Burning fossil fuels raises atmospheric carbon dioxide, strengthening the greenhouse effect and acidifying the oceans. Some pollutants concentrate up food chains.

Biodiversity includes genetic diversity within species, the diversity of species, and the diversity of ecosystems. Habitat loss, invasive species, pollution and overharvesting drive extinctions. Ecosystems provide services such as clean water and pollination, and conservation protects habitats and species.

Some behaviors are innate, such as reflexes and fixed action patterns triggered by a specific stimulus. Others are learned, and imprinting combines both, happening only during a sensitive period. Most real behavior blends inherited tendencies with experience.

Habituation is learning to ignore a repeated harmless stimulus. In classical conditioning, an animal links a neutral stimulus to a meaningful one; in operant conditioning, it links a behavior to its reward or punishment. Animals also learn by trial and error, by insight and by watching others.

Helping relatives can spread shared genes, so kin selection can favor altruism. Unrelated animals may help each other when the favor is likely to be returned. In eusocial species, such as honeybees, most individuals do not reproduce at all, and ritual displays often settle disputes without injury.

Animals communicate with chemical signals, visual displays, sounds and, in honeybees, dances that show the direction of food. Bright warning colors advertise that an animal is toxic. Daily circadian rhythms and seasonal cycles are kept in step mainly by light.

Optimal foraging theory predicts that animals choose food that gives the most energy for the time and risk involved. In mate choice, the choosier sex often favors costly ornaments or displays, which can persist through sexual selection even when they hurt survival.

Infectious diseases are caused by pathogens and can spread from person to person. Noninfectious diseases come from genetics, lifestyle, nutrient shortages or wear with age, and most chronic diseases have several contributing causes.

Germ theory holds that many diseases are caused by microorganisms, replacing the old idea that bad air caused illness. Koch's postulates set a test for linking a specific microbe to a specific disease: find it in every case, grow it, use it to cause the disease again, and recover it.

Infections spread through direct contact, respiratory droplets, contaminated food and water, or vectors such as mosquitoes and ticks. A reservoir is where the pathogen normally lives, and the incubation period is the time from infection to symptoms.

A disease that is constantly present at a usual level in an area is endemic. A rise in cases clearly above that usual level is an epidemic, and an epidemic that spreads over several countries or continents is a pandemic.

Each control measure breaks a different link in the chain of transmission: sanitation removes the pathogen's route, vaccination protects people before exposure and can create herd immunity, isolation separates the sick, and quarantine separates people who were exposed.

Antibiotics do not create resistance; they select for bacteria that already carry resistance genes, which survive and multiply when an antibiotic kills the rest. Bacteria can also pass resistance genes to one another, so overuse and misuse of antibiotics speed its spread.