Biology, oriented

Science moves from observation to a testable hypothesis, and a good hypothesis must be possible to prove wrong. Life's chemistry rests on water: its molecules cling together through hydrogen bonds, which gives water a high capacity for heat and makes it an excellent solvent. Carbon forms four bonds and builds the skeletons of the four big molecule classes: carbohydrates, lipids, proteins and nucleic acids. Most are polymers joined by removing water and broken apart by adding it back. A protein's sequence of amino acids decides how it folds, and its fold decides what it does.

Every cell is wrapped in a membrane, a double layer of phospholipids studded with proteins. Small nonpolar molecules slip through it, while ions and larger polar molecules need channels or carriers. Moving a substance down its concentration gradient costs no energy; pumping it the other way does. Water follows dissolved particles by osmosis, so a cell placed in a saltier solution loses water and shrinks.

Eukaryotic cells divide their work among organelles. The nucleus holds the DNA, ribosomes build proteins, the endoplasmic reticulum and the Golgi apparatus process and ship them, and mitochondria release energy from food. Prokaryotic cells, such as bacteria, have no nucleus and are usually much smaller.

Rule: ask what a structure's shape or location lets it do; in biology, form and function nearly always explain each other.

Cells run on adenosine triphosphate, or ATP. Breaking off one of its phosphate groups releases energy that drives otherwise uphill reactions, and the cell rebuilds it constantly. Enzymes speed reactions by lowering the energy barrier they must cross, without being used up and without changing whether a reaction releases energy overall.

Cellular respiration releases the energy stored in glucose. Glycolysis splits glucose in the cytoplasm for a small ATP gain; the citric acid cycle in the mitochondria strips off carbon dioxide and loads electron carriers; and the electron transport chain uses those electrons to pump protons, whose flow back through ATP synthase makes most of the ATP. Oxygen is the final electron acceptor. Without oxygen, fermentation keeps glycolysis running but yields far less energy.

Photosynthesis runs the overall process in reverse. In the chloroplast's thylakoids, light splits water, releasing oxygen and making ATP and a loaded electron carrier. In the stroma, the Calvin cycle spends both to fix carbon dioxide into sugar. Chlorophyll absorbs mostly red and blue light, which is why leaves look green.

Cells also talk to one another. A signal binds a receptor, sets off a chain of reactions that amplifies it, and produces a response, after which the signal must be switched off.

Rule: track where the energy and the electrons go; most metabolism questions become simple once you follow them.

Before dividing, a cell copies its DNA so each chromosome has two identical sister chromatids. In mitosis these separate, giving two cells genetically identical to the parent, for growth and repair. Checkpoints stop the cycle if something is wrong, and cancer begins when those controls fail.

Meiosis makes gametes. Homologous chromosomes, one from each parent, pair up and swap segments by crossing over, then separate, and the sister chromatids separate in a second division. The result is four haploid cells, each genetically different. Errors in separation produce an extra or missing chromosome.

Mendel showed that traits pass as discrete units. Each parent passes one of its two alleles, chosen at random, so crossing two heterozygotes gives a 3:1 ratio of dominant to recessive traits. Genes on different chromosomes are inherited independently. Real traits add complications: incomplete dominance, codominance, multiple alleles, and traits shaped by many genes plus the environment.

Genes on the X chromosome behave differently in males, who have only one X. A single recessive allele on a male's X shows up in his phenotype, so X-linked recessive conditions are far more common in males. Genes close together on one chromosome tend to be inherited together.

Rule: write the genotypes of the parents first and list the gametes each can make; every inheritance question follows from that list.

Deoxyribonucleic acid, DNA, is a double helix whose two strands pair base to base: adenine with thymine and guanine with cytosine. When it copies itself, each new molecule keeps one old strand. Copying runs in one direction only, so one strand is built continuously and the other in short pieces.

A gene is expressed in two steps. Transcription copies it into ribonucleic acid, RNA, and translation reads that RNA three bases at a time, each codon calling for an amino acid or a stop. In eukaryotes the RNA is processed first: noncoding introns are cut out, and splicing the same RNA different ways lets one gene make several proteins. A mutation that changes one base may change one amino acid, stop the protein early, or have no effect; adding or removing a base shifts the whole reading frame.

Nearly every cell in your body has the same DNA, so cells differ by which genes they use. Bacteria switch whole groups of genes with operons. Eukaryotes control access to DNA by how tightly it is packed, and use proteins that bind DNA to turn genes up or down.

Biotechnology builds on these mechanisms. Restriction enzymes cut DNA at specific sequences, the polymerase chain reaction copies a chosen region millions of times, gel electrophoresis sorts fragments by size, and sequencing reads the bases in order.

Rule: when a question involves a change in DNA, follow it to the RNA and then to the protein before you judge its effect.

Natural selection needs three things: variation in a trait, inheritance of that trait, and differences in survival or reproduction linked to it. Over generations, helpful traits become more common. Individuals do not evolve; populations do, as their allele frequencies change. Selection also does not respond to need; it works only on variation already present.

Several forces change allele frequencies. Selection favors some alleles, genetic drift changes them by chance and matters most in small populations, gene flow moves them between populations, and mutation supplies new ones. New species form when populations stop interbreeding, often after a physical barrier separates them.

The evidence comes from many directions. Fossils show change over time, homologous structures reveal common ancestry, all life shares the same genetic code, and resistance to antibiotics and pesticides shows evolution happening within years. Phylogenetic trees map that ancestry: read relatedness from the shared branch points, not from how close two names sit at the tips. Life falls into three domains, Bacteria, Archaea and Eukarya.

Microbes are central to that diversity. Viruses are genetic material in a protein coat and can reproduce only inside host cells, so they are not counted as cells. Bacteria and archaea have no nucleus, and many fix nitrogen or decompose dead matter.

Rule: look for variation, inheritance and differential success; if any of the three is missing, natural selection cannot be the explanation.

Plants lift water through xylem largely because it evaporates from their leaves, transpiration, pulling the water column up behind it. Guard cells open and close the pores called stomata, trading water loss for carbon dioxide. Phloem carries sugar from where it is made to where it is used, and hormones such as auxin steer growth toward light.

Animals keep internal conditions stable through homeostasis, mostly by negative feedback that counteracts a change. The heart pumps blood through arteries, capillaries and veins, with valves keeping it moving one way. In the kidney, nephrons filter blood and reclaim what the body needs, letting waste leave in urine. Digestion breaks food into small molecules that the small intestine absorbs.

Neurons carry fast signals. A neuron receives input on its dendrites and sends an electrical impulse down its axon, faster where the axon is wrapped in myelin, then passes the message chemically across a synapse. Hormones carry slower, longer-lasting signals through the blood from glands such as the pituitary, thyroid and pancreas.

The immune system defends in two layers. Innate defenses, such as skin, inflammation and fever, act fast against anything. Adaptive defenses target specific invaders: B cells make antibodies, T cells kill infected cells, and memory cells make a second response faster.

Rule: for any body system, name the variable it controls and the feedback loop that controls it.

Energy enters an ecosystem through producers that capture sunlight and passes to consumers, but only a small share moves from each level to the next, because most is used or lost as heat. That is why food chains are short. Nutrients, unlike energy, cycle: carbon moves through photosynthesis, respiration and burning, and nitrogen depends on bacteria to become usable.

A population with unlimited resources grows faster and faster, but real populations level off at the carrying capacity of their environment. Species compete, prey on one another and live in partnerships that may help both, help one, or harm one. Removing a keystone species can ripple through a whole community.

Human activity changes these systems. Fertilizer runoff feeds algae whose decay strips water of oxygen, creating dead zones, and burning fossil fuels adds carbon dioxide that warms the climate. Behavior matters too: many animals keep daily rhythms set mainly by light.

Infectious diseases spread through contact, droplets, food and water, or animal carriers. A disease that is always present at a usual level is endemic; a clear rise above that level is an epidemic, and one that spreads across several countries or continents is a pandemic. Vaccination, sanitation and isolation each cut a different link in the chain of spread. Antibiotics select for bacteria that are already resistant, which is why overuse speeds resistance.

Rule: follow the flow of energy and the links of transmission; most ecology and disease questions turn on where a chain is weak.