Matter is anything that takes up space and has mass. It exists as solid, liquid, or gas. All matter is made of elements — pure substances that cannot be broken down by ordinary chemical processes. The smallest stable unit of matter is an atom. Atoms are so small that one million placed side by side would only span the width of a period on a page.

Isotopes are atoms of the same element that differ in the number of neutrons. Isotopes have the same atomic number but different mass numbers. The presence or absence of neutrons does not change chemical behavior. Unstable isotopes are radioactive — they spontaneously emit subatomic particles or radiation. Weak radioisotopes are used in diagnostic procedures.

Electron shells: Electrons occupy ordered shells around the nucleus. The first shell holds a maximum of 2 electrons. The second shell holds up to 8. Only electrons in the outermost shell interact with other atoms. A full outer shell = chemically stable (inert, will not react). An unfilled outer shell = unstable and reactive.

When an atom gains or loses electrons it becomes an ion — a charged particle. Ions with a positive charge are cations (+). Ions with a negative charge are anions (−).

An ionic bond is the electrical attraction between a cation and an anion. Example: sodium (Na) loses one electron → becomes Na+ (cation). Chlorine (Cl) gains that electron → becomes Cl− (anion). The attraction between Na+ and Cl− forms sodium chloride (NaCl) — table salt, an ionic compound.

A covalent bond forms when two atoms share electrons to fill their outer shells. Covalent bonds are strong — the shared electrons physically tie atoms together.

A hydrogen bond is the weak attraction between a slightly positive hydrogen atom in one polar covalent bond and a slightly negative oxygen or nitrogen atom in another polar covalent bond. The two atoms can be in different molecules or in different parts of the same large molecule.

Hydrogen bonds are too weak to form molecules on their own. Their effects are significant because they occur in large numbers. They can alter molecular shapes and pull molecules together.

Metabolism refers to all chemical reactions in the body. Cells use these reactions to maintain homeostasis and perform essential functions. Three types are critical to physiology:

Activation energy is the amount of energy required to start a chemical reaction. Without help, most reactions needed to sustain life would not occur at body temperature and normal pH. For example, breaking down complex sugar in a lab requires boiling it in acid — conditions that would kill cells.

Enzymes are protein molecules that act as catalysts. A catalyst accelerates a chemical reaction without being permanently changed or consumed. Cells make one enzyme molecule for each specific reaction they need to control.

Enzymes work by lowering the activation energy threshold. This makes the reaction proceed faster under normal body conditions. Lowering activation energy affects only the rate of the reaction, not its direction, not the products formed. An enzyme cannot cause a reaction that is chemically impossible.

Water (H2O) makes up to two-thirds of total body weight. A change in the body's water content can have fatal consequences because virtually all physiological systems are affected. Water is a polar molecule — oxygen's stronger pull on electrons creates a slightly negative oxygen end and slightly positive hydrogen ends — which explains all three of its critical properties.

A hydrogen atom involved in a chemical bond can easily lose its electron to become a hydrogen ion (H+). In excessive numbers, H+ ions break chemical bonds, change the shapes of complex molecules, and disrupt cell and tissue functions. The concentration of hydrogen ions must be precisely regulated.

pH is a number from 0 to 14 that represents the concentration of hydrogen ions (H+) in a solution.

Buffers are compounds that stabilize pH by either removing or replacing hydrogen ions. They prevent dangerous swings in pH when acids or bases enter body fluids.

Antacids such as Alka-Seltzer, Rolaids, and Tums are buffers that tie up excess hydrogen ions in the stomach. The major physiological buffer is sodium bicarbonate (baking soda). A variety of buffers in body fluids maintain pH between 7.35 and 7.45 in most tissues.

A carbohydrate is an organic molecule containing carbon, hydrogen, and oxygen in a near 1:2:1 ratio. Familiar examples: sugars and starches. Despite being the primary energy source, carbohydrates account for only about 1% of total body weight. Three major types:

Lipids contain carbon, hydrogen, and oxygen but have relatively less oxygen than carbohydrates — the ratio is NOT 1:2:1. May also contain phosphorus, nitrogen, or sulfur. Familiar types: fats, oils, waxes. Most lipids are insoluble in water; special transport mechanisms carry them in blood. Lipids provide roughly twice as much energy per gram as carbohydrates. Account for 12–18% of body weight in adult men and 18–24% in adult women.

Proteins are the most abundant organic components of the human body, accounting for about 20% of total body weight. All proteins contain carbon, hydrogen, oxygen, and nitrogen. Smaller quantities of sulfur and phosphorus may also be present. Proteins determine cell shape, tissue properties, and virtually all cellular functions.

Seven functions:

Protein structure — amino acids and peptide bonds:

Proteins are chains of amino acids linked by peptide bonds. Each amino acid has a central carbon bonded to: a hydrogen atom, an amino group (–NH2), a carboxyl group (–COOH), and a variable R group (side chain). The R group distinguishes one amino acid from another — 20 different amino acids exist in the body. A typical protein contains 1,000 amino acids; the largest complexes have 100,000 or more.

Denaturation: Body temperatures over 43°C (110°F) or extreme pH changes alter a protein's three-dimensional shape. Denatured proteins are nonfunctional. Loss of structural proteins and enzymes causes irreparable damage to organs. A single amino acid change in a protein of 10,000+ amino acids can destroy its function — sickle cell anemia results from one amino acid substitution in hemoglobin.

Nucleic acids are large organic molecules made of carbon, hydrogen, oxygen, nitrogen, and phosphorus. They store and process information at the molecular level inside cells. Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

Both are built from subunits called nucleotides. Each nucleotide has three parts: a five-carbon sugar, a phosphate group (PO43−), and a nitrogenous (nitrogen-containing) base.

Complementary base pairing in DNA: Because of their shapes, adenine bonds only with thymine (A–T), and cytosine bonds only with guanine (C–G). These are complementary base pairs. The two DNA strands are held together by hydrogen bonds between these pairs. The double helix resembles a spiral staircase — the sugar-phosphate backbones are the railings, and the base pairs are the steps.

Cells obtain energy by breaking down organic molecules (catabolism of glucose). To use that energy for cellular work, it must be transferred efficiently between molecules. The body does this through high-energy bonds — covalent bonds that store unusually large amounts of energy. In cells, high-energy bonds typically connect a phosphate group (PO43−) to an organic molecule, creating a high-energy compound. Most high-energy compounds are derived from nucleotides.

The most important high-energy compound in the body is ATP (adenosine triphosphate). ATP is built from the nucleotide AMP (adenosine monophosphate) plus two additional phosphate groups attached by high-energy bonds.

ATP powers: protein synthesis, muscle contraction, active transport across membranes, and all other energy-requiring cellular functions. Cells continuously generate ATP from ADP using energy obtained from catabolism of glucose and other organic molecules.