The process of photosynthesis converts light energy to stored chemical energy by converting carbon dioxide plus water into sugars plus released oxygen. The sugar molecules thus formed contain carbon, hydrogen, and oxygen; their hydrocarbon backbones are used to make amino acids and other carbon-based molecules that can be assembled into larger molecules (such as proteins or DNA), used for example to form new cells. As matter and energy flow through different organizational levels of living systems, chemical elements are recombined in different ways to form different products. As a result of these chemical reactions, energy is transferred from one system of interacting molecules to another. For example, aerobic (in the presence of oxygen) cellular respiration is a chemical process in which the bonds of food molecules and oxygen molecules are broken and new compounds are formed that can transport energy to muscles. Anaerobic (without oxygen) cellular respiration follows a different and less efficient chemical pathway to provide energy in cells. Cellular respiration also releases the energy needed to maintain body temperature despite ongoing energy loss to the surrounding environment. Matter and energy are conserved in each change. This is true of all biological systems, from individual cells to ecosystems.

Each atom has a charged substructure consisting of a nucleus, which is made of protons and neutrons, surrounded by electrons. The periodic table orders elements horizontally by the number of protons in the atom's nucleus and places those with similar chemical properties in columns. The repeating patterns of this table reflect patterns of outer electron states. The structure and interactions of matter at the bulk scale are determined by electrical forces within and between atoms. Stable forms of matter are those in which the electric and magnetic field energy is minimized. A stable molecule has less energy, by an amount known as the binding energy, than the same set of atoms separated; one must provide at least this energy in order to take the molecule apart.