The Chemistry of Microbiology Level of organizations as arranged in ascending order; atoms, molecules, cell organelles, cells, tissues, organs, organ systems, organisms, population, community, ecosystem, and biomes. Atoms Atoms have three parts neutrons, protons, and electrons. Protons are positively charged, electrons negatively charged, and neutrons have no charge. In the periodic table, elements are named according to the number of protons; for example, helium is number two since it has two protons. Cations are positively charged atm, which has lost an electron, while an anion is a negatively charged atom since it has gained an electron. Isotopes have the same number of protons but different numbers of protons.