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Biology LibreTexts

2.2: Atoms and Basic Chemistry

  • Page ID
    16416
  • A. Overview of Elements and Atoms

    The difference between elements and atoms is often confused in casual conversation. Both terms describe matter, substances with mass. Different elements are different kinds of matter distinguished by different physical and chemical properties. In turn, the atom is the fundamental unit of matter…, that is, of an element.

    The number of positively charged protons and neutral neutrons in an atomic nucleus account for most of the mass of an atom. Each negatively charged electron that orbits a nucleus is about 1/2000th of the mass of a proton or neutron. Thus, they do not add much to the mass of an atom. Electrons stay in atomic orbits because of electromagnetic forces, i.e., their attraction to the positively charged nuclei. Nuclear size (mass) and the cloud of electrons around its nucleus define structure of an atom. And that structure dictates the different properties of the elements.

    Recall that atoms are chemically most stable when they are electrically uncharged, with an equal number of protons and electrons. Isotopes of the same element are atoms with the same number of protons and electrons, but a different number of neutrons. Therefore, isotopes are also chemically stable, but they may not be physically stable. For example, the most abundant isotope of hydrogen contains one proton, one electron and no neutrons. The nucleus of the deuterium isotope of hydrogen contains one neutron and that of tritium contains two neutrons. Both isotopes can be found in water molecules. Deuterium is stable. In contrast, the tritium atom is radioactive, subject to nuclear decay over time. Whether physically stable or not, all isotopes of an element share the same chemical and electromagnetic properties and behave the same way in chemical reactions.

    The electromagnetic forces that keep electrons orbiting their nuclei allow the formation of chemical bonds in molecules. We model atoms to illustrate the average physical location of electrons (the orbital model) on one hand, and their potential energy levels (the Bohr, or shell model) on the other. Look at the models for helium illustrated below.

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    Up to two electrons move in a space defined as an orbital. In addition to occupying different areas around the nucleus, electrons exist at different energy levels, moving with different kinetic energy. Electrons can also absorb or lose energy, jumping or falling from one energy level to another.

    A unique atomic number (number of protons) and atomic mass (usually measured in Daltons, or Da) characterize different elements. A unique symbol with a superscripted atomic number and a subscripted atomic mass number defines each element. Take the most common isotope of carbon (C) for example. Its atomic number is 6 (the number of protons in its nucleus) and its mass is 12 Da (6 protons and 6 neutrons at 1 Da each!). Remember that the mass of the electrons in a carbon (C) atom is negligible!

    Find the C atom and look at some of the other atoms of elements in the partial periodic table below.

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    This partial periodic table shows the elements essential for all life in greater or lesser amounts, as well as some that may also be essential in humans.

    122 Atoms and Elements

    B. Electron Configuration – Shells and Subshells

    The Bohr model of the atom reveals how electrons can absorb and release energy. The shells indicate the energy levels of electrons. Electrons can absorb different kinds of energy (radiation, light, electrical). For example, beaming UV light at atoms can excite electrons. If an electron absorbs a full quantum of energy (or a photon of radiant energy), it will be boosted from the ground state (the shell it normally occupies) into a higher shell, an excited state. Excited electrons move at greater speed around the nucleus, with more kinetic energy than it did at ground. Excited electrons also have more potential energy than ground state electrons. This is because they are unstable, releasing some of the energy gained during excitation as they return to ground, i.e., their starting energy level (shell), as shown below.

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    Electrons falling back to ground typically release excitation energy as heat. Atoms whose excited electrons release their energy as light fluoresce; they are fluorescent. A fluorescent light is an example of this phenomenon; electrical energy excites electrons out of atomic orbitals in molecules coating the interior surface of the bulb. As all those excited electrons return to ground state, they fluoresce, releasing light. These atoms can be repeatedly excited by electricity. As we shall see, biologists and chemists have turned fluorescence into tools of biochemistry, molecular biology and microscopy. The ground state is also called the resting state, but electrons at ground are by no means resting! They just move with less kinetic energy excited electrons.

    123 Electron Energy & Fluorescence