6 Atoms of Life
The key biologically relevant elements are hydrogen (H), carbon (C), nitrogen (N), oxygen (O), phosphorous (P) and sulfur (S). These elements represent more than 95 percent of the mass of a cell. Carbon is a major component of nearly all biological molecules.
Elements are characterized by their atomic structure. While the subatomic structure of the atom is a major topic of interest in chemistry, physics and biophysics, we will only discuss the basic structure that will provide sufficient information for the construction of molecules in the context of this course. Atoms have a central nucleus with positively charged protons and neutral neutrons; negatively charged electrons circle the nucleus. The electrons that are involved in chemical bonding are those electrons in the outermost orbit, referred to as valence electrons.
Atomic mass, the sum of the number of protons and neutrons in the atomic structure, is a particularly useful measure of each element. By summing the atomic mass of all the atoms in a molecule, one can estimate the molecular mass of the molecule, which is then expressed in atomic mass units, or Daltons. This table shows the masses of the six atoms of the elements listed above.
| Atom | Mass | Valence Electrons | Covalent Bonds |
|---|---|---|---|
| H | 1 | 1 | 1 |
| C | 12 | 4 | 4 |
| N | 14 | 5 | 3 or 4 (e.g. NH4+) |
| O | 16 | 6 | 2 |
| P | 31 | 5 | 3 |
| S | 32 | 6 | 2 |
| Cl | 35 | 7 | 1 |
To calculate the mass of a molecule, we find the mass of each individual atom in the molecule and add them together. For example, a water molecule (H2O) contains one oxygen atom that has a mass of 16 amu (atomic mass units) and two hydrogen atoms that each have a mass of one amu. Therefore, the mass of a water molecule is 16 amu + 2 x 1 amu = 18 amu.
The electronegativity of an element is the degree to which an atom will attract electrons in a chemical bond. Elements with higher electronegativities, such as N, O and F (fluorine), have a strong attraction for electrons in a chemical bond and will therefore “pull” electrons away from less electronegative atoms. Elements with low electronegativity, such as metals, tend to “give away” electrons easily. The electrons are shared between two atoms, however, the two atoms don’t necessarily share the electrons equally. Some atoms are more likely to draw the shared electrons closer to themselves. Atoms have a high electronegativity if they tend to draw the electrons towards them. Electronegativity increases as one moves from the left to the right across the periodic table. In the image below of the partial periodic table, Hydrogen is moderately electronegative, with a value of 2.1, carbon is somewhat more electronegative, with a value of 2.5, and fluorine is the most electronegative atom, with a value of 4.0 [1].
- Image title: Electronegativities of Biologically Important Atoms, Image description: From left to right: Top row: Hydrogen (2.1) Middle row: Lithium (1.0), Beryllium (1.5), B (2.0), Carbon (2.5), Nitrogen (3.0), Oxygen (3.5), Fluorine (4.0) Bottom row: Sodium (0.9), Magnesium (1.2), Aluminum (1.5), Silicon (1.8), Phosphorus (2.1), Sulfer (2.5), Chlorine (3.0) ↵
