Making Molecules - A molecule is comprised of two or more chemically bonded atoms. The atoms may be of the same type of element, or they may be different. Many elements are found in nature in molecular form - two or more atoms (of the same type of element) are bonded together. Oxygen, for example, is most commonly found in its molecular form "O2" (two oxygen atoms chemically bonded together). There are three primary types of bonds holding atoms together.
Covalent Bonds: Covalent bonds are formed from shared pairs of electrons. They usually occur between atoms of near equal electronegativity. Atoms share electrons to temporarily fill, or empty their outer shells (satisfy the octet rule) . Applied to covalent bonding, the octet rules states that when atoms form covalent bonds, they tend to share sufficient electrons so as to achieve an outer shell having eight electrons (except for hydrogen and helium, which have a stable outer shell of 2 electrons). Covalent bonds are represented in many molecular images as "sticks" or "rods". See the covalent bonds holding the two Hydrogen atoms (white) to the Oxygen atom (red) forming a water molecule, H20, in the image on the left.
Not all electrons involved in covalent bonds are shared equally. In our water molecule example, Oxygen is more electronegative than Hydrogen. The shared electrons will spend more time near the O atom and less time near the H. This results in a partial negative charge surrounding the O atom and a partial negative charge surrounding the H. This unequal sharing of electrons results in polar covalent bonds; covalent bonds with partial charges at each "pole" (think North and South pole). Bonded atoms that share electrons equally have non-polar covalent bonds, the example of Non-polar covalent bonds we will encounter are those between C and H. Water is a polar molecule. The covalent electrons are shared unequally. The greek delta symbols in the above image mean that the charges caused by the unequal sharing of electrons by the atoms are only partial charges. These atoms are not Ions.
Ionic bonds usually occur
beween atoms with large differences in electronegativity. Ionic bonds are formed when there is a complete transfer of electrons
from one atom to another forming two oppositely charged ions.
One atom gains an electron (and becomes negatively charged, an anion), one atom loses an electron (and becomes positively charged, a cation). The opposite charges attract the two atoms and holds them together forming an Ionic bond. One of the critical features of ionic compounds is that they are electrically neutral. Their net positive and negative charges must cancel.
Hydrogen Bonds : This is primarily an intermolecular bond (between molecules) and occurs between polar molecules like the two water molecules below. Partial charges on the molecules attract each other and form a weaker, transitory, H-bond. They are called Hydrogen bonds since, most of the time, Hydrogen is one of the partially charged atoms involved in the bond.
The number and type of bond formed between atoms depends on the nature of the atoms involved. More specifically, the valence electron arrangement and the relative electronegativity of the atoms. To predict the type of chemical bonds that might be formed, you can consult the periodic table and determine the above parameters. This is important for our work later in the class
However, considering the small number of elements we must deal with, You probably should just memorize the elements and their characteristics in this little table. These are the elements most often involved in forming Bio-molecules.
In the next section we look at Biomolecules, focussing on their structure and function.
As you study them ask yourself; What am I looking at, What does it do, and How do I know?