Atoms are the basic unit of chemistry. They are composed of three basic parts:

1)      Neutrons:  Neutrons are uncharged particles that are found in the center of the atom (the nucleus). Neutrons give mass (weight) to the atom but do not participate in chemical reactions.

2)      Protons: Protons are positively charged particles that are also found in the nucleus. Like neutrons, protons give mass to the atom but do not participate in chemical reactions. The number of protons an atom has is called the atom’s atomic number, and determines the atom’s identity (e.g. carbon atoms have 6 protons, oxygen atoms have 8 protons).

3)      Electrons: Electrons are negatively charged particles that are found in electron shells surrounding the nucleus. They have essentially no mass but are important in chemical reactions. The first electron shell can hold 2 electrons. For most biologically relevant atoms, additional electron shells (if present) can hold up to eight electrons.

Each atom contains equal numbers of protons and electrons. The number of neutrons may vary within atoms of a particular type. (For example, carbon atoms may have 6, 7, or 8 neutrons).  Atoms that vary only in the number of neutrons are called isotopes.

Bonds

Atomic stability:

    The stability of atoms depends on whether or not their outer-most shell is filled with electrons.  If the outer shell is filled, the atom is stable.  Atoms with unfilled outer shells are unstable, and will usually form chemical bonds with other atoms to achieve stability.

 

The two types of chemical bonds that atoms can form to achieve stability are called ionic bonds and covalent bonds. In ionic bonds, atoms donate or receive electrons to achieve stability. In covalent bonds, atoms share electrons to achieve stability. The type(s) of bond a particular atom can form depends on the numbers of electrons in their outer shells.

 

Ionic bonds:

  Ionic bonds result from the transfer of electrons between atoms. If an atom has only a few electrons in its outer shell, it can achieve stability by donating these electrons to an atom that has an outer shell that is almost full.

 

For example:

 

 An atom of sodium has only one electron in its outer shell. An atom of chlorine has seven outer electrons (almost a full shell).

 

  

 

 

If the lone sodium outer electron is transferred to the chlorine atom, both atoms would have full outer shells and so would achieve stability. 

 

 

 

 

When clorine gains an extra electron, it is called chloride.

 

 

 

Since chlorine gained a negatively charged electron, it now has more electrons than protons and has a net negative charge. Since sodium lost an electron, it now has more protons than electrons and so has a net positive charge.  Charged particles (like sodium and chlorine after the transfer of electrons) are called ions.  (Specifically, positively charged ions are called cations and negatively charged ions are called anions). Due to the opposite charge of the two ions (negative chloride and positive sodium), the two ions are attracted to each other and form an ionic bond.  The resulting compound is referred to as an ionic compound.  Note that ionic compounds have totally different properties than either of the atoms that make them up. Sodium is a highly reactive silver metal. Chlorine is a toxic green gas. Sodium chloride is table salt.

 

The animation below further illustrates the formation of the ionic compound sodium chloride.

 

Ionic compounds can form from the transfer of one or two (occasionally three) electrons.

 

 Note that in the watery environment of cells or solutions, the water molecules disrupt the ionic bonds by keeping the different ions separate.  Ions are also called electrolytes. Sodium, chloride, calcium, and potassium are biologically important electrolytes.

 

Covalent bonds:

Covalent bonds occur when atoms achieve stability by sharing electrons. In the picture below, the central carbon atom is sharing one pair of electrons with 4 different hydrogen atoms, forming a molecule of CH₄ (methane). Note that if you count all the electrons in the outer shell of carbon, there are 8, so it is stable. If you count all the electrons in each hydrogen outer shell, there are 2. Since the first shell only holds two electrons, the hydrogen atoms are also stable.

 

 

The animation below shows another view of how the atoms in methane share electrons.

 

 

 

 It is also possible for atoms to share two or three pairs of electrons. In the picture below, the two oxygen atoms are sharing two pairs of electrons, forming a molecule of oxygen gas (O₂).

 

Covalent bonds are often represented as single lines in chemical formulas. For example, in the covalent compounds shown below, each line represents a shared pair of electrons.

 

 

 

 

The pH scale measures how many hydrogen ions, H⁺, are present in a solution. Since concentration means how much of a substance is present in a solution, the pH scale measures hydrogen ion concentration. Because the range in hydrogen ion concentration is extremely large, a logarithmic scale is needed to express the number of hydrogen ions present. Using a logarithmic scale means for each whole number change, the number of hydrogen ions in solution changes by a factor of 10. Low pH values represent the greatest number of hydrogen ions present and large numbers represent the least number of hydrogen ions present.

 

Water molecules are composed of two hydrogen atoms and one oxygen atom covalently bound together. But, sometimes one of the hydrogen atoms leaves the water molecule as a hydrogen ion. (The hydrogen electron stays with the oxygen.) Consequently, water has a mixture of H⁺ and OH^-. When there is an equal number of H⁺ and OH^-, the value on the pH scale is 7. If there are more H⁺ than OH^- in a solution, the pH scale values are less than 7. If there are less H⁺ than OH^- in a solution, the pH scale values are greater than 7. How does a solution get unequal amounts of H⁺ and OH^-?