Basic Biological Chemistry

 
                                               
       
       
       
       
       
       
       
       
                                       
  Introduction

 

All living things are made up of elements.  An element is defined as a substance that cannot be broken down by ordinary chemical reactions.  There are 92 naturally occurring elements.  Elements are composed of atoms, which are composed of sub atomic particles known as neutrons, protons, and electrons.  Neutrons and protons are found in the nucleus of the atom.  The number of protons in the nucleus is referred to as the atomic number.  The number of electrons in an atom is equal to the number of protons.  The electrons are found outside the nucleus in a volume of space called the orbital.  The first orbital can contain a maximum of two electrons.  Each subsequent outer orbital can contain a maximum of eight electrons (a.k.a. the octet rule).  The number of electrons that an atom must gain or lose to complete its outer orbital is called its valence.  For example, oxygen has an atomic number of eight and so needs two electrons to fill its second orbital.  Thus, oxygen has a valence of +2.  Sodium, on the other hand, has an atomic number of eleven.  Because it is easier to lose one electron than to gain seven, we say that sodium has a valence of –1.

            If the outer orbital of an atom contains less than the maximum number of electrons that it can hold (i.e., less than 2 or 8), the atom can share electrons with other atoms in order to fill its outer orbital.  The kind of bond that forms when electrons are shared between two atoms is called a covalent bond.  Another kind of bond is called an ionic bond.  This chemical bond occurs when a positively charged atom (has more protons than electrons) is attracted to a negatively charged atom (having more electrons than protons).  In today’s lab, we will practice forming covalent bonds, as they are the most common of the chemical bonds.  We will practice with molecules known as inorganic molecules.  These molecules lack one or more of these three elements—oxygen, carbon, or hydrogen.  They are easier to work with because of their small size.  Organic molecules are generally larger than inorganic molecules and are defined, for our purposes, as having carbon, oxygen, and hydrogen.

            To help you understand the structure of atoms and how covalent bonds can form, we will first practice determining valences for the most common elements found in living cells.  For the following atoms below, determine the number of electrons in the outer orbital and the valence, using the periodical chart.  Remember to include the “plus” and “minus” signs.

 

 

#electrons

valence

carbon

 

 

nitrogen

 

 

hydrogen

 

 

magnesium

 

 

phosphorus

 

 

chlorine

 

 

            Next, we will practice drawing Lewis diagrams, as these will also help you understand how covalent bonds form.  Lewis diagrams are sometimes called electron-dot diagrams.  Don’t worry, your lab instructor will help you get started.  You will also construct some three-dimensional models of molecules after you have practiced with the Lewis diagrams.  While you are practicing drawing the molecules, keep the following points in mind:

 

1)         Each atom in the molecule must be surrounded by four pairs of electrons with the exception of the hydrogen atom, which only needs one pair of electrons.  Remember, hydrogen has an atomic number of “one” and thus only needs one more electron to fill its first and only orbital.

 

2)         A pair of electrons may lie between two atoms and be “shared” by both atoms.  That is to say they are counted as one of the necessary four pairs.  A “shared” pair of electrons constitutes a covalent bond and is portrayed as a straight line between the two atoms.

 

3)         Two atoms may share two pairs of electrons.  This would be described as a “double” covalent bond and be indicated using two straight lines.  If two atoms share three pairs of electrons, this would be called a “triple” covalent bond and would be indicated with three straight lines.