Organic Chemistry

An updated version of this lesson is available at Visionlearning: Organic Chemistry

        How do we fit into this universe that we just described?  To understand life on Earth, we must first understand organic chemistry.  Organic chemicals (also known as hydrocarbons) contain carbon bonded to hydrogen (some also contain other elements).  Because of the unique bonding properties of carbon, there are millions of different organic chemicals.  Each one has unique properties.  There are organic chemicals that make up your hair, your skin, even your fingernails.  All life as we know it is made up of organic compounds.  Why is carbon such a special element?  Let's look at its chemistry in a little more detail.
        Carbon (C) appears in the 2nd row of the periodic table and has atomic number of 6.  Given our discussion of electron shells it is easy to see that carbon has 4 electrons in its valence shell.  Since carbon needs 8 electrons to fill its valence shell, it forms 4 bonds with other atoms (each bond consisting of one of carbon's electrons and one of the bonding atom's).  Every valence electron participates in bonding, thus a carbon atom's bonds will be distributed evenly over the atom's surface.  These bonds form a tetrahedron, as illustrated below:

        An organic molecule (hydrocarbon) is formed when carbon bonds to hydrogen.  The simplest hydrocarbon consists of 4 hydrogen atoms bonded to a carbon atom (called methane):

In addition to binding to hydrogen, carbon can also bind to other carbon atoms, as illustrated below:

In fact the uniqueness of carbon comes from the fact that it can bind to itself.  Carbon atoms can form long chains:

branched chains:

rings:

in fact, there appears to be almost no limit to the number of different structures that carbon can form.  To add to the complexity of organic chemistry, neighboring carbon atoms can form double and triple bonds in addition to single carbon-carbon bonds:
 

Table I
A carbon-carbon single bond
A carbon-carbon double bond
A carbon-carbon triple bond

Keep in mind that each carbon atom forms 4 bonds.  As you increase the number of bonds between carbon atoms, the number of hydrogen atoms in the molecule decreases (as can be seen in the table above).

Nomenclature (naming compounds):
        The simplest hydrocarbons are those that contain only carbon and hydrogen.  As we have seen, these come in three varieties: 1) alkanes, molecules with only single bonds, 2) alkenes, those with one or more double bond and 3) alkynes, those with one or more triple bond.  Basic organic chemistry can be thought of as a molecular Erector Set, if you know the number of carbon atoms and the type of bonds in a molecule, you can build the molecular structure.  To describe the number of carbon atoms in a hydrocarbon, chemists use prefixes in the molecule's name.  The first 10 prefixes used in organic chemistry are shown below.  To complete the hydrocarbon name, the prefix is attached to the ending of the root word (drop the alk- from the words alkane, alkene or alkyne) to describe the type of bonding on the molecule.  The hydrocarbon names (also called nomenclature) is described in Table II using the first 10 alkanes as examples.

Table II
 
 
ie.: Alkanes
Hydrocarbon prefix # of carbon atoms name formula     structure*
           Meth
1
methane CH4
           Eth
2
ethane C2H6
           Prop
3
propane C3H8
           But
4
butane C4H10
           Pent
5
pentane C5H12
           Hex
6
hexane C6H14
           Hept
7
heptane C7H16
           Oct
8
octane C8H18
           Non
9
nonane C9H20
           Dec
10
decane C10H22
* only the first 4 are illustrated




As we have discussed, each carbon atom has 4 bonds.  As you add carbon to a molecule, the empty carbon bonds are filled with hydrogen atoms (or other elements, as we will soon see).  You can calculate the number of H atoms in the simple alkanes.  The number of H atoms in a simple alkane equals two times the number of carbon atoms plus 2, or (2n + 2), where n is the number of carbon atoms in the molecule.  The simple alkenes have 1 double bond and 2 fewer H atoms in the molecule; the number of H atoms in the simple alkenes = (2n).  Simple alkynes contain 1 triple bond 2 fewer H atoms than the alkene, or (2n - 2) H atoms.

        The simple hydrocarbons are fairly common.  Methane, for example, is released by decaying organic matter and is the main compound in natural gas.  These chemicals are generally gases or liquids in nature and are very flammable.  Butane is used in cigarette lighters.  Ethyne, also known as acetylene, is used in welding.

        In addition to carbon and hydrogen, hydrocarbons can also contain other elements.  The alcohols, for example, are a group of hydrocarbons in which a hydroxol (-OH) group is bound to a carbon skeleton.  These compounds are named like the simple hydrocarbons, a prefix attached to a root ending (-anol for the alcohols).  Thus ethanol, is a 2 carbon alcohol with the structure:

Most people are familiar with this organic compound as it is the active ingredient in "alcoholic" beverages such as beer and wine.

        While the simple hydrocarbons are important, they do not themselves commonly occur in living organisms (except for during the occasional bout of methane flatulence).  The simple hydrocarbons are the building blocks of more complex molecules that make up living organisms.  In the next lesson, we will introduce some of these molecules and their biochemistry, the chemistry of life.

There are several good sites on the Web for exploring organic chemistry in further detail.  The one hitch with many of these sites is that most require you to have some type of molecule-viewing software.  One choice of software available for free is the Chemscape Chime 2.0 viewing software.  Once you have installed this plug-in, you can may want to visit some of the sites below for more information on organic chemistry:

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