Carbon and Molecular Diversity - 1 Although water is the most abundant compound of living organisms, and the "medium" for the existence of life, most of the molecules from which living organisms are composed are based on the element, carbon. Carbon has the ability to form large, complex and diverse molecules. The cells and tissues of virtually all organisms are made up of the same basic molecules: carbohydrates, lipids, proteins and the nucleic acids which are based on carbon. For this reason, it is beneficial to look at the properties of carbon as our introduction to the molecules of living organisms. As a field of study, organic chemistry deals with the chemistry of carbon, or carbon hydrogen molecules, which are called hydrocarbons. It is the versatility of carbon that provides for the uniformity of chemicals and atomic proportions of the elements found in living organisms. From simple carbon backbones, living organism can manufacture a multitude of different substances needed to sustain life. It is the variation among this multitude of organic molecules from species to species and individual to individual that distinguishes one from another. Our immediate goal is to become familiar with the structure and function of the macromolecules of living organisms. Before reviewing the structure of the major groups of compounds of living organisms, we need to look at the element, carbon, what a hydrocarbon is, and also study the molecules called functional groups, which bond to hydrocarbons, altering the chemical nature of the resulting compound. Properties of Carbon As you know, the chemical characteristics and bonds formed by an atom are determined by the atom s electrons. Carbon is one of the elements that makes covalent bonds to become stable. The carbon atom has 6 electrons, 2 in the inner shell and 4 in its outer shell. Carbon has a valence of 4 so each carbon atom makes 4 bonds. (And generally in 4 different directions. This is known as carbon s tetravalence.) Carbon may make bonds with other carbon atoms forming chains, branching chains or rings of linked carbon atoms. Ring compounds are common in living organisms. Carbon makes single covalent (bonding angle 109, forming a tetrahedron shaped molecule) double covalent and triple covalent bonds. Double and triple bonds alter the bonding angles and shape of the resulting molecule. The bonding of carbons to carbons is called the carbon skeleton.
Carbon and Molecular Diversity - 2 When carbon is not bonding to other carbon atoms, it covalently bonds to a number of other atoms, notably hydrogen, oxygen and nitrogen. In fact, the basic carbon compound is a hydrocarbon, formed from carbon and hydrogen. Several hydrocarbon examples are shown here of the carbon skeleton. Let s look now at the properties of Hydrocarbons Hydrocarbons, like carbon, typically vary in: The number of carbons on the chain Straight, branching chains or ring compounds Where and how many hydrogen atoms are attached to the carbon chain Most hydrocarbons have very similar properties for example the C H bond is energy rich; so hydrocarbons make good fuels (methane, propane, butane, heptane) Hydrocarbon variations that differ only in the arrangement of atoms are called isomers. Isomers are very important in biology, and we shall see many examples. There are three types of isomers: structural, geometric and enantiomers. Structural isomers vary in their covalent bonding arrangement.
Carbon and Molecular Diversity - 3 Geometric isomers share common covalent bonding, but because double bonds are inflexible (prevent rotation), the differing shape of geometric isomers can dramatically affect their biological function. (This is sometimes called the cistrans difference.) Geometric isomers are important in vision. Light hitting the pigment, rhodopsin, in the rods of the eye causes a change in structure, which triggers the nerve transmission. Cis-trans changes also occur when one partially hydrogenates fats, forming trans-fatty acids. Enantiomers are molecules that have the same molecular formula but are mirror images of each other. Enantiomers are formed when four different molecular groups are bonded to a central (asymmetric) carbon so that they can be arranged in just two different ways. As with other types of isomers, the different shapes of enantiomers can dramatically alter function. One example of this is vitamin E. There are L and D forms; one is more active, and found naturally. The other is frequently in vitamin pills but lacks the same biological activity. Your text illustrates a similar situation with L-dopa, a drug that helps treat Parkinson's disease. D- dopa is biologically inactive. Hydrocarbons can, in general, have other variations in bonding which result in compounds that are different in shape and often function. For example, the covalent bond angles in a ring compound determine the molecule's shape. The primary difference between cellulose and starch, two carbohydrate macromolecules, is that starch is formed by α 1-4 linkages of glucose, forming a helical molecule, and cellulose is formed from β 1-4 linkages, forming a straight molecule. Starch and cellulose are not isomers, although they are composed of the polymers of the monosaccharide, glucose.
Carbon and Molecular Diversity - 4 Function Groups and Compounds of Living Organisms The major compounds of living organisms are modifications of hydrocarbons with something (very precise) added. These components of the molecules formed are most often involved in the chemical reactions that occur and are called functional groups. Functional groups are molecular fragments which, when substituted for one or more hydrogen atoms in a hydrocarbon, confer particular chemical properties to the new compound. The functional group determines the "behavior" of the molecule and is consistent in different organic molecules. We shall look briefly at some common functional groups: Hydroxyl CarbonylCarboxyl Amino Sulfhydryl Phosphate Methyl Functional Groups Important in Living Organisms
Carbon and Molecular Diversity - 5 The Hydrocarbon and the Methyl Functional Group The hydrocarbon backbone of most molecules is formed from an alkane, a molecule with all single bonded carbons and hydrogens attached at the other carbon bonds. The smallest alkane is methane, CH 4, a single carbon atom bonded to 4 hydrogen atoms. The hydrocarbon backbone is lengthened by adding methyl functional groups, CH 3, a carbon with 3 hydrogen atoms attached. The naming convention for alkanes is important because this naming convention is used for most carbon compounds. The prefix is determined by the number of carbon atoms. 1 carbon = methane 2 carbons = ethane 3 carbons = propane 4 carbons = butane 5 carbons = pentane Hydroxyl Functional Group The hydroxyl function group is formed by an oxygen bonded to a hydrogen, with the second bond of the oxygen free to attach to the carbon chain ( OH). Hydroxyl functional groups confer properties of an alcohol to hydrocarbons. Hydroxyl functional groups are polar (the oxygen end's electronegativity), and attract water. This helps dissolve in water those macromolecules, such as sugars, which have hydroxyl functional groups in their structure. The naming convention for alcohols is to have the alcohol end in "ol" and the prefix be determined by the number of carbons (based on the alkane or pure hydrocarbon naming convention). For example, the two-carbon alcohol is ethanol. An alcohol can have more than one hydroxyl functional group. Such molecules are called poly-hydroxy alcohols. Carbonyl Functional Group The carbonyl functional group is a double bonded oxygen (=O). Carbonyl functional groups confer properties of aldehydes or ketones to hydrocarbons. Because double bonds restrict flexibility and rotation on the carbon skeleton, the location of the carbonyl functional group affects structure, and function. Carbonyl functional groups attached to an "end" carbon form aldehydes. Carbonyl functional groups attached to a non-end carbon form ketones. The naming convention for ketones uses the suffix "one" and aldehydes the suffix "al". The prefix may be determined by the number of carbons. It is not always so. For example, propanal is the 3-carbon aldehyde, but the 3-carbon ketone, by convention, is called acetone.
Carbon and Molecular Diversity - 6 Carboxyl Functional Group The carboxyl function group combines the hydroxyl and the carbonyl functional groups attached to a common carbon atom. The carboxyl functional group will always be at the end of a carbon chain. Carboxyl functional groups form organic (or carboxylic) acids. The -OH portion of the functional group dissociates in solution, donating a H +. This dissociation is aided by the electronegativity of the =O of the carbonyl portion of the functional group. Amino Functional Group The amino function group is - NH 2. The amino functional group added to organic compounds forms amines. Most amines in living organisms are found in molecules which also have carboxyl function groups and form the important class of molecules called amino acids. The amino functional group is a base. The nitrogen region of the amino functional group can attract a proton (generally attached to a hydrogen, thereby removing hydrogen ions from solution) resulting in a positive charge. Sulfhydryl Functional Group Sulfur, like oxygen, forms two covalent bonds. The sulfhydryl functional group (-SH) is similar to the hydroxyl functional group. Sulfhydryl functional groups are important in the structure of proteins, where the sulfur bonds help stabilize the protein's functional structure. Compounds containing sulfhydryl groups are called -thiols. Phosphate Functional Group Phosphate is a negative ion composed of phosphate bonded to 4 oxygen atoms. (PO 4 ), formed by the dissociation of phosphoric acid. The loss of two hydrogen ions from the acid results in the negative charge. One of the oxygen molecules of the phosphate functional group bonds to the carbon chain. Phosphate functional groups are important in energy transfer. We will study the energy transfer molecule, ATP, later. Having had this brief introduction/review of carbon and functional groups, we can now turn to the macromolecules from which we, and all living organisms, are composed!