Biochemistry For Dummies. John T. Moore

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Chapter 3

      Fun with Carbon: Organic Chemistry

      IN THIS CHAPTER

      

Understanding why carbon is fundamental to biochemistry

      

Measuring the strength of different kinds of bonds

      

Finding out about functional groups

      

Checking out isomerism

      Most biologically important molecules are composed of organic compounds, compounds of carbon. Therefore, you, as a student of biochemistry, must have a general knowledge of organic chemistry, which is the study of carbon compounds, in order to understand the functions and reactions of biochemical molecules. In this chapter, we go over the basics of organic chemistry, including the various functional groups and isomers that are important in the field of biochemistry. (We’re sure that this chapter will bring back fond memories of your organic chemistry classes and labs.)

      If you feel you need a little more background in organic chemistry, refer to Organic Chemistry I For Dummies (written by Arthur Winter and published by Wiley); Organic Chemistry II For Dummies, by these two wonderful authors (Wiley); and even Chemistry For Dummies, by John (Wiley). (Shameless plugs for others of our books!)

The Role of Carbon in the Study of Life

Long ago, scientists believed that all carbon compounds were the result of biological processes, which meant that organic chemistry was synonymous with biochemistry under what was known as the Vital Force theory. In the mid-1800s, though, researchers such as Friedrich Wöhler debunked that long-held notion; the synthesis of urea, CO(NH₂)₂, from an inorganic material (ammonium cyanate, NH₄OCN) showed that other paths to the production of carbon compounds existed. Organic chemists now synthesize many important organic chemicals without the use of living organisms; however, biosynthesis is still an important source of many organic compounds.

      Why are there so many carbon compounds? The answer lies primarily in two reasons, both tied to carbon’s versatility in creating stable bonds:

       Carbon bonds to itself. Carbon atoms are capable of forming stable bonds to other carbon atoms. The process of one type of atom bonding to identical atoms is catenation. Many other elements can catenate, but carbon is the most efficient at it. There appears to be no limit to how many carbon atoms can link together. These linkages may be in chains, branched chains, or rings, as shown in Figure 3-1.

       Carbon bonds to other elements. Carbon is capable of forming stable bonds to a number of other elements. These include the biochemically important elements hydrogen, nitrogen, oxygen, and sulfur. The latter three elements form the foundation of most of the functional groups (reactive groups of a molecule) necessary for life. Bonds between carbon and hydrogen are usually unreactive under biochemical conditions; thus, hydrogen often serves as an inert substituent (an atom or group of atoms taking the place of another atom or group or occupying a specified position in a molecule).

FIGURE 3-1: Top: straight chain hydrocarbon expanded and condensed. Middle: branched chain hydrocarbon. Bottom: ring hydrocarbon.

It’s All in the Numbers: Carbon Bonds

Carbon is capable of forming four bonds. In bonding to itself and other elements, carbon uses a variety of types of hybridization. When it bonds to other atoms, for example, possible hybridizations include four single bonds, one double and two single bonds, two double bonds, or a triple and a single bond. Double bonds to oxygen atoms are particularly important in many biochemicals. Table 3-1 shows the number of bonds carbon may form with some selected nonmetals, along with the hybridization of those bonds.

TABLE 3-1 Possible Bonds of Carbon and Selected Nonmetals

Element	Number of Possible Bonds with Carbon	Some Possible Hybridizations for Second Period Elements
Carbon (C)	4	4 single (sp3); 2 single and 1 double (sp2); 1 single and 1 triple (sp); 2 double (sp)
Nitrogen (N)	3	3 single (sp3); 1 single and 1 double (sp2); 1 triple (sp)
Oxygen (O)	2	2 single (sp3); 1 double (sp2)
Sulfur (S)	2	2 single (sp3); 1 double (sp2)
Hydrogen (H)	1	1 single
Fluorine (F)	1	1 single
Chlorine (Cl)	1	1 single
Bromine (Br)	1	1 single
Iodine (I)	1	1 single

When Forces Attract: Bond Strengths

      Covalent bonds are important intramolecular forces (forces within the same molecule) in biochemistry. Intermolecular forces (forces between chemical species) are also extremely important. Among other things, intermolecular forces are important to hydrophilic (water-loving) and hydrophobic (water-hating) interactions. (Phobias involve fear or hate, so hydrophobic is water-hating.)

      Everybody has ‘em: Intermolecular forces

      All intermolecular forces are van der Waals forces — that is, they’re not true bonds in the sense of sharing or transferring electrons but are weaker attractive forces. These forces include London dispersion forces, dipole-dipole forces, hydrogen bonding, and ionic interactions, all of which we discuss in the following sections.

      London dispersion forces

      London dispersion forces are very weak and short-lived