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The second ionization of phosphoric acid, Ka2, is the primary intracellular buffer system. The pH of this conjugate acid-base pair (
Calculating a buffer’s pH
To determine a buffer’s pH, you can use a Ka or Kb calculation, as we discuss in the section “Swapping hydrogens between acids and bases,” earlier in this chapter, or you can use the Henderson-Hasselbalch equation, which is a shortcut.
The Henderson-Hasselbalch equation takes two forms:
and
The terms in either form are the same as those we define earlier in the chapter. For example, suppose you want to calculate the pH of a buffer composed of 0.15 M pyruvic acid and 0.25 M sodium pyruvate. Referring back to Table 2-2, you see that the Ka of pyruvic acid is
The pKa would be 2.50. Therefore:
Chapter 3
Fun with Carbon: Organic Chemistry
IN THIS CHAPTER
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
