CHEMISTRY THE CENTRAL SCIENCE
24 THE CHEMISTRY OF LIFE: ORGANIC AND BIOLOGICAL CHEMISTRY
24.10 NUCLEIC ACIDS
Nucleic acids are a class of biopolymers that are the chemical carriers of an organism's genetic information. Deoxyribonucleic acids (DNA) are huge molecules whose molecular weights may range from 6 million to 16 million amu. Ribonucleic acids (RNA) are smaller molecules, with molecular weights in the range of 20,000 to 40,000 amu. Whereas DNA is found primarily in the nucleus of the cell, RNA is found mostly outside the nucleus in the cytoplasm, the nonnuclear material enclosed by the cell membrane. DNA stores the genetic information of the cell and specifies which proteins the cell can synthesize. RNA carries the information stored by DNA out of the cell nucleus into the cytoplasm, where the information is used in protein synthesis.
FIGURE 24.26 Structure of a phospholipid.
Why do phospholipids form bilayers but not monolayers in water?
FIGURE 24.27 The cell membrane. Living cells are encased in membranes typically made of phospholipid bilayers. The bilayer structure is stabilized by the favorable interactions of the hydrophobic tails of the phospholipids, which point away from both the water inside the cell and the water outside the cell, while the charged head groups face the two water environments.
The monomers of nucleic acids, called nucleotides, are formed from a five-carbon sugar, a nitrogen-containing organic base, and a phosphate group. An example is shown in FIGURE 24.28.
The five-carbon sugar in RNA is ribose, and that in DNA is deoxyribose:
FIGURE 24.28 A nucleotide. Structure of deoxyadenylic acid, the nucleotide formed from phosphoric acid, deoxyribose, and the organic base adenine.
Deoxyribose differs from ribose only in having one fewer oxygen atom at carbon 2.
There are five nitrogen-containing bases in nucleic acids:
The first three bases shown here are found in both DNA and RNA. Thymine occurs only in DNA, and uracil occurs only in RNA. In either nucleic acid, each base is attached to a five-carbon sugar through a bond to the nitrogen atom shown in color.
The nucleic acids RNA and DNA are polynucleotides formed by condensation reactions between a phosphoric acid OH group on one nucleotide and a sugar OH group on another nucleotide. Thus, the polynucleotide strand has a backbone consisting of alternating sugar and phosphate groups with the bases extending off the chain as side groups (FIGURE 24.29).
Is DNA positively charged, negatively charged, or neutral in aqueous solution at pH 7?
FIGURE 24.29 A polynucleotide. Because the sugar in each nucleotide is deoxyribose, this polynucleotide is of the form found in DNA.
The DNA strands wind together in a double helix (FIGURE 24.30). The two strands are held together by attractions between bases (represented by T, A, C, and G). These attractions involve dispersion forces, dipole-dipole forces, and hydrogen bonds. (Section 11.2) As shown inFIGURE 24.31, the structures of thymine and adenine make them perfect partners for hydrogen bonding. Likewise, cytosine and guanine form ideal hydrogen-bonding partners. We say that thymine and adenine are complementary to each other and cytosine and guanine are complementaryto each other. In the double-helix structure, therefore, each thymine on one strand is opposite an adenine on the other strand, and each cytosine is opposite a guanine. The double-helix structure with complementary bases on the two strands is the key to understanding how DNA functions.
The two strands of DNA unwind during cell division, and new complementary strands are constructed on the unraveling strands (FIGURE 24.32). This process results in two identical double-helix DNA structures, each containing one strand from the original structure and one new strand. This replication allows genetic information to be transmitted when cells divide.
The structure of DNA is also the key to understanding protein synthesis, the means by which viruses infect cells, and many other problems of central importance to modern biology. These themes are beyond the scope of this book. If you take courses in the life sciences, however, you will learn a good deal about such matters.
FIGURE 24.30 The DNA double helix.
Which pair of complementary bases, AT or GC, would you expect to bind more strongly?
FIGURE 24.31 Hydrogen bonding between complementary bases.
FIGURE 24.32 DNA replication. The original DNA double helix partially unwinds, and new nucleotides line up on each strand in complementary fashion. Hydrogen bonds help align the new nucleotides with the original DNA chain. When the new nucleotides are joined by condensation reactions, two identical double-helix DNA molecules result.
SAMPLE INTEGRATIVE EXERCISE Putting Concepts Together
is formed in the body from carbohydrate metabolism. In muscles, it is reduced to lactic acid in the course of exertion. The acid-dissociation constant for pyruvic acid is 3.2 × 10–3. (a) Why does pyruvic acid have a higher acid-dissociation constant than acetic acid? (b) Would you expect pyruvic acid to exist primarily as the neutral acid or as dissociated ions in muscle tissue, assuming a pH of about 7.4 and an acid concentration of 2 × 10–4M? (c) What would you predict for the solubility properties of pyruvic acid? Explain. (d) What is the hybridization of each carbon atom in pyruvic acid? (e) Assuming H atoms as the reducing agent, write a balanced chemical equation for the reduction of pyruvic acid to lactic acid (Figure 24.14). (Although H atoms do not exist as such in biochemical systems, biochemical reducing agents deliver hydrogen for such reductions.)
(a) The acid-dissociation constant for pyruvic acid should be somewhat greater than that of acetic acid because the carbonyl function on the α-carbon atom of pyruvic acid exerts an electron-withdrawing effect on the carboxylic acid group. In the C—O—H bond system the electrons are shifted from H, facilitating loss of the H as a proton. (Section 16.10)
(b) To determine the extent of ionization, we first set up the ionization equilibrium and equilibrium-constant expression. Using HPv as the symbol for the acid, we have
Let [Pv–] = x. Then the concentration of undissociated acid is 2 × 10–4 – x. The concentration of [H+] is fixed at 4.0 × 10–8 (the antilog of the pH value). Substituting, we obtain
Solving for x, we obtain x[3.2 × 10–3 + 4.0 × 10–8] = 6.4 × 10–7.
The second term in the brackets is negligible compared to the first, so
x = [Pv–] = 6.4 × 10–7/3.2 × 10–3 = 2 × 10–4M
This is the initial concentration of acid, which means that essentially all the acid has dissociated. We might have expected this result because the acid is quite dilute and the acid-dissociation constant is fairly high.
(c) Pyruvic acid should be quite soluble in water because it has polar functional groups and a small hydrocarbon component. It is miscible with water, ethanol, and diethyl ether.
(d) The methyl group carbon has sp3 hybridization. The carbon of the carbonyl group has sp2 hybridization because of the double bond to oxygen. Similarly, the carboxylic acid carbon is sp2 hybridized.
(e) The balanced chemical equation for this reaction is
Essentially, the ketonic functional group has been reduced to an alcohol.
STRATEGIES IN CHEMISTRY
If you are reading this box, you have made it to the end of our text. We congratulate you on the tenacity and dedication that you have exhibited to make it this far!
As an epilogue, we offer the ultimate study strategy in the form of a question: What do you plan to do with the knowledge of chemistry that you have gained thus far in your studies? Many of you will enroll in additional courses in chemistry as part of your required curriculum. For others, this will be the last formal course in chemistry that you will take. Regardless of the career path you plan to take—whether it is chemistry, one of the bio-medical fields, engineering, the liberal arts, or another field—we hope that this text has increased your appreciation of the chemistry in the world around you. If you pay attention, you will be aware of encounters with chemistry on a daily basis, from food and pharmaceutical labels to gasoline pumps, sports equipment to news reports.
We have also tried to give you a sense that chemistry is a dynamic, continuously changing science. Research chemists synthesize new compounds, develop new reactions, uncover chemical properties that were previously unknown, find new applications for known compounds, and refine theories. The understanding of biological systems in terms of the underlying chemistry has become increasingly important as new levels of complexity are uncovered. You may wish to participate in the fascinating venture of chemical research by taking part in an undergraduate research program. Given all the answers that chemists seem to have, you may be surprised at the large number of questions that they still find to ask.
Finally, we hope you have enjoyed using this textbook. We certainly enjoyed putting so many of our thoughts about chemistry on paper. We truly believe it to be the central science, one that benefits all who learn about it and from it.