an, Biological Science, 4e, Chapter 4
Chapter 4 - Nucleic Acids and the RNA World
Learning Objectives: Students should be able to...
• Sketch a nucleotide, label its three basic parts, and identify the 2', 3', and 5' carbons.
• Make another sketch showing the primary and secondary structures of DNA.
• Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.
• Explain why and how the secondary structure of DNA allows organisms to store and copy information.
• Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.
I. What Is a Nucleic Acid?
A. What is a nucleic acid made of?
1. A nucleic acid is a polymer that is made up of monomers called nucleotides.
2. One nucleotide consists of a phosphate group, a sugar, and a nitrogenous base. (Fig. 4.1a)
3. The sugar can be either ribose or deoxyribose. (Fig. 4.1b) a. Ribonucleotides contain the sugar ribose; deoxyribonucleotides contain the sugar deoxyribose.
b. On the 2' carbon, ribose has an −OH group; deoxyribose has an −H.
4. The nitrogenous bases: (Fig. 4.1c)
a. There are two classes of nitrogenous bases: purines and
(1) Adenine (A) and guanine (G) are purines.
(2) Cytosine (C), uracil (U), and thymine (T) are pyrimidines. b. Ribonucleotides can have the bases A, G, C, and U.
c. Deoxyribonucleotides can have the bases A, G, C, and T.
5. Students should be able to sketch a nucleotide using a ball, pentagon, and hexagon to depict the phosphate group, sugar,
and nitrogenous base. Students should also be able to label the 2', 3', and 5'carbons on the sugar molecule, and add the atoms that are bonded to the 2' carbon.
B. Could chemical evolution result in the production of nucleotides? 1. No one has yet observed the formation of a nucleotide via chemical evolution.
2. The ribose problem:
a. On early Earth, sugars could have been easily synthesized from heated formaldehyde molecules.
b. But, it is not clear how ribose became the predominant sugar.
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an, Biological Science, 4e, Chapter 4
3. The pyrimidine problem:
a. On early Earth, purines could have been readily synthesized from HCN molecules.
b. But, no one has yet discovered a plausible mechanism for
pyrimidine production via chemical evolution.
C. How do nucleotides polymerize to form nucleic acids?
1. Nucleic acids form when nucleotides polymerize.
a. The polymerization occurs via a condensation reaction that forms a phosphodiester linkage, linking the 5' carbon of one nucleotide to the 3' carbon of the sugar of the next nucleotide. (Fig. 4.2) b. A polymer of ribonucleotides is ribonucleic acid (RNA); a polymer of deoxyribonucleotides is deoxyribonucleic acid (DNA).
c. The sequence of nitrogenous bases forms the primary structure of the RNA or DNA molecule.
2. DNA and RNA strands are directional. (Figs. 4.2 and 4.3)
a. One end has an unlinked 5' carbon with a free phosphate group. b. The other end has an unlinked 3' carbon with a free −OH group, where new nucleotides can be added.
c. The sequence of bases of a strand of DNA or RNA is
conventionally written from the 5' to the 3' end.
d. Students should be able to draw a simplified diagram of a phosphodiester linkage between two nucleotides, mark the 3'
and 5' ends, and indicate where the next nucleotide would be added.
3. Polymerization is an endergonic process that requires energy. a. The free energy of the nucleotides is first raised by the addition of two phosphate groups to each nucleotide. (Fig. 4.4)
b. This raises the potential energy of the substrate molecules enough to make the polymerization reaction possible.
c. Phosphorylation is used in many other cellular reactions to make endergonic reactions possible.
4. Could nucleic acids form in the prebiotic soup?