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Thymine

Hydrogen Pump Plasma Membrane

3.26 Hydrogen Bonding in RNA When a single-stranded RNA folds in on itself, hydrogen bonds can stabilize it into a three-dimensional shape.

DNA is a purely informational molecule. The information in DNA is encoded in the sequence of bases carried in its strands—the information encoded in the sequence TCAG is different from the information in the sequence CCAG. The information can be read easily and reliably, in a specific order.

The three-dimensional appearance of DNA is strikingly uniform. The segment shown in Figure 3.27 could be from any DNA molecule. The variations in DNA—the different sequences of bases—are strictly "internal." Through hydrogen bonding, the two complementary polynucleotide strands pair and twist to form a double helix. When compared with the complex and varied tertiary structures of different proteins, this uniformity is surprising. But this structural contrast makes sense in terms of the functions of these two classes of macromolecules.

It is their different and unique shapes that permit proteins to recognize specific "target" molecules. The unique three-dimensional form of each protein matches at least a portion of the surface of the target molecule. In other words, structural diversity in the molecules to which proteins bind requires corresponding diversity in the structure of the proteins themselves.

In DNA, then, the information is in the sequence of the bases; in proteins, the information is in the shape of the molecule.

DNA is a guide to evolutionary relationships

Because DNA carries hereditary information between generations, a theoretical series of DNA molecules with changes in base sequences stretches back through evolutionary time. Of course, we cannot study all of these DNA molecules, because many of their organisms have become extinct. However, we can study the DNA of living organisms, which are judged to have changed little over millions of years. Comparisons and contrasts of these DNA molecules can be added to evidence from fossils and other sources to reveal the evolutionary record, as we will see in Chapter 24.

Closely related living species should have more similar base sequences than species judged by other criteria to be more distantly related. The examination of base sequences has confirmed many of the evolutionary relationships that have been inferred from the more traditional study of body structures, biochemistry, and physiology. For example, the closest living relative of humans (Homo sapiens) is the chimpanzee (genus Pan), which shares more than 98 percent of its DNA base sequence with human DNA. This confirmation of well-established evolutionary relationships gives credibility to the use of DNA to elucidate relationships when studies of structure are not possible or are not conclusive. For example,

The yellow phosphorus atoms and their attached red oxygen atoms form the two helical backbones.

The paired bases are stacked in the center of the coil (blue nitrogen atoms and gray carbon atoms).

3.27 The Double Helix of DNA The backbones of the two strands in a DNA molecule are coiled in a double helix.The small white atoms represent hydrogen.

The yellow phosphorus atoms and their attached red oxygen atoms form the two helical backbones.

The paired bases are stacked in the center of the coil (blue nitrogen atoms and gray carbon atoms).

3.27 The Double Helix of DNA The backbones of the two strands in a DNA molecule are coiled in a double helix.The small white atoms represent hydrogen.

DNA studies revealed a close evolutionary relationship between starlings and mockingbirds that was not expected on the basis of their anatomy or behavior.

DNA studies support the division of the prokaryotes into two domains, Bacteria and Archaea. Each of these two groups of prokaryotes is as distinct from the other as either is from the Eukarya, the third domain into which living things are classified (see Chapter 1). In addition, DNA comparisons support the hypothesis that certain subcellular compartments of eukaryotes (the organelles called mitochondria and chloroplasts) evolved from early bacteria that established a stable and mutually beneficial way of life inside larger cells.

RNA may have been the first biological catalyst

The three-dimensional structure of a folded RNA molecule presents a unique surface to the external environment (see Figure 3.26). These surfaces are every bit as specific as those of proteins. We noted above that an important role of proteins in biology is to act as catalysts, speeding up reactions that would ordinarily take place too slowly to be biologically useful, and that the spatial property of proteins is vital to this role.

As we will see, certain RNA molecules can also act as catalysts, using their three-dimensional shapes and other chemical properties. They can catalyze reactions on their own nu-cleotides as well as in other cellular substances. These catalytic RNAs are called ribozymes. Their discovery had implications for theories of the origin of life.

The Miller-Urey experiment and other such experiments in prebiotic chemistry yielded both amino acids and nu-cleotides. Organisms can synthesize both RNA and proteins from these monomers. As we noted above, in current organisms on Earth, protein synthesis requires DNA and RNA, and nucleic acid synthesis requires proteins (as enzymes). So the question is, when life originated, which came first, the proteins or the nucleic acids?

The discovery of catalytic RNAs provided a solution to this dilemma and led to the hypothesis that early life was part of an "RNA world." RNA can be informational (in its nucleotide sequence) as well as catalytic. So when RNA was first made, it could have acted as a catalyst for its own replication, as well as for the synthesis of proteins. Then DNA could have eventually evolved by being made from RNA. There is some laboratory evidence supporting this scenario:

► RNAs of different sequences have been put in a test tube and made to replicate on their own. Such self-replicating ribozymes speed up the synthesis of RNA 7 million-fold.

► In living organisms today, the formation of peptide linkages (see Figure 3.5) is catalyzed by a ribozyme.

► In certain viruses called retroviruses, there is an enzyme called reverse transcriptase that catalyzes the synthesis of DNA from RNA.

Nucleotides have other important roles

Nucleotides are more than just the building blocks of nucleic acids. As we will see in later chapters, there are several nu-cleotides with other functions:

► ATP (adenosine triphosphate) acts as an energy transducer in many biochemical reactions (see Chapter 6).

► GTP (guanosine triphosphate) serves as an energy source, especially in protein synthesis. It also has a role in the transfer of information from the environment to the body tissues (see Chapters 12 and 15).

► cAMP (cyclic adenosine monophosphate), a special nucleotide in which a bond forms between the sugar and phosphate groups within adenosine monophosphate, is essential in many processes, including the actions of hormones and the transmission of information by the nervous system (see Chapter 15).

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