Nucleic Acids: Informational and Catalytic Macromolecules

The nucleic acidsare polymers specialized for the storage, transmission, and use of information. There are two types of nucleic acids: DNA(deoxyribonucleic acid) and RNA(ribonucleic acid). DNA molecules are giant polymers that encode hereditary information and pass it from generation to generation. Through an RNA intermediate, the information encoded in DNA is also used to specify the amino acid sequence of proteins. Information flows from DNA to DNA in reproduction, but in the nonreproductive activities of the cell, information flows from DNA to RNA to proteins which ultimately carry out these functions. In addition, certain RNAs act as catalysts for important reactions in cells.

The nucleic acids have characteristic chemical properties

Nucleic acids are composed of monomers called nucleotides, each of which consists of a pentose sugar, a phosphate group, and a nitrogen-containing base—either a pyrimidine or a purine. (Molecules consisting of a pentose sugar and a nitrogenous base, but no phosphate group, are called nucleosides.) In DNA, the pentose sugar is deoxyribose, which differs from the ribose found in RNA by one oxygen atom. In both RNA and DNA, the backbone of the macromolecule consists of alternating pentose sugars and phosphates (sugar—phosphate—sugar—phosphate). The bases are attached to the sugars and project from the chain. The nucleotides are joined by phosphodiester linkages between the sugar of one nucleotide and the phosphate of the next (-diester refers to the two covalent bonds formed by —OH groups reacting with acidic phosphate groups). The phosphate groups link carbon 3 in one pentose sugar to carbon 5 in the adjacent sugar. Most RNA molecules consist of only one polynucleotide chain. DNA, however, is usually double-stranded; it has two polynucleotide strands held together by hydrogen bonding between their nitrogenous bases. The two strands of DNA run in opposite directions. This antiparallel orientation is necessary for the strands to fit together in three-dimensional space.

The uniqueness of a nucleic acid resides in its nucleotide sequence

Only four nitrogenous bases—and thus only four nucleotides— are found in DNA. The DNA bases and their abbreviations are adenine (A), cytosine (C), guanine (G), and thymine (T). A key to understanding the structure and function of nucleic acids is the principle of complementary base pairing. In double-stranded DNA, adenine and thymine always pair (A-T), and cytosine and guanine always pair (C-G). Base pairing is complementary because of three factors: the sites for for hydrogen bonding on each base, the geometry of the sugar–phosphate backbone, which brings opposite bases near each other, and the molecular sizes of the paired bases. Adenine and guanine are both purines consisting of two fused rings. Thymine and cytosine are both pyrimidines, consisting of only one ring. The pairing of a large purine with a small pyrimidine ensures stability and consistency in the double-stranded molecule of DNA. Ribonucleic acids are also made up of four different monomers, but their nucleotides differ from those of DNA. In RNA the nucleotides are termed ribonucleotides (the ones in DNA are deoxyribonucleotides). They contain ribose rather than deoxyribose, and instead of the base thymine, RNA uses the base uracil (U). The other three bases are the same as in DNA. Although RNA is generally single-stranded, complementary hydrogen bonding between ribonucleotides can take place. These bonds play important roles in determining the shapes of some RNA molecules and in associations between RNA molecules during protein synthesis. When the base sequence of DNA is copied in the synthesis of RNA, complementary base pairing also takes place between ribonucleotides and deoxyribonucleotides. In RNA, guanine and cytosine pair (G-C), as in DNA, but adenine pairs with uracil (A-U). Adenine in an RNA strand can pair either with uracil (in another RNA strand) or with thymine (in a DNA strand).

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 variations in DNA—the different sequences of bases—are strictly “internal.” Through hydrogen bonding, 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 threedimensional 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.

Because DNA carries hereditary information between generations, a theoretical series of DNA molecules with changes in base sequences stretches back through evolutionary time. 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, 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. 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. 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 nucleotides as well as in other cellular substances. These catalytic RNAs are called ribozymes. Their discovery had implications for theories of the origin of life. Organisms can synthesize both RNA and proteins from these monomers. As we noted above, in current organisms on the Earth, protein synthesis requires DNA and RNA, and nucleic acid synthesis requires proteins (as enzymes). The discovery of catalytic RNAs 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 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 nucleotides with other functions: ATP (adenosine triphosphate) acts as an energy transducer in many biochemical reactions.

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. 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.

All Life from Life

The concepts conveyed throughout this chapter—that large molecules obey the mechanistic laws of physics and chemistry, and that life could have arisen from inanimate, self-replicating macromolecules—have come to be generally accepted by the scientific community. So should we expect to see new life forms arise at any time from the biochemical environment? During the Renaissance (a period from about 1350 to 1700 A.D., marked by the birth of modern science), most people thought that at least some forms of life arose directly from inanimate or decaying matter by spontaneous generation. For instance, it was suggested that mice arose from sweaty clothes placed in dim light, frogs came from moist soil, and flies were produced from meat. These ideas were attacked by scientists such as the Italian doctor and poet Francisco Redi using the relatively new idea of using experiments to test an idea. In 1668, Redi proposed that flies arose not by some mysterious transformation of decaying meat but from other flies, who laid their eggs on the meat. The eggs developed into wormlike maggots (the immature form of flies). Redi set out several jars containing chunks of meat. One jar contained meat exposed both to the air and to flies.

A second jar contained meat in a container wrapped in a fine cloth so that the meat was exposed to the air, but not to flies. The meat in the third jar was in a sealed container and thus was not exposed to either air or flies. As he had hypothesized, Redi found maggots, which then hatched into flies, only in the first container. The idea that a complex organism like a fly could come from a totally different substance was laid to rest. With the invention of the microscope in the 1660s, a vast new biological world was unveiled. Under microscopic observation, virtually every environment on Earth was found to be teeming with tiny organisms such as bacteria. Some scientists believed that these organisms arose spontaneously from their rich chemical environment. The experiments that disproved this idea were done by the great French scientist Louis Pasteur. His experiments showed that microorganisms come only from other microorganisms and that an environment without life remains lifeless unless contaminated by living creatures. These experiments by Redi, Pasteur and others provided solid evidence that neither small (bacteria) nor large (flies) organisms come from inanimate matter, but instead come from living parent organisms. Indeed, life on Earth no longer arises from nonliving materials. This is because the atmospheric and planetary conditions that exist on Earth today are vastly different from those on the prebiotic, anaerobic planet. The oxygen present in today’s atmosphere would break down the prebiotic molecules before they could accumulate. In addition, the necessary energy sources—including constant lightning strikes, immense volcanic eruptions and bombardment by intense ultraviolet light—are no longer present with anything like their primeval force.

Life may have come from outside Earth. The evidence for this proposal comes primarily from chemicals contained in meteorites that have landed on Earth. The theory of chemical evolution proposes that life on Earth originated on the Earth. Experiments using model systems that attempt to duplicate the ancient Earth have shown that chemical evolution could have produced the four types of macromolecules that distinguish living things.

Macromolecules are polymers constructed by the formation of covalent bonds between smaller molecules called monomers. Macromolecules in living organisms include polysaccharides, proteins, and nucleic acids. Macromolecules have specific, characteristic three-dimensionalshapes that depend on the structure, properties, and sequence of their monomers. Different functional groups give local sites on macromolecules specific properties that are important for their biological functioning and their interactions with other macromolecules.

Monomers are joined by condensation reactions, which release a molecule of water for each bond formed. Hydrolysis reactions use water to break polymers into monomers.

The functions of proteins include support, protection, catalysis, transport, defense, regulation, and movement. Protein function sometimes requires an attached prosthetic group. There are 20 amino acids found in proteins. Each amino acid consists of an amino group, a carboxyl group, a hydrogen and a side chain bonded to the carbon atom. The side chains or R groups of amino acids may be charged polar or hydrophobic; there are also special cases, such as the —SH groups of cysteine, which can form disulfide bridges. The side chains give different properties to each of the amino acids.

Amino acids are covalently bonded together into polypeptide chains by peptide linkages, which form by condensation reactions between the carboxyl and amino groups. Polypeptide chains are folded into specific three-dimensionalshapes to form functional proteins. Four levels of protein structureare possible: primary, secondary, tertiary and quaternary.The primary structure of a protein is the sequence of aminoacids bonded by peptide linkages. This primary structure determinesboth the higher levels of structure and protein function. The two types of secondary structure a-helices and b-pleatedsheets—are maintained by hydrogen bonds between atomsof the amino acid residues. The tertiary structure of a protein is generated by bending and folding of the polypeptide chain. The quaternary structure of a protein is the arrangement of two or more polypeptides into a single functional protein consisting of two or more polypeptide subunits. Weak chemical interactions are important in the three-dimensional structure of proteins and in their binding to other molecules. Proteins denatured by heat, alterations in pH or certain chemicals lose their tertiary and secondary structure as well as their biological function. Renaturation is not often possible. Chaperonins assist protein folding by preventing binding to inappropriate ligands.

All carbohydrates contain carbon bonded to hydrogen atoms and hydroxyl groups. Hexoses are monosaccharides that contain six carbon atoms. Examples of hexoses include glucose, galactose, and fructose, which can exist as chains or rings. The pentoses are five-carbon monosaccharides. Two pentoses,ribose and deoxyribose, are components of the nucleic acidsRNA and DNA, respectively.They covalently link monosaccharides into larger unitssuch as disaccharides, oligosaccharides, and polysaccharides.Cellulose, a very stable glucose polymer, is the principal componentof the cell walls of plants. Starches, less dense and less stable than cellulose, store energyin plants. Chemically modified monosaccharides include the sugarphosphates and amino sugars. A derivative of the amino sugarglucosamine polymerizes to form the polysaccharide chitinwhich is found in the cell walls of fungi and the exoskeletons ofinsects.

Although lipids can form gigantic structures, these aggregations are not chemically macromolecules because the individual units are not linked by covalent bonds. Fats and oils are triglycerides, composed of three fatty acids covalently bonded to a glycerol molecule by ester linkages. Saturated fatty acids have a hydrocarbon chain with no double bonds. The hydrocarbon chains of unsaturated fatty acids have one or more double bonds that bend the chain, making close packing less possible. Phospholipids have a hydrophobic hydrocarbon “tail” and a hydrophilic phosphate “head.”In water, the interactions of the hydrophobic tails andhydrophilic heads of phospholipids generate a phospholipidsbilayer that is two molecules thick. The head groups are directedoutward, where they interact with the surrounding water. The tails are packed together in the interior of the bilayer. Carotenoids trap light energy in green plants. Carotene can be split to form vitamin A, a lipid vitamin. Some steroids, such as testosterone, function as hormones.Cholesterol is synthesized by the liver and has a role in cell membranes,as well as in the digestion of fats. Vitamins are substances that are required for normal functioning, but must be acquired from the diet.

DNA is the hereditary material. Both DNA and RNA play roles in the formation of proteins. Information flows from DNA to RNA to protein. Nucleic acids are polymers made up of nucleotides. A nucleotide consists of a phosphate group, a sugar (ribose in RNA and deoxyribose in DNA), and a nitrogen-containing base. In DNA the bases are adenine, guanine, cytosine, and thymine, but in RNA uracil substitutes for thymine. In the nucleic acids, the bases extend from a sugar–phosphatebackbone. The information content of DNA and RNA resides intheir base sequences. RNA is single-stranded. DNA is a double strandedhelix in which there is complementary, hydrogenbondedbase pairing between adenine and thymine (A-T) and guanine and cytosine (G-C). The two strands of the DNA doublehelix run in opposite directions. Base pairing of single-stranded RNAs can lead to three-dimensionalBase pairing of single-stranded RNAs can lead to threedimensionalstructures, which can be catalytic. This finding hasled to the proposal that in the origin of life, RNA preceded protein. Comparing the DNA base sequences of different living speciesprovides information on their evolutionary relationships.

1.3.2. Physics and Chemistry of the Living Cell

In general, anything that has mass and takes up space is matter. Matter is made of small nonliving particles called atoms. Atoms themselves are composed of still smaller parts. In organisms, however, atoms are never broken down. Instead, they are only rearranged into new combinations. About 100 kinds of atoms are found naturally on the earth. They correspond to the 100 natural elements, substances that cannot be broken down chemically into simpler substances. 6 elements are especially important to life: carbon, hydrogen, oxygen, sulfur, nitrogen and phosphorus. Hydrogen and oxygen atoms make up water, carbon atoms form coal, diamonds and some forms of carbon dioxide in the air, nitrogen atoms make up part of fertilizers, etc. About 20 others play lesser, but important role.

Atoms are seldom found alone in nature. Usually, they join together to form larger particles called molecules. A molecule consists of two or more atoms joined by chemical bonds.