PART 1 Introduction
2.2. CELL CONSTRUCTION 1. Introduction
2.2.5. Nucleic Acids, RNA, and DNA
Nucleic acidsplay the central role in reproduction of living cells. Deoxyribonucleic acid (DNA) stores and preserves genetic information. Ribonucleic acid(RNA) plays a central role in protein synthesis. Both DNA and RNA are large polymers made of their corre- sponding nucleotides.
40 An Overview of Biological Basics Chap. 2
Nucleotides are the building blocks of DNA and RNA and also serve as molecules to store energy and reducing power. The three major components in all nucleotides are phosphoric acid, pentose (ribose or deoxyribose), and a base (purine or pyrimidine). Fig- ure 2.15 depicts the structure of nucleotides and purine-pyrimidine bases. Two major purines present in nucleotides are adenine (A) and guanine (G), and three major pyrim- idines are thymine (T), cytosine (C), and uracil (U). Deoxyribonucleic acid (DNA) con- tains A, T, G, and C, and ribonucleic acid (RNA) contains A, U, G, and C as bases. It is the base sequence in DNA that carries genetic information for protein synthesis. In Chap- ters 4 and 8 we discuss how this information is expressed and passed on from one genera- tion to another.
In Chapter 5 we will discuss further the role of nucleotides in cellular energetics.
The triphosphates of adenosine and to a lesser extent guanosine are the primary energy currency of the cell. The phosphate bonds in ATP (adensosine triphosphate) and GTP (guanosine triphosphate) are high-energy bonds. The formation of these phosphate bonds or their hydrolysis is the primary means by which cellular energy is stored or used. For example, the synthesis of a compound that is thermodynamically unfavorable can be
Figure 2.14. Examples of important steroids. The basic numbering of the carbon atoms in these molecules is also shown.
Figure 2.15. (a) General structure of ribonucleotides and deoxyribonucleotides. (b) Five nitroge- nous bases found in DNA and RNA. (With permission, from J. E. Bailey and D. F. Ollis, Biochemical Engineering Fundamentals, 2d ed., McGraw-Hill Book Co., New York, 1986, p. 43.)
coupled to ATP hydrolysis to ADP (the diphosphate) or AMP (the monophosphate). The coupled reaction can proceed to a much greater extent, since the free-energy change be- comes much more negative. In reactions that release energy (for example, oxidation of a sugar), the energy is “captured” and stored by the formation of a phosphate bond in a cou- pled reaction where ADP is converted into ATP.
In addition to using ATP to store energy, the cell stores and releases hydrogen atoms from biological oxidation-reduction reactions by using nucleotide derivatives. The two most common carriers of reducing power are nicotinamide adenine dinucleotide(NAD) and nicotinamide adenine dinucleotide phosphate(NADP).
In addition to this important role in cellular energetics, the nucleotides are important monomers. The polynucleotides (DNA and RNA) are formed by the condensation of nu- cleotides. The nucleotides are linked together between the 3¢and 5¢carbons’ successive sugar rings by phosphodiester bonds. The structures of DNA and RNA are illustrated in Fig. 2.16.
DNA is a very large threadlike macromolecule (MW, 2 ¥109D in E. coli) and has a double-helical three-dimensional structure. The sequence of bases (purines and pyrim- idines) in DNA carries genetic information, whereas sugar and phosphate groups perform a structural role. The base sequence of DNA is written in the 5¢ Æ3¢direction, such as pAGCT. The double-helical structure of DNA is depicted in Fig. 2.17. In this structure, two helical polynucleotide chains are coiled around a common axis to form a double- helical DNA, and the chains run in opposite directions, 5¢ Æ3¢and 3¢ Æ5¢. The main fea- tures of double-helical DNA structure are as follows:
1. The phosphate and deoxyribose units are on the outer surface, but the bases point toward the chain center. The planes of the bases are perpendicular to the helix axis.
2. The diameter of the helix is 2 nm. The helical structure repeats after ten residues on each chain, at an interval of 3.4 nm.
3. The two chains are held together by hydrogen bonding between pairs of bases. Ade- nine is always paired with thymine(two H bonds); guanine is always paired with cytosine(three H bonds).This feature is essential to the genetic role of DNA.
4. The sequence of bases along a polynucleotide is not restricted in any way, although each strand must be complementary to the other. The precise sequence of bases car- ries the genetic information.
The large number of H bonds formed between base pairs provides molecular stabi- lization. Regeneration of DNA from original DNA segments is known as DNA replication. When DNA segments are replicated, one strand of the new DNA segment comes directly from the parent DNA, and the other strand is newly synthesized using the parent DNA segment as a template. Therefore, DNA replication is semiconservative, as depicted in Fig. 2.18. The replication of DNA is discussed in more detail in Chapter 4.
Some cells contain circular DNA segments in cytoplasm that are called plasmids.†
Plasmids are nonchromosomal, autonomous, self-replicating DNA segments. Plasmids are easily moved in and out of the cells and are often used for genetic engineering. Naturally oc- curring plasmids can encode factors that protect cells from antibiotics or harmful chemicals.
†Linear rather than circular plasmids can be found in some yeasts and other organisms.
Figure 2.16. Structure of DNA and RNA chains. Phosphodiester bonds are formed between 3¢and 5¢carbon atoms. (With permission, from A. Lehninger, Biochemistry, 2d ed., Worth Publishing, New York, 1975, p. 319.)
Figure 2.17. Double-helical structure of DNA, showing overall process of replication by complementary base pairing. (With per- mission, from T. D. Brock, D. W. Smith, and M. T. Madigan, Biology of Microorganisms, 4th ed., Pearson Education, Upper Saddle River, NJ, 1984, p. 276.)
Figure 2.18. Semiconservative replication of DNA.
The major function of DNA is to carry genetic information in its base sequence. The genetic information in DNA is transcribed by RNA molecules and translated in protein synthesis. The templates for RNA synthesis are DNA molecules, and RNA molecules are the templates for protein synthesis. The formation of RNA molecules from DNA is known as DNA transcription, and the formation of peptides and proteins from RNA is called translation.
Certain RNA molecules function as the genetic information-carrying intermediates in protein synthesis (messenger,m-RNA), whereas other RNA molecules [transfer(t-RNA) and ribosomal (r-RNA)] are part of the machinery of protein synthesis. The ribosomal r-RNA is located in ribosomes which are small particles made of protein and RNA. Ribo- somesare cytoplasmic organelles (usually attached on the inner surfaces of endoplasmic reticulum in eucaryotes) and are the sites of protein synthesis.
RNA is a long, unbranched macromolecule consisting of nucleotides joined by 3¢–5¢
phosphodiester bonds. An RNA molecule may contain from 70 to several thousand nu- cleotides. RNA molecules are usually single stranded, except some viral RNA. However, certain RNA molecules contain regions of double-helical structure, like hairpin loops.
Figure 2.19 describes the cloverleaf structure of t-RNA (transfer RNA). In double-helical regions of t-RNA, A pairs with U and G pairs with C. The RNA content of cells is usually two to six times higher than the DNA content.
Let us summarize the roles of each class of RNA species:
Messenger RNA(m-RNA) is synthesized on the chromosome and carries genetic in- formation from the chromosome for synthesis of a particular protein to the ribosomes.
The m-RNA molecule is a large one with a short half-life.
Transfer RNA(t-RNA) is a relatively small and stable molecule that carries a spe- cific amino acid from the cytoplasm to the site of protein synthesis on ribosomes. t-RNAs contain 70 to 90 nucleotides and have a MW range of 23 to 28 kD. Each one of 20 amino acids has at least one corresponding t-RNA.
Ribosomal RNA(r-RNA) is the major component of ribosomes, constituting nearly 65%. The remainder is various ribosomal proteins. Three distinct types of r-RNAs present in the E. coliribosome are specified as 23S, 16S, and 5S, respectively, on the basis of their sedimentation coefficients (determined in a centrifuge). The symbol S denotes a Svedberg unit. The molecular weights are 35 kD for 5S, 550 kD for 16S, and 1,100 kD for 23S.
These three r-RNAs differ in their base sequences and ratios. Eucaryotic cells have larger ribosomes and four different types of r-RNAs: 5S, 7S, 18S, and 28S. Ribosomal RNAs make up a large fraction of total RNA. In E. coli, about 85%of the total RNA is r-RNA, while t-RNA is about 12%and m-RNA is 2%to 3%.
2.3. CELL NUTRIENTS