DNA and RNA strands are large polymers that have very similar structures. Each has a linear sugar–phosphate backbone that has alternating residues of a five-carbon sugar and a phosphate, with a nitrogenous base attached to each sugar residue (Figure 1A). The sugars are ribose in RNA and deoxyribose in DNA, and they differ in either lacking or possessing an –OH group at their 2′-carbon positions (Figure 1B).
Fig1. Repeat units in nucleic acids. (A) The linear backbone of nucleic acids consists of alternating phosphate (P) and sugar residues. Attached to each sugar is a base. The basic repeat unit (pale peach shading) consists of a base + sugar + phosphate = a nucleotide. (B) Ribose, the sugar in RNA, and deoxyribose, the sugar in DNA, both have five carbon atoms numbered 1′ to 5′. Deoxyribose lacks the hydroxyl (OH) group attached to carbon 2 of ribose (the proper name is 2′-deoxyribose).
Unlike the sugar and phosphate residues, the bases of a nucleic acid molecule vary, and it is the sequence of bases that identifies the nucleic acid and determines its function. The bases of a nucleic acid each consist of heterocyclic rings of carbon and nitrogen atoms and can be divided into two structural classes: purines, which have two inter locked rings, and pyrimidines, which have a single ring. In both DNA and RNA there are four principal types of base, two purines and two pyrimidines. Three types of base adenine (A), cytosine (C), and guanine (G) are common to both DNA and RNA. The fourth base is thymine (T) in DNA and the closely related uracil (U) in RNA. Uracil lacks the 5-methyl group found in thymine (Figure 2A).
Fig2. Purines, pyrimidines, nucleosides, and nucleotides. (A) The common bases in nucleic acids. The bases A, C, and G occur in both DNA and RNA, but T is found in DNA while U is a closely related analog found in RNA. (B and C) Examples of nucleosides and nucleotides. A nucleoside is a base + sugar residue, as shown by the example in (B), which is adenosine. A nucleotide is a nucleoside + phosphate group attached to the 3′ or 5′ carbon of the sugar. The two examples shown in (C) are adenosine 5′-monophosphate (AMP; left) and 2′-deoxycytidine 5′-triphosphate (dCTP; at the right). The bold lines at the bottom of the ribose and deoxyribose rings mean that the plane of the sugar ring is at an angle of 90° with respect to the plane of the chemical groups that are linked to the 1′ to 4′ carbon atoms within the ring. If the plane of the base is represented as lying on the surface of the page, the 2′ and 3′ carbons of the sugar could be viewed as projecting upward out of the page, while the oxygen atom of the sugar ring projects downward below the surface of the page. Phosphate groups are numbered sequentially (α, β, γ, etc.), according to their distance from the sugar ring.
In nucleic acids, each base is covalently attached to the sugar by an N-glycosidic bond that joins a nitrogen atom (nitrogen 1 of a pyrimidine or nitrogen 9 of a purine) to the carbon 1′ (one prime) of the sugar. A sugar with an attached base is called a nucleoside (Figure 2B). A nucleoside with a phosphate group attached at the 5′ or 3′ carbon of the sugar is the basic repeat unit of a DNA strand, and is called a nucleotide (Figure 2C and Table 1).
Table1. NOMENCLATURE FOR BASES, NUCLEOSIDES, AND NUCLEOTIDES
As described below, DNA also contains a few types of minor base produced by chemical modification, but base modification is much more common in RNA where a large variety of chemical modifications of both bases and ribose sugars are known to occur.
Polypeptides
Proteins are composed of one or more polypeptide chains that may be modified by the addition of carbohydrate side chains or other chemical groups. Like DNA and RNA, poly peptides are polymers that have a linear sequence of repeating units. The basic repeat unit is called an amino acid.
Amino acids get their name because in its electrically neutral form a single unbound amino acid has an amino group (–NH2) connected by a central α-carbon atom to a carboxyl group (–COOH). The central carbon atom also bears an identifying side chain that determines the chemical nature of the amino acid. At physiological pH, the amino group acquires a proton and becomes positively charged and the carboxyl group loses a proton and becomes negatively charged (Figure 3A). According to the type of amino acid, the side chain may or may not have a charge, as detailed below.
Fig3. The general structure of an amino acid and a polypeptide. (A) Amino acid structure. At the left is the uncharged form of a generalized individual amino acid. A central α carbon is linked to three major groups: an amino group (NH2 ), a carboxyl group (COOH), and a side chain R, giving the general formula H2 N–CH(R)–COOH. At physiological pH, as shown at the right, the end groups are ionized: the amino group acquires a positive charge and the carboxyl group acquires a negative charge. The gray shading shows an amino acid repeating unit as found in a polypeptide. (B) Polypeptide structure. A polypeptide forms by sequential addition of amino acid monomers in a condensation reaction involving the carboxyl group of the last amino acid to be incorporated and the amino group of the next amino acid to be incorporated. The amino acid monomers (highlighted by gray shading) are therefore connected by amide bonds (–CO–NH–), known in this context as peptide bonds. One end of the polypeptide backbone will retain the charged amino group of the original amino acid and is known as the N-terminal end; the other end has the charged carboxyl group of the last amino acid to be incorporated, and is the C-terminal end.
Polypeptides are formed by sequential condensation reactions between the amino group of one amino acid and the carboxyl group of the next amino acid to be incorporated into the polymer. As a result, a polypeptide has a repeating backbone where the amino acid residues are linked by amide groups (–CO–NH–) that are referred to as peptide bonds (Figure 3B), and where the side chain (generally called an R-group) can differ from one amino acid to another (Figure 4).
Fig4. Side chains of the 20 common amino acids, grouped according to chemical class. In 19 of the 20 common amino acids the side chain is connected by a single covalent bond (red) to the α-carbon atom of the amino acid backbone; for these, we give the structure of the side chain only. Proline is the exception and we give its full structure here. Its side chain (-CH2 CH2-CH2-) is connected to the backbone by two covalent bonds (red), with one end joined to the central α carbon atom, and the other end to the nitrogen atom of the backbone amino group. The convention for naming carbon atoms in a side chain is to use sequential Greek letters, counting out from the central α carbon atom (β, γ, δ, and so on; for example, in lysine’s side chain, the carbon atom joined to the amino group, is the ε or epsilon carbon atom). Some amino acids have side chains with polar groups (pale peach shading) that may be uncharged or charged. The uncharged polar amino acids comprise three with a free hydroxyl group (serine, threonine, and tyrosine), two with amide groups (asparagine and glutamine), plus cysteine (which is only weakly polar). The charged amino acids comprise two acidic amino acids, aspartic acid (= aspartate) and glutamic acid (= glutamate), with a negatively charged carboxyl ion on their side chain at physiological pH, plus three basic amino acids. The latter include two strongly basic amino acids, lysine and arginine, each with a positively-charged nitrogen atom in the side chain at physiological pH, plus the very weakly basic histidine. Note: at physiological pH histidines are predominantly neutral, but at low pH they can be positively charged (as shown here).
Twenty different amino acids are common in nature and can be classified into three main groups according to their side chains (see Figure 4). Nine amino acids have a nonpolar side chain. In most of these cases the side chain is a simple aliphatic group, but phenylalanine and tryptophan have aromatic side chains and proline has a very unusual side chain that connects the central carbon atom to the N-terminal amino group (see Figure 4). The nonpolar neutral amino acids are hydrophobic (repel water), often inter acting with one another and with other hydrophobic groups.
Six amino acids are polar but electrically neutral overall. Their side chains carry polar groups with fractional electrical charges (often denoted as δ+ or δ−). Five amino acids have a charged side chain that either has a negative charge at physiological pH (acidic) or a net positive charge (basic, see Figure 4). In general, charged and uncharged polar amino acids are hydrophilic while nonpolar amino acids are hydrophobic. However, glycine and cysteine occupy intermediate positions on the hydrophilic–hydrophobic scale ( glycine has just a single hydrogen as its side chain, and the –SH group is not so polar as an –OH group).
The amino acids of proteins often undergo chemical modification of the side chains. Quite often a very simple chemical group is added to the side chain of the amino acid, but sometimes a large carbohydrate, lipid, or even another protein is joined to the side chain, as described below.
