# Lecture 21: Nucleic Acids: Structure
## Organic Chemistry II
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## Learning Objectives
By the end of this lecture, students will be able to:
1. Identify the components of nucleotides (base, sugar, phosphate) and nucleosides
2. Distinguish between DNA and RNA at the chemical level
3. Describe Watson-Crick base pairing and its hydrogen bonding patterns
4. Explain the double helical structure of DNA
5. Describe the primary structure (phosphodiester backbone) and higher-order structures of nucleic acids
6. Relate the chemical structure of nucleic acids to their biological function
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## Lecture Content
### I. Components of Nucleotides
Nucleotides are the monomeric building blocks of nucleic acids, and each consists of three components: a nitrogenous base, a pentose sugar, and a phosphate group.
The nitrogenous bases fall into two structural categories, both of which are aromatic heterocycles. The purines -- adenine (A), a 6-aminopurine, and guanine (G), a 2-amino-6-oxopurine -- contain a two-ring system formed by fusing a pyrimidine ring with an imidazole ring. The pyrimidines -- cytosine (C), thymine (T), and uracil (U) -- contain a single six-membered ring. Thymine (5-methyl-2,4-dioxopyrimidine) is found exclusively in DNA, while uracil (2,4-dioxopyrimidine) replaces it in RNA.
The pentose sugar is 2-deoxyribose in DNA (lacking a hydroxyl at the 2' position) and ribose in RNA (retaining the 2'-OH). Sugar carbons are numbered with primes (1', 2', 3', 4', 5') to distinguish them from the numbering of the base. The base attaches at the 1' position through an N-glycosidic bond in the beta configuration: purines connect through N9, and pyrimidines through N1. The phosphate group, derived from phosphoric acid, is esterified to the 5' position of the sugar and carries negative charges at physiological pH.
### II. Nucleosides and Nucleotides
A nucleoside is simply a base attached to a sugar without a phosphate group. The nucleosides are adenosine, guanosine, cytidine, thymidine, and uridine, with the prefix "deoxy" added for DNA versions. A nucleotide adds one or more phosphate groups to a nucleoside, making it a nucleoside monophosphate (AMP, GMP, etc.), diphosphate (ADP), or triphosphate (ATP).
ATP (adenosine triphosphate) is the universal energy currency of the cell. Hydrolysis of the gamma-phosphate bond (ATP to ADP + Pi) releases approximately 30.5 kJ/mol. The term "high-energy bond" is somewhat misleading: it is not the bond itself that is strong but rather the products of hydrolysis that are stabilized by resonance, relief of electrostatic repulsion among the closely spaced negative charges, and improved solvation.
Cyclic nucleotides such as cAMP (3',5'-cyclic AMP) serve as second messengers in signal transduction cascades. Many coenzymes essential to metabolism -- NAD+, FAD, and coenzyme A -- contain nucleotide components as part of their structure.
### III. Primary Structure: The Phosphodiester Backbone
Nucleotides are linked into polynucleotide chains by 3',5'-phosphodiester bonds. Each phosphate group bridges the 3'-OH of one nucleotide to the 5'-OH of the next, creating a repeating sugar-phosphate backbone from which the bases project like rungs on a ladder. The chain has inherent directionality, with a 5' end (bearing a free 5'-phosphate) and a 3' end (bearing a free 3'-OH). By convention, sequences are written 5' to 3'.
A critical chemical difference between DNA and RNA backbones determines their biological roles. DNA uses deoxyribose, which lacks the 2'-OH and is therefore resistant to base-catalyzed hydrolysis, making DNA chemically stable enough for long-term genetic storage. RNA uses ribose, and the 2'-OH can attack the adjacent phosphodiester bond, making RNA inherently less stable. This chemical lability is one reason evolution selected DNA rather than RNA as the permanent repository of genetic information.
Panel A: Detailed structure of a dinucleotide (e.g., dApdT in DNA) showing the 3',5'-phosphodiester bond connecting two nucleotides. The 5' end is at the top and the 3' end is at the bottom. The deoxyribose sugars, phosphate groups, and bases (adenine and thymine) are all clearly labeled, with prime-numbered sugar carbons (1' through 5'). Panel B: Comparison of ribose (RNA) and 2-deoxyribose (DNA), highlighting the 2'-OH in ribose and the 2'-H in deoxyribose, with an arrow showing how the 2'-OH in RNA can participate in intramolecular cleavage of the phosphodiester bond.
### IV. Watson-Crick Base Pairing
Complementary base pairing is the chemical foundation of the double helix. Adenine pairs with thymine (in DNA) or uracil (in RNA) through two hydrogen bonds. Guanine pairs with cytosine through three hydrogen bonds, making G-C base pairs stronger than A-T (or A-U) pairs.
These pairing rules were anticipated by Chargaff's experimental observations, made before the structure of DNA was solved: in double-stranded DNA, the concentration of adenine always equals that of thymine, and the concentration of guanine always equals that of cytosine. The ratio of [A+T] to [G+C] varies between species but is constant within a given species. Watson-Crick base pairing elegantly explains all of Chargaff's rules.
In addition to hydrogen bonding, base stacking interactions contribute significantly to the stability of the double helix. The aromatic bases are stacked on top of one another along the helix axis, engaging in van der Waals (London dispersion) interactions between their pi electron systems. The hydrophobic effect also contributes, as the relatively nonpolar bases are removed from the aqueous environment and sequestered in the interior of the helix. The combined contributions of base stacking are comparable to or even greater than those of hydrogen bonding.
### V. The DNA Double Helix
The Watson-Crick model, proposed in 1953 and based on X-ray crystallography data from Rosalind Franklin and Maurice Wilkins, describes DNA as two polynucleotide strands wound around each other in a right-handed double helix. The strands are antiparallel: one runs 5' to 3' while the other runs 3' to 5'. The sugar-phosphate backbones are on the outside, and the bases face inward, perpendicular to the helix axis.
The base pairs are stacked approximately 3.4 angstroms apart, with 10 base pairs per complete turn of the helix, giving a pitch of 34 angstroms. The diameter is approximately 20 angstroms. The geometry of base pairing creates two grooves of unequal width: the major groove is wider and more accessible, serving as the primary site for protein-DNA interactions, while the minor groove is narrower.
B-form DNA is the most common form under physiological conditions, and it is the form described above. A-form DNA is a right-handed helix that is wider and shorter, found in RNA-RNA and RNA-DNA duplexes. Z-form DNA is a left-handed helix with a zigzag backbone, occurring in sequences with alternating purines and pyrimidines under conditions of high salt concentration.
Panel A: Watson-Crick base pairs drawn with hydrogen bonds shown as dashed lines. A-T pair with two hydrogen bonds labeled (donor/acceptor atoms identified). G-C pair with three hydrogen bonds labeled. The glycosidic bonds to deoxyribose are indicated to show the relative width of the base pair (~10.85 A C1' to C1' distance). Panel B: Side view of the B-form DNA double helix showing the antiparallel strand orientation (5' to 3' arrows), the major and minor grooves, base pair spacing (3.4 A), full turn (34 A, 10 bp), and diameter (20 A). The sugar-phosphate backbones are shown as ribbons and the base pairs as horizontal bars.
### VI. RNA Structure
RNA is typically single-stranded but forms extensive intramolecular secondary structures through self-complementary base pairing. Messenger RNA (mRNA) carries genetic information from DNA to the ribosome. Transfer RNA (tRNA) is the adapter molecule that delivers amino acids during translation; it has a characteristic cloverleaf secondary structure and an L-shaped tertiary structure, with the anticodon loop pairing with mRNA codons and the 3'-CCA end accepting the amino acid. Ribosomal RNA (rRNA) is both a structural and catalytic component of the ribosome; the peptidyl transferase activity that forms peptide bonds is catalyzed by rRNA, not by protein, making the ribosome a ribozyme. Additional classes of RNA, including snRNA, miRNA, and siRNA, perform various regulatory functions.
Common secondary structures in RNA include hairpin loops (stem-loops), in which short complementary regions form a double-stranded stem topped by an unpaired loop. Internal loops, bulges, junctions, and pseudoknots create the complex three-dimensional architectures needed for RNA function. Standard Watson-Crick pairs (A-U and G-C) predominate, but non-Watson-Crick interactions, such as the G-U wobble pair, are common and play important roles in tRNA recognition and other processes.
### VII. Chemical Modification and Damage to Nucleic Acids
The chemical integrity of nucleic acids is constantly threatened by spontaneous and environmental damage. Deamination removes an amino group from a base: cytosine deaminates to uracil, and adenine to hypoxanthine. If unrepaired, cytosine deamination produces a C-to-T mutation. This reaction occurs spontaneously at low rates and is accelerated by nitrous acid (HNO2).
Depurination, the loss of a purine base by hydrolysis of the N-glycosidic bond, occurs approximately 10,000 times per cell per day and is repaired by the base excision repair (BER) pathway. Reactive oxygen species can oxidize bases, producing lesions such as 8-oxoguanine, which mispairs with adenine instead of cytosine. Alkylating agents, including dimethyl sulfate and nitrogen mustards, can alkylate bases, with N7 of guanine being the most nucleophilic and therefore the primary target. Many anticancer drugs function as DNA alkylating agents.
UV radiation induces the formation of thymine dimers (cyclobutane pyrimidine dimers) between adjacent thymines on the same strand. These lesions are repaired by the nucleotide excision repair (NER) pathway. Defects in NER cause xeroderma pigmentosum, a hereditary condition of extreme UV sensitivity and elevated skin cancer risk.
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