Unit 3: Nucleic Acids

I. Orientation — Molecular information and energy systems

Nucleic acids are biological polymers that store, transmit, and express genetic information. DNA is the principal hereditary material, while RNA performs informational, catalytic, structural, and regulatory roles. Their properties arise from nucleotide composition, phosphodiester bonding, hydrogen bonding, base stacking, and interaction with water and ions.

• Basic principle: Information is encoded in the sequence of nitrogenous bases, especially in DNA and messenger RNA.
• Polymer convention: Nucleic-acid sequences are normally written from the 5′ end to the 3′ end.
• Backbone principle: Sugars and phosphate groups form the repeating, negatively charged backbone; bases project inward or outward depending on the nucleic acid.
• Pairing principle: Adenine pairs with thymine in DNA or uracil in RNA; guanine pairs with cytosine.
• Complementarity: A strand determines its complementary strand through specific hydrogen-bonding patterns.
• Biological roles: Nucleotides function not only as monomers but also as energy carriers, activated intermediates, second messengers, and cofactors.

II. Purines and pyrimidines — Nitrogenous bases

A. Purines and pyrimidines

Purines and pyrimidines are nitrogen-containing aromatic bases that differ in ring structure and combine with sugars to form nucleosides.

• Purines: Purines contain two fused rings: a six-membered pyrimidine ring joined to a five-membered imidazole ring.
  • Adenine (A): A purine with an amino group at carbon 6; it pairs with thymine or uracil.
  • Guanine (G): A purine with a carbonyl group at carbon 6 and an amino group at carbon 2; it pairs with cytosine.
• Pyrimidines: Pyrimidines contain one six-membered nitrogen-containing ring.
  • Cytosine (C): Contains an amino group at carbon 4 and pairs with guanine.
  • Thymine (T): A 5-methylated pyrimidine found mainly in DNA.
  • Uracil (U): Similar to thymine but lacks the 5-methyl group; it is characteristic of RNA.
• Base pairing: G–C pairs form three hydrogen bonds, whereas A–T and A–U pairs form two hydrogen bonds.
• Tautomerism: Rare imino or enol forms can alter hydrogen-bonding patterns and produce replication errors.
• Biological modification: 5-methylcytosine is an important modified base involved in gene regulation and epigenetic marking.

III. Nucleosides and nucleotides — Structural units of nucleic acids

A. Nucleosides and nucleotides

A nucleoside consists of a nitrogenous base linked to a pentose sugar, whereas a nucleotide is a nucleoside esterified with one or more phosphate groups.

• Nucleoside structure: The base attaches to the sugar through a β-N-glycosidic bond.
  • Purine linkage: The bond involves N9 of the purine and C1′ of the sugar.
  • Pyrimidine linkage: The bond involves N1 of the pyrimidine and C1′ of the sugar.
• DNA nucleosides: Adenosine, guanosine, cytidine, and thymidine contain 2-deoxyribose.
• RNA nucleosides: Adenosine, guanosine, cytidine, and uridine contain ribose.
• Nucleotide structure: A phosphate is usually attached to the 5′-hydroxyl group, producing compounds such as AMP, ADP, and ATP.
• Phosphate naming: One, two, or three phosphate groups are designated mono-, di-, or triphosphate.
• Polymer formation: Nucleotides join through 3′–5′ phosphodiester bonds.

Nucleotide polymer: 5′-sugar–phosphate–sugar–phosphate-3′

• Chemical distinction: Ribose has a 2′-OH group, while deoxyribose has a 2′-H group; this makes RNA more chemically reactive than DNA.
• Charge: At physiological pH, phosphate groups are negatively charged, increasing nucleic-acid solubility in water.

IV. Biologically important nucleotides — Energy, signaling, and metabolism

A. Biologically important nucleotides

Biologically important nucleotides act as energy currencies, intracellular signals, activated metabolic intermediates, and components of cofactors.

• ATP: Adenosine triphosphate transfers phosphoryl groups and couples favorable and unfavorable reactions.
  • Hydrolysis: ATP hydrolysis commonly produces ADP and inorganic phosphate.

ATP + H₂O → ADP + Pi + energy

• Symbols: ATP is adenosine triphosphate, ADP is adenosine diphosphate, Pi is inorganic phosphate.
  • GTP: Guanosine triphosphate powers protein synthesis, signal transduction, and microtubule assembly; GTP hydrolysis controls molecular switches such as G proteins.
  • cAMP: Cyclic AMP is produced from ATP by adenylyl cyclase and activates protein kinase A in many hormone responses.
  • cGMP: Cyclic GMP regulates processes including smooth-muscle relaxation and visual signal transduction.
  • Nucleotide sugars: UDP-glucose transfers glucose during glycogen synthesis and carbohydrate metabolism; the UDP group acts as a leaving group that activates glucose.
  • Activated intermediates: CDP-linked compounds participate in phospholipid synthesis, while S-adenosylmethionine transfers methyl groups.
  • Cofactor components: Nucleotides occur in NAD⁺, FAD, and coenzyme A, where they assist electron transfer or acyl-group transfer.
  • Energy interpretation: ATP hydrolysis is useful because its products are stabilized by resonance, hydration, and reduced electrostatic repulsion; “high-energy” refers to large negative free-energy change, not an unusually strong bond.

V. Structure of DNA — Stable genetic information

A. Structure of DNA

DNA is a polymer of deoxyribonucleotides arranged in two antiparallel, complementary strands that form a double helix.

• Primary structure: Nucleotides are connected by 3′–5′ phosphodiester bonds between the 3′-OH of one deoxyribose and the 5′-phosphate of the next nucleotide.
• Antiparallel strands: One strand runs 5′→3′ and the complementary strand runs 3′→5′.
• Complementary pairing: Adenine pairs with thymine through two hydrogen bonds; guanine pairs with cytosine through three.
• Double-helical arrangement: In the common B-DNA form, hydrophilic sugar-phosphate groups face the aqueous exterior and hydrophobic bases stack inside.
• Dimensions of B-DNA: The helix is approximately 2 nm wide, has about 10.5 base pairs per turn, and rises approximately 0.34 nm per base pair.
• Grooves: The major and minor grooves expose different chemical patterns, allowing proteins to recognize particular DNA sequences.
• Stabilization: Base stacking contributes strongly to stability; hydrogen bonds provide pairing specificity.
• Sequence notation: A sequence such as 5′-AGCT-3′ has the complementary strand 3′-TCGA-5′.
• Alternative forms: A-DNA is shorter and wider than B-DNA, while Z-DNA is a left-handed helix associated with certain sequence and ionic conditions.
• Packaging: In eukaryotes, DNA wraps around histone proteins to form nucleosomes, allowing a very long molecule to fit inside the nucleus.
• Replication relevance: Complementary, antiparallel structure permits each parental strand to serve as a template for a new strand.

VI. Structure of RNA — Diverse single-stranded molecules

A. Structure of RNA

RNA is generally a single-stranded ribonucleotide polymer whose 2′-OH group permits flexible folding and diverse biological functions.

• Primary structure: RNA nucleotides are connected through 3′–5′ phosphodiester bonds, just as in DNA, but contain ribose and uracil.
• Secondary structure: An RNA strand folds back on itself to form stems, hairpin loops, bulges, internal loops, and pseudoknots.
  • Stem formation: Complementary sequences form A–U and G–C pairs.
  • Noncanonical pairing: G–U wobble pairs are common in RNA and are important during translation.
• Tertiary structure: Long-range interactions, metal ions, and base stacking produce compact three-dimensional structures.
• Messenger RNA: mRNA carries coding information from DNA to ribosomes; eukaryotic mRNA commonly contains a 5′ cap and a 3′ poly(A) tail.
• Transfer RNA: tRNA carries amino acids and contains an anticodon that pairs with an mRNA codon.
• Ribosomal RNA: rRNA forms the structural and catalytic core of ribosomes; peptide-bond formation is catalyzed by ribosomal RNA.
• Catalytic RNA: Ribozymes demonstrate that RNA can function as an enzyme, as in self-splicing introns and the ribosome’s peptidyl-transferase center.
• RNA modifications: Modified bases and sugars, such as pseudouridine and methylated nucleotides, improve folding, stability, and recognition.
• Chemical limitation: The 2′-OH can attack the adjacent phosphodiester bond, making RNA more susceptible to alkaline hydrolysis than DNA.

VII. Physical and chemical properties of nucleic acids — Stability, behavior, and analysis

A. Physical and chemical properties of nucleic acids

Nucleic-acid behavior depends on charge, base composition, hydrogen bonding, aromatic stacking, solvent conditions, and chemical reactivity.

• Solubility: Nucleic acids are generally soluble in water because their ionized phosphate groups interact with polar solvent molecules.
• Acidic character: Phosphate groups behave as acids and remain largely negatively charged near physiological pH.
• UV absorption: Aromatic bases absorb ultraviolet light maximally near 260 nm; absorbance at 260 nm is used to estimate nucleic-acid concentration.
• Hyperchromic effect: Denaturation separates stacked bases, increasing absorbance at 260 nm. Renaturation decreases absorbance as the helix reforms.
• Melting temperature: The melting temperature, or Tm, is the temperature at which half of a double-stranded nucleic-acid population is denatured.
  • GC effect: Greater G–C content generally raises Tm because G–C pairing and stacking stabilize the helix.
  • Salt effect: Higher ionic strength shields negative phosphate charges and usually raises duplex stability.
• Denaturation: Heat, extreme pH, urea, or formamide can disrupt hydrogen bonding and base stacking without breaking the covalent backbone.
• Renaturation: Complementary strands can reassociate when suitable temperature, salt concentration, and time permit sequence alignment.
• Hydrolysis: RNA is alkali-labile because its 2′-OH promotes intramolecular cleavage; DNA is more resistant under the same conditions.
• Acid damage: Strong acid can remove purine bases from DNA, producing abasic sites; prolonged harsh conditions can also damage the sugar-phosphate backbone.
• Nucleases: DNases and RNases hydrolyze phosphodiester bonds; exonucleases remove terminal nucleotides, whereas endonucleases cut within a strand.
• Electrophoresis: Because nucleic acids are negatively charged, they migrate toward the positive electrode in an electric field; agarose gels separate DNA mainly by length.
• Hybridization: Complementary strands from different sources can pair, allowing techniques such as probe detection and sequence identification.
• Chemical reactivity: DNA’s deoxyribose improves long-term stability, whereas RNA’s ribose supports catalytic folding but increases susceptibility to degradation.