Biochemistry
Nucleotide Structure
Building blocks of DNA and RNA — phosphate, sugar, base
A nucleotide is the building block of nucleic acids (DNA, RNA). Three components: (1) Phosphate group (PO₄³⁻). (2) Pentose sugar — deoxyribose (DNA) or ribose (RNA). (3) Nitrogenous base — A, T, G, C in DNA; A, U, G, C in RNA. Bases categorized: purines (A, G) — two-ring; pyrimidines (T, C, U) — single-ring. Bases pair: A-T (or A-U) via 2 H-bonds; G-C via 3 H-bonds. Nucleotides linked via phosphodiester bonds — backbone. Plus ATP (energy currency), NAD⁺ (electron carrier), cAMP (signaling) — all nucleotides.
- ComponentsPhosphate + sugar + nitrogenous base
- DNA sugarDeoxyribose (no -OH at 2' position)
- RNA sugarRibose (-OH at 2' position)
- Bases (DNA)A, T, G, C
- Bases (RNA)A, U, G, C (U replaces T)
- PairsA-T (2 H-bonds), G-C (3 H-bonds)
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Why nucleotides matter
- Genetics. Genetic information storage.
- Protein synthesis. mRNA, tRNA, rRNA.
- Energy. ATP is universal fuel.
- Signaling. cAMP, cGMP, GTP.
- Drugs. Antiviral, anticancer (target nucleotide chemistry).
- Diagnostics. PCR, DNA sequencing.
- Forensics. DNA fingerprinting.
Common misconceptions
- DNA and RNA are the same. Different sugar, base, structure, role.
- All nucleotides are in nucleic acids. ATP, NAD⁺ also nucleotides.
- 4 bases in all nucleic acids. RNA has U; modified bases exist.
- Base pairing arbitrary. Specific H-bonding requires complementarity.
- DNA can't make RNA. Transcription creates RNA from DNA.
- RNA is short DNA. Different chemistry; many forms.
Frequently asked questions
What's a nucleotide?
Three components covalently linked. (1) Phosphate group. (2) Pentose sugar (5-C). (3) Nitrogenous base. Sugar (DNA: deoxyribose; RNA: ribose) has phosphate at 5' position, base at 1' position. Nucleotide = "phosphorylated nucleoside." Nucleoside = sugar + base only.
What's the difference between DNA and RNA?
(1) Sugar: DNA = deoxyribose (no OH at 2'); RNA = ribose (OH at 2'). (2) Base: DNA = A, T, G, C; RNA = A, U, G, C (uracil replaces thymine). (3) Structure: DNA = double helix; RNA = single strand (mostly). (4) Function: DNA = genetic storage; RNA = protein synthesis, regulation, catalysis (some). (5) Stability: DNA more stable (chemical, thermodynamic).
What are purines and pyrimidines?
Two structural classes of nitrogenous bases. Purines: two fused rings. Adenine (A), guanine (G). Pyrimidines: single ring. Thymine (T), cytosine (C), uracil (U). Different sizes — purines bigger. Pairing rules: purine pairs with pyrimidine (consistent helix width). A-T: 2 H-bonds. G-C: 3 H-bonds (stronger). U replaces T in RNA.
How are bases paired?
Hydrogen bonds. A-T: 2 H-bonds (A's NH₂ + T's CO; A's N + T's NH). G-C: 3 H-bonds (more stable). Watson-Crick base pairing. Specific pairing because: (1) Geometric: purine + pyrimidine fits double helix. (2) Functional groups: H-bond donors and acceptors complement only between specific bases.
How do nucleotides link?
Phosphodiester bond. Phosphate of one nucleotide bonds to 3'-OH of previous (3' to 5' direction). Each phosphate bonds to two sugars (one of each end). Backbone: sugar-phosphate-sugar-phosphate, with bases hanging off. Polymer with 5' end (free phosphate) and 3' end (free OH). Sequence read 5' to 3'.
What's ATP?
Adenosine triphosphate. Adenine + ribose + 3 phosphates. Energy currency of cell. Hydrolysis ATP → ADP + Pi releases ~30 kJ/mol of usable energy. Fuels: protein synthesis, muscle contraction, transport. Generated via cellular respiration. Total ATP cycled: body's weight equivalent every day.
What's the genetic code?
Mapping from nucleotide sequences to amino acids in proteins. 3 nucleotides (codon) = 1 amino acid. 64 codons (4³) → 20 amino acids + stop. Some redundancy (multiple codons per amino acid). Universal across nearly all life. Codon table: AUG = Met (start), UAA/UAG/UGA = stop, CCC = Pro, etc. Based on RNA (mRNA), used in translation.