11.1 Structure and properties of nucleotides

Nucleotides are the building blocks of DNA and RNA. They're made of a nitrogenous base, a sugar, and phosphate groups. These components work together to store and transmit genetic information in living organisms.

Understanding nucleotides is crucial for grasping how genetic material functions. The structure of nucleotides determines how DNA and RNA form, replicate, and carry out their roles in biological processes like protein synthesis and gene expression.

Nucleotide Components

Building Blocks of Nucleic Acids

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• Nucleotides are the fundamental building blocks of nucleic acids (DNA and RNA)
• Consist of three main components: a nitrogenous base, a pentose sugar, and one or more phosphate groups
• Nucleosides are nucleotides without the phosphate group(s)
  • Composed of only the nitrogenous base and the pentose sugar
• Nitrogenous bases are heterocyclic aromatic compounds that contain nitrogen
  • Serve as the information-carrying portion of the nucleotide
  • Can be either purines or pyrimidines (adenine, guanine, cytosine, thymine, and uracil)

Sugar and Phosphate Backbone

• Pentose sugars in nucleotides are either ribose (RNA) or deoxyribose (DNA)
  • Ribose contains a hydroxyl group at the 2' position, while deoxyribose lacks this hydroxyl group
• Phosphate groups are attached to the 5' carbon of the pentose sugar
  • Nucleotides can have one, two, or three phosphate groups (mono-, di-, or triphosphates)
• The sugar and phosphate groups form the backbone of the nucleic acid strand
  • Phosphodiester bonds link the 3' hydroxyl of one nucleotide to the 5' phosphate of the next

Nitrogenous Bases

Purine and Pyrimidine Structures

• Purines are double-ringed structures with a six-membered and a five-membered nitrogen-containing ring fused together
  • Adenine (A) and guanine (G) are the purine bases found in nucleic acids
• Pyrimidines are single-ringed structures with a six-membered nitrogen-containing ring
  • Cytosine (C), thymine (T), and uracil (U) are the pyrimidine bases found in nucleic acids
  • Thymine is found in DNA, while uracil replaces thymine in RNA

Nomenclature and Tautomerism

• Nucleotide nomenclature is based on the type of pentose sugar and the nitrogenous base
  • For example, deoxyadenosine triphosphate (dATP) contains deoxyribose, adenine, and three phosphate groups
• Tautomerism is the ability of certain nitrogenous bases to exist in different structural isomers (tautomers)
  • Tautomers can interchange between keto (C=O) and enol (C-OH) forms
  • Tautomerism can lead to non-canonical base pairing and potential mutations during replication

Nucleotide Interactions

Hydrogen Bonding and Base Pairing

• Hydrogen bonding is a key interaction between nucleotides in nucleic acids
  • Occurs between the nitrogenous bases of complementary nucleotides
• In DNA, adenine (A) pairs with thymine (T) through two hydrogen bonds, while guanine (G) pairs with cytosine (C) through three hydrogen bonds
  • These specific base-pairing rules (A-T and G-C) maintain the genetic integrity of DNA
• In RNA, uracil (U) replaces thymine and pairs with adenine (A) through two hydrogen bonds
• Hydrogen bonding between complementary bases stabilizes the double-stranded structure of DNA and contributes to the formation of secondary structures in RNA (hairpins, loops, and stems)