BCM 301

Nucleic Acid Bases

Overview of Nucleic Acids

  • Nucleic acids are biopolymers essential for all known forms of life.

  • Main components:

    • Nucleosides

    • Nucleotides

    • DNA (Deoxyribonucleic Acid)

    • RNA (Ribonucleic Acid)

Nucleotide Structure

Components of a Nucleotide

  • Structure consists of three components:

    1. Base: Could be a Purine or Pyrimidine.

    2. Pentose Sugar: 5-carbon sugar which could be ribose (in RNA) or deoxyribose (in DNA).

    3. Phosphate Group: Can be mono-, di-, or triphosphate.

Bonding and Configuration

  • B-glycosidic bond: Links a base to the sugar.

  • Nucleotide organization:

    • 5' end: Phosphoryl group can be located here.

    • 3' end: Hydroxyl group is present.

Nucleic Acid Base Types

Purines

  • Adenine (A)

    • Structure includes NH₂ group.

  • Guanine (G)

    • Structure includes NH₂ group and an oxygen functional group.

Pyrimidines

  • Cytosine (C)

    • Contains NH group and a double-bonded oxygen.

  • Thymine (T)

    • Known as 5-methyluracil; characterized by a methyl group and two carbonyls.

  • Uracil (U)

    • Found in RNA, lacks the methyl group on Thymine.

Pentose Sugars

Characteristics of Pentoses

  • Sugar configuration is "primed" for identification:

    • 1' to 5' numbering convention is used.

Types of Pentose Sugars

  • D-Ribose

    • Formula: C₅H₁₀O₅

    • Hydroxyl (OH) groups on 2', 3', and 4'.

  • 2'-Deoxyribose

    • Formula: C₅H₁₀O₄

    • Lacks and has Hydroxyl (OH) only on 3' and 4' with a Hydrogen (H) on 2'.

Nucleosides

Formation of Nucleosides

  • Result from the linkage of a sugar with a purine or pyrimidine base via an N-glycosidic linkage:

    • Purines bond to the C1’ carbon of the sugar at their N9 atoms.

    • Pyrimidines bond to C1’ carbon at their N1 atoms.

Example: Adenosine

  • Structure of Adenosine:

    • Contains configurations of N-glycosidic Linkage attached to its sugar component.

Phosphate Groups

Types of Phosphates

  • Phosphate groups can be mono-, di-, or triphosphates.

  • Linking Sites: Phosphates can bond to either the C3 or C5 atoms of the sugar, integral to nucleotide structure.

Nucleotides

Definition of Nucleotides

  • Formed when one or more phosphate groups link with a nucleoside at the 5’ end through esterification.

Types of Nucleotides

  • RNA (Ribonucleic Acid): Polymer of ribonucleotides.

  • DNA (Deoxyribonucleic Acid): Polymer of deoxyribonucleotides.

Common Bases in Nucleotides

  • Both types contain Adenine, Guanine, and Cytosine:

    • Ribonucleotides include Uracil.

    • Deoxyribonucleotides include Thymine.

Functions of Nucleotides

Biological Importance

  1. Building Blocks: Serve as the foundational elements for nucleic acids (DNA and RNA).

  2. Energy Storage: Involved in processes like muscle contraction, active transport, maintenance of ion gradients.

  3. Activated Intermediates: Play a role in biosynthesis (example: UDP-glucose, S-adenosylmethionine).

  4. Coenzymes: Components include NAD+, NADP+, FAD, FMN, and CoA.

  5. Metabolic Regulation:

    • Second Messengers: Such as cyclic AMP (cAMP) and cyclic GMP (cGMP).

    • Phosphate Donors: In signaling processes (e.g., ATP).

    • Enzyme Regulation: Via adenylation or uridylylation mechanisms.

Naming Conventions for Nucleic Acids

Nucleosides

  • Purine Nucleosides: End with “-sine”

    • Examples: Adenosine, Guanosine.

  • Pyrimidine Nucleosides: End with “-dine”

    • Examples: Thymidine, Cytidine, Uridine.

Nucleotides

  • Derived from nucleoside name with the addition of “mono-”, “di-”, or “triphosphate” prefixes.

    • Examples: Adenosine Monophosphate (AMP), Cytidine Triphosphate (CTP), Deoxythymidine Diphosphate (dTDP).