Chapter 4 Nucleic Acids, Sections 4.1-4.3

Definition: Nucleic Acids (NAs) are polymers of nucleotides.
Components of a Nucleotide: Each nucleotide is comprised of three primary components:
1. Base: An aromatic heterocyclic molecule, either a Purine or a Pyrimidine.
2. Sugar Molecule: A pentose sugar, specifically Deoxyribose (in DNA) or Ribose (in RNA).
3. Phosphate Group: Typically attached to the 5' carbon of the sugar, but can be attached at other hydroxyl positions (e.g., 2', 3').
- The base and phosphate group are generally positioned above the plane of the sugar.

Nature: Bases are aromatic, heterocyclic molecules that vary between different nucleotides.
Primary Classes based on Ring Structure:
1. Purines: Consist of a fused five-membered and six-membered ring system (e.g., Adenine (A), Guanine (G)).
2. Pyrimidines: Consist of a single six-membered ring system (e.g., Cytosine (C), Uracil (U) in RNA, Thymine (T) in DNA).
Structural Characteristics:
- Despite their aromaticity, the rings are not perfectly flat due to exocyclic groups.
- They are still considered fully aromatic.
Tautomerization: Purine and pyrimidine bases can exist in different tautomeric forms, primarily Keto-Enol and Amino-Imino tautomerism. This property is crucial for hydrogen bonding within nucleic acids.

Definition: A nucleoside consists of a base covalently linked to a pentose sugar.
Two Classes in Nature:
- Ribonucleosides: Contain Ribose as the sugar, found in RNA.
- Deoxyribonucleosides: Contain Deoxyribose as the sugar, found in DNA. Deoxyribose is distinguished by the absence of a hydroxyl group at the 2' carbon position.

Definition: A nucleotide is a nucleoside with one or more phosphate groups attached.
Role: Nucleotides are the fundamental monomer units that polymerize to form DNA and RNA.
Phosphate Attachment:
- Most Common Position: The phosphate group is most frequently attached at the 5' position of the pentose sugar in both RNA and DNA.
- Alternative Positions: Phosphate groups can attach to any available hydroxyl group of the sugar (e.g., 2', 3', 5') depending on the context.
Phosphorylation State: Nucleotides can be mono-, di-, or tri-phosphorylated (e.g., AMP, ADP, ATP).
Nomenclature: By default, a 5'-phosphate is assumed unless explicitly stated otherwise in the nucleotide name (e.g., Adenosine monophosphate typically refers to Adenosine 5'-monophosphate).
- Knowing the name should allow one to derive the structure (e.g., Adenosine 2'-monophosphate, Adenosine 3'-monophosphate, Adenosine 5'-monophosphate, or cyclic AMP).

Process: Nucleic acids are synthesized by linking individual nucleotides (also called