Biology: Nitrogenous Bases Overview

Bases in DNA and RNA

• Nucleotide bases include adenine (A), cytosine (C), guanine (G), thymine (T for DNA), and uracil (U for RNA).
• Bases are categorized into two classes: purines (A, G) and pyrimidines (C, T, U).
• Purines have a dual-ring structure; pyrimidines have a single-ring structure.

DNA Structure

• DNA forms a double helix with two strands held together by hydrogen bonds between complementary bases: A pairs with T, and G pairs with C.
• A-T pairs consist of two hydrogen bonds; G-C pairs are more stable due to three hydrogen bonds.
• Strands are anti-parallel, with one running 5' to 3' and the other 3' to 5'.
• Base stacking, involving overlapping pi molecular orbitals, contributes to the stability of the helix.

Types of DNA Structures

• B-form DNA is the most common and exists as a right-handed helix.
• A-form DNA is also right-handed and slightly elongated.
• Z-form DNA is rare, left-handed, and typically occurs in localized regions during unwinding.

Key Bonds in Nucleic Acids

• Phosphodiester bonds link nucleotides in the DNA backbone.
• Different types of bonds correlate with distinct macromolecules: peptide bonds for proteins, phosphodiester bonds for nucleic acids, and glycosidic bonds for carbohydrates.

Nucleotides vs. Nucleosides

• Nucleotides consist of a sugar (ribose or deoxyribose), a nitrogenous base, and one or more phosphate groups.
• Nucleosides lack the phosphate group and consist only of the sugar and base.

Ribose vs. Deoxyribose

• RNA contains ribose, with a hydroxyl (OH) group on carbon 2.
• DNA contains deoxyribose, lacking the OH group on carbon 2, which contributes to DNA's stability and its tendency to form double helices.

Structural Implications

• The absence of the hydroxyl group in DNA leads to increased stability compared to RNA, which is primarily single-stranded.
• RNA can occasionally form double-helical structures but is less stable than DNA due to the presence of the hydroxyl group.

Important Concepts

• Watson-Crick base pairing is the primary reference for base interactions in DNA.
• AT-rich regions promote easier unwinding for processes like replication and transcription due to fewer hydrogen bonds.

Nucleic Acids Overview

• Nucleic acids consist of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
• Key difference: RNA contains ribose sugar, while DNA contains deoxyribose (lacks hydroxyl group on carbon 2).

Nucleotides and Nucleosides

• Nucleosides consist of a sugar and a nitrogenous base.
• Nucleotides are formed when a phosphate group is added to a nucleoside, classified as:
  • Nucleotide monophosphate (1 phosphate)
  • Nucleotide diphosphate (2 phosphates)
  • Nucleotide triphosphate (3 phosphates)

Sugar Structures

• Ribose and deoxyribose are five-carbon sugars.
• Ribose has a hydroxyl (-OH) group on carbon 2.
• Deoxyribose lacks this -OH group, having two hydrogens instead.

Stability and Structure

• DNA nucleotides are more stable than RNA nucleotides due to the absence of the -OH group.
• DNA typically forms a double helix structure, while RNA usually exists as single-stranded, with occasional double-helix regions.

Nitrogenous Bases

• DNA bases: Adenine (A), Cytosine (C), Guanine (G), Thymine (T).
• RNA bases: Adenine (A), Cytosine (C), Guanine (G), Uracil (U).
• Bases are categorized into purines (A and G) and pyrimidines (C, U in RNA, T in DNA).
  • Purines have a two-ring structure; pyrimidines have a single-ring structure.

Base Pairing and Bonding

• Base pairing occurs between one purine and one pyrimidine.
• The AT base pair is connected by two hydrogen bonds, while the GC base pair is joined by three hydrogen bonds.
• DNA strands are anti-parallel: one strand runs 5' to 3' and the other runs 3' to 5'.

DNA Structures

• Most common form is B-form DNA, a right-handed helix.
• A-form DNA is also right-handed but elongated, while Z-form DNA is a less common left-handed helix, often localized in regions under strain.

DNA Bonding

• Phosphodiester bonds link nucleotides in the DNA backbone.
• The Watson-Crick base pairing model defines the hydrogen bonding patterns between bases, crucial for replication and transcription.

Intercalating Agents

• Intercalating agents can insert between base pairs, potentially causing mutations during DNA replication due to structural disruption.

Functional Significance

• AT-rich regions of DNA facilitate unwinding for biological processes like replication and transcription due to weaker hydrogen bonding.