Nucleic Acid Structure: DNA, RNA, and Their Biological Functions

Nucleotides: The Building Blocks of Nucleic Acids

Structural Components of Nucleotides

Nucleotides are the fundamental units of nucleic acids, such as DNA and RNA. Each nucleotide consists of three main components:

• Phosphate group: Provides negative charge and enables linkage between nucleotides.

• Monosaccharide (sugar): Ribose in RNA, deoxyribose in DNA.

• Heterocyclic nitrogen base: Purines (adenine, guanine) and pyrimidines (cytosine, thymine, uracil).

Nucleosides are similar to nucleotides but lack the phosphate group.

Nitrogenous Bases

The nitrogenous bases are classified as:

• Purines: Adenine (A), Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only)

These bases are aromatic, planar, and participate in hydrogen bonding.

Formation of Nucleic Acids

Condensation and Hydrolysis Reactions

Nucleotides are joined together by condensation reactions (loss of water), forming phosphodiester bonds. Hydrolysis reactions break these bonds by adding water.

• Condensation: Formation of nucleosides (sugar + base) and nucleotides (nucleoside + phosphate).

• Hydrolysis: Breakdown of nucleic acids into nucleotides.

Polynucleotide Structure

Nucleic acids are linear polymers of nucleotides, connected by phosphodiester bonds between the 3' and 5' carbons of the sugar.

• Directionality: Written from 5' phosphate end to 3' OH end.

• Sequence example: 5' AGTC 3'

DNA vs. RNA: Structural and Functional Differences

Major Differences

DNA and RNA differ in several key aspects:

Feature	DNA	RNA
Bases	A, G, C, T	A, G, C, U
Sugar	Deoxyribose	Ribose
Strandedness	Double-stranded	Single-stranded

3D Structure of DNA: The Double Helix

Key Structural Features

Double-stranded DNA forms a double helix, with the following characteristics:

• Antiparallel strands: One strand runs 5' to 3', the other 3' to 5'.

• Phosphate backbone: Located on the outside, bases point inward.

• Planar bases: Perpendicular to the backbone, stacked like steps of a spiral staircase.

Structural Stability

The stability of the double helix is due to:

• Dispersion forces: Between stacked aromatic bases (stacking energy).

• Hydrogen bonding: Between complementary base pairs (A-T, G-C).

Base-Pairing and Complementarity

Chargaff’s Rules

Chargaff’s rules state that in double-stranded DNA:

• The number of A equals T.

• The number of G equals C.

This complementarity allows for accurate replication and information transfer.

Reverse Complement

To write the reverse complement of a DNA sequence, pair each base with its complement and reverse the direction:

• A pairs with T

• G pairs with C

Example: 5' ATT GCC AGG 3' → 3' TAA CGG TCC 5'

DNA Organization in the Cell

Genes, Chromosomes, Chromatin, and Nucleosomes

DNA is highly compacted in the cell:

• Chromatin: Orderly tangle of DNA in non-dividing cells.

• Chromosomes: Highly compacted, visible during cell division.

• Nucleosomes: DNA wrapped around histone proteins (rich in Arg and Lys).

• Gene: Segment of DNA directing synthesis of a single polypeptide.

Protein-DNA Interactions

General Principles

Proteins interact with DNA primarily through ionic interactions:

• Positively-charged amino acids: Arg, Lys, His on proteins.

• Negatively-charged phosphates: On DNA backbone.

• Interactions are called salt bridges.

Mutations in DNA

Causes and Consequences

A mutation is a change in the DNA sequence, often caused by mutagens such as ionizing radiation or chemical agents. Mutations can alter base-pairing and, if not repaired, are propagated during DNA replication.

• Example: Cytosine deamination produces uracil, which pairs with adenine instead of guanine.

• Semiconservative replication: Each new DNA double helix contains one old and one new strand.

Central Dogma of Molecular Biology

Information Flow

The central dogma describes the flow of genetic information:

• Replication: DNA → DNA

• Transcription: DNA → RNA

• Translation: RNA → Protein

Each process involves initiation, elongation, and termination phases.

Summary Table: DNA vs. RNA

Feature	DNA	RNA
Base	A, G, C, T	A, G, C, U
Sugar	Deoxyribose	Ribose
Strandedness	Double-stranded	Single-stranded
Function	Genetic storage	Genetic decoding, catalysis

Additional info: These notes expand on the original lecture slides by providing definitions, examples, and structural context for nucleic acids, their organization, and their biological functions. All included images directly reinforce the structural and functional explanations provided.