Nucleotides, Nucleic Acids, and Genetic Information: Structure and Function

4. Nucleotides, Nucleic Acids, and Genetic Information

4.1 Nucleotides

Nucleotides are the fundamental building blocks of nucleic acids, which are essential for the storage and transmission of genetic information in all living organisms.

• Nucleotides consist of three components:

  • Nitrogenous base (adenine, guanine, cytosine, thymine, or uracil)

  • Pentose sugar (ribose in RNA, deoxyribose in DNA)

  • Phosphate group (mono-, di-, or triphosphate)

• Nucleosides are composed of a nitrogenous base linked to a sugar, without the phosphate group.

• Nitrogenous bases are planar, aromatic heterocyclic compounds, classified as either purines (adenine, guanine) or pyrimidines (cytosine, thymine, uracil).

• Sugars in nucleotides are pentoses: ribose (RNA) or deoxyribose (DNA).

• The majority of nucleotides in cells are found in polymeric form as RNA or DNA, functioning in the transfer and storage of genetic material.

Example:

Adenosine diphosphate (ADP) is a nucleotide consisting of adenine (base), ribose (sugar), and two phosphate groups.

4.2 Nucleic Acid Structure

Nucleic acids are polymers of nucleotides, forming long chains that encode genetic information.

• Phosphodiester bonds link the 3' and 5' positions of neighboring ribose units, forming the backbone of nucleic acids.

• Phosphates make nucleic acids polyanions at physiological pH.

• Phosphodiester bonds are formed by a condensation reaction catalyzed by DNA ligase.

• Nucleic acid sequences are written from the 5' to 3' direction, with a free phosphate at the 5' end.

• DNA and RNA differ in their sugar (deoxyribose vs. ribose) and base composition (thymine in DNA, uracil in RNA).

Equation:

$\text{Phosphodiester bond:} \quad \text{Sugar}_1 - \text{Phosphate} - \text{Sugar}_2$

Example:

A trinucleotide consists of three nucleotides linked by phosphodiester bonds.

4.3 Nucleic Acid Function

Nucleic acids play a central role in the storage, transmission, and expression of genetic information.

• DNA stores genetic information in the sequence of its bases.

• RNA transmits genetic information and can also catalyze biochemical reactions (ribozymes).

• Single-stranded DNA is rare and mainly found in certain viruses; double-stranded RNA is also found in some viruses.

• RNA often forms compact structures, such as stem-loop motifs, due to base pairing.

Example:

Messenger RNA (mRNA) carries genetic information from DNA to ribosomes for protein synthesis.

4.4 Chargaff's Rule and Double Helix Model

Chargaff's Rule and structural observations led to the discovery of the DNA double helix.

• Chargaff's Rule: DNA has equal numbers of adenine and thymine (A = T), and equal numbers of guanine and cytosine (G = C).

• Double helix model:

  • DNA is a helical molecule with two antiparallel strands forming a right-handed helix.

  • Bases are stacked with a spacing of 3.4 Å and occupy the core of the helix.

  • 10.4 bases per turn of the helix.

  • Major and minor grooves are present on the surface.

  • Bases pair via hydrogen bonds: A with T, G with C.

Equation:

$\text{A} = \text{T}, \quad \text{G} = \text{C}$

Example:

Watson and Crick's model of DNA explains the molecular basis of heredity.

4.5 DNA and Chromatin Organization

DNA is packaged in cells with proteins to form chromatin and chromosomes.

• Histones are small, positively charged proteins that bind tightly to DNA, aiding in its packaging.

• Nucleosome is the fundamental unit of chromatin, consisting of DNA wrapped around histone proteins.

• Chromatin is the complex of DNA and proteins in the nucleus.

• Chromosomes are highly condensed structures of chromatin, each containing a single, long DNA molecule.

• Humans have 23 pairs of chromosomes (46 total).

Example:

Human chromosome 1 contains over 200 million base pairs of DNA.

Comparison Table: Purines vs. Pyrimidines

Type	Bases	Structure
Purines	Adenine (A), Guanine (G)	Double-ring
Pyrimidines	Cytosine (C), Thymine (T), Uracil (U)	Single-ring

Comparison Table: DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Strands	Double (usually)	Single (usually)
Function	Genetic storage	Genetic transmission, catalysis

Additional info:

• RNA can catalyze reactions (ribozymes), a property not shared by DNA.

• DNA packaging is essential for genome stability and regulation of gene expression.