Properties of Nucleotides

Introduction to Nucleotides

Nucleotides are the fundamental building blocks of nucleic acids, such as DNA and RNA. They serve as information and energy-carrying molecules in cells.

• Nucleotides are composed of three parts:

  • Phosphate group – contains phosphorous

  • Sugar – ribose (RNA) or deoxyribose (DNA)

  • Nitrogen-containing base – purines or pyrimidines

• The chemical structure of a nucleotide includes a phosphate attached to the 5' carbon of the sugar, which is linked to a nitrogenous base at the 1' carbon via a glycosidic bond.

• Nucleoside: Consists of a sugar and a base only (no phosphate).

• Nucleotide: Consists of a sugar, base, and one or more phosphate groups.

Phosphate Linkages and ATP

Additional phosphate groups can be added to nucleotides to form di-phosphates (e.g., ADP) and tri-phosphates (e.g., ATP). ATP is the primary energy currency of the cell, and its energy comes from the hydrolysis of phosphoanhydride bonds.

• Phosphoanhydride bonds are formed by condensation of two phosphoric acids.

• Hydrolysis of these bonds releases energy used in cellular processes.

Phosphoanhydride and Phosphate Ester Bonds

Phosphoanhydride bonds are found in molecules like ATP, GDP, and CTP. Phosphate ester bonds are present in nucleotides such as AMP.

Table: Nucleic Acid Bases, Nucleosides, and Nucleotides

Structures of Nitrogenous Bases

Pyrimidines and Purines

Nitrogenous bases are classified as pyrimidines (single ring) or purines (double ring). These bases form hydrogen bonds that stabilize the structure of DNA and RNA.

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

  • Single ring structure

  • Conjugated (planar), can form H-bonds

  • A pairs with T (or U), G pairs with C

• Purines: Adenine (A), Guanine (G)

  • Double ring structure

  • Conjugated (planar), can form H-bonds

Biologically Active Compounds Related to Bases

• Orotic acid: a metabolite

• Caffeine: plant compound, affects adenosine receptors in the brain

• Flucytosine: anti-fungal drug

• Theobromine: plant compound, toxic to dogs

Summary Point: Many biologically active compounds beyond DNA and RNA bases are purines and pyrimidines.

Structure and Backbone of Nucleic Acids

Sugar Components: Ribose vs. 2'-Deoxyribose

The backbone of nucleic acids consists of alternating sugar and phosphate groups. The difference between DNA and RNA is the sugar component:

• Ribose (RNA): Contains a hydroxyl group (-OH) at the 2' position.

• 2'-Deoxyribose (DNA): Lacks the 2' hydroxyl group (has -H instead).

This difference affects secondary structure and stability:

• Oxygen at the 2' position in RNA can act as a nucleophile, making RNA more susceptible to hydrolysis.

• RNA is less stable (more labile) than DNA, both structurally and functionally.

• Many enzymes (RNases) catalyze RNA breakdown.

Phosphodiester Bonds and Hydrolysis

The backbone of nucleic acids is formed by phosphodiester linkages between the 5' phosphate and 3' hydroxyl groups of adjacent nucleotides.

• Alkaline hydrolysis of RNA can occur via a cyclic intermediate, leading to backbone cleavage.

• Enzymes called nucleases catalyze the hydrolysis of phosphodiester bonds, resulting in 3' OH and 5' P ends.

Restriction Enzymes and DNA Fragmentation

Restriction Endonucleases

Restriction enzymes hydrolyze both strands of DNA, yielding two fragments. These fragments can have staggered ('sticky') or blunt ends.

• Sticky ends have overhanging single-stranded regions that can anneal with complementary sequences.

• Blunt ends have no overhangs.

• Fragments are labeled by their 5' and 3' ends; the 5' ends contain the phosphate group.

Polymerization of DNA and RNA

Mechanism of Polymerization

Polymerases synthesize DNA and RNA by reading the template strand 3' to 5' and building the new strand 5' to 3'. The reaction requires a 3' hydroxyl group and incoming dNTPs (deoxynucleoside triphosphates).

• The 3' OH acts as the nucleophile, attacking the alpha phosphate of the incoming dNTP.

• Polymerization is driven by the high free energy yield of phosphoanhydride bond hydrolysis.

Key Equation:

Red arrows in diagrams represent thermodynamic favorability.

Historical Connections: Nobel Prizes in Nucleic Acid Research

Restriction Enzymes

• Werner Arber, Daniel Nathans, and Hamilton O. Smith received the Nobel Prize in 1978 for the discovery of restriction enzymes and their application to molecular genetics.

• Arber postulated that restriction enzymes bind to DNA at specific sites containing recurring structural elements.

• Nathans applied restriction enzymes to genetics, enabling the construction of genetic maps.

DNA Polymerase

• Arthur Kornberg received the Nobel Prize in 1959 for the discovery of DNA polymerase.

• His work enabled the understanding of DNA replication mechanisms.

Additional info: The notes also reference the role of adenosine in sleep regulation and the effects of caffeine on adenosine receptors, as well as the toxicity of theobromine to dogs.