Lecture 5 fall 2025

General Biochemistry I

  • Course Code: 4375/5475

  • Topic: Nucleotides & Nucleic Acids I

  • Visual Reference: M.C. Escher, Möbius strip II

Learning Goals

  • Understand structures and organization of nucleic acids.

  • Comprehend ATP hydrolysis and its high energy releases.

  • Recognize DNA as a source of genetic information.

  • Understand the role of topoisomerase in regulating DNA supercoiling.

Nucleic Acids Overview

  • Nucleotides and their polymers (nucleic acids) are fundamental to various cellular functions:

    • Participation in oxidation-reduction reactions.

    • Energy transfer processes.

    • Facilitation of intracellular signaling.

    • Involvement in biosynthetic reactions.

    • Storage and decoding of genetic information.

    • Structural and catalytic activities.

Nucleotides

  • Eight common nucleotide varieties:

    • Composed of a nitrogenous base linked to a sugar with at least one phosphate group.

    • Bases can be classified as:

      • Purines: Adenine (A), Guanine (G).

      • Pyrimidines: Cytosine (C), Uracil (U), and Thymine (T).

      • Structural Features:

        • Planar, aromatic, heterocyclic.

        • Purines bond to five-carbon sugar via N9.

        • Pyrimidines bond via N1.

    • Ribonucleotides contain ribose (RNA).

    • Deoxyribonucleotides contain 2’-deoxyribose (DNA).

Nucleotide Structure and Classification

  • In ribo- or deoxyribonucleotides, phosphate groups bond to C3’ or C5’ of the sugar:

    • Phosphate absence yields nucleosides; e.g., 5’-nucleotide = nucleoside-5’-phosphate.

    • Nucleotides are categorized as mono-, di-, or tri-phosphates depending on phosphate count at the C5’ position.

Metabolic Functions of Nucleotides

  • Free nucleotides facilitate various metabolic functions:

    • ATP is the principal energy carrier/transfer agent.

    • ATP produced through processes like photosynthesis or degradation of nutrients.

    • Energy is released through ATP hydrolysis, converting to ADP (adenosine diphosphate).

ATP Hydrolysis

  • ATP hydrolysis features very negative standard state free energy (ΔG°’= -31 kJ/mol):

    • The reaction is highly exergonic, favoring products and considered essentially irreversible.

    • The concept of high energy phosphate bonds is considered overly simplified; rather, it involves unique properties of reactants/products.

Factors Influencing ΔG°’ of ATP Hydrolysis

  • Factors contributing to high ΔG°’ include:

    1. Resonance stability of phosphate products.

    2. Electrostatic repulsion between charged products.

    3. Enhanced hydration of hydrolysis products.

    4. Effects of pH and ionic strength of solutions.

Genetic Information in Nucleic Acids

  • Nucleic acids are vital carriers of genetic information:

    • Early belief attributed genetic information to proteins.

    • Groundbreaking experiment by Avery, MacLeod, and McCarty demonstrated DNA from a bacterial strain carried genetic information.

Avery-MacLeod-McCarty Experiment

  • Methodology included:

    • Killing S strain cells and fractionating them into nucleic acids, proteins, carbohydrates.

    • Only nucleic acids successfully transformed R strain bacteria to S strain.

Hershey and Chase Experiment

  • Confirmed DNA's role as genetic information carrier:

    • Used labeled viral DNA and identified that DNA, not protein, transmitted genetic information to bacteria.

Structural Features of Nucleic Acids

  • Nucleic Acids consist of:

    • Polymers of nucleotides: DNA and RNA.

    • Backbone formed by phosphodiester bonds between adjacent ribose units.

    • Physiological pH renders nucleic acids as polyanions.

Chargaff’s Rules

  • Established by Erwing Chargaff:

    • DNA contains equal amounts of A&T and G&C.

    • RNA composition varies in ribonucleotide counts.

3-D Structure of DNA

  • Rosalind Franklin's X-ray diffraction indicated DNA's helical structure.

  • Watson & Crick's model incorporates chemical insights to depict DNA's double helical structure:

    • Two right-handed helical polynucleotide chains.

    • Antiparallel strand configuration.

    • Sugar-phosphate backbone with base pairing in the helix center.

DNA Conformations

  • Three conformations:

    • A-DNA, B-DNA (biologically common), Z-DNA.

    • Variations in helical sense, dimensions, base pairing phenomena.

Forces Stabilizing Nucleic Acids

  • Stabilizing forces include:

    • Hydrogen bonds for specificity.

    • Stacking interactions resulting from hydrophobic and van der Waals interactions.

    • Stacking energy varies by sequence, influenced by enthalpy rather than increasing entropy.

DNA Supercoiling and Topoisomerases

  • Bacterial genome has supercoiled circular DNA (plasmids), which are essential for DNA packing.

  • Topoisomerases control DNA supercoiling:

    • Type I: Relaxation of negative supercoils.

    • Type II: Requires ATP hydrolysis, producing double-strand cleavages.

Topoisomerase Inhibitors

  • Inhibitors linked to antibiotics and anticancer agents:

    • Significant cellular impact through DNA damage in rapidly dividing cells.

Learning Objectives

  • Familiarity with eight common nucleotide structures.

  • Understanding of energy roles played by nucleotides.

  • Explanation of historical experiments establishing DNA as genetic material.

  • Identification of forces stabilizing DNA and implications of supercoiling/topoisomerase actions.