Lecture 5 (II) DNA Double Helix and ATP F24 NEW

Secondary Structure of DNA

  • Chargaff's Rules:

    • Erwin Chargaff and colleagues discovered:

      • The number of adenine (A) residues equals thymidine (T) residues (A = T).

      • The number of guanine (G) residues equals cytosine (C) residues (G = C).

    • Variability: The percentages of GC and AT vary among different organisms.

X-ray Crystallography and DNA Identification

  • Contribution of Rosalind Franklin and Maurice Wilkins:

    • Used X-ray crystallography to investigate the secondary structure of DNA.

    • Challenges:

      • Chromosomes are long DNA molecules that shear and fragment during isolation, which complicates crystal formation.

      • Fragments are similar but not identical, making it difficult to obtain high-resolution patterns.

    • Advancement in technology has led to synthesizing small oligonucleotides that form well-ordered crystals.

Photo 51: Key X-ray Diffraction Image

  • Franklin's Photo 51:

    • The first useful X-ray diffraction image of DNA.

    • Evidence revealed:

      • DNA molecules are helical.

      • Two periodicities exist along the long axis: a primary of 3.4 Å and a secondary of 34 Å.

Model Formation by Watson and Crick

  • In 1953, utilizing existing data on DNA structure, Watson and Crick developed their model.

  • Notably, Fred Sanger also detailed the amino acid sequence of insulin in the same year.

Structure of DNA According to Watson and Crick

  • Description: Proposed a structure with two helical chains coiling around the same axis based on assumptions about phosphate diester linkages between deoxyribose residues.

    • Configuration:

      • Each chain has phosphates on the outside and bases on the inside.

      • Both chains follow right-handed helices, running in opposite directions due to a dyad perpendicular to the fiber axis.

Geometry of the Double Helix

  • Characteristics:

    • Two DNA chains wind around a single axis forming a right-handed double helix.

    • Backbone: Hydrophilic sugar-phosphate backbone faces water; hydrophobic bases are stacked inside perpendicular to the axis.

    • Each base of one strand pairs with an opposite base of the other strand, A with T and C with G.

Antiparallel Structure and Dimensions

  • The two strands of DNA are antiparallel; phosphodiester bonds run in opposite directions.

  • Important measurements:

    • Vertically stacked base pairs are 3.4 Å apart.

    • Each helix turn contains approximately 10 base pairs (totaling 34 Å).

    • The diameter of the double helix measures 20 Å (2 nm).

Self-Complementarity in DNA

  • Self-complementarity allows each strand of the double helix to serve as a template for the synthesis of new daughter strands.

  • Implications for biology: essential for mitosis, meiosis, heredity, and DNA repair mechanisms.

Hydrogen Bonding in Base Pairs

  • Watson-Crick base pairs consist of:

    • Three hydrogen bonds between cytosine (C) and guanine (G).

    • Two hydrogen bonds between adenine (A) and thymine (T).

  • Higher GC to AT ratios make separating DNA strands more challenging.

Structural Dynamics of DNA

  • The strands of the double helix are coiled (plectonemically coiled) and cannot be separated without unwinding from an end.

  • DNA undergoes "supercoiling," resulting in compact structures, similar to a phone cord.

Major and Minor Grooves in DNA

  • DNA has two grooves: Major and Minor:

    • Angles created by glycosidic bonds lead to varying widths (minor groove is narrower than the major groove).

    • Grooves alternate around the double helix, lined with potential hydrogen-bonding atoms from the bases, facilitating specific protein interactions.

Forces Stabilizing the DNA Double Helix

  • The secondary structure is largely independent of base sequence due to similar shapes and properties of base pairs.

  • Stabilization forces include:

    1. Hydrophobic effect (hidings bases in the core).

    2. Hydrogen bonding between base pairs.

    3. van der Waals stacking of bases.

Base Composition Insights

  • For a DNA strand with [A] = 30% and [G] = 24%, the calculations yield:

    • [T] = 30% (due to A = T) and [C] = 24% (due to G = C).

    • Further calculations indicate [C] + [T] = 46%, though their individual values remain indeterminate.

Complementary Strand Base Composition

  • The complementary strand must have:

    • [T] = 30% and [C] = 24%, hence [A] + [G] = 46% (this reflects the complementarity in base pairing).

The Central Dogma of Molecular Biology

  • Conceptual framework for biological information flow:

    • DNA → RNA → Protein

    • Processes involved: transcription, translation, and replication.

Adenosine Triphosphate (ATP) - Energy Currency

  • ATP is essential for cellular energy transactions, discovered by Fritz Lipmann.

  • Composition: consists of a base (adenine), sugar (ribose), and three phosphate groups (alpha, beta, gamma).

  • A human uses about 40 kg of ATP during a restful day, linking food energy conversion to cellular processes.

ATP Functionality

  • ATP serves as a bridge between catabolism and anabolism:

    • Cells catabolize nutrients to synthesize ATP, which donates energy for anabolic reactions and cellular processes including transport and motion.

  • ATP turnover is rapid, with a typical lifespan of seconds to minutes.

Free Energy Change for ATP Hydrolysis

  • Hydrolysis of ATP is energetically favorable, releasing substantial free energy:

    • ΔG for ATP hydrolysis = -50 kJ/mol.

    • Energy transfer processes occur primarily at the phosphate groups of ATP.