Molecular Structure of DNA and RNA

Chapter 09: Molecular Structure of DNA and RNA

The Central Dogma of Biology

  • Fundamental Concept: DNA, RNA, and proteins interact in a central framework that governs biological processes.

9.1 Identification of DNA as the Genetic Material

  • Criteria for Genetic Material: To fulfill its role, genetic material must meet several criteria:

    • Information: Contains necessary information for the creation of an organism.

    • Transmission: Passed from parent to offspring.

    • Replication: Must be replicable to ensure continuity.

    • Variation: Capable of change to explain genetic diversity.

Griffith's Experiments with Streptococcus pneumoniae

  • Study Subject: Griffith studied S. pneumoniae, a bacterium.

  • Strains of S. pneumoniae:

    • Type S:

    • Smooth appearance due to a polysaccharide capsule.

    • Protects the bacterium from the immune response of hosts.

    • Type R:

    • Rough appearance, lacking a capsule.

Transforming Principle

  • Experiment Outcome:

    • Griffith concluded that dead type S bacteria could transform type R bacteria into type S through a mysterious "transforming principle."

    • The nature of this principle was unknown at the time.

Significance of Transformation

  • Evaluation of Properties:

    • The capsule's formation by transformed bacteria satisfies the criteria for genetic material, including:

    • Acquisition of information to produce a capsule.

    • Variability in capsule production.

    • Replication and transmission of the necessary information.

9.2 The Experiments of Avery, MacLeod, and McCarty

  • Context: By the 1940s, it was established that DNA, RNA, proteins, and carbohydrates are essential components of cells, but the specific genetic material was not identified.

  • Significant Breakthrough: Using Griffith's findings, Avery, MacLeod, and McCarty sought to determine the genetic material.

9.3 Overview of DNA and RNA Structure

  • Nucleic Acids: DNA and RNA, recognized as nucleic acids, were first identified by Friedrich Miescher in 1869, who termed it "nuclein" from cell nuclei.

  • Properties: DNA and RNA release H+ in water, establishing their classification as acids.

  • Complexity: Nucleic acids exhibit multiple structural levels.

    • Nucleotides are the repeating structural units linked to form strands.

    • DNA strands can interact to form a double helix, while the three-dimensional structures arise from their folding and interactions with proteins, forming chromosomes.

9.4 Nucleotide Structure

  • Components of Nucleotides: Each nucleotide consists of:

    • Phosphate Group

    • Pentose Sugar:

    • Ribose in RNA

    • Deoxyribose in DNA

    • Nitrogenous Base: Includes purines (Adenine, Guanine) and pyrimidines (Cytosine, Thymine in DNA, Uracil in RNA).

Terminology of Nucleic Acid Units

  • Nucleoside: Combination of a base and sugar. Examples:

    • Adenine + ribose = Adenosine

    • Adenine + deoxyribose = Deoxyadenosine

  • Nucleotide: Base + sugar + phosphate.

9.5 Structure of a DNA Strand

  • Covalent Bonds: Nucleotides in DNA are linked via covalent (ester) bonds forming phosphodiester linkages.

    • Orientation: Each DNA strand has a directional 5′ to 3′ orientation, with all sugars oriented the same way.

  • Backbone: The backbone of the nucleic acid strand is formed by phosphates and sugars, with bases projecting outward.

9.6 Discovery of the Double Helix

  • Watson and Crick: In 1953, Watson and Crick determined the double helical structure of DNA using contributions from:

    • Linus Pauling (helical structures)

    • Rosalind Franklin and Maurice Wilkins (X-ray diffraction)

    • Erwin Chargaff (base ratios).

Contributions to DNA Structure

  • Rosalind Franklin: Conducted X-ray diffraction studies on DNA fibers that indicated key features:

    • Helical structure

    • Existence of multiple strands

    • 10 base pairs per turn.

  • Erwin Chargaff's Rule: Noted that the percentage of adenine equals that of thymine, and cytosine equals guanine, leading to the formulation of Chargaff's rule, which was pivotal in establishing the DNA structure.

9.7 Structure of the DNA Double Helix

  • Configuration: The double helix has:

    • 10 base pairs per turn and a diameter of about 2 nm, with strands oriented in an antiparallel fashion (one 5′-3′, the other 3′-5′).

  • Stabilization: Key to stability:

    • Hydrogen bonding between bases (A with T via 2 H-bonds; C with G via 3 H-bonds).

    • Base stacking interactions enhance stability.

Grooves in the Helix

  • Major and Minor Grooves: Two asymmetrical grooves exist on the outside:

    • Major Groove: Allows protein binding.

    • Minor Groove: Also allows certain proteins to bind, facilitating interactions with specific base sequences.

9.8 RNA Structure

  • Differences from DNA:

    • RNA uses uracil instead of thymine.

    • RNA contains ribose sugar with a 2′ OH group.

  • Length: RNA molecules can span hundreds to thousands of nucleotides in length, with one strand serving as a template during synthesis.

RNA Secondary Structure

  • Formation: Despite being mostly single-stranded, RNA can form short double-stranded regions due to A-U and C-G base-pairing:

    • Typically right-handed helices with 11 to 12 base pairs per turn.

    • Varieties of secondary structures include bulge loops, internal loops, multibranched loops, and stem loops.