DNA: The Chemical Nature of the Gene

Chapter 10 Overview

  • Characteristics of the genetic material
  • DNA is the genetic material - Griffith - Avery - Hershey-Chase
  • RNA as genetic material
  • Nucleic acid structure
  • Base composition (Chargaff)
  • Base pairing
  • X-ray diffraction (Franklin)
  • The Double Helix (Watson and Crick)
  • Animal & Plant Viruses (Ch. 9)

10.1 Contributions to the Structure of DNA

  • Key contributors to the understanding of DNA:
    • Theodor Boveri: proposed that chromosomes may transmit heredity.
    • Walter Sutton: developed the Chromosome Theory of Inheritance.

10.2 Johann Friedrich Miescher

  • Performed the first chemical analysis of DNA in 1869.
  • Isolated DNA from white blood cells.

10.3 Genetic Material Characteristics

  • Genetic material must contain complex information.
  • Must encode the phenotype.
  • Must replicate faithfully.
  • Must have the capacity to vary.

10.4 Fred Griffith's Discovery of the Transforming Principle

  • Year: 1928.
  • Isolated multiple strains of Streptococcus pneumoniae:
    • Types include IIS, IIR, IIIS, IIIR (S for smooth, R for rough forms).
    • Smooth type (S): disease-causing form with a polysaccharide coat.
    • Rough type (R): non-virulent form without a polysaccharide coat.

10.5 Identification of the Transforming Principle

  • Researchers: Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944).
  • Key finding: Treatment with DNase (degrades DNA) eliminated the transformation ability.
  • Investigated the effects of enzymatic destruction of RNA, protein, or DNA on the ability of heat-killed IIIS filtrate to transform IIR bacteria.

10.6 Concept Check 1

  • Question: If RNase and DNase treated samples transformed while those treated with protease did not, what conclusion would be drawn?
    • Protease is necessary for transformation.
    • RNA and DNA are deemed the genetic materials.
    • Proteins are not the genetic material.
    • Transformation requires both RNase and DNase.

10.7 Alfred Hershey & Martha Chase

  • Year: 1952.
  • Utilized a biochemical approach to confirm that DNA is the genetic material.
  • Experiment:
    • Infected E. coli with T2 phage.
    • Cultured in medium with 35S (incorporates into proteins, not DNA) and 32P (incorporates into DNA, not proteins).

10.8 Structure of DNA & RNA

Building Blocks: Nucleotides

  • Composed of:
    • Sugar
    • Nitrogenous base
    • Phosphate group

10.9 Sugar Composition of Nucleotides

  • Ribose: sugar in RNA.
  • Deoxyribose: sugar in DNA.
  • Structural differences between ribose and deoxyribose include the presence of a hydroxyl group on the 2' carbon for ribose, and a hydrogen atom for deoxyribose.

10.10 Nitrogenous Bases

  • Purines (double-ring structures):
    • Adenine (A)
    • Guanine (G)
  • Pyrimidines (single-ring structures):
    • Cytosine (C)
    • Thymine (T) - present in DNA
    • Uracil (U) - present in RNA

10.11 Nucleotide Forms

Nucleotide Composition:

  • Names and symbols are listed including:
    • Adenine (Base: A, Nucleotide: dAMP, Nucleoside: dA)
    • Guanine (Base: G, Nucleotide: dGMP, Nucleoside: dG)
    • Thymine (Base: T, Nucleotide: dTMP, Nucleoside: dT)
    • Cytosine (Base: C, Nucleotide: dCMP, Nucleoside: dC)

10.12 RNA Structure

  • Generally single-stranded.
  • Nucleotide strands connected by 5’ to 3’ phosphodiester bonds.
  • Strands synthesized in a 5’ to 3’ direction.

10.13 Chargaff’s Rules

  • Empirical rules derived from base composition of DNA:
    • Amount of purines equals amount of pyrimidines.
    • A = T and G = C.
    • The G+C content versus A+T content is species-specific and often represented as %(G+C).

10.14 Double Helix Structure

  • Proposed by James Watson & Francis Crick (1953).
  • Based on Chargaff’s rules and X-ray diffraction data from Rosalind Franklin.
  • Structure dimensions:
    • Diameter of the double helix is 2 nm.
    • 10 base pairs per turn of the helix.
    • Distance between base pairs is 0.34 nm (3.4 Å).

10.15 DNA Strand Structure

  • DNA is usually double-stranded with two antiparallel strands.
  • Antiparallel strands refer to the 5’ to 3’ directionality.
  • Base pairing: A pairs with T via 2 hydrogen bonds; G pairs with C via 3 hydrogen bonds.

10.16 Primary and Secondary Structures in DNA

  • Primary Structure: Sequence of base pairs.
  • Secondary Structure: B form double helix.

10.17 Alternative Secondary Structures

  • A form: Exists under lower humidity.
  • Z form: Left-handed zigzag structure, potentially exists in vivo.
  • More complex secondary structures can form due to intramolecular base pairing in single-stranded nucleic acids.

10.18 Complex Secondary Structures

  • Example: DNA during replication shows complex arrangements.
  • Many RNA molecules also exhibit complex secondary structures.

10.19 Base Pairing Mechanics

  • Strands of DNA or RNA can pair if they have complementary bases:
    • Example pairing:
    • Strand 1: 3’-CGAAATGCTCCATGCCAGACCTTTGCTGCGCACTACGA-5’
    • Strand 2: 5’-CTGCGGAATGCTACGGTCTGGAAACGAGCCCTTAATCG-3’
  • The strands must be antiparallel to pair.

10.20 Suggested Problems

  • Problems: 1, 3-5, 7-13, 15, 19, 24, 26, 27, 29-32, 35-37 to reinforce the chapter content.

Chapter 9 Overview: Plant and Animal Viruses

  • Some viruses contain DNA genomes; others are RNA genomes.

Examples of DNA and RNA viruses:

DNA Viruses:
  • Adenoviruses
  • Herpesviruses
  • Papillomaviruses
  • Parvoviruses
RNA Viruses:
  • Retroviruses (e.g., HIV)
  • Negative-strand RNA viruses (e.g., Influenza, Ebola, Rabies)
  • Positive-strand RNA viruses (e.g., Rhinoviruses, West Nile virus, Coronaviruses)

9.25 Retroviruses

  • Method of action: uses reverse transcription to incorporate RNA into host DNA.
  • Reverse Transcriptase synthesizes a double-stranded DNA copy from the virus’ RNA genome.
  • Integrated viral DNA (provirus) can be transcribed to make viral proteins.

Evolution of HIV-1

  • Evolved from recombination between retroviruses that infect monkeys.
  • Likely originated in humans through contact with chimpanzees.

Influenza Virus Overview

Major Strain Information:

  • 1918: Spanish Flu - H1N1
  • 1957: Asian Flu - H2N2
  • 1968: Hong Kong Flu - H3N2
  • 2009: Swine Flu - H1N1
Types of Influenza:
  • Influenza A, B, and C with A subtypes based on Hemagglutinin (HA) & Neuraminidase (NA).

Influenza Evolution

  • Antigenic Drift: High mutation rates due to error-prone RNA replication.
  • Antigenic Shift: Reassortment of RNA strands from different influenza strains during simultaneous infections.

Coronaviruses and Cellular Mechanisms

  • Entry into cells is mediated by specific proteins such as LMPRSS2 and ACE2 creating the viral genomic RNA and membrane fusion.
  • SARS-CoV-2 genomes have similar sequences to previous coronaviruses with a low mutation rate due to “proofreading.”