Chapter 13: The Molecular Basis of Inheritance

Overview: Life’s Operating Instructions

  • In 1953, James Watson and Francis Crick introduced the double-helical model for DNA structure.
  • Hereditary information in DNA directs biochemical, anatomical, physiological, and behavioral traits.
  • DNA replication reproduces hereditary information in all body cells.

Concept 13.1: DNA Is the Genetic Material

  • Identifying inheritance molecules was a major challenge in the early 20th century.

The Search for the Genetic Material: Scientific Inquiry

  • T. H. Morgan’s group located genes on chromosomes.
  • DNA and protein were candidates for the genetic material.
  • Proteins initially seemed more likely.
  • The role of DNA was determined by studying bacteria and their infecting viruses.

Evidence That DNA Can Transform Bacteria

  • Frederick Griffith's research in 1928:
    • Worked with pathogenic and harmless strains of bacteria.
    • Mixing heat-killed pathogenic strain with live harmless strain made some cells pathogenic.
    • He termed this transformation: a change in genotype and phenotype due to foreign DNA assimilation.
  • Oswald Avery identified DNA as the transforming substance.
  • Many were skeptical due to limited knowledge about DNA.

Evidence That Viral DNA Can Program Cells

  • Studies of viruses infecting bacteria provided more evidence.
    • Bacteriophages (phages) are widely used in molecular genetics research.
    • A virus is DNA (or RNA) enclosed by a protein coat.
    • Viruses infect cells and use their machinery to reproduce.
  • Alfred Hershey and Martha Chase (1952) showed DNA is the genetic material of phage T2.
    • Only the DNA of the T2 phage, not protein, enters E. coli cells during infection.
    • Injected DNA provides the genetic information.

Additional Evidence That DNA Is the Genetic Material

  • Erwin Chargaff (1950) reported that DNA composition varies between species.
  • Diversity made DNA a credible genetic material candidate.
  • Chargaff’s rules:
    • Base composition of DNA varies between species.
    • In any species, the percentages of adenine (A) and thymine (T) are equal, and guanine (G) and cytosine (C) are equal.
    • A=TA = T and G=CG = C
    • The double helix discovery later explained these rules.

Building a Structural Model of DNA: Scientific Inquiry

  • James Watson and Francis Crick determined DNA's structure.
  • Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study molecular structure.
  • Franklin’s X-ray images enabled Watson to deduce DNA was helical.
  • X-ray images helped deduce helix width and nitrogenous base spacing.
  • Photo patterns suggested a double helix.

Further Insights from Franklin's Work

  • Franklin's images of DNA enabled Watson:
    • Identified DNA's helical structure.
    • Determined the width of the helix.
    • Determined the spacing of nitrogenous bases.
  • The images indicated a double-stranded structure.

Model Building and Backbone Arrangement

  • Watson and Crick built double helix models conforming to X-ray measurements and DNA chemistry.
  • Franklin concluded sugar-phosphate backbones were on the outside with nitrogenous bases paired inside.
  • Watson's model had antiparallel backbones (subunits running in opposite directions).

Base Pairing Specificity

  • Watson and Crick determined base pairing was specific due to base structures.
  • Adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C).
    • A−TA-T and G−CG-C
  • The Watson-Crick model explained Chargaff’s rules:
    • Amount of A = Amount of T.
    • Amount of G = Amount of C.

Concept 13.2: Many Proteins Work Together in DNA Replication and Repair

  • The relationship between structure and function is evident in the double helix.
  • Watson and Crick suggested specific base pairing implies a copying mechanism for genetic material.

The Basic Principle: Base Pairing to a Template Strand

  • DNA strands are complementary; each stores information to reconstruct the other.
  • In DNA replication, the parent molecule unwinds, and new daughter strands are built based on base-pairing rules.
  • The semiconservative model predicts each daughter molecule has one old and one new strand.
  • Other models:
    • Conservative: parent strands rejoin.
    • Dispersive: each strand is a mix of old and new.
  • Experiments by Matthew Meselson and Franklin Stahl supported the semiconservative model.

DNA Replication: A Closer Look

  • DNA copying is fast and accurate.
  • More than a dozen enzymes and other proteins participate.
  • Much is known about this “replication machine” in bacteria.
  • The process is similar in prokaryotes and eukaryotes.

Getting Started

  • Replication starts at origins of replication, where DNA strands separate, forming a replication “bubble.”
  • Replication fork: Y-shaped region at each end of the bubble where parental DNA strands are unwinding.
  • Eukaryotes have multiple replication bubbles that fuse, speeding up DNA copying.

Proteins Involved in Unwinding

  • Helicases: untwist the double helix at replication forks.
  • Single-strand binding proteins: stabilize single-stranded DNA.
  • Topoisomerase: relieves strain ahead of the replication fork by breaking, swiveling, and rejoining DNA strands.

Synthesizing a New DNA Strand

  • Enzymes that synthesize DNA (DNA polymerases) can only add nucleotides to an existing chain paired with the template.
  • The initial nucleotide strand is a short RNA primer.
  • Primase starts an RNA chain with a single RNA nucleotide and adds RNA nucleotides one at a time using the parental DNA as a template.
  • The primer is short (5–10 nucleotides long).
  • DNA polymerases catalyze the elongation of new DNA at a replication fork.
  • They add nucleotides to the 3′ end of a preexisting chain.
  • Most DNA polymerases require a primer and a DNA template strand.
  • The elongation rate is about 500 nucleotides per second in bacteria and 50 per second in human cells.

Antiparallel Elongation

  • New DNA strands must be formed antiparallel to the template strand.
  • DNA polymerases add nucleotides only to the free 3′ end of a growing strand.
  • Strands can only elongate in the 5′ to 3′ direction.
  • Leading Strand:
    • DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork on one template strand of DNA.
    • Only one primer is required.
  • Lagging Strand:
    • To elongate the other new strand (lagging strand), DNA polymerase must work in the direction away from the replication fork.
    • The lagging strand is synthesized as a series of segments called Okazaki fragments.
    • Okazaki fragments are 100–200 nucleotides long in eukaryotes and 1,000–2,000 nucleotides long in E. coli.
  • After Okazaki fragment formation, DNA polymerase I removes RNA primers and replaces the nucleotides with DNA.
  • DNA ligase joins the remaining gaps.

Proofreading and Repairing DNA

  • Errors in completed DNA molecules: one in 10 billion.
  • DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides.
  • Mismatch repair: enzymes correct errors in base pairing.
  • Hereditary defect in mismatch repair enzyme is associated with colon cancer.
  • Defect allows cancer-causing errors to accumulate faster.
  • DNA can be damaged by chemical or physical agents (e.g., X-rays).
  • DNA bases can undergo spontaneous changes.
  • Nuclease cuts out and replaces damaged stretches of DNA.
  • Nucleotide excision repair: DNA repair system.
  • DNA repair enzymes in skin repair genetic damage from UV light.

Evolutionary Significance of Altered DNA Nucleotides

  • Error rate after proofreading repair is low but not zero.
  • Sequence changes may become permanent and be passed on to the next generation (mutations).
  • Mutations are the source of genetic variation upon which natural selection operates.

Replicating the Ends of DNA Molecules

  • Linear DNA replication machinery cannot complete the 5′ ends of daughter strands.
  • Repeated replication rounds produce shorter DNA molecules with uneven ends.
  • Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called telomeres.
  • Telomeres do not contain genes.
  • They consist of multiple repetitions of one short nucleotide sequence.
  • Telomeres postpone the shortening of DNA molecules but do not prevent it.
  • Telomere shortening is connected to aging.
  • Telomerase lengthens telomeres in germ cells.
  • Telomerase is not active in most human somatic cells but shows activity in some cancer cells.
  • Telomerase is under study as a target for cancer therapies.

Concept 13.3: A Chromosome Consists of a DNA Molecule Packed Together with Proteins

  • Bacterial chromosome: double-stranded, circular DNA molecule associated with a small amount of protein.
  • Eukaryotic chromosomes: linear DNA molecules associated with a large number of proteins.
  • In bacteria, DNA is “supercoiled” and found in the nucleoid region.
  • Chromatin: complex of DNA and protein in eukaryotic cells.
  • Chromosomes fit into the nucleus through multilevel packing.
  • Chromatin undergoes changes in packing during the cell cycle.
  • Histones are responsible for the first level of DNA packing in chromatin.
  • Four types of histones are most common in chromatin.
  • A nucleosome consists of DNA wound twice around a protein core of eight histones (two of each main histone type).

Editing Genes and Genomes

  • CRISPR-Cas9 system:
    • Cas9 is a nuclease that cuts double-stranded DNA molecules as directed by a guide RNA complementary to the target gene.
    • Used to “knock out” (disable) a gene to determine its function.
    • Modified to repair a gene that has a mutation.
    • Used in attempts to correct the genetic defect causing sickle-cell disease.
    • Used to alter genes in insects to prevent disease transmission.
    • Gene drive: engineering a new allele to favor its inheritance over the wild type allele, driving the engineered allele through the population.
  • Ethical considerations are important for CRISPR technology.