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Life’s Operating Instructions

  • In 1953, James Watson and Francis Crick introduced an elegant double-helical model for the structure of deoxyribonucleic acid (DNA).
  • Hereditary information is encoded in DNA and reproduced in all cells of the body.
  • The DNA program directs the development of biochemical, anatomical, physiological, and, to some extent, behavioral traits.

Concept 16.1: DNA is the Genetic Material

  • Early in the 20th century, identifying the molecules of inheritance was a significant challenge for biologists.
  • T. H. Morgan’s group demonstrated that genes are located on chromosomes, making the two components of chromosomes—DNA and protein—candidates for the genetic material.

Additional Evidence That DNA is the Genetic Material

  • DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group.
  • The nitrogenous bases can be adenine (A), thymine (T), guanine (G), or cytosine (C).
  • In 1950, Erwin Chargaff reported that DNA composition varies between species, contributing to its credibility as the genetic material.
Chargaff’s Rules
  • Two main points known as Chargaff’s rules:   - The base composition of DNA varies between species.   - In any species, the number of adenine (A) and thymine (T) bases is equal, and the number of guanine (G) and cytosine (C) bases is equal.
  • The basis for these rules was understood following the discovery of the double helix.

Building a Structural Model of DNA: Scientific Inquiry

  • After DNA was accepted as the genetic material, a major challenge emerged: determining how its structure accounts for its role in heredity.
  • Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study molecular structure, producing a significant picture of the DNA molecule.
Insights from X-ray Crystallography
  • Franklin’s images of DNA enabled Watson to deduce the molecule's helical structure, its width, and the spacing of the nitrogenous bases.
  • The pattern suggested that the DNA molecule was composed of two strands forming a double helix.

Watson and Crick’s Model of DNA

  • Franklin never collaborated with Watson and Crick; her data was shown to them without her knowledge by Wilkins.
  • It was noted that Watson and Crick's model conformed to the evidence available from the X-rays and chemistry of DNA.
Antiparallel Backbones and Base Pairing
  • Watson built a model depicting antiparallel backbones, which means their subunits run in opposite directions.
  • Initially, Watson and Crick assumed bases paired similarly (A with A), but this led to inconsistent widths.
  • Realizing that pairing a purine (A or G) with a pyrimidine (C or T) resulted in a consistent width led to correct base pairing rules:   - Adenine (A) pairs exclusively with thymine (T).   - Guanine (G) pairs exclusively with cytosine (C).
  • This specificity explained Chargaff’s rules: the amount of A = T and the amount of G = C in any organism.

Concept 16.2: Many Proteins Work Together in DNA Replication and Repair

  • The interrelationship of structure and function is evident in the double helix structure identified by Watson and Crick.
  • The specific base pairing suggested a potential copying mechanism for genetic material.

Base Pairing as a Template for Replication

  • Each DNA strand is complementary, serving as a template for building a new strand during replication.
  • In replication, the parent molecule unwinds, and daughter strands are constructed based on base-pairing rules.
Semiconservative Model of DNA Replication
  • Watson and Crick proposed a semiconservative model, predicting that each daughter molecule consists of one old strand (conserved from the parent) and one newly synthesized strand.
  • Competing models:   - Conservative model: two parent strands rejoin.   - Dispersive model: each strand is a mix of old and new.

DNA Replication Process

  • Replication starts at specific sites known as origins of replication.
  • Eukaryotic chromosomes may have numerous origins, allowing replication to proceed bidirectionally until the entire molecule is copied.
Replication Fork and Enzymes
  • At each replication bubble, a replication fork is formed, indicating new DNA strands' elongation.
  • Key enzymes include:   - Helicase: untwists the double helix at replication forks.   - Single-strand binding proteins: stabilize single-stranded DNA.   - Topoisomerase: alleviates twisting strain by breaking and rejoining DNA strands.
Synthesizing New DNA Strands
  • DNA polymerases synthesize new DNA at the replication fork, requiring a primer, which is a short RNA sequence created by the enzyme primase.
  • The primer is short (5-10 nucleotides long), with its 3′ end as the starting point for the new DNA strand.
  • DNA polymerases can only extend strands in the 5′ to 3′ direction, which influences the overall replication process.

Leading and Lagging Strands

  • DNA polymerase synthesizes a leading strand continuously toward the replication fork.
  • The lagging strand is synthesized in segments known as Okazaki fragments, which are joined later by DNA ligase.

Proofreading and Repair Mechanisms

  • DNA polymerases proofread the newly synthesized DNA, correcting incorrect nucleotides.
  • Mismatch repair processes rectify base pairing errors.
  • DNA can be damaged by chemical agents or undergo spontaneous changes; nucleotide excision repair removes damaged regions.

Evolutionary Significance of DNA Changes

  • Despite effective proofreading and repair, errors can occur, leading to mutations, which serve as genetic variation sources for evolution.

Replicating Linear DNA Ends

  • DNA polymerase difficulties pose issues for linear eukaryotic DNA, leading to shorter DNA strands with each replication.
  • Prokaryotic DNA, being circular, does not face this problem.

Telomeres and Their Role

  • Eukaryotic chromosomes feature specialized nucleotide sequences at their ends known as telomeres.
  • Telomeres help mitigate the loss of essential genes during replication, though they do not prevent shortening.
  • Telomere shortening is associated with aging, while the enzyme telomerase can lengthen telomeres in germ cells.

Chromosome Structure and DNA Packaging

  • A chromosome is defined as a DNA molecule associated with proteins. Eukaryotic chromosomes have linear DNA associated with a substantial amount of protein, while bacterial chromosomes feature circular DNA with minor protein interaction.
  • In eukaryotes, DNA combines with proteins to form chromatin, characterized by a highly organized packing system within the nucleus.

Nucleosomes and Gene Regulation

  • Nucleosomes, the fundamental units of DNA packaging, consist of DNA wrapped around histone proteins.
  • Chemical modifications to histones can influence chromatin condensation and affect gene expression.

Changes During the Cell Cycle

  • Chromatin undergoes regular packing changes throughout the cell cycle, transitioning from a less condensed state during interphase to a densely packed formation in preparation for mitosis.