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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.