L16: Nucleic Acid Structure and DNA Replication

Lesson 16: Nucleic Acid Structure and DNA Replication

Learning Objectives

This lesson covers the structure and function of DNA, the experiments that established DNA as the genetic material, and the mechanisms of DNA replication in prokaryotes and eukaryotes.

• Experimental Evidence for DNA as Genetic Material: Analyze key experiments by Griffith, Hershey and Chase, Chargaff, Watson and Crick, Franklin, Wilkins, Meselson, and Stahl.

• Structure of Nucleotides and DNA: Describe the structure of nucleotides and the double helix, including base pairing and the sugar-phosphate backbone.

• DNA Replication Mechanism: Understand the process of DNA replication, including the roles of leading and lagging strands, and the function of key enzymes.

• DNA Repair and Chromosome Compaction: Explain DNA repair mechanisms and how DNA is packaged in eukaryotic chromosomes.

• Eukaryotic Chromosome Structure: Outline the levels of chromosomal compaction in eukaryotes.

Key Terms and Definitions

• DNA Replication: The process by which a cell duplicates its DNA before cell division.

• Virus: A non-living infectious agent composed of nucleic acid and protein coat.

• Genetic Material: Molecules responsible for heredity and variation, primarily DNA in most organisms.

• Semi-conservative Model: Each new DNA molecule consists of one old strand and one newly synthesized strand.

• Single Strand Binding Proteins: Proteins that stabilize unwound DNA during replication.

• Leading Strand: The DNA strand synthesized continuously in the 5' to 3' direction.

• Lagging Strand: The DNA strand synthesized discontinuously as Okazaki fragments.

• Telomere: The repetitive DNA sequence at the end of eukaryotic chromosomes, protecting them from degradation.

• Transformation: Uptake of foreign DNA by a cell, demonstrated by Griffith's experiment.

• Antiparallel: The opposite orientation of the two strands in a DNA double helix.

• Cytosine: A pyrimidine nitrogenous base found in DNA and RNA.

• Origins of Replication: Specific DNA sequences where replication begins.

• Helicase: Enzyme that unwinds the DNA double helix during replication.

• Primase: Enzyme that synthesizes RNA primers for DNA polymerase to begin synthesis.

• Nucleotide Excision Repair: DNA repair mechanism that removes and replaces damaged DNA segments.

• Histone: Protein that DNA wraps around to form nucleosomes in eukaryotic chromatin.

• Bacteriophage: A virus that infects bacteria.

• Adenine: A purine nitrogenous base found in DNA and RNA.

• Origin: The starting point of DNA replication.

• Replication Fork: The Y-shaped region where DNA is split into two strands for replication.

• Topoisomerase: Enzyme that relieves tension ahead of the replication fork.

• DNA Polymerase III: Main enzyme that synthesizes new DNA strands in prokaryotes.

• Okazaki Fragments: Short DNA fragments synthesized on the lagging strand.

• Mismatch Repair: Correction of errors missed by DNA polymerase during replication.

• Nucleosome: Structural unit of chromatin, consisting of DNA wrapped around histone proteins.

Major Experiments Establishing DNA as Genetic Material

Griffith's Transformation Experiment

• Demonstrated that a substance from dead bacteria could genetically transform living bacteria.

• Suggested the existence of a "transforming principle," later identified as DNA.

Hershey and Chase Experiment

• Used bacteriophages labeled with radioactive isotopes to show that DNA, not protein, is the genetic material.

Chargaff's Rules

• Found that the amount of adenine equals thymine, and cytosine equals guanine in DNA.

• Led to the base-pairing rules: A pairs with T, C pairs with G.

Watson, Crick, Franklin, and Wilkins

• Determined the double helix structure of DNA using X-ray diffraction data.

Meselson and Stahl Experiment

• Demonstrated the semi-conservative model of DNA replication using isotopic labeling.

Structure of DNA and Nucleotides

• Nucleotide: The building block of DNA, consisting of a phosphate group, deoxyribose sugar, and a nitrogenous base (adenine, thymine, cytosine, or guanine).

• Double Helix: DNA consists of two antiparallel strands forming a right-handed helix.

• Base Pairing: Adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G) via hydrogen bonds.

• Sugar-Phosphate Backbone: The sides of the DNA ladder are formed by alternating sugar and phosphate groups.

DNA Replication Process

• Initiation: Replication begins at origins of replication, where helicase unwinds the DNA.

• Elongation: DNA polymerase synthesizes new DNA strands in the 5' to 3' direction. The leading strand is synthesized continuously, while the lagging strand is synthesized in Okazaki fragments.

• Enzymes Involved:

  • Helicase: Unwinds the DNA double helix.

  • Single-Strand Binding Proteins: Stabilize unwound DNA.

  • Primase: Synthesizes RNA primers.

  • DNA Polymerase III: Main enzyme for DNA synthesis in prokaryotes.

  • DNA Ligase: Joins Okazaki fragments on the lagging strand.

  • Topoisomerase: Relieves supercoiling ahead of the replication fork.

• Termination: Replication ends when the entire DNA molecule has been copied.

Equation for DNA Synthesis Direction:

$5' \rightarrow 3'$

DNA Repair Mechanisms

• Mismatch Repair: Corrects errors missed by DNA polymerase during replication.

• Nucleotide Excision Repair: Removes and replaces damaged DNA segments.

Chromosome Structure and Compaction

• Nucleosome: DNA wrapped around histone proteins, forming the basic unit of chromatin.

• Higher-Order Structures: Nucleosomes coil to form chromatin fibers, which further fold to form chromosomes.

• Telomeres: Repetitive DNA sequences at chromosome ends, protecting them from degradation.

Table: Key Enzymes and Their Functions in DNA Replication

Enzyme	Function
Helicase	Unwinds the DNA double helix
Single-Strand Binding Proteins	Stabilize unwound DNA strands
Primase	Synthesizes RNA primers
DNA Polymerase III	Synthesizes new DNA strands (prokaryotes)
DNA Ligase	Joins Okazaki fragments
Topoisomerase	Relieves supercoiling ahead of the replication fork

Virtual Learning Resources

• Pearson Modified Mastering Lesson 16 Assignment

• Chapter 16 BioFlix® Animation: DNA Replication

• Chapter 16, Figure 16-5 Walk Through: Addition of a Nucleotide to a DNA Strand

• Chapter 16, HHMI Biointeractive Video: Great Discoveries in Science: The Double Helix