11.2 DNA Replication

DNA replication is a crucial process that ensures genetic information is accurately copied and passed on to new cells. This complex mechanism involves various enzymes and steps, working together to create identical DNA molecules from a parent template.

The semiconservative model and bidirectional nature of DNA replication are key concepts to understand. These processes, along with the formation of Okazaki fragments, allow for efficient and accurate copying of genetic material in both prokaryotic and eukaryotic cells.

DNA Replication Models and Processes

Semiconservative model of DNA replication

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• Two strands of parent DNA molecule separate during replication
  • Each parent strand serves as template for synthesis of new complementary strand (template strand)
• Newly synthesized strands paired with respective parent strands
  • Forms two daughter DNA molecules
• Each daughter DNA molecule consists of one parent strand and one newly synthesized strand
  • Daughter molecules considered "semiconservative" as they contain half of original parent DNA (conserves one strand from parent)

Bidirectional nature of DNA replication

• DNA replication occurs simultaneously in both directions from origin of replication
  • Bidirectional replication speeds up process (allows for faster completion)
• Leading strand synthesized continuously in 5' to 3' direction
  • DNA polymerase synthesizes leading strand without interruption as it moves along template strand (no stopping and starting)
• Lagging strand synthesized discontinuously in short fragments called Okazaki fragments
  • DNA polymerase synthesizes lagging strand in 5' to 3' direction, but opposite direction of replication fork movement
  • Discontinuous synthesis due to antiparallel nature of DNA strands (strands run in opposite directions)

Okazaki fragments in DNA replication

• Okazaki fragments are short segments of DNA synthesized on lagging strand
  • About 100-200 nucleotides long in bacteria (1000-2000 in eukaryotes)
• Formation of Okazaki fragments necessary due to:
  1. Antiparallel nature of DNA (strands run in opposite directions)
  2. Unidirectional activity of DNA polymerase (only synthesizes in 5' to 3' direction)
• RNA primase synthesizes short RNA primers that provide starting point for DNA polymerase to initiate Okazaki fragment synthesis
• DNA polymerase I removes RNA primers and fills gaps between Okazaki fragments
• DNA ligase seals nicks between Okazaki fragments, creating continuous strand of DNA (joins fragments together)

Enzymes and Steps in DNA Replication

Key steps of bacterial DNA replication

1. Initiation: DNA helicase unwinds double-stranded DNA at origin of replication
   • Single-stranded DNA binding proteins (SSB) stabilize single-stranded DNA (prevents reannealing)
2. Primer synthesis: RNA primase synthesizes short RNA primers complementary to single-stranded DNA
   • Primers provide starting point for DNA synthesis (DNA polymerase requires primer to begin)
3. Elongation: DNA polymerase III (DNA pol III) extends primers, synthesizing new DNA strands
   • Leading strand synthesis occurs continuously, lagging strand synthesis occurs discontinuously through Okazaki fragments
4. Primer removal and gap filling: DNA polymerase I (DNA pol I) removes RNA primers and replaces with DNA
   • DNA pol I also fills gaps between Okazaki fragments (creates continuous strand)
5. Joining fragments: DNA ligase seals nicks between newly synthesized DNA fragments, creating continuous strand

Bacterial vs eukaryotic DNA replication

• Similarities:
  • Both use semiconservative replication (each parent strand serves as template for new strand synthesis)
  • Both have bidirectional replication with leading and lagging strands
  • Both require similar enzymes (helicase, primase, DNA polymerases, ligase)
• Differences:
  • Eukaryotes have multiple origins of replication, bacteria typically have single origin
  • Eukaryotic DNA replication occurs during S phase of cell cycle, bacterial replication occurs throughout cell cycle
  • Eukaryotes have multiple types of DNA polymerases (DNA pol α, δ, ε), bacteria primarily use DNA pol III
  • Okazaki fragments shorter in eukaryotes (100-200 nucleotides) compared to bacteria (1000-2000 nucleotides)

Rolling circle replication mechanism

• Alternative mechanism of DNA replication found in some viruses and plasmids
• Single-stranded DNA molecule replicated to form long, continuous strand with multiple copies of original sequence
• Process begins with nick in one strand of double-stranded DNA molecule
  • Nicked strand displaced and serves as template for synthesis of new complementary strand
• Newly synthesized strand continuously extended, forming long, linear DNA molecule with multiple copies of original sequence
• Long, linear DNA molecule then cleaved into individual units, each representing copy of original DNA molecule
• Important for replication of certain genetic elements:
  • Single-stranded DNA viruses (bacteriophages)
  • Plasmids in bacteria (extrachromosomal DNA)
  • Mitochondrial DNA in some eukaryotes (organelle DNA)

DNA Replication Fidelity and Chromosome Ends

• Complementary base pairing ensures accurate DNA replication
  • Adenine pairs with thymine, guanine pairs with cytosine
• Replication fork is the Y-shaped region where DNA strands separate for replication
• DNA polymerases have proofreading ability to correct errors during replication
  • Enhances accuracy of DNA replication
• Telomeres are specialized structures at chromosome ends
  • Protect chromosome ends from degradation and fusion