DNA Replication Notes (Biology Honors)

Why Replicate DNA?

• DNA contains the information for imperative characteristics and codes for making proteins.
• DNA is found in the nucleus of eukaryote cells and in the cytosol of prokaryotes.
• Cells must replicate their DNA before dividing to ensure each daughter cell has a complete set of genetic information.
• Without replication, cell division would result in cells lacking the necessary code to function.

DNA Structure

• DNA has repeating subunits called monomers or nucleotides, each with a phosphate group, a sugar (deoxyribose), and a nitrogen base.
• The four nitrogen bases in DNA are adenine (A), thymine (T), cytosine (C), and guanine (G).
• Adenine and guanine are purines (two-ring structure), while cytosine and thymine are pyrimidines (one-ring structure).
• A purine always pairs with a pyrimidine: A with T, and C with G.
• DNA is double-stranded, forming a double helix structure.
• The sides of the DNA molecule consist of a backbone made of alternating sugar and phosphate molecules.
• The nitrogen bases are on the inside, forming hydrogen bonds to link the two strands.
• A and T form two hydrogen bonds (A=T) , while C and G form three hydrogen bonds (C≡G) . Thus, a t two c g three.
• DNA strands are complementary; knowing one strand allows prediction of the other.

DNA Replication Overview

• DNA replication occurs in the nucleus during the S phase of interphase.
• The process follows a semiconservative model, where each new DNA molecule contains one original strand and one newly synthesized strand.
• The original DNA strands serve as templates for creating complementary strands.
• The result is two identical DNA molecules, each with one old and one new strand (daughter strands).

Enzymes Involved in DNA Replication

• Helicase: Unzips the DNA by breaking hydrogen bonds and unwinding the double helix, creating a replication fork.
• Topoisomerase: Relieves tension ahead of the replication fork by creating temporary nicks in the helix, preventing the DNA from getting too tightly wound and breaking.
• Primase: Synthesizes short RNA primers that provide a starting point for DNA polymerase to begin replication.
• DNA Polymerase: Adds free nucleotides to the template DNA, matching complementary bases (A with T, C with G). It also proofreads and corrects any base pairing mistakes.
• Ligase: Joins DNA fragments together, including Okazaki fragments on the lagging strand. It also fixes any broken bonds in the DNA.

Detailed Enzyme Functions

• Helicase:
  • Unwinds and separates the double-stranded DNA by breaking hydrogen bonds.
  • Creates a replication fork, which is the point where DNA separation occurs.
• Topoisomerase:
  • Relieves torsional stress ahead of the replication fork.
  • Prevents the DNA from supercoiling and breaking by creating temporary nicks.
• DNA Polymerase:
  • Adds free nucleotides to create a new DNA sequence complementary to the template strand.
  • Matches complementary bases (A with T, C with G).
  • Proofreads the new strand and corrects errors, though not perfectly (leading to DNA mutations).
• Primase:
  • Synthesizes RNA primers.
  • These primers are short sequences of RNA that provide a starting point for DNA polymerase.
  • DNA polymerase recognizes these primers and begins adding nucleotides from there.
• Ligase:
  • Joins Okazaki fragments on the lagging strand.
  • Seals nicks in the DNA by creating phosphodiester bonds.

Leading vs. Lagging Strand

• DNA polymerase can only add DNA bases in the 5' to 3' direction.
• The leading strand is synthesized continuously in the 5' to 3' direction towards the replication fork.
• The lagging strand is synthesized discontinuously in the 5' to 3' direction away from the replication fork, resulting in Okazaki fragments.
• Okazaki fragments are short DNA fragments on the lagging strand that are later joined together by DNA ligase.

Replication Process

• Origin of replication is identified.
• DNA strands separate using helicase.
• Primers are made by primase.
• Elongation occurs as DNA polymerase adds nucleotides, creating longer fragments.
• Termination occurs when the process is complete, and there's a specific sequence that tells the polymerase that it's time to stop.
• Ligase seals up all the little parts.

Detailed Replication Steps

• Initiation:
  • Helicase unwinds and separates the DNA strands.
  • Topoisomerase relieves tension to prevent supercoiling.
  • Single-stranded binding proteins prevent the strands from re-annealing.
  • Primase synthesizes RNA primers.
• Elongation:
  • DNA polymerase adds nucleotides in the 5' to 3' direction.
  • The leading strand is synthesized continuously.
  • The lagging strand is synthesized discontinuously, forming Okazaki fragments.
  • DNA polymerase proofreads and corrects errors.
• Termination:
  • Replication forks meet.
  • DNA polymerase detaches.
  • Ligase seals the gaps between fragments.

Anti-Parallel Strands

• DNA strands run anti-parallel to each other.
• One strand runs 5' to 3', while the other runs 3' to 5'.
• The 5' and 3' designations refer to the carbon atoms on the deoxyribose sugar.
• Replication can only occur in the 5' to 3' direction.

Implications of Errors

• If mismatched base pairs occur (e.g., A paired with C), the DNA helix can be distorted.
• DNA polymerase proofreads to minimize errors, but mutations can still arise. These mutations can alter protein synthesis or have no effect.

Multiple Origins of Replication

• Chromosomes have multiple origins of replication to speed up the replication process.
• Replication bubbles form at each origin and eventually merge.