3.3 The Nucleus and DNA Replication

The nucleus is the control center of the cell, housing our genetic material. It's surrounded by a double membrane that acts like a gatekeeper, allowing specific molecules in and out. This protective barrier ensures our DNA stays safe and organized.

Inside the nucleus, we find the nucleolus, chromatin, and nuclear matrix. These components work together to manage DNA, produce ribosomes, and support the nucleus's structure. Understanding the nucleus is key to grasping how our cells function and replicate.

The Nucleus

Structure and function of nuclear membrane

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• Double membrane structure encloses genetic material
  • Outer membrane continuous with rough endoplasmic reticulum facilitates communication and transport between nucleus and cytoplasm
  • Inner membrane contains unique proteins and lipids that regulate nuclear processes and maintain nuclear integrity
• Nuclear pores allow selective bidirectional transport of molecules (proteins, RNA) between nucleus and cytoplasm
  • Regulated by nuclear pore complexes that recognize and transport specific cargo
• Provides a protective barrier between genetic material and cytoplasm preventing unauthorized access and maintaining optimal environment for DNA
• Maintains nuclear shape and integrity by providing structural support and resisting mechanical stresses

Key components of nucleus

• Nucleolus serves as site of ribosomal RNA (rRNA) synthesis and ribosome subunit assembly
  • Appears as dense, spherical structure within nucleus due to high concentration of rRNA and proteins
  • Plays crucial role in protein synthesis by producing ribosomes
• Chromatin consists of DNA and associated proteins (histones) in non-dividing cells
  • Exists in two forms: euchromatin (less condensed, transcriptionally active) and heterochromatin (highly condensed, transcriptionally inactive)
  • Chromatin state regulates gene expression by controlling access to DNA
• Nuclear matrix provides structural support for nucleus as a protein scaffold
  • Plays a role in DNA replication, transcription, and repair by organizing chromatin and localizing enzymes

DNA organization in nucleus

• DNA wrapped around histone proteins to form nucleosomes, the basic unit of chromatin
  • Each nucleosome consists of eight histone proteins (two each of H2A, H2B, H3, and H4) that DNA wraps around
  • Linker DNA connects adjacent nucleosomes and is associated with histone H1
• Nucleosomes further coiled and condensed to form chromatin fibers
  • 30 nm fibers (solenoid structure) formed by interactions between nucleosomes and histone H1
  • Compacts DNA and regulates accessibility for transcription
• Higher-order chromatin packaging organizes chromatin into loops and domains
  • Chromatin loops and domains associated with nuclear matrix
  • Allows for efficient storage and regulation of genetic material (approximately 2 meters of DNA in each nucleus)
• Telomeres protect chromosome ends from degradation and fusion

DNA Replication

Steps of DNA replication

1. Initiation begins when origin of replication is recognized by initiator proteins
   • DNA helicase unwinds double helix, creating replication fork
   • Single-stranded DNA binding proteins stabilize single-stranded DNA and prevent reannealing
2. Elongation involves synthesis of new DNA strands
   • DNA primase synthesizes short RNA primers complementary to template strands
   • DNA polymerase III extends primers, synthesizing new DNA strands in 5' to 3' direction
     • Leading strand synthesized continuously
     • Lagging strand synthesized discontinuously as Okazaki fragments
   • DNA polymerase I replaces RNA primers with DNA nucleotides ensuring complete DNA synthesis
3. Termination occurs when entire genome is duplicated
   • DNA ligase seals nicks between Okazaki fragments on lagging strand creating continuous strand

• Importance in cell division
  • Ensures accurate transmission of genetic information to daughter cells by replicating DNA
  • Maintains genome integrity and stability preventing mutations and errors
  • Essential for cell growth, development, and repair by providing genetic blueprint

DNA replication mechanism

• Semiconservative replication ensures each daughter cell receives one parental DNA strand and one newly synthesized strand
• Base pairing (A-T, G-C) guides accurate DNA synthesis, resulting in complementary strands
• Deoxyribonucleotides are joined by phosphodiester bonds to form the DNA backbone