Chapter 16: The Structural Basis of Cellular Information: DNA, Chromosomes & the Nucleus

Chapter 16: The Structural Basis of Cellular Information: DNA, Chromosomes & the Nucleus

DNA Structure

  • Double-Stranded Nature:

    • DNA is composed of two strands that are anti-parallel, meaning they run in opposite directions.

    • The strands are oriented according to the sugar-phosphate backbone.

    • One strand runs from the 5′ to the 3′ direction, while the complementary strand runs from the 3′ to the 5′ direction.

Major and Minor Grooves of DNA

  • Groove Characteristics:

    • DNA has major and minor grooves which are regions of varied accessibility.

    • Proteins often bind at the major groove, where they can interact with specific sequences to regulate gene expression.

Types of DNA in the Nucleus

  • Major Forms of DNA:

    • DNA exists in three primary forms within the nucleus: A-DNA, B-DNA, and Z-DNA.

B-DNA

  • Characteristics:

    • Most Common Form:

    • This form is prevalent under physiological conditions.

    • Helical Structure:

    • Right-handed helix with approximately 10 base pairs per turn.

    • Dimensions:

    • Diameter ranges from 2 nm to 3.4 nm, with each base pair measuring about 0.34 nm apart.

A-DNA

  • Characteristics:

    • Condition for Formation:

    • Forms under dehydrated conditions or when DNA is hybridized with RNA.

    • Helical Properties:

    • Right-handed and more compact than B-DNA, being shorter and wider.

Z-DNA

  • Characteristics:

    • Formation Conditions:

    • Can form under high salt concentrations (high ionic strength).

    • May arise during negative supercoiling or when exposed to specific sequences like alternating purine-pyrimidine repeats, such as “CGCGCG”.

    • Helical Orientation:

    • This structure is characterized as left-handed.

Supercoiling of DNA

  • Definition:

    • Refers to the extra twisting of the DNA double helix, impacting accessibility for replication or transcription.

  • Types of Supercoiling:

    • Positive Supercoiling:

    • Right-handed, loosens helix, facilitating transcription.

    • Negative Supercoiling:

    • Left-handed, tightens helix, hindering access, and builds tension ahead of replication forks, necessitating relief.

Topoisomerases

  • Definition:

    • Enzymes that alleviate torsional stress in DNA by cutting and subsequently rejoining DNA strands.

  • Types of Topoisomerases:

    • Type I:

    • Cuts one strand of DNA without utilizing ATP.

    • Important during unwinding of DNA for replication/transcription.

    • Type II:

    • Cuts both strands and requires ATP for function, resolving knots particularly prior to cell division.

DNA Gyrase

  • Overview:

    • A specific type II topoisomerase found in prokaryotes and mitochondria.

    • Functions to induce negative supercoiling, thereby relieving positive supercoiling that arises ahead of replication forks and preventing over-winding and tangling of the DNA.

DNA Packaging

  • Nucleosome Formation:

    • DNA wraps around proteins known as histones to form nucleosomes, the fundamental units of chromatin.

    • Each nucleosome contains 146 base pairs of DNA.

Chromatin Structure

  • Definition:

    • Chromatin is a complex of DNA and associated proteins that organizes genetic material in eukaryotic cell nuclei.

  • Major Types of Chromatin:

    • Euchromatin:

    • Loosely packed, transcriptionally active.

    • Heterochromatin:

    • Constitutive:

      • Permanently condensed, includes structures like centromeres and telomeres.

    • Facultative:

      • Can switch between active and inactive states (e.g., X-chromosome inactivation).

Chromatin Dynamics During Cell Cycle

  • Mitosis/Meiosis:

    • Chromatin condenses into visible structures called chromosomes solely during prophase.

  • Interphase:

    • Chromosomes occupy distinct territories within the nucleus, each having specific subdomains.

The Cell Nucleus

  • Definition:

    • The nucleus functions as the control center of the cell, housing the cell's DNA.

  • Structure:

    • Surrounded by a nuclear envelope comprising two membranes.

  • Outer Membrane:

    • Continuously connected to the rough endoplasmic reticulum (ER).

  • Inner Membrane:

    • Anchors chromatin and possesses a nuclear lamina structure, with a substance filling the inner space.

Nuclear Pore Complexes

  • Functionality:

    • Comprises large protein assemblies that regulate transport across the nuclear envelope.

    • Allows passive transport of small molecules while controlling active transport for larger items, such as proteins and RNA.

  • Structure:

    • Each pore consists of a double ring of eight proteins surrounding a central channel protein, with fibers that form a basket-like structure on either side.

Import Mechanism of Proteins into the Nucleus

  • Nuclear Localization Signals (NLS):

    • Cargo proteins that require entry into the nucleus possess NLS sequences, which bind transport receptors (importin).

    • This complex carries the proteins through the nuclear pore complexes.

  • Ran-GTP Cycle:

    • Inside the nucleus, Ran-GTP binds to importin, causing the release of the cargo.

    • The importin-Ran-GTP complex is then exported back to the cytoplasm, hydrolyzing Ran-GTP into Ran-GDP, resetting the cycle.

    • Exportins functions like importin but take cargo outside of the cell with help of Ran-GTP

The Nucleolus

  • Function:

    • Primarily responsible for rRNA transcription, processing, and assembly of ribosomal subunits.

  • Dense Structure:

    • Lacks a membrane and contains:

    • rRNA genes (DNA)

    • rRNA molecules

    • Ribosomal proteins

    • Enzymes for rRNA processing.

  • Components of the Nucleolus:

    • Fibrillar Centers (FC):

    • Composed of ribosomal DNA (rDNA); the site of rRNA transcription.

    • Dense Fibrillar Component (DFC):

    • Contains new pre-rRNA and processing enzymes; site for rRNA processing.

    • Granular Component (GC):

    • Contains assembled ribosomal proteins and processed rRNA; site of ribosomal assembly.

  • Both the small and large ribosomal subunits are only assembled in the nucleolus and bind together during mRNA translation in the cytoplasm.

  • Nucleolar Stress:

    • Disruption in ribosome production (due to DNA damage, nutrient deprivation, or mutations) can lead to the swelling and fragmentation of the nucleolus, sometimes resulting in the formation of 'stress caps'— activating p53 and other stress responses that lead to cell cycle arrest or apoptosis.

Progeria (Hutchinson-Gilford Progeria Syndrome)

  • Causes:

    • Results from a mutation in the LMNA gene leading to the production of progerin, a defective form of mature lamin A. This disrupts the nuclear lamina and leads to misshapen nuclei and impaired chromatin organization.

  • Consequences:

    • Loss of heterochromatin, altered gene expression, defective DNA repair mechanisms, increased nucleolar stress, and premature cellular senescence. Senescence refers to a state in which a cell permanently ceases division while remaining metabolically active, contributing to aging and inflammation.

  • Research Advancement:

    • Longitudinal studies by NIH have facilitated the development of the first FDA-approved treatment for progeria, such as Lonafarnib, which acts as an orally active farnesyltransferase (FPTase) inhibitor, targeting mutated signaling pathways affecting cellular proliferation and migration, promoting vascular health.