Chromosomes, DNA Replication, and Repair

Posted on Jun 20, 2024 in Biology

Chromosomes and DNA Organization

Transposable Elements (TE) (“Jumping genes” or “transposons”) make up >40% of the human genome.

Eukaryotic Chromosome Structure

  • Telomeres: Located at chromosome ends, protecting against genetic material loss during replication and preventing chromosome fusion.
  • Centromere Types:
    • Monocentric: Single centromere per chromosome (most common).
    • Holocentric: Multiple centromeres per chromosome (e.g., C. elegans, plants).

Genetic Information Storage

  • Prokaryotes: 1:1 ratio of gene length to mRNA length.
  • Eukaryotes: Genes are much longer than mRNA due to intron removal (prokaryotes lack introns). Complex eukaryotes have genes spaced further apart with more non-coding DNA in between, while simpler eukaryotes resemble prokaryotes in gene spacing.

DNA Packaging

DNA is packaged with histone proteins to form nucleosomes, which bundle into chromatin. Chromatin forms loops, condensing further into condensed chromatin loops, ultimately forming chromosomes.

DNA Replication

Cell Cycle and Replication Regulation

  • Cell Cycle: Regulates pre-replication and initiation complexes.
  • S Phase: DNA replication occurs.
  • Cyclin-Dependent Kinases (CDKs): Regulate DNA replication by binding to the Origin of Replication (ORC) and initiating replication.
  • ORC, Cdc6, Cdt1, and MCM Complex: Orchestrate the assembly and activation of the helicase, unwinding DNA for replication.
  • Cdt1 and Cdc6 Degradation: Prevents excessive replication after initiation.
  • 3D Configuration: Essential for molecular binding and proper replication processes.

Replication Bubble

  • Multiple Origins: Present in eukaryotic cells, while prokaryotic cells have only one.
  • Leading Strand: Synthesized continuously in the 5′ to 3′ direction towards the replication fork.
  • Lagging Strand: Synthesized discontinuously as Okazaki fragments in the 5′ to 3′ direction, away from the replication fork.
    • Okazaki fragments are formed due to the need for DNA polymerase to wait for the parent strand to unwind.
    • Each fragment has a primer that is eventually removed and replaced with DNA.

Telomeres and Chromosome Shortening

  • Eukaryotic chromosome ends shorten with each replication round.
  • Telomerase: A ribonucleoprotein that prevents chromosome shortening by adding telomeric repeats to the ends.
    • Active telomerase prevents shortening; most cells cease expression after embryonic development.
    • Germ cells, somatic stem cells, and cancer cells maintain telomerase activity, contributing to their immortality.

DNA Mutations and Repair

Types of Mutations

  • Endogenous (Internal):
    • Spontaneous mutations: Deamination, depurination.
    • Replication slippage: Errors during replication, such as loops in the template strand.
  • Exogenous (External):
    • Industrial pollutants
    • Tobacco smoke
    • Food-related mutagens
    • UV light

DNA Proofreading and Mismatch Repair (MMR)

  • DNA Proofreading: Corrects errors during replication with an error rate of about 1 in 100,000 nucleotides.
    • Identifies incorrect base pairs through 3D configuration.
    • The daughter strand is nicked, a section is digested, and DNA polymerase replaces the incorrect nucleotides. Ligase seals the backbone.
    • In bacteria, methylation distinguishes the parent strand, as the daughter strand is methylated after replication.
  • UV Damage Repair:
    • UV light causes pyrimidine dimerization (mainly T-T), distorting the helix and blocking replication.
    • UvrA: Identifies dimerization within the UvrA-UvrB complex.
    • UvrB: Recruits UvrC, forming a complex that cleaves DNA on both sides of the damage.
    • UvrD: Removes the damaged fragment.

Meiotic Recombination and DNA Repair

Meiotic Recombination: Increases genetic diversity through the exchange of genetic material between homologous chromosomes during meiosis.

Meiosis and Recombination

  • Prophase I: Homologous chromosomes align, and chiasmata (crossing-over points) become visible.
  • Synaptonemal Complex: Forms between chromatids of homologous chromosomes, facilitating recombination.
  • Zygotene: Chromosomes pair with homologs along the synaptonemal complex, forming a bivalent or tetrad.
  • Pachytene: Full synapsis of homologs occurs, and recombination nodules appear along the synaptonemal complex.

Double-Strand Break (DSB) Model of Recombination

  • Spo11: Creates a DSB, and the Spo11-Dmc1 complex initiates strand degradation at the break, yielding single-stranded ends.
  • Strand Exchange: Opposing chromatids exchange DNA segments to maintain complementarity.
  • Holliday Junction: A four-way DNA junction formed during recombination, where single strands are exchanged between homologous chromatids.

DSB Repair

  • DSBs are hazardous, potentially leading to chromosomal rearrangements, cell death, or cancer.
  • Meiotic recombination utilizes homologous chromosomes for DSB repair.
  • Non-Homologous End Joining (NHEJ): A repair mechanism used when a homologous template is unavailable, potentially leading to genetic information loss but preferable to an unrepaired DSB.

Consequences of DNA Repair Gene Mutations and Cancer

Clonal Expansion and Mutation Accumulation

  • Mutations in DNA repair genes can lead to the accumulation of mutations in daughter cells.
  • Multiple Parallel Clonal Expansions:
    • An initial mutation leads to the expansion of a cell population carrying that mutation.
    • Subsequent mutations arise in subsets of these cells, leading to further clonal expansions with different mutation combinations.
    • This process continues, resulting in a heterogeneous tumor cell population with various mutations.

Oncogenes and Tumor Suppressor Genes

  • Initial mutations often affect oncogenes or tumor suppressor genes, disrupting normal cell growth and proliferation control.
  • Oncogenes: Mutated genes that promote excessive cell growth and proliferation.
  • Tumor Suppressor Genes: Genes that normally inhibit uncontrolled cell growth; their loss can lead to cancer.
    • Gatekeepers: Regulate cell cycle progression.
    • Caretakers: Maintain genome integrity.

DNA Damage Response

ATM and ATR Kinases

  • ATM (Ataxia Telangiectasia Mutated): Activated by double-strand breaks, phosphorylating specific substrates involved in DNA repair and cell cycle arrest.
  • ATR (ATM and Rad3-related): Responds to UV lesions, stalled replication forks, and some ATM substrates, activating downstream pathways for DNA repair and cell cycle control.

p53: Guardian of the Genome

  • p53: A crucial tumor suppressor gene and a key target of ATM and ATR kinases.
  • Activated by DNA damage and hyperproliferative stress.
  • Induces cell cycle arrest or programmed cell death (apoptosis) in response to damage, preventing the propagation of damaged cells.
  • p53 Loss of Function (LOF): Common in various cancers, either as an initial driver mutation or a later event contributing to tumor progression.

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