DNA Repair and Recombination Lecture Quiz

DNA Repair and Recombination

• Lecture date: 9/14/2024
• Presenter: Tobias Weinrich, PhD
• Affiliation: School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley

Learning Objectives

• Describe mechanisms ensuring accurate DNA replication
• Compare and contrast DNA damage types and excision repair methods
• Explain how DNA repair defects lead to cancer
• Summarize mechanisms for repairing double-strand breaks
• Explain mobile genetic elements, their transposition methods, and influence on gene expression
• Describe types of viruses and their genomes

Lecture Structure

• Fidelity of DNA replication
• DNA damage
• DNA repair mechanisms:
  • Single-strand – excision repair
  • Mismatch Repair
  • Base excision repair
  • Nucleotide excision repair
  • Double-strand breaks
    • Nonhomologous end joining (NHEJ)
    • Homologous recombination
• Mobile genetic elements
  • Transposons
  • Retrotransposons
• Retroviruses
• Viruses (DNA or RNA genome)
• Viral morphologies
• Viral cycle

Mutation Rate and DNA Damage

• Mutation: Permanent nucleotide sequence change in DNA (positive/neutral/negative)
• Mutation rate = copying errors x unrepaired DNA damage
• DNA replication fidelity:
  • Errors per nucleotide added during replication steps: -5'→ 3' polymerization: 1 in 10⁵ -3'→ 5' exonucleolytic proofreading: 1 in 10² -Strand-directed mismatch repair: 1 in 10³ -Combined error rate: 1 in 10¹⁰
• DNA damage:
  • Spontaneous: DNA tautomers, strand slippage, damage to individual bases
  • Induced by mutagens (physical and chemical):
    • Physical: UV radiation, ionizing radiation
    • Chemical: base analogues, base-modifying agents, intercalating agents
    • Biological: mobile genetic elements

Defects in DNA Repair

• Accumulated unrepaired DNA events over time
• Defects in repair mechanisms lead to increased mutation accumulation, potentially causing cancer

Table 5-2: Inherited Human Syndromes

• Presents various human conditions related to DNA repair deficiencies and their corresponding phenotypes (e.g., colon cancer, skin cancer, UV sensitivity, neurological abnormalities)

DNA Damage - Spontaneous Mutations

• Tautomeric forms: Rare alternate resonance structures of nitrogenous bases cause base pair mismatches
• Strand Slipping: DNA polymerase may replicate a short DNA segment twice, especially regions with highly repetitive DNA
• Trinucleotide repeat disorders: Diseases associated with repeat expansions
  • Specific diseases (fragile X syndrome, Friedrich ataxia, Huntington disease, myotonic dystrophy, spinal and bulbar muscular atrophy, spinocerebellar ataxia), their respective repeat sequences, and typical symptoms.

DNA Damage – Mutagens

• Base analogues: Resemble nitrogenous bases in structure, leading to different base pairings
• Base-modifying agents: Chemically alter DNA bases, creating adducts
• Intercalating agents: Intercalate between bases, distorting the local 3D shape of DNA
• Radiation:
  • UV radiation: Causes pyrimidine dimers (covalent bonds between adjacent thymidines)
  • Ionizing radiation: Removes electrons from biological molecules. Causes double-strand breaks.

Repair System

• Direct repair: Chemical reversion
• Excision repair systems:
  • Mismatch repair: Occurs during or immediately after replication, distinguishing parental/newly synthesized strands
  • Base excision repair
  • Nucleotide excision repair
  • Translesion DNA polymerase
  • Light-dependent repair
    • Pyrimidine dimers are primarily the target

Base Excision Repair

• DNA glycosylase removes base; AP endonuclease removes abasic nucleotide; Repair DNA Pol fills gap; DNA ligase seals the nick

Nucleotide Excision Repair

• Repair machinery recognizes DNA distortion; Excision nuclease cuts on each side; DNA helicase removes segment; Repair DNA polymerase fills gap; DNA ligase seals the nick
• Xeroderma pigmentosum: Defects in nucleotide excision repair leading to skin cancer

Double-Strand Repair

• Causes: Ionizing radiation, replication fork mishaps, strong oxidizing agents, metabolites (anticancer drugs)
• Repair mechanisms:
  • Nonhomologous end joining (NHEJ): Predominant method, but may introduce mutations
  • Homologous recombination: Flawless repair, no information loss

Nonhomologous End Joining (NHEJ)

• Repair process loses base pairs; introduces mutations by deletions
• Introns and most DNA being non-coding make this not as problematic as other types of damage
• Translocation – unlikely

Homologous Recombination

• Exchange of strands between separate DNA molecules, using the undamaged homologous chromosome as a template
• Flawless repair preserving genetic information
• BRCA-1/BRCA-2 defects linked to breast cancer risk

Replication Collapse in Homologous Recombination

• Replication collapse due to presence of "nicks" blocks DNA polymerase progress

Mobile Genetic Elements

• Transposons: Mobile genetic elements moving in a genome
  • When moving, transposons can change gene order, generate new information, or moderately repeat in the genome -Allow for homologous recombination, being a mechanism for repair and evolution -Molecular parasites: Cells cannot get rid of them; no apparent function except for maintenance -Encode enzymes for movement, including transposase, integrase, and reverse transcriptase.

DNA Transposons and Retrotransposons

• DNA transposons: Conservative (cut and paste) & replicative (copy and paste) transposition mechanisms
• Retrotransposons: Copy and paste transposition mechanism, utilizing RNA intermediate and reverse transcriptase

Viruses – DNA or RNA genome

• Viruses: Small parasites replicating only in host cells; examples listed
• Viral genomes: DNA or RNA, single-stranded or double-stranded. Examples of viruses with each type are included in Table 6-2.

Viruses – Morphologies

• Naked, enveloped, helical, icosahedral, complex morphologies are presented in the visual aids; examples are given in the visual aids (e.g., T4 phage, bacterial virus, Potato virus X, Adenovirus, human+ virus, Influenza virus)

Viruses – Cycle

• Obligate cellular parasites: Rely on cell machinery to replicate
• Replication cycle (stages of viral replication) illustrated through a diagram, showing adsorption, endocytosis, fusion, replication, transcription, etc.

Retroviruses – RNA Genome

• Retroviruses integrate into host cells through DNA by recombination with reverse transcriptase; steps in retroviral replication are shown.

Mobile Genetic Elements – β-globin Cluster

• Shows location of Alu and L1 elements within the human β-globin cluster, highlighting their frequency in our genomes. Percentage of genome composition is given.

Test your understanding of DNA repair mechanisms and the role they play in preventing cancer. This quiz covers topics such as DNA damage types, excision repair methods, and mobile genetic elements discussed in the lecture. Assess your knowledge of the fidelity of DNA replication and the effects of mutations.