week 1

• Why is it important to maintain high sequence similarity during DNA replication?

  To ensure genetic fidelity and prevent mutations
• What is the role of DNA polymerase in DNA replication?

  To synthesize new DNA strands by adding nucleotides
• What happens to the amino acid sequence if there is a change in the nucleic acid sequence?

  It can lead to changes in protein shape, function, or expression
• What mechanisms preserve DNA integrity in eukaryotes?

  • Presence of a nuclear envelope
  • Condensation of chromatin
  • Semi-conservative replication
  • Chromosomal structures: telomeres and centromeres
• What are telomeres?

  Repeating sequences of DNA that protect chromosome ends
• What is the function of the nuclear envelope?

  To separate the contents of the nucleus from the cytoplasm
• What is the structure of chromatin composed of?

  Two molecules of each of four histones (H2A, H2B, H3, H4)
• How does DNA wind around histones to form nucleosomes?

  146 nucleotides of DNA wind 1.65 times around the histone core
• What is the role of single-stranded binding (SSB) proteins during DNA replication?

  To prevent secondary structures from forming on single-stranded DNA
• What are the steps of DNA replication?

  1. Separation of the double helix into two strands
  2. DNA Primase synthesizes RNA primers
  3. DNA Polymerase adds nucleotides to the template strand
  4. On the lagging strand, Okazaki fragments are formed and joined by DNA ligase

  
• What is the function of DNA helicase in DNA replication?

  To separate the double helix into two template strands
• What is the direction of DNA synthesis by DNA polymerase?

  5' to 3' direction
• What are Okazaki fragments?

  Short sections of DNA synthesized on the lagging strand
• What is the role of DNA ligase in DNA replication?

  To join Okazaki fragments together
• How do replication forks function in DNA replication?

  They are bidirectional, synthesizing DNA continuously on the leading strand and discontinuously on the lagging strand
• What is the function of topoisomerase during DNA replication?

  To relieve torsional stress caused by the unwinding of DNA strands
• What is the difference between Type I and Type II topoisomerases?

  Type I nicks one strand, while Type II forms a double strand break
• What is the role of the sliding clamp in DNA replication?

  To keep DNA polymerase attached to the DNA template
• What happens when the final RNA primer cannot be replaced with DNA?

  It leads to incomplete replication of the lagging strand
• What is the function of telomerase in DNA replication?

  To extend the telomeres at the ends of chromosomes
• What is the proofreading ability of DNA polymerase?

  It allows the enzyme to remove incorrectly paired nucleotides
• What are the types of DNA repair mechanisms?

  • Nucleotide Excision Repair (for pyrimidine dimers)
  • Base Excision Repair (for deamination)
  • Mismatch Repair (for replication errors)
• What happens if DNA repair mechanisms fail?


  It generates a variant in the gene sequence
• What is depurination in DNA?

  A loss of a base from the DNA sequence
• What effects can a deletion of a base due to depurination have on protein sequence?

  It can cause a frameshift mutation or a premature stop to translation
• What are the genetic disorders associated with inefficient DNA repair?

  • Cancer
  • Genetic syndromes
  • Other hereditary diseases
• What is the consequence of failure to remove incorrectly paired bases during DNA proofreading?

  It leads to a "mismatched" pair in the DNA sequence.
• What happens after a mismatched pair is detected in DNA?

  A repair is attempted.
• What determines the repair mechanism for a DNA error?

  The type of error that has been incorporated.
• What are the types of DNA repair mechanisms mentioned?

  • Nucleotide Excision Repair (pyrimidine dimer)
  • Base Excision Repair (deamination)
  • Mismatch Repair (replication errors)
• What is the result of failure in DNA repair mechanisms?


  It generates a variant in the gene sequence.
• What occurs during depurination in DNA?

  There is a deletion of a base without changing the base pair sequence.
• What potential effects can a deletion of a base have on the protein sequence?

  It can lead to a single amino acid change, frameshift mutation, premature stop to translation, or changed splicing.
• What is initiated when there is a break in a single strand of the DNA double helix?

  Single Strand Break Repair is initiated.
• What happens when both strands of the double helix break?

  Double Strand Break Repair is initiated.
• What are the two mechanisms of Double Strand Break Repair?

  • Non-Homologous End Joining: more error-prone, often occurs outside S-phase.
  • Homologous Recombination: uses the second homologous chromosome as a template, no loss of nucleotides.

  
• Where does crossing over occur during meiosis?

  During Prophase I.
• What is the purpose of crossing over in meiosis?

  To generate diversity.
• What are linked genes?

  Genes that are located physically close to one another on a chromosome and are part of a linkage group.
• What is the effect of the proximity of genes on a chromosome during crossing over?

  The closer genes are to one another, the lower the chance they will be separated during crossing over.