PY411 Lectures

• DNA


  A molecule composed of two strands held together by hydrogen bonds between paired bases
• DNA


  • Double helix structure
  • Four bases: adenine, thymine, guanine, cytosine (Watson and Crick base pairing)
  • Base-pairing enables faithful copying of DNA
• DNA Replication


  1. Double helix opens at pre-determined sites called replication origins

  2. Replication bubble formed when DNA is unwound at origin of replication

  3. Eukaryotic cells have multiple sites of replication

  4. Helicase enzymes unwind dsDNA to form replication fork
• Unwinding of dsDNA by helicase

  Introduces positive supercoils into the DNA
• Relaxation of positive supercoils


  1. By type II topoisomerases: DNA gyrase introduces negative supercoils in bacteria

  2. Topoisomerase IV assists in relaxing positive supercoiling in bacteria

  3. Type I and II topoisomerases relax both positive and negative DNA torsional stress in eukaryotes
• Topoisomerase IV has a role in resolving interlinked DNA strands after replication in bacteria
• Quinolone antibiotics interfere with bacterial DNA replication and transcription by targeting DNA gyrase and Topoisomerase IV
• DNA Replication at Replication Forks


  1. Replication forks formed at origins of replication

  2. Leading strand synthesised continuously

  3. Lagging strand synthesised in Okazaki fragments

  4. DNA primase synthesises RNA primers for lagging strand synthesis
• DNA Synthesis


  • Deoxyribonucleotides added to 3'-hydroxyl end
  • Nucleotides enter as nucleoside triphosphates (dNTPs)
  • Phosphodiester bonds formed by DNA polymerase
• Lagging Strand Synthesis


  1. DNA polymerase adds to new RNA primer to start Okazaki fragments

  2. DNA polymerase finishes DNA fragment

  3. Old RNA primer erased and replaced by DNA

  4. DNA ligase joins new Okazaki fragments
• RNA


  • Single-stranded molecule, can fold into variety of shapes
  • Uracil instead of Thymine
  • Ribose sugar instead of deoxyribose
• Transcription


  1. Incorporation of nucleotides into mRNA from DNA template

  2. mRNA sequence corresponds to DNA coding strand

  3. Transcription initiated at promoter

  4. RNA polymerase moves 3'-5' on DNA template to synthesise 5'-3' mRNA

  5. Transcription stops at terminator sequence
• In prokaryotes, mRNA sequence is colinear with translated protein sequence
• In eukaryotes, mRNA must be processed to remove extra sequences before translation
• Types of RNA


  • mRNA
  • tRNA
  • rRNA
  • snRNA
  • miRNA
• Genetic Code


  • Universal, Degenerate, Non-overlapping
  • AUG is start codon, UAA/UAG/UGA are stop codons
  • Triplet codons in mRNA code for amino acids
  • tRNAs carry different amino acids based on anticodon
• Ribosome


  • Molecular machine that interprets the genetic code
  • Prokaryotic ribosomes are different from eukaryotic ribosomes
• Translation


  1. Initiation: Ribosome binds mRNA at start codon

  2. Elongation: Amino acids added to polypeptide chain via tRNA-mRNA codon interaction

  3. Termination: Stop codon reached, polypeptide released, ribosome dissociates
• Prokaryotic mRNAs are often polycistronic, while eukaryotic mRNAs are usually monocistronic
• Eukaryotic translation initiation


  mRNA bound to 40S ribosomal subunit via 5' cap, with help of initiation factors
• Prokaryotic translation initiation


  mRNA Shine-Dalgarno sequence aligns with 16S rRNA, with help of initiation factors
• Epigenetics


  • Changes in gene expression without altering DNA sequence
  • Includes DNA methylation, histone modifications, and non-coding RNAs
• Epigenetic changes


  Can be passed on to daughter cells or next generation
• Consequences of Epigenetics


  • Cell differentiation during development
  • Role in diseases like infections, cancers
  • Influenced by factors like diet, stress, toxins