Topic 4: Central dogma

• Nucleic acids are polymeric macromolecules forming the chemical basis for the transmission of genetic trait

  
• Two main classes of nucleic acids

  • deoxyribonucleic acid (DNA)
  • ribonucleic acid (RNA)

  
• Nucleotide


  Monomer made of 5-carbon sugar, nitrogenous base, and phosphate group

  
• Nucleoside


  Sugar + Base
• Nitrogenous bases


  • Adenine (A)
  • Guanine (G)
  • Thymine (T)
  • Cytosine (C)
  • Uracil (U)

  
• Purines

  Adenine (A) and Guanine (G)

  
• Pyrimidines


  Thymine (T), Cytosine (C) and Uracil (U)

  
• Base pairing in DNA

  • G ≡ C (3 H-bond)
  • A = T (2 H-bond)

  
• Total concentration of purines equals the concentration of pyrimidines in DNA

  
• 1. bonds between nucleotides are the key to the specificity of all nucleic acid-based tests used in the molecular laboratory

  
• GC rich region


  Higher melting temperature (Tm)

  
• AT rich region


  Lower Tm
• Nucleotide


  Nucleoside with a phosphate group attached at carbon atom 5'

  
• Polynucleotide


  Two nucleotides covalently bonded with a 3'-5' phosphodiester bond

  
• General structure of DNA

  • Two polynucleotide strands coiled in a double helix
  • Complementary and anti-parallel sugar-phosphate backbones
  • Bases oriented towards central axis, forming H-bonds and stacking interactions

  
• Major DNA conformations


  • A-form
  • B-form
  • Z-form
• Differences between DNA conformations

  • Helix sense, base pairs per turn, diameter of helix, distance between adjacent base pairs, rotation per base pair

  
• Functions of DNA


  • Store genetic information
  • Direct RNA transcription
  • Contain instructions for development, survival, and reproduction
• Denaturation of DNA


  Loss of the helical structure (double strand to single strand)

  
• Methods to denature DNA

  • Thermal denaturation
  • Alkaline method
  • Other denaturing agents
• Hypochromic effect


  Decreasing ability to absorb light
• Hyperchromic effect


  Increasing ability to absorb light
• Melting temperature (Tm)


  Temperature at which half of the DNA molecules are denatured

  
• Renaturation of DNA (Annealing)

  Rewinding of denatured DNA strands to form double helix

  
• Central Dogma of Molecular Biology


  Genetic information flows from DNA to RNA to protein

  
• Transcription


  DNA template to RNA by RNA Polymerase

  
• Translation


  RNA to protein
• Naked DNA is roughly 2 nm in diameter, but the length of a stretched single molecule may be up to several dozens of centimetres
• DNA compaction in prokaryotes and eukaryotes

  • Prokaryotes: nucleoid-associated proteins
  • Eukaryotes: DNA wrapped around histone proteins to form nucleosomes and chromatin

  
• Kingdoms of Life


  • Monera
  • Protista
  • Fungi
  • Plantae
  • Animalia
• Prokaryotes are classified into Bacteria and Archaea
• Differences between prokaryotic and eukaryotic cells

  • Presence of membrane-bound organelles, nuclear envelope, cytoskeleton, and complex internal structures in eukaryotes
• Nuclei


  Eukaryotic nuclei are ~10 μm in diameter and contain 46 chromosomes (2× 3.3G base pairs), consisting of ~2.2 m of DNA in total
• If DNA is stored naked inside a nucleus or a cell, it would become tangled
• Prokaryotes


  • Nucleoid-associated proteins resemble the functions of the histone proteins found in eukaryotes
• Eukaryotes


  • Double helix DNAs are wrapped around spools of histone proteins to form nucleosomes, which package together to produce chromatin

  
• Kingdoms of Life


  • Monera
  • Bacteria
  • Archaebacteria
• A classification for living organisms can be 5-Kingdom or 6-Kingdom
• Prokaryotic and eukaryotic cells have differences and exceptions
• Eukaryotes include animal and plant cells