bio120 sample

• DNA replication


  The process by which a DNA molecule is copied to produce two identical DNA molecules

  
• Video of DNA replication machinery


  • https://dnalc.cshl.edu/view/15478-DNA-replication-3D-animation-with-sound-effects-only.html
• Same animation, but with narration


  • https://dnalc.cshl.edu/view/15509-DNA-replication-animation-3D-animation-with-basic-narration.html
• Watson and Crick's model for DNA replication

  It is referred to as "semi-conservative" replication

  
• Three proposed models of replication at the time

  • semi-conservative
  • conservative
  • dispersive

  
• Conservative


  Refers to if the original double helix is retained or not following replication
• Meselson and Stahl Experiment

  1. Grew bacteria in medium containing 15N to make all their DNA heavy

  2. Put them in 14N and let them grow, so newly made DNA is light and previous DNA is heavy

  3. Sampled over time and looked at relative proportions of 14N and 15N

  
• Isotopes


  Differ in the number of neutrons, allowing separation using centrifugation
• Meselson and Stahl video


  • https://www.youtube.com/watch?v=yDQg7uXShUs
• Appearance of heavy, hybrid, and light DNA bands after centrifugation


  • https://en.wikipedia.org/wiki/Meselson%E2%80%93Stahl_experiment
  • https://www.khanacademy.org/science/biology/dna-as-the-genetic-material/dna-replication/a/mode-of-dna-replication-meselson-stahl-experiment

  
• Meselson and Stahl's experiment showed that DNA replication is semi-conservative

  
• Challenges to replicating DNA

  • Separate the two strands, pull them apart, and keep them apart
  • Unwind the double helix
  • Make a copy of each strand at the same time...in opposite directions (because they are antiparallel)
  • Don't make any mistakes while you're at it

  
• DNA


  Deoxyribonucleic acid, a polynucleotide (a polymer of nucleotides)

  
• Four nucleotides in DNA

  • Adenine
  • Guanine
  • Cytosine
  • Thymine

  
• Covalent and hydrogen bonds in DNA

  • Covalent bonds in the sugar-phosphate backbone
  • Hydrogen bonds between bases of a base pair

  
• DNA strands are polar


  Having 3' and 5' ends, referring to the carbon position on the ribose

  
• DNA polymerase synthesizes the new strand from the template strand

  Adds nucleotides at the 3' end

  
• Nucleotide


  The general term, the specific term is deoxyribonucleoside triphosphate (dNTP)

  
• DNA Polymerase "Hand" Model


  Active site where new nucleotides are added
• Origin of replication (ORI)


  Where DNA replication begins, forming a replication bubble flanked by two replication forks

  
• Leading strand, lagging strand, Okazaki fragment


  Terms describing the basic pattern of DNA synthesis

  
• Synthesis is bidirectional because DNA polymerase can only add at the 3' end
• Summary of enzymes for DNA replication

  • Helicase
  • Single-stranded binding proteins
  • Topoisomerase
  • Primase
  • DNA polymerase III
  • DNA polymerase I
  • Sliding clamp
  • DNA ligase

  
• DNA polymerase III is the main replication enzyme in E. coli
• DNA polymerase I uses its 5' to 3' exonuclease activity to remove the RNA of the previously synthesized Okazaki fragment, and uses its 5' to 3' polymerization activity to replace the RNA nucleotides with DNA nucleotides

  
• Sliding clamp


  Tethers DNA polymerase III to the DNA template, making replication more efficient
• DNA ligase seals the nick left between adjacent fragments after RNA primers replaced with DNA