10 Things you need to know about Replication

Watson and Crick published their hypothesis for how DNA replicates in a second paper in 1958. Then, Matthew Meselson and Franklin Stahl devised a clever experiment that suggested that DNA replication is semiconservative. This experiment was growing E. coli bacteria in a nutrient medium that was rich in heavy isopotes of nitrogen then changing this medium that was rich in light isotope of nitrogen. They used density gradient centrifugation to analyze the density of DNA (cesium chloride solution) and they found out that layer of intermediate DNA was kept as generations had passed. In other words, DNA replication is semiconservative, but not conservative.

Prokaryotic cells and eukaryotic cells have the same semiconservative pattern of DNA replication. The only difference is that prokaryotic cells usually have only one replication origin while eukaryotic cells have multiple origins of replication. 

Replication Fork: the region where the enzymes replication a DNA molecule are bound to untwisted (region where helicase is attached)

Replication Bubble: the region where two replication forks are in close proximity to each other, oriducing a bubble in the replicating DNA.

Steps of DNA Replication

Initiation:

1. DNA helicase: the enzyme that unwinds double-helical DNA by disrupting hydrogen bonds
2. SS binding protein or SSBs(Single-Stranded binding protein): a protein that keeps separated strands of DNA apart/ keeps away from annealing
3. DNA gyrase: the bacterial enzyme that relieves the tension produced by the unwinding of DNA during replication
4. DNA primase: produce primers(a sequence of 10 to 60 RNA bases) which signals the DNA polimerase 3 

Elongation:

1. DNA polymerase 3: 

• recognizes RNA primers
• elongate new DNA strand 5' to 3' direction
• leading strand towards the fork; lagging strand (or Okazaki fragments) away from the fork

Termination:

1. DNA polymerase 1: an enzyme that replaces RNA primers with appropriate deoxyribonucleotides; proof reads and cut out a mistaken nucleotides acting as exonuclease.
2. DNA ligase: an enzyme that joins DNA fragments together by catalyzing the formation of a bond between the 3' hydroxyl group and a 5' phosphate group on the sugar-phosphate backbones.

Important Facts to know

• Deoxyribonucleoside triphosphates are added by DNA polymerase 3 then two phosphates are removed and reclycled again.
• New strands are formed starting from the bubble.