19. DNA replication

Last updated on January 11, 2020 at 12:44


  • Nucleosomes are lengths of DNA wound around histones, a type of protein
  • There are five types of histones. H1, H2A, H2B, H3 and H4
  • Nucleosomes coil into 30 nm fibres, which coils on itself many times to become the chromatids
  • The more coiled DNA is around histones, the harder the DNA is to transcribe from. Chromatin remodelling complexes, like SWI/SNF control how coiled the DNA is, to control the rate of transcription.
  • DNA can only be synthesized in the 5’ -> 3’ direction
  • Primers are synthesized by primase and removed by DNA polymerase I
  • Aspartate and Mg2+ are needed for DNA elongation
  • There are three types of DNA polymerases, the enzymes that replicate DNA. DNA polymerase III has the highest processivity
  • Proofreading is done by the 3’ -> 5’ exonuclease activity of DNA polymerase
    • DNA polymerase I, II and III in bacteria have proofreading
    • DNA polymerase δ and ε in eukaryotes have proofreading

DNA replication is complicated

DNA strands have direction, which means they’re not symmetrical. They have one 5’ end, and the other end is called the 3’ end. The two parallel strands in the DNA helix are oriented in the opposite direction, as seen on the blue strands on the figure on the right. When DNA should be replicated, these two strands has to be separated, so each of them can serve as a template for the two new strands.

A schematic of how DNA replication is performed. Note that lagging and leading strand refer to the red strands, not the blue.

DNA is wound around proteins called histones. There exist five main types of histones, H1, H2A, H2B, H3 and H4. A complex of DNA around a histone is called a nucleosome. Each nucleosome is composed of 8 histones. The nucleosome coils into a fibre called the 30nm fibre, which coils even more to become the chromatid. The more tightly wound DNA is around the histone, the harder it is to transcribe from. The DNA-histone interaction therefore has big effects on gene expression, as we’ll see later.

DNA polymerase
Gene that encodes it polA polB polC
Has proofreading (3’ -> 5’ exonuclease) Yes Yes Yes
Has 5’ -> 3’ exonuclease Yes No No
Speed Low Low High
Processivity Low Slightly higher Very high

DNA polymerase is the enzyme that performs the replication. There are three types, the differences of which are shown in the table above (the table shows the prokaryotic DNA polymerases, not the eukaryotic ones). Processivity is a measure of how many nucleotides it can produce before the protein dissociates from the DNA. Because DNA pol III has the highest processivity, it’s the one that’s used for synthesis of both the leading and the lagging strand. DNA pol I and II are used for repair, and filling in gaps.

They all have proofreading (3’ -> 5’ exonuclease) activity. This means that if the DNA polymerase inserts a wrong or damaged base by accident, it will remove it, insert the correct base, and then continue replicating. This is because exonucleases can remove nucleotides on the end of a DNA-strand.

Because DNA polymerase only can synthesize DNA in the 5’ to 3’ direction, and not the 3’ to 5’ direction, something clever must be done to create the new strand that is to go in the 3’ to 5’ direction (check the figure above). This is solved by creating small fragments of DNA (in the 5’ to 3’ direction) with spaces in between them (“nicks”), which DNA ligase then binds together. This is why this strand is called the “lagging” strand, because it is synthesized in small parts at a time.

DNA polymerase cannot start the replication without some nucleotides being present. These nucleotides, called a primer, are synthesized by primase. This primer is actually RNA, not DNA, and is removed by DNA polymerase I after DNA pol III has started synthesis of the new strands.

There are many proteins present in the replication fork, all needed for successful DNA replication. They are helicase, which unwinds the double stranded DNA into two single strands, DNA gyrase, which uncoils the supercoiled DNA to help helicase, single-strand binding protein (SSB), which binds the two single strands to keep them stable and separated, primase, DNA polymerase I and III and DNA ligase. 7 in all. They all have enzymatic activity, except for SSB, which just binds to stuff.

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18. Genes and chromosomes

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20. DNA repair

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