Summary: Biochemistry And Bioinformatics

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• DNA Replication

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• What is needed for DNA synthesis in vitro?

  Prepare a DNA template, DNA polymerase, add dNTPs, protein fractions then measure over time and HELICASE

• What kind of labelling is used in order to measure DNA synthesis?

  Radioactive labelling

• What do the replicative DNA polymerases have in common (Pol α, Pol δ, and Pol ε) 

  Are B family polymerases because they have a low error rate and therefore high fidelity

• What are the differences between different replication DNA polymerases (Pol α, Pol δ, and Pol ε) 

  - Epsilon demonstrates high processivity
  - Alpha and delta interact together for DNA switching in the early phase of DNA replication 
  - Delta polymerase is able to interact with McM helicase because it is the first polymerase in the initiation of DNA repliation 

• What considerations do we need to make when we want to model a replication fork?

  Need to take into account for the protein-chromatin interactions called nucleosomes

• Define a replication fork

  Marks where DNA replication is occurring at specific sites in the DNA

• Name the proteins found in a replication fork

  DNA pol A
  DNA pol Delta
  Proliferating Cell Nuclear Antigen 
  Replication factor C
  Replication protein A
  Fen1 and Rnase H
  MCM helicase protein complex 
  GIN5 and Cdc45 proteins
  Polymerase epsilon

• The function of DNA polymerase alpha in DNA replication initiation is 

  A catalytic enzyme that is able to synthesize an RNA primer to offer the 3' end hydroxyl group for DNA pol to extend from 
  Starts DNA synthesis for both the leading and lagging strand 

• What is the function of polymerase delta for initiating DNA replication?

  The two subunit polymerase is able to catalyze the synthesis of DNA after DNA polymerase alpha. This is a sensible action because delta polymerase demonstrates proof-reading activity as it is able to remove wrong bases incorporated

• The function of the proliferating cell nuclear antigen (PCNA)

  Is able to clamp and therefore secure polymerase epsilon onto the DNA thereby, heightens processivity creating longer DNA strands and low frequency of spontaneous stopping of DNA synthesis