Questions: 10. Compare and contrast PCR and DNA replication in vivo. Explain the biochemical basis for any differences, including the type of primers and which enzymes are required in each case. (PCR is fair game for the exam.)

PCR (Polymerase Chain Reaction) and DNA replication in vivo are both processes that involve the synthesis of DNA, but they differ in several key aspects, including their purpose, conditions, and the biochemical components involved.

1. Purpose and Context:

   • PCR: This is an artificial method used in laboratories to amplify specific segments of DNA. It is used for various applications such as cloning, sequencing, and forensic analysis.
   • DNA Replication in Vivo: This is a natural process that occurs in living cells to duplicate the entire genome before cell division, ensuring that each daughter cell receives a complete set of genetic information.

2. Primers:

   • PCR: Uses synthetic DNA primers. These are short, single-stranded DNA sequences that are designed to anneal to specific sequences flanking the target DNA region. They provide a starting point for DNA synthesis.
   • DNA Replication in Vivo: Uses RNA primers. These are short RNA sequences synthesized by the enzyme primase. They are later removed and replaced with DNA.

3. Enzymes:

   • PCR: The main enzyme used is Taq polymerase, a heat-stable DNA polymerase derived from the bacterium _Thermus aquaticus_. It synthesizes new DNA strands by adding nucleotides to the 3' end of the primers.
   • DNA Replication in Vivo: Involves several enzymes, including DNA polymerase (e.g., DNA polymerase III in prokaryotes), helicase (to unwind the DNA double helix), primase (to synthesize RNA primers), and ligase (to join Okazaki fragments on the lagging strand).

4. Conditions:

   • PCR: Conducted in vitro (outside a living organism) and involves repeated cycles of denaturation (heating to separate DNA strands), annealing (cooling to allow primers to bind), and extension (DNA synthesis).
   • DNA Replication in Vivo: Occurs in the cellular environment at physiological temperatures and is a continuous process during the S phase of the cell cycle.

5. Fidelity and Error Correction:

   • PCR: Taq polymerase lacks proofreading ability, which can lead to errors in the amplified DNA.
   • DNA Replication in Vivo: DNA polymerases have proofreading activity, which helps maintain high fidelity by correcting errors during DNA synthesis.

In summary, while both PCR and DNA replication in vivo involve DNA synthesis, they differ in their purpose, the type of primers used, the enzymes involved, and the conditions under which they occur. PCR is a laboratory technique for amplifying specific DNA sequences, whereas DNA replication in vivo is a natural process for duplicating the entire genome in living cells.