Question

Summarize and compare the properties of DNA polymerase I II, and III.

Short answer

DNA polymerases I, II, and III have some common properties such as 5' to 3' polymerase activity and 3' to 5' exonuclease activity. The differences between these enzymes lie mainly in their roles and functions. DNA Polymerase I is primarily responsible for removing RNA primers and filling in gaps with DNA nucleotides, and it uniquely has 5' to 3' exonuclease activity. DNA Polymerase II is mainly involved in DNA repair, particularly in error-prone repair, which may introduce errors during the repair process. DNA Polymerase III is the primary enzyme for DNA replication, and unlike the other two polymerases, it lacks 5' to 3' exonuclease activity and does not have a role in removing RNA primers.

Step-by-step solution

1. Introduce DNA Polymerases

DNA polymerases are enzymes that play a crucial role in DNA replication. These enzymes construct new DNA strands by adding nucleotides to a pre-existing DNA molecule or RNA primer. In this exercise, we will focus on the properties of DNA polymerase I, II, and III, which are found in prokaryotes, specifically in E. coli.

2. DNA Polymerase I

DNA Polymerase I plays a role in DNA replication, repair, and recombination. Its primary function is to remove RNA primers and replace them with DNA nucleotides during replication. DNA Polymerase I has three notable activities: 1. 5' to 3' polymerase activity – This allows it to synthesize DNA in the 5' to 3' direction by adding nucleotides to the 3' end of the growing strand. 2. 3' to 5' exonuclease activity – This proofreading activity corrects errors that may occur during replication by removing mismatched nucleotides. 3. 5' to 3' exonuclease activity – This activity allows DNA Polymerase I to remove RNA primers and replaces them with the appropriate DNA nucleotides.

3. DNA Polymerase II

DNA Polymerase II has a primary role in DNA repair rather than replication, and it functions in error-prone repair, meaning that it might incorporate incorrect bases in the process of repairing DNA. Its two main activities are: 1. 5' to 3' polymerase activity – Like DNA polymerase I, it synthesizes DNA in the 5' to 3' direction. 2. 3' to 5' exonuclease activity – It also has proofreading activity that helps correct any errors during DNA synthesis. Unlike DNA Polymerase I, Polymerase II lacks 5' to 3' exonuclease activity and is not involved in the removal of RNA primers.

4. DNA Polymerase III

DNA Polymerase III is the primary enzyme responsible for DNA replication in prokaryotes. It synthesizes new DNA strands at the replication fork. Its key activities include: 1. 5' to 3' polymerase activity – It synthesizes DNA in the 5' to 3' direction, much like DNA polymerases I and II. 2. 3' to 5' exonuclease activity – It also has proofreading abilities to correct mistakes that occur during DNA synthesis. However, DNA Polymerase III lacks 5' to 3' exonuclease activity, and it does not play a role in removing RNA primers during DNA synthesis.

5. Comparison of DNA Polymerases

Now that we have examined the properties and functions of each DNA polymerase individually, we can summarize and compare their properties as follows: 1. All three polymerases possess 5' to 3' polymerase activity and 3' to 5' exonuclease activity. 2. DNA Polymerase I is mainly involved in removing RNA primers and filling in the gaps with DNA nucleotides, while DNA Polymerase III is the primary enzyme for replication. DNA Polymerase II is more focused on DNA repair processes. 3. Only DNA Polymerase I has 5' to 3' exonuclease activity, which is responsible for the removal of RNA primers. 4. DNA Polymerase II functions in error-prone DNA repair, meaning it may introduce errors during repair. In conclusion, DNA Polymerase I, II, and III have some common properties, but they perform distinct roles in DNA replication, repair, and recombination processes.

Key concepts

DNA replication

DNA replication is a vital biological process ensuring that each daughter cell receives an accurate copy of the genetic material from the parent cell. This process occurs during the S phase of the cell cycle in prokaryotic and eukaryotic cells, though we will focus on prokaryotic replication here. **In prokaryotes, three DNA Polymerases – I, II, and III – are particularly crucial.**

- **DNA Polymerase I**: This enzyme plays a supportive role in DNA replication. It is not the key player but is crucial for replacing RNA primers with DNA nucleotides.
- **DNA Polymerase III**: This is the primary enzyme responsible for synthesizing new DNA strands by adding nucleotides in the 5' to 3' direction.

Each DNA polymerase has to accurately copy the DNA sequence to avoid mutations. This accuracy is not only due to their selection of appropriate nucleotides but also because of their proofreading ability, thanks to their exonuclease activity.

Error-prone repair

Error-prone repair is a DNA repair mechanism that, while aiming to fix genetic injuries, can sometimes introduce errors. It stands in contrast to more accurate repair methods which ensure integrity and fidelity of the genetic material.

DNA Polymerase II is most associated with error-prone repair activities. It participates in repairing damaged DNA by filling gaps, albeit with lower accuracy.

- **Purpose**: While it might sound detrimental, error-prone repair allows organisms to bypass replication blocks caused by severely damaged DNA. The trade-off is sometimes incorporating incorrect nucleotides.
- **Consequences**: Such errors, if not further corrected, may lead to mutations that could be harmful, neutral, or occasionally beneficial.

Despite being termed "error-prone," this repair style is part of a broader strategy to maintain genetic continuity under stress conditions where more precise methods may not suffice.

Exonuclease activity

Exonuclease activity is an essential feature of many DNA polymerases, offering a mechanism to improve the fidelity of DNA replication. These enzymes can remove nucleotides from the ends of a DNA strand, functioning in two main directions.

- **3' to 5' Exonuclease Activity**: This activity provides a proofreading function. As DNA polymerases synthesize a new strand, they occasionally incorporate the wrong nucleotide. The 3' to 5' exonuclease activity allows immediate error correction by excising the mismatched nucleotide.
- **5' to 3' Exonuclease Activity**: Found only in DNA Polymerase I among the prokaryotic polymerases. It plays a unique role in removing RNA primers from the Okazaki fragments during DNA replication.

By excising erroneous or unnecessary fragments, exonuclease activity ensures that the newly synthesized DNA is accurate and ready to function properly in subsequent cellular processes. This activity is crucial for maintaining genetic stability across replication cycles.