Difference Between DNA Polymerase 1 and 3

Main Difference – DNA Polymerase 1 vs 3

DNA polymerase 1 and 3 are two types of DNA polymerases involved in prokaryotic DNA replication. DNA polymerases assist the synthesis of a new DNA strand by assembling the nucleotides to the parent strand. Both DNA polymerase 1 and 3 possess replicative activity in the 5’ to 3’ direction. DNA polymerase 1 possesses both 5’ to 3’ and 3’ to 5’ exonuclease activity. However, DNA polymerase 3 only possess 3’ to 5’ exonuclease activity. The main difference between DNA polymerase 1 and 3 is that DNA polymerase 1 is involved in the removal of primers from the fragments and replacing the gap by relevant nucleotides whereas DNA polymerase 3 is mainly involved in the synthesis of the leading and lagging strands.  

Key Areas Covered

1. What is DNA Polymerase 1
      – Definition, Structure, Function
2. What is DNA Polymerase 3
      – Definition, Structure, Function
3. What are the Similarities Between DNA Polymerase 1 and  3
      – Outline of Common Features
4. What is the Difference Between DNA Polymerase 1 and 3
      – Comparison of Key Differences

Key Terms: DNA Polymerase 1, DNA Polymerase 3, 3’ To 5’ Exonuclease Activity, 5’ To 3’ Exonuclease Activity, Gap Filling, Klenow Fragment, Polymerization, Proofreading, Prokaryotic DNA Replication

What is DNA Polymerase 1

DNA polymerase 1 is a type of DNA polymerases that possesses polymerization activity, proofreading activity, and primer removal activity. DNA polymerase 1 was first discovered by Arthur Kornberg in 1956. He was awarded the Nobel Prize for this discovery in 1959. DNA polymerase 1 is encoded by the polA gene. The size of the polA gene is 3000 bp. DNA polymerase 1 is involved in prokaryotic DNA replication since it aids the synthesis of a new DNA strand in the 5’ to 3’ direction. Moreover, DNA polymerase 1 is involved in filling gaps, repair, and recombination. The enzyme, DNA polymerase 1 fills the gaps in the double-stranded DNA, which is important in DNA repair. DNA polymerase 1 possesses both 3’ to 5’ exonuclease activity and the 5’ to 3’ exonuclease activity. The 5’ to 3’ exonuclease activity degrades both single- and double-stranded DNA in the 5’ to 3’ direction. Once the 5’ to 3’ exonuclease activity is removed from the DNA polymerase 1 holoenzyme, the remaining molecule is called the Klenow fragment.

Figure 1: Functional domains of DNA polymerase 1

The Klenow fragment is a useful molecule in DNA amplification reactions. This is important in mismatch repair. The three functional domains of DNA polymerase 1 is shown in figure 1. 

What is DNA Polymerase 3

DNA polymerase 3 is the main enzyme involved in prokaryotic DNA replication. DNA polymerase 3 possesses 5’ to 3’ polymerization activity where new nucleotides are added to the growing chain at its 3’ end. The enzyme aids the base pairing of incoming nucleotides with the template strand. The other function of DNA polymerase 3 is proofreading the replicated DNA. DNA polymerase 3 possess 3’ to 5’ exonuclease activity. Hence, this enzyme reads the just added nucleotides, and if there is any mismatch with the template strand, it will be removed and resynthesized. Therefore, DNA polymerase 3 is important in maintaining the stability of the genome.

Figure 2: DNA polymerase 3

DNA polymerase 3 holoenzymes is composed of ten subunits, which are arranged into two DNA polymerases. The α subunit is the catalytic subunit. The ε subunit has 3’ to 5’ proofreading activity. The θ subunit has an unknown function. The α subunit is encoded by the dnaE gene. The ε and θ subunits are encoded by the dnaQ and holE genes. The structure of the DNA polymerase 3 is shown in figure 2. 

Similarities Between DNA Polymerase 1 and 3

• DNA polymerase 1 and DNA polymerase 3 are two families of DNA polymerases.
• Both DNA polymerase 1 and DNA polymerase 3 are involved in the prokaryotic DNA replication.
• Both DNA polymerase 1 and DNA polymerase 3 possess both polymerase activity as well as the exonuclease activity.
• Both DNA polymerases carry out DNA replication in a semi-conservative

Difference Between DNA Polymerase 1 and 3

Definition

DNA Polymerase 1: DNA polymerase 1 is a DNA polymerase encoded by the polA gene and is involved in the prokaryotic DNA replication.

DNA Polymerase 3: DNA polymerase 3 is the main enzyme that aids prokaryotic DNA replication.

Discovery

DNA Polymerase 1: DNA polymerase 1 was first discovered by Arthur Kornberg in 1956.

DNA Polymerase 3: DNA polymerase 3 was first discovered by Thomas Kornberg and Malcolm Gefer in 1970.

Encoded by

DNA Polymerase 1: DNA polymerase 1 is encoded by polyA gene.

DNA Polymerase 3: DNA polymerase 3 is encoded by dnaE, dnaQ, and holE genes.

Family

DNA Polymerase 1: DNA polymerase 1 belongs to the DNA polymerase family A.

DNA Polymerase 3: DNA polymerase 3 belongs to the DNA polymerase family C.

Exonuclease Activity

DNA Polymerase 1: DNA polymerase 1 has both  3’ to 5’ exonuclease activity and 5’ to 3’ exonuclease activity.

DNA Polymerase 3: DNA polymerase 3 only has  3’ to 5’ exonuclease activity.

Function

DNA Polymerase 1: DNA polymerase 1 removes the RNA primer from 5’ to 3’ direction.

DNA Polymerase 3: DNA polymerase 3 adds deoxyribonucleic acids to the 3’ end.

RNA Primer

DNA Polymerase 1: DNA polymerase 1 removes the RNA primer.

DNA Polymerase 3: DNA polymerase 3 requires an RNA primer to synthesize the DNA.

DNA Synthesis

DNA Polymerase 1: DNA polymerase 1  adds nucleotides to the growing polynucleotide chain.

DNA Polymerase 3: DNA polymerase 3 is the key enzyme for synthesizing DNA in prokaryotes.

Lagging/Leading Strands

DNA Polymerase 1: DNA polymerase 1 only acts on the lagging strand.

DNA Polymerase 3: DNA polymerase 3 acts on both leading and lagging strands of the replication fork.

Rate of DNA Synthesis

DNA Polymerase 1: DNA polymerase 1 can add 10 to 20 nucleotides per second.

DNA Polymerase 3: DNA polymerase 3 can add around 1000 nucleotides per second.

Conclusion

DNA polymerase 1 and 3 are two types of DNA polymerases involved in prokaryotic DNA replication. Both types of DNA polymerases possess 5’ to 3’ polymerizing activity. In addition, both enzymes possess 3’ to 5’ exonuclease activity for proofreading. The main function of DNA polymerase 3 is its function in the polymerization. However, DNA polymerase 1 possesses 5’ to 3’ exonuclease activity. By 5’ to 3’ exonuclease activity, DNA polymerase 1 is capable of primer removing. The forming gap is also filled by the DNA polymerase 1. Therefore, the main difference between DNA polymerase 1 and 3 is their roles in the prokaryotic DNA replication.

Reference:

1. “DNA Polymerase I.” Worthington Enzyme Manual. N.p., n.d. Web. Available here. 09 Aug. 2017. 
2. Marians, Kenneth J., Hiroshi Hiasa, and Deok Ryong Kim. “Role of the Core DNA Polymerase III Subunits at the Replication Fork α IS THE ONLY SUBUNIT REQUIRED FOR PROCESSIVE REPLICATION.” Journal of Biological Chemistry. N.p., 23 Jan. 1998. Web. Available here. 09 Aug. 2017. 

Image Courtesy:

1. “PolymeraseDomains” By (unknown) “Molecule of the Month”, March 2000 – Protein Data Bank (Public Domain) via Commons Wikimedia
2. “DNA polymerase III (with subunits)” By Alepopoli – Own work (CC BY-SA 3.0) via Commons Wikimedia

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