DNA Polymerase

DNA polymerase is a complex enzyme. It is an enzyme that carries out polymerization of DNA, as it is clear from its name DNA polymerase. It is mainly of three types in prokaryotes viz; pol-I, pol-II and pol-III and in eukaryotes, it is of five kinds viz; pol-α, pol-β, pol-Ƴ, Pol- δ and pol-Ɛ. The first polymerase activity was seen in E.coli observed by Arthur Kornberg in 1958 and named it as E.coli DNA-pol I.

Later three types of DNA polymerases were introduced and named as DNA-pol I, DNA-pol II and DNA-pol III. On further discovery, it was found that the DNA polymerase not only shows the polymerization activity but also the exonuclease activity. Here we will discuss all the properties, structure and activities showed by all the three polymerases.

Content: DNA Polymerase

  1. Definition of DNA Polymerase
  2. DNA Polymerases in Prokaryotes
  3. Comparison Chart on Functions of Prokaryotic DNA Polymerases
  4. Characteristics

Definition of DNA Polymerase

DNA-polymerase also refers as “DNA replicase” which forms DNA by adding nucleotides in the replication process. Polymerase enzyme always moves along with the parental strand (template strand) in 3’-5’ direction but forms daughter strand (complementary strand) in 5’-3’ direction.

DNA Polymerases in Prokaryotes

In prokaryotes, primarily there are three polymerases enzymes namely: DNA pol-I, II and III.
prokaryotic polymerases

DNA Polymerase I

It is the first polymerase enzyme that was discovered by Arthur Kornberg in 1958. It consists of a single polypeptide chain. In starting it was believed that it is a replication enzyme, but after further study, it was evidenced that it is more a DNA repair enzyme rather than a replication enzyme. In pol-I, there is one atom of zinc present per chain, and that’s why it also refers to “Metalloenzymes”.

Activities found in DNA pol-I:

  • 5’-3’ polymerase activity: Involves the addition of nucleotide bases for the synthesis of a new DNA strand.
  • 3’-5’ exonuclease activity: Involves the deletion of mismatched nucleotide bases or helps in nick translation.
  • 5’-3’ exonuclease activity: It involves the deletion of RNA primers from the 5’end of the complementary DNA strand.

Structure: The structure of Pol-I resembles the right hand of the human. The structure consist of three regions:

  • Palm region: It is the catalytic active site contains conserved sequences. It acts as an active site of pol-I. Palm region is made of β- pleated sheet. Its primary function is the processing the addition of deoxyribonucleotide triphosphate.
  • Finger region: It is the template site, where once the base pairing is done it encloses the deoxyribonucleotide triphosphate. Its primary function is to catalyze the synthesis of incoming nucleotides by the help of catalyst known as metal ions.
  • Thumb region: It is the region which binds the DNA and maintains the correct position of the primer and active site.

dna pol 1

DNA Polymerase II

It was discovered by Thomas Kornberg in 1970. Its efficiency of polymerization is slower than the pol-I. It also consists of a single polypeptide chain. Pol-II acts as backup enzyme or alternative to the process of replication as in absence of pol-I it elongates the Okazaki fragments.

Activities found in DNA pol-II:

  • 5’-3’ polymerase activity: Involves the addition of nucleotide bases for the synthesis of a new DNA strand.
  • 3’-5’ exonuclease activity: Involves the deletion of mismatched nucleotide bases or helps in nick translation.

Structure: The structure of pol-II is quite unknown.

DNA Polymerase III

It is the primary holoenzyme that mainly participates in the process of replication. It consists of two polypeptide chains. Pol-III contain subunit of many enzymes that perform different functions also refers to “heteromultimeric enzyme”. Pol-III contains 10 subunits in its structure that make pol-III a complete enzyme, i.e. “holoenzyme”.

Activities found in DNA pol-III:

  • 5’-3’ polymerase activity: Involves the addition of nucleotide bases for the synthesis of a new DNA strand.
  • 3’-5’ exonuclease activity: Involves the deletion of mismatched nucleotide bases or helps in nick translation.

Structure: The structure of pol-III consist of 10 subunits namely:

  • α: It encodes DNA E gene and helps in DNA synthesis.
  • Ɛ: Codes for DNA Q gene and helps in 3’-5’ proofreading activity.
  • Ɵ: Encodes hol E gene and acts as accessory protein and involves in proofreading function.
  • Ʈ: It codes for DNA X gene and promotes dimerization of the core protein complex.
  • Ƴ: It codes for DNA Y gene.
  • δ: Encodes hol A gene.
  • δ’: Codes for hol B gene.
  • χ  : encodes hol C gene.
  • Ψ: codes for hol D gene.
  • β: encodes DNA N gene. It acts as “clamp protein” that holds the DNA molecule and responsible for the processivity factor.Ƴ, δ, δ’, χ and Ψ all acts as “clamp loader complex and helps the β- clamp loader protein to bind with the DNA.

dna pol 3

Comparison Chart on Functions of Prokaryotic DNA Polymerases

PropertiesDNA pol-IDNA pol- IIDNA pol-III
5’-3’ polymerase activityPresentPresentPresent
3’-5’ exonuclease activityPresentPresentPresent
5’-3’ exonuclease activityPresentAbsentAbsent
RNA dependent polymerizationIt can carry out RNA dependent polymerizationIt can notIt can not
DNA repairing characteristicsPresentPresentAbsent
Ligation propertyPresentAbsentAbsent
Involvement in replicationParticipates Does not participatePlays a major role

Characteristics

DNA- polymerase has some specific characteristics like:

  1. Polymerization activity
  2. Fidelity, i.e. proofreading ability
  3. Processivity, i.e. processing of  DNA and its bases
  4. Thermostability, i.e. stable at high temperature
    Example: Taq- DNA polymerase of Thermus aquaticus bacterium.

These all properties make it useful in molecular processes like PCR, DNA sequencing etc.

Leave a Comment

Your email address will not be published. Required fields are marked *