DNA Polymerase

DNA Polymerase 

DNA polymerases taking part in replication are sometimes also called replicases .Prokaryotes have three major types of DNA synthesizing enzymes called DNA A polymerases, III,II and I. All  of them add nucleotide in 5'➡️3' direction on 3' ➡️5' strand. They also possess 3' ➡️5' exonuclease activity.That mean all these enzymes can degrade DNA. But as long as deoxyribonucleotide precursors are present in even moderate amounts, the synthetic activity of a DNA polymerase is greatly favored over its degradation activity.While DNA polymerase III is mainly involved in DNA replication, Polymerase I is major repair enzyme.Polymerase II is minor repair enzyme.DNA polymerase I also has 5' ➡️3' exconuclease  activity and specially helps in removal of primer. Most other DNA Polymerases including DNA polymerase III lack a 5' ➡️3'exonuclease activity.Eukaryotic cells contain several types of DNA polymerases like æ,ß,Y, ó,£.DNA polymerase ó  is the nuclear replicate; DNA polymerase æ is concerned with priming (initiating) replication. ß and £ polymerases participate in DNA repair while  Ý polymerase is responsible for the replication of mitochondrial DNA. All DNA polymerases have a configuration of gripping hand with thumb on one side, fingers on the other and the palm like concave catalytic site for combining template and base pairs.

What are the polymerase structure and functions?

DNA polymerase are enzymes that are responsible for responsible for synthesizing new DNA strands by adding nucleotides in a template_ dependent manner. They play a crucial role in DNA replication, repair, and recombination. 

Structure of   DNA  polymerase: 

DNA polymerase have a similar structural architecture, consisting of several domains:

1: Palm domain: This is the catalytic core of the enzyme and contains the active site that accommodates the template DNA and incoming nucleotides. 
2): Fingers Domain:This domain interacts with the template DNA and allows for the movement of the polymerase along the DNA strand during synthesis. 

3): Thum domain:This domain helps to stabilize the enzymes interaction with the DNA template. 

4):Exonuclease Domain ( proofreading domain): Many DNA polymerases also possess an exonuclease domain that can proofread the newly synthesized DNA strands. This domain has 3' to 5' exonuclease activity, allowing the enzyme to remove incorrectly incorporated nucleotides. 

Functions of DNA polymerase:

1):DNA Replication:DNA polymerase are essential for DNA replication, where they synthesize new DNA strands by adding complementary nucleotides to the template DNA strand.They strat synthesizing the new strands by adding a short RNA primer.During replication, DNA polymerases also proofread their synthesized DNA strand, correcting any errors that may occurs.

2): DNA Repair : When DN is damaged by various factors such as radiation, chemicals,or error during replication, DNA polymerases are involved in DNA repair processes. They can excise and replace damaged or incorrect nucleotides in the DNA  strand, ensuring its proper integrity. 
3): DN Recombination:In DNA recombination and repair processes, DNA Polymerases help in the synthesis of new DNA strands to repair damaged or missing regions, using intact DNA strands as templates. 

Proof reading and DNA repair: Sometimes a wrong base is introduced in the DNA strandduring replication. But their frequency is only one in 10,000.3'➡️5' excouclease activity of polymerases carries out a critical  " proof  reading " or editing "function that is necessary for the high degree of fidelity characteristic of DNA replication. When presented with a template primer DNA that has a terminal mismatch ( an unpaired or incorrectly paired base or sequence of bases at the 3' end of the primer, the 3➡️5' exconuclease of the polymerase clips off the unpaired base or bases. When an appropriately base paired terminus results,  the polymerase begins resynthesis by adding  nucleotides to the 3' end of the primer strand and continue until the template is exhausted.

DNA polymerase III is unable to distinguish uracil  from thymine so it is incorporated in place of thymine. It is corrected by many enzymes. There is a separate repair mechanism for any damage caused to DNA due to exposure or mismatching that escapes proof reading. A nick or break is caused, by an endonuclease near the region of repair, DNA polymerase I removes the mismatched or wrong nucleotides if present and synthesises a correct replacement by using the intact strand as template. The newly formed segment is sealed by DNAA ligase.

4):DNA  Amplification ( PCR):Certain DNA polymerases such as Tag DNA polymerase, are used as Taq DNA polymerase, are used in Polymerase chain Reaction ( PCR) to amplify specific DNA sequence. In PCR, the DNA polymerase chain Reactions (PCR) to amplify specific DNA sequences. In PCR, the DNA  polymerase can  repeatedly synthesize new DNA strands from a template DNA, resulting in the production of millions of copies of the target DNA sequence. 
Overall, DNA polymerases play a vital role in maintaining the fidelity and integrity of the DNA molecule, as well as in DNA replication, repair, recombination, and amplification processes. 

Eukaryotic DNA polymerase Types and Function:

Prokaryotic cell, Eukaryotic cells also have many DNA polymerases, which perform different functions, e.g.mitochondrial DNA replication, nuclear DNA replication, nuclear DNA replication,etc The nuclear DNA replication is mainly done by DNA polymerase 𝝳 and  𝜶 .There are at least 15 DNA polymerases identified in human beings. 

DNA polymerase  𝝳 : It is the main enzyme for replication in eukaryotes. It also has 3' ➡️5' exonuclease activity for proofreading.

☆ DNA polymerase  𝟄: The main function  is DNA repair. It removes primers for Okazaki fragments from the lagging strand.

☆DNA polymerase  𝝲: It is the main replicative enzyme for mitochondrial DNA. 

☆DNA Polymerase  𝜶  : The main function of DNA polymerase  𝜶 is to synthesize primers.The smaller subunit has a primase activity.The largest subunit has polymerization activity. It forms a primer for Okazaki fragments, which is then extended by DNA polymerase 𝝳.

Prokaryotic DNA polymerase Types and Function:

There are five DNA polymerase identified in E.coli.All the DNA polymerases differ in structure, functions and  rate of polymerization and progressivity. 

DNA polymerase I : It is coded  by polA gene.It is a single polypeptide and  has a role in recombination and repair. It has both 5' ➡️3' and 3'➡️5'exonuclease activity.DNA polymerase I removes the RNA primer from lagging strand by 5'➡️3' exconuclease activity and also fills the gap.

DNA Polymerase II is coded by polA gene.It is made up of 7 subunits. It main role is in repair and also a backup of DNA polymerase III. It had 3' ➡️5' exconuclease activity.

DNA polymerase III is the main enzymes for replication in E.coli
 It is coded by polC gene. The polymerization and processivity rate is maximum in DNA polymerase III. It also has proofreading 3' ➡️5' exonuclease activity.

DNA polymerase III of E. Coli is made up of a total of 13 subunits, which comprises 9 different types of subunits. 

☆ It consist of two core domains made up of      𝜶, 𝟄, and 𝞱 subunits. It is attached to the complex or clamp_ loading complex, which is made up of five subunits, T2Yóó .Additional subunits X and ₩ are attached to the clamp_ loading complex. ß subunits make two clamps with a dimer each.They increase the processivity of the DNA polymerase III.

DNA polymerase IV is coded by dibB gene. It main role is in DNA repair during SOS response, when DNA replication is stalled at the replication fork.DNA polymerase II, IV and V are translesion polymerases. 

DNA polymerase V is also involved in translesion synthesis during SOS responds and DNA repair.It is made up of UmuC monomer and UmuD dimer.

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