DNA Polymerase- definition, structure, types (vs RNA polymerase)
DNA is the molecule that carries the genetic information of living organisms. It consists of two strands of nucleotides that are complementary and antiparallel to each other, forming a double helix structure. Each nucleotide has a nitrogenous base (adenine, thymine, cytosine or guanine), a sugar (deoxyribose) and a phosphate group. The bases on one strand pair with the bases on the other strand through hydrogen bonds, forming the base pairs A-T and C-G.
In order to pass on the genetic information to the next generation of cells, DNA needs to be replicated before cell division. This process involves separating the two strands of DNA and using each strand as a template to synthesize a new complementary strand. The result is two identical copies of DNA, each with one original strand and one new strand.
The enzyme that is responsible for synthesizing the new DNA strands is called DNA polymerase. DNA polymerase belongs to a family of enzymes that can catalyze the formation of new DNA molecules from nucleotides, using an existing DNA or RNA strand as a template. DNA polymerase can only add nucleotides to the 3` end of a growing DNA strand, so it always works in the 5` to 3` direction. It also requires a primer, which is a short RNA or DNA fragment that provides a free 3` hydroxyl group for the first nucleotide addition.
DNA polymerase is essential for life, as it ensures the accurate and faithful replication of DNA. It also plays a role in repairing damaged DNA and preventing mutations. There are different types of DNA polymerase that have different functions and characteristics in different organisms and cellular compartments. Some of them have proofreading abilities that can correct errors during DNA synthesis, while others can bypass lesions or gaps in the template strand.
In this article, we will explore the definition, structure, types and mechanism of DNA polymerase, as well as compare it with RNA polymerase, which is another enzyme that synthesizes RNA from DNA. We will also discuss some of the applications and implications of DNA polymerase in biotechnology and medicine.
- DNA polymerase is a group of enzymes that catalyze the template-directed synthesis of DNA, which is essential for DNA replication and repair.
- DNA polymerase was first discovered in 1955 by Arthur Kornberg and his colleagues, who isolated and purified an enzyme from Escherichia coli that could synthesize DNA from a DNA template and four deoxyribonucleoside triphosphates (dNTPs) .
- The enzyme was named DNA polymerase I and it was the first of many types of DNA polymerases that have been identified in prokaryotic and eukaryotic cells.
- DNA polymerase I has two main functions:
- It removes the RNA primers that initiate the synthesis of the Okazaki fragments on the lagging strand during DNA replication, using its 5` to 3` exonuclease activity.
- It fills in the gaps left by the removal of the primers, using its 5` to 3` polymerase activity.
- DNA polymerase I also has a 3` to 5` exonuclease activity that allows it to proofread and correct errors during DNA synthesis.
- Other types of DNA polymerases have different functions and properties, such as:
- DNA polymerase II, III and V are involved in DNA replication and repair in prokaryotes, with DNA polymerase III being the main replicative enzyme. They belong to different families (B, C and Y) based on their structural and sequence similarities.
- DNA polymerase γ is responsible for replicating and repairing mitochondrial DNA in eukaryotes. It belongs to family A, which also includes DNA polymerase I.
- DNA polymerase α, δ and ε are involved in nuclear DNA replication in eukaryotes, with DNA polymerase α initiating the synthesis of both leading and lagging strands, and DNA polymerase δ and ε extending them. They belong to family B, which also includes DNA polymerase II.
- DNA polymerase β, λ and μ are involved in base excision repair and non-homologous end joining in eukaryotes. They belong to family X, which has a distinct structure from other families.
- DNA polymerase η, ι and κ are involved in translesion synthesis, which is a mechanism of bypassing DNA lesions that block replication. They belong to family Y, which is prone to errors and lacks exonuclease activity.
- Terminal deoxynucleotidyl transferase (TdT) is a unique type of DNA polymerase that adds random nucleotides at the ends of DNA molecules, without a template. It is involved in the diversification of immunoglobulin genes in vertebrates.
DNA polymerases are enzymes that synthesize new DNA strands from existing templates. They have a common structural framework consisting of three subdomains: the palm, the fingers, and the thumb. These subdomains resemble an open right hand that grips the DNA template and the incoming nucleotide.
- The palm subdomain contains the catalytic site where the phosphodiester bond between the nucleotides is formed. It also has a 3` to 5` exonuclease activity that proofreads and corrects errors during DNA synthesis .
- The fingers subdomain is responsible for binding and positioning the incoming nucleotide that is complementary to the template base. It also undergoes a conformational change to close around the nucleotide and bring it closer to the catalytic site .
- The thumb subdomain interacts with the DNA backbone and stabilizes the DNA polymerase-DNA complex. It also regulates the processivity and fidelity of DNA synthesis by controlling the movement of the DNA template .
In addition to these three subdomains, different types and families of DNA polymerases have other domains that are specific for their functions and interactions with other proteins. For instance, some DNA polymerases have a 5` to 3` exonuclease domain that removes RNA primers from the Okazaki fragments on the lagging strand. Some also have a little finger domain that enhances DNA binding and polymerase activity.
The structure of DNA polymerase is well-adapted to its function of accurately and efficiently replicating DNA. By having a conserved core structure and variable accessory domains, DNA polymerases can perform various roles in DNA replication, repair, and recombination.
DNA polymerases are a group of enzymes that can synthesize new DNA strands from existing templates. They are essential for DNA replication and repair in both prokaryotic and eukaryotic cells. Based on sequence homology and structural features, DNA polymerases can be classified into seven different families: A, B, C, D, X, Y and RT . Some viruses also encode special DNA polymerases, such as Hepatitis B virus DNA polymerase. The table below summarizes the main types and functions of DNA polymerases in prokaryotes and eukaryotes.
|Family||Prokaryotic types||Eukaryotic types||Functions|
|A||Pol I||Pol γ||Replication and repair of mitochondrial DNA; excision repair; removal of RNA primers|
|B||Pol II||Pol α, Pol δ, Pol ε||Replication and repair of nuclear DNA; initiation of replication; synthesis of leading and lagging strands|
|C||Pol III||-||Replication and repair of bacterial DNA; main polymerase for replication|
|D||-||-||Replication and repair of archaeal DNA|
|X||-||Pol β, Pol λ, Pol μ||Base excision repair; non-homologous end joining; rejoining of DNA double-strand breaks|
|Y||Pol IV, Pol V||Pol η, Pol ι, Pol κ||Translesion synthesis; bypass of DNA lesions; error-prone replication|
|RT||-||Telomerase, Retroviral RTs||Synthesis of telomeric DNA; reverse transcription of RNA into DNA|
DNA polymerase is an enzyme that synthesizes new DNA strands from nucleotides, using a template DNA strand. The mechanism of DNA polymerase involves the following steps:
- DNA polymerase binds to the template strand and the primer, which is a short RNA or DNA sequence that provides a 3` end for the polymerase to start adding nucleotides.
- DNA polymerase adds nucleotides to the 3` end of the primer, complementary to the template strand, in the 5` to 3` direction. The nucleotides are joined by phosphodiester bonds, which are formed by the hydrolysis of the high-energy phosphate groups of the nucleotides.
- DNA polymerase uses two metal ions, usually magnesium, to catalyze the reaction. One metal ion activates the 3` hydroxyl group of the primer, while the other metal ion stabilizes the negative charges of the phosphate groups and facilitates their nucleophilic attack on the incoming nucleotide.
- DNA polymerase also proofreads its work by using its 3` to 5` exonuclease activity. This activity removes any mismatched or incorrect nucleotides that are incorporated into the new strand and replaces them with the correct ones.
- DNA polymerase continues to synthesize the new strand until it reaches the end of the template strand or encounters another primer. Then, it dissociates from the DNA and moves to another site.
The mechanism of DNA polymerase is different for the leading and lagging strands during DNA replication. The leading strand is synthesized continuously by one DNA polymerase, while the lagging strand is synthesized discontinuously by multiple DNA polymerases. The lagging strand consists of short segments called Okazaki fragments, which are initiated by primers and later joined by DNA ligase.
The mechanism of DNA polymerase also varies depending on the type and family of the enzyme. Different types of DNA polymerases have different structures, functions, and roles in DNA replication and repair. For instance, some DNA polymerases have additional domains or subunits that help them interact with other proteins or bind to specific regions of DNA. Some DNA polymerases also have other activities, such as 5` to 3` exonuclease or lyase, that are involved in removing primers or repairing damaged bases.
DNA polymerase is a highly accurate and efficient enzyme that ensures faithful copying and maintenance of genetic information in cells. It is essential for life and evolution.
DNA polymerase and RNA polymerase are both enzymes that synthesize nucleic acids, but they have different functions and characteristics. Some of the main differences between them are:
- DNA polymerase synthesizes DNA from a DNA template, while RNA polymerase synthesizes RNA from a DNA template .
- DNA polymerase requires a primer, which is a short nucleic acid sequence that provides a free 3` OH group for the addition of nucleotides, while RNA polymerase does not require a primer and can initiate synthesis de novo .
- DNA polymerase uses deoxyribonucleotides (dATP, dGTP, dCTP, and dTTP) as substrates, while RNA polymerase uses ribonucleotides (ATP, GTP, CTP, and UTP) as substrates . The difference in the sugar moiety (deoxyribose vs ribose) and the base (thymine vs uracil) affects the stability and function of the nucleic acids.
- DNA polymerase produces a double-stranded DNA molecule that is complementary and antiparallel to the template strand, while RNA polymerase produces a single-stranded RNA molecule that is complementary and antiparallel to the template strand . The double-stranded DNA forms a helical structure with base pairing between the strands, while the single-stranded RNA can fold into various secondary and tertiary structures with base pairing within the strand.
- DNA polymerase has a proofreading system that can correct errors during synthesis by using its 3` to 5` exonuclease activity, while RNA polymerase has no proofreading system and is more error-prone . The accuracy of DNA replication is essential for maintaining genetic integrity, while the errors in RNA transcription can be tolerated or even beneficial for generating diversity.
- DNA polymerase is involved in DNA replication, which occurs only once per cell cycle in preparation for cell division, while RNA polymerase is involved in transcription, which occurs continuously throughout the cell cycle in response to gene expression regulation . The amount and timing of DNA replication are tightly controlled by checkpoints and signals, while the amount and timing of transcription are modulated by various factors such as transcription factors, enhancers, silencers, chromatin structure, etc.
- DNA polymerase is found in both prokaryotes and eukaryotes, but there are different types and families of DNA polymerases with different roles and specificities . For instance, in eukaryotes, there are five main types of DNA polymerases: α, β, γ, δ, and ε. Polymerase γ is responsible for mitochondrial DNA replication, while polymerases α, δ, and ε are responsible for nuclear DNA replication. Polymerases β and ε are also involved in DNA repair mechanisms.
- RNA polymerase is also found in both prokaryotes and eukaryotes, but there are different types and subunits of RNA polymerases with different roles and specificities . For instance, in prokaryotes, there is only one type of RNA polymerase that synthesizes all types of RNA (mRNA, rRNA, tRNA), but it requires different sigma factors to recognize different promoters. In eukaryotes, there are three main types of RNA polymerases: I, II, and III. Polymerase I synthesizes rRNA (except for 5S rRNA), polymerase II synthesizes mRNA and some small RNAs (such as snRNA), and polymerase III synthesizes tRNA and some small RNAs (such as 5S rRNA).
These are some of the major differences between DNA polymerase and RNA polymerase. Both enzymes are essential for life as they enable the flow of genetic information from DNA to RNA to protein. Understanding how they work can help us appreciate the complexity and diversity of biological systems.
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