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DNA polymerase

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DNA polymerase is a vital family of enzymes that catalyze the synthesis of DNA molecules. These enzymes are responsible for building DNA from molecular precursors known as nucleoside triphosphates. This process is essential for DNA replication, which occurs every time a cell divides. During replication, DNA polymerase works to create two identical DNA duplexes from a single original duplex. This ensures that genetic information is passed accurately from one generation of cells to the next.

DNA polymerase
DNA polymerase

Before the enzyme can begin its work, the DNA molecule must be prepared. An enzyme called helicase unwinds the tightly woven DNA molecule. Helicase functions by breaking the hydrogen bonds between the nucleotide bases. This action "unzips" the double-stranded DNA into two separate single strands. These single strands then serve as templates for the replication process. DNA polymerase reads these existing strands to guide the creation of matching new strands.

To build the new strand, DNA polymerase adds nucleotides to the 3' end of the growing chain. This process results in the elongation of the new strand in a 5' to 3' direction. Because of this, the enzyme must move along the original template strand in a 3' to 5' direction. This specific movement creates two strands that are antiparallel, meaning they run in opposite directions. The enzyme ensures accuracy by pairing nucleotides with specific bases. For example, cytosine always pairs with guanine, and thymine always pairs with adenine.

The discovery of these enzymes changed our understanding of biology. In 1956, Arthur Kornberg and his colleagues discovered DNA polymerase I in the bacterium Escherichia coli. They were able to describe how the enzyme copies the base sequence of a template strand. For this groundbreaking work, Kornberg was awarded the Nobel Prize in 1959. Later, in 1970, Thomas Kornberg and Malcolm E. Gefter discovered DNA polymerase II. Other types, including DNA polymerase III, were found in the 1970s, while polymerases IV and V were identified in 1999.

Replication fork
Replication fork

DNA polymerase is highly efficient due to a characteristic called processivity. Processivity refers to the average number of nucleotides an enzyme adds each time it binds to a template. While a nonprocessive enzyme might add only one nucleotide per second, processive enzymes add many more. In some cases, such as phage T4 DNA elongation in E. coli, the rate can reach 749 nucleotides per second. To maintain this speed, the enzyme often associates with a ring-shaped protein called a sliding DNA clamp. This clamp prevents the polymerase from diffusing away from the DNA template.

Although these enzymes are fast, they are not perfect. DNA polymerase makes approximately one mistake for every billion base pairs copied. To maintain high fidelity, many polymerases possess an exonuclease domain for proofreading. If the enzyme detects an incorrect base pair, it uses 3'-5' exonuclease activity to excise the wrong nucleotide. The enzyme then moves backward, removes the error, and re-inserts the correct base. This correction is vital because mismatches can lead to dysfunctional proteins or even cancer.

DNA polymerase
DNA polymerase

The physical structure of DNA polymerase is remarkably consistent across different species. This is known as a conserved structure, which suggests the enzyme performs an irreplaceable function. The shape of the enzyme is often compared to a human right hand, consisting of palm, finger, and thumb domains. The palm domain is where the chemical reaction is catalyzed. The finger domain binds the nucleoside triphosphates to the template base. Finally, the thumb domain helps with the positioning and translocation of the DNA.

DNA polymerase
DNA polymerase

Scientists categorize DNA polymerases into several distinct families based on their sequence homology. These include families A, B, C, D, X, Y, and RT. For instance, Family A includes repair polymerases like Pol I, which is found in prokaryotes. Family RT includes reverse transcriptase, an unusual enzyme used by retroviruses to polymerize DNA from an RNA template. These enzymes are also essential in biotechnology. Since 1983, they have been used in the polymerase chain reaction, or PCR. Since 1988, thermostable versions have been used to make the PCR process more efficient.

DNA polymerase
DNA polymerase
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Shared primase-binding peptide in...
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