DNA polymerase assembles DNA out of nucleotides. DNA is the molecule that codes for proteins, carries the genes, and transmits heredity. DNA polymerase is one enzyme that makes this possible. It constructs new DNA strands that precisely copy old ones. Sometimes, though, polymerase inserts the wrong component in a strand, and must correct its error.
DNA is usually coiled up and twisted within cells. An enzyme called helicase opens it. Untwisted, it is a length of two strands, like the sidepieces of a ladder, with cross pieces that can be thought of as the rungs of a ladder. To replicate, the ladder splits the long way, like a zipper, and each half serves as a template for the construction of a new other half.
Each molecule of the ladder has a specific shape, like a puzzle piece, and will only correctly fit with a matching piece. When the DNA strand splits down the middle, it exposes the centers of its cross pieces so that they can be matched. There are only four bases of DNA. Each only matches a specific partner: Adenine matches Thymine while Guanine matches Cytosine. In DNA, a base is combined with a sugar, a deoxyribose, and three phosphates. Deoxyribose, the sugar, is the D in DNA.
DNA copying proceeds in only one direction. It starts at what is called the five prime end. The ends of the DNA strand are described as the five prime ends and the three prime ends. These names refer to the number of carbon atoms in the molecules where new nucleotides will attach.
The DNA polymerase finds deoxyribonucleases, molecules that match the exposed end of the DNA strand. It bonds to them and brings them to the leading edge of DNA construction. There it assembles them onto the DNA strand. This happens in a strict order, assembling molecules from one end of the strand only (from 5 to 3), and only after another enzyme, primase, has begun construction. (Technically, the leading strand is assembled from one end to the other. The lagging strand is assembled in segments, so that the polymerase can work in the correct direction.)
The DNA polymerase assembles the ladder, piece by piece, matching each new deoxyribonuclease to one that is already there. Each nucleotide has three phosphate groups. One group connects the nucleotide to the last nucleotide to have been added, building a bit of the side rail of the ladder. The other two phosphate groups are removed. The polymerase is only active at the leading edge of the construction.
Construction must be done right. DNA errors can mean cell death, cell malfunction, birth defects, or cancer. Therefore, some DNA polymerase is able to detect and repair its own assembly mistakes. This function is called, appropriately enough, proofreading.
All polymerases in prokaryotic cells proofread. In eukaryotic cells like those of plants and animals, only certain polymerase enzymes can proofread. The process begins when an incorrect nucleotide is inserted. Further additions to the DNA strand stop. The error creates a sort of roadblock. The polymerase can actually track backward to a mistake.
An exonuclease, another enzyme, then removes the mistaken nucleotide. It breaks the bonds between the incorrect nucleotide and the DNA under construction. It cleaves the mistake away from the growing face of the DNA. The nucleotide itself is actually saved, or, you might say, recycled.
That done, the DNA polymerase resumes its duplication of the DNA strand. DNA duplication is called semi-conservative, because a new DNA strand is half-new, while it conserves half the old strand. The proof reading process might be called very conservative, because it makes DNA replication 10 to 100 times as accurate as it would otherwise have been.
The cell does have other DNA repair techniques as well, and needs them. Causes of damage include radiation, chemicals, and even everyday metabolic processes. Proofreading, however, can be said to be the first line of DNA defense, because it happens as the DNA is being created.
DNA polymerase repairs errors in a process called proofreading. It stops adding new nucleotides to the strand under construction, and the mistake is snipped away and replaced. This process contributes a great deal to the essential accuracy of DNA replication.
