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dna replication

DNA is unique among all known molecules because it is the only one that is capable of duplicating itself. The process of duplication is called replication.

Replication is somewhat complex, but what basically happens is that the two complementary strands which form the DNA molecule unzip and then are used as templates from which new new strands are made as free nucleotides combine with their complementary bases.

Replication of DNA is semi-conservative. That is, one side of each new DNA strand is "old" and the other side is "new".

nucleoside triphosphates

Before the steps of replication are looked at, let's just briefly examine nucleoside triphosphates.

Replication involves large numbers of free nucleoside triphosphates. A nucleoside triphosphate is much like a nucleoside except that instead of having one phosphate molecules, it has three. A representation of a nucleoside triphosphate is shown below.

In the diagram, P represents a phosphate molecule, S represents a sugar molecule (deoxyribose or ribose), and B represents the base. There are eight types of nucleoside triphosphates involved in replication. They are:

• dATP - deoxyribose adenosine triphosphate
• dTTP - deoxyribose thymine triphosphate
• dCTP - deoxyribose cytosine triphosphate
• dGTP - deoxyribose guanine triphosphate
• ATP - ribose adenosine triphosphate
• TTP - ribose thymine triphosphate
• CTP - ribose cytosine triphosphate
• GTP - ribose guanine triphosphate

These molecules will pair with the bases on the template strands during the replication process. The high energy of the triphosphates is used to form bonds between the nucleotides. The two outermost phosphates are liberated, leaving the innermost group still attached. Once the two outermost phosphates have been released, the nucleoside triphosphate has become a nucleotide.

This remaining phosphate forms a link between the two deoxyribose subunits. The free 3'-OH group of the deoxyribose in the first nucleotide then reacts with the first 5' phosphate of the second nucleotide to form a sugar-phosphate-sugar linkage. The 3'-OH group of the second nucleotide is free to, and will, react with the 5' phosphate of the third nucleotide and so on.

unzipping the dna

All references to 3', 5', and other primes refer to the primes on the new parts of the daughter strands.

The process of replication begins in the DNA molecules at thousands of sites called origins of replication. At these sites, which look like little bubbles, the hydrogen bonds between the bases are broken and the paired bases seperate. The helix begins to pull apart or unwind.

The unwinding of the helix is facilitated by an enzyme called helicase, which is part of the replication complex - a group of enzymes and other proteins that take care of the replication process. There are two replication complexes at each origin of replication. As unwinding continues, they move in opposite directions creating two Y-shaped replication forks. Replication proceeds in both directions until the bubbles meet.

The image below shows an orgin of replication. The green arrows indicate the directions that the helix will unravel in. New bases (in blue) are coming in and attaching to their complementary bases on the old strand.

As the strands unwind, another enzyme, gyrase prevents an accumulation of twists by making temporary single-strand nicks in the DNA. Where the DNA is nicked, the helix can unwind around the connected strand. The nick will be sealed later by another enzyme called ligase

Replication complexes also contain single-strand binding proteins to help keep the two template strands apart and a familily of enzymes of vital importance to replcation - DNA polymerases.

adding bases

DNA polyermerase III is the primary enzyme responsible for replication. It's main function is to add the 5' phosphate of a new nucleotide to and existing 3'-OH group. A limitation of DNA polymerase III is that it can't begin a new daughter strand by itself - it requires that there already be a 3'-OH end to add the next nucleotide to.

Though there may already be origins of replication on a strand of DNA, replication does not really begin until an enzyme called primase adds a primer of a few RNA nucleotides in a 5' to 3' direction. This primer provides the free 3'-OH needed by DNA polymerase III. The primer is later removed and replaced by DNA.

Another limitation of DNA polymerase III is that it can only add new bases to the 3'-OH end of a growing strand. New DNA strands always grow from the 5' to the 3' end (of the daughter strand). Since the original DNA strand unzips, replication can occur in a 5' to 3' direction on one side and in a 3' to 5' direction on the other side. But DNA polymerase work in a 3' to 5' direction. This problem is ingeniously solved as we will soon see.

As replication moves from an origin along an unowund segment the addition and joingin of bases on one strand can proceed continually in a 5' to 3' direction. This strand is referred to as the leading strand.

The other parent strand is copied discontinuously, creating a lagging strand. As the leading strand is continuously synthesized, unpaired bases accumulate on the laggin strand, joing with their complementary bases but not to each other as DNA polymerase III is needed for that, until a long enough segment has been created to allow first primes then DNA polymerase III to begin working on it in a 5' to 3' direction. The short segments of newly assembled DNA are called Okazaki fragments. As replication proceeds and nucleotides are added to the 3' end of the Okazaki fragments, they come to meet each other. When DNA polyerase III meets the RNA primer from a previous segment, DNA polymerase I comes along and excises the primer, fills the gap with DNA, and leaves. The Okazaki fragments are joined together by ligase.

The image below shows replication. The helix will unwind in the direction of the green arrow. The yellow bases are RNA molecules - the primer. The purple ellipses are DNA polymerases which are linking the new bases together. They move in the direction of the black arrows.

As the new strands form, DNA polymerase II moves along the strands and proof-reads them for errors, which we also refer to as mutations.

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