Genes, Unzipped
Before a cell can divide into two daughter cells, all of the DNA of the parent cells must be copied so that each daughter gets a copy. The DNA of a cell carries all of the organism’s genetic material—and instructions on how to use it.
DNA Structure
The structure of DNA is a double helix (spiral shape around a common axis) consisting of anti-parallel (running in opposite directions) strands of nucleic acid. It might be helpful to picture the DNA molecule as a ladder. Each leg of the ladder represents one strand of DNA and the rungs represent the nucleotide bases that hold the entire structure together. In DNA, the nucleotides on one strand are always paired with a partner in a very consistent manner.
DNA nucleotides
Nucleotides (the building blocks of DNA) are made up of a sugar molecule, a phosphate, and a nucleobase. DNA pairs contain only four different nucleotides, whose bases are either adenine (A), thymine (T), guanine (G), or cytosine (C).
DNA strands are made up of a repeated pattern of a sugar (deoxyribose) and a phosphate. The sugar-phosphate molecule is called a ring compound because of its shape. The sugar is a form of ribose that has lost an oxygen atom (de-oxy meaning “minus oxygen”). If you think of the sugar molecule as being formed in the shape of a pentagon, then there are five angles where other molecules could attach.
Imagine the base of the pentagon on the bottom and the point at the top. The first angle to the right of the top point is called 1', or 1 prime. Going in a clockwise direction, the second angle would be called 2', or 2 prime, and so on until all five angles are numbered. This helps scientists discuss where these molecules on a ring compound are attaching to each other.
In DNA, in one nucleotide, the phosphate group attaches to the sugar at 5' and links to another nucleotide at the 3'. In this way, DNA strands exist as a one-way street that runs 5' to 3' in biochemical terms. But remember that DNA strands are connected to each other (the legs on the ladder). So, while one strand (the coding strand) is read left to right as 5' to 3', the other strand of the double helix (the complementary strand) is present 5' to 3' in the opposite direction.
Preparing for Replication
Before the DNA double helix can be replicated, it must be separated into single strands. This is like unzipping a pair of pants. On the DNA molecule, helicase, an enzyme, binds and separates the nucleotide pairs, freeing one strand from its partner. Although both strands are being replicated at the same time, for simplicity the strands and their replication will be considered separately.
How does helicase work?
Helicase breaks down the hydrogen bond at the center of a segment of DNA, where the bases connect to each other. This exposes the bases so that new bases can attach. Adenine always attaches to thymine and guanine always attaches to cytosine.
Once the strands are unzipped, they no longer take a double helix shape. They are linear strands of nucleotides (denoted with the letters A, T, G, and C).
Leading Strand Replication
The so-called “complementary” strand of DNA is the “opposite” partner for the genetic code (coding strand). But it is used as a template to produce a new double helix for one daughter cell. By using each strand as a template, each daughter cell contains one new strand and one inherited strand from the parent and therefore forms the basis of semi-replicative division.
With the DNA unzipped, an enzyme called DNA polymerase reads the template strand in a 3' to 5' direction, and assembles a new coding strand in a 5' to 3' direction. For example, if the sequence on the complementary DNA strand were 3'-A-T-C-G-G-T-T-A–5', then the new coding strand would be assembled in this order: 5'-T-A-G-C-C-A-A-T-3'. Since this is also the direction in which the DNA helicase enzyme is unzipping the double helix, DNA polymerase simply follows along until the entire strand has been copied into a long new coding strand, which is called the leading strand.
Lagging Strand Replication
Although the leading strand is continuously synthesized as one long new strand, the other replication, which uses the coding strand as a template, is more complex. Instead of a strand being continuously replicated, the lagging strand is produced in discontinuous pieces.
Recall that as DNA helicase is unzipping the double helix, it moves in one direction. This works great for the leading strand replication because the new strand can be generated in the same direction that helicase is moving.
However, for the other template, the new strand is generated in the opposite direction. This causes the new lagging strand to be generated in pieces. As soon as an area of single-stranded DNA is exposed, a new strand is being generated. But, in this case, the new strand is being formed in the opposite direction from the way the helicase is unzipping DNA. Thus, as helicase unzips away from the new strand segments, a gap of single-stranded DNA will be present between the new strand and the helicase. This is called an Okazaki fragment. The process of unzipping and replicating will continue producing distinct Okazaki fragments along the length of this template into a discontinuous lagging strand with gaps remaining between the fragments.
These fragments have to be linked together to form a new, continuous strand of DNA. The gluing, or ligation, of these fragments into one long continuous strand is the function of first DNA polymerase and then DNA ligase, which bind to the gap site between adjacent Okazaki fragments and ligates them all together into a complete strand.