DNA Replication

Define the terms describing DNA replication: semiconservative, origin, bidirectional, replication fork, Okazaki fragment.

Semiconservative: When DNA replicates, each daughter molecule of DNA has one strand from the original DNA and one new strand. This means that it is semiconservative (as opposed to conservative in which the entire daughter molecule would be made of original DNA).
Origin: The place at which DNA replication takes place. Eukaryotic chromosomes often have multiple origins.
Bidirectional: Proceeding in two directions at once.
Replication fork: The area where the DNA is currently being replicated. The two DNA strands are separated in this area with DNA replication taking place on both.
Okazaki fragment: Fragments of DNA that are formed on the lagging strand. (I'll explain this in a bit.)

Understand the mechanism of leading and lagging strand replication and role of the RNA primer.

After the DNA has been opened up to reveal the replication fork, DNA synthesis takes place on both strands. DNA is antiparallel so the two strands are running in opposite directions to each other, and thus synthesis must take place in opposite directions as well.

Synthesis, however, must run from 5' to 3'. On one strand, this works quite well, and the DNA can be synthesised continuously. This strand is known as the leading strand. On the other strand, otherwise known as the lagging strand, the DNA is synthesised in little fragments at a time as the helix is opened up. These fragments are known as Okazaki fragments.

About primers- DNA polymerase can only join nucleotides to already existing nucleotides. The cell gets around this by using RNA primers, as RNA doesn't need already existing nucleotides to form a new strand. An RNA primer is placed at the start of every leading strand and at the start of every Okazaki fragment on the lagging strand. In the case of the lagging strand, most of these RNA primers are removed by RNAse H before DNA polymerase "overwrites" them with DNA.

Understand the functions of the proteins at the DNA replication fork.

There are several different proteins at the DNA replication fork. They cooperate to form what is known as the "replication machine." One of these is helicase, which unzips the double helix. (There's a really bad joke that goes "If I was an enzyme, I'd be helicase so that I can unzip you.") The sliding clamp is a protein that holds DNA Polymerase in place during replication, whereas the clamp loader assembles the clamp onto the DNA using energy from ATP. There are also single strand DNA-binding proteins that stabilise the unwound strands of DNA, preventing them from "snapping back together."

List major DNA polymerases of prokaryotes and eukaryotes and their functions.

There are three main types of DNA polymerase in prokaryotes such as E. coli. These are very imaginatively named DNA polymerase I, II and III. DNA polymerase I has functions in DNA repair as well as the maturation of Okazaki fragments (i.e. the removal of the RNA primer and the "stitching up" of Okazaki fragments to form a continuous strand). DNA polymerase II also plays roles in DNA repair. DNA polymerase III is the main DNA replication enzyme in prokaryotes, and it has a much higher affinity for deoxynucleotides than the other two types of DNA polymerase and is therefore able to add nucleotides much more rapidly.

There are five main types of DNA polymerase in eukaryotes. They are similar to those in prokaryotes but have some more protein components. Also, instead of being named I, II, III etc., they are named after letters of the Greek alphabet. Alpha DNA polymerase elongates primers, beta DNA polymerase repairs DNA, gamma DNA polymerase replicates mitochondrial DNA, delta DNA polymerase plays roles in the synthesis of the lagging strand and epsilon DNA polymerase plays roles in the synthesis of the leading strand. Please do note, however, that the roles of delta and epsilon DNA polymerases are still controversial.