Replication of DNA occurs at a molecular junction that is usually drawn schematically as a fork and is hence called a replication fork. Figure 24.6 depicts a replication fork in E. coli along with many of the proteins that participate in DNA replication. The figure shows that leading strand and lagging strand replication occur on opposite strands at the same replication fork and that replication proceeds for both strands in the 5' to 3' direction. The terms in Figure 24.6 are described below:
Topoisomerase - an enzyme that relieves the torsional stress that arises ahead of the replication fork when the helicase enzyme unwinds the DNA strands (Figure 24.30, Figure 24.31).
DNA polymerase - catalyzes the chemical reactions for polymerization of nucleotides.
Helicase - (Figure 24.27) an enzyme that unwinds DNA strands ahead of the DNA polymerase. Each strand of parental DNA has it own helicase. The one associated with the lagging strand is complexed with primase as part of a unit called the primosome.
Primase - an enzyme that copies a DNA template strand by making an RNA strand complementary to it. The RNA serves as a priming site where DNA polymerase can begin to synthesize a DNA strand.
Primosome - a complex containing a primase and helicase. It helps to initiate DNA replication by synthesizing an RNA primer and to elongate it by unwinding the strands in advance of the replication complex.
Single-strand DNA-binding protein (SSB) - binds single-stranded DNA to stabilize it so that the hydrogen-bonding surfaces of the DNA bases are spatially oriented toward the incoming nucleotides (Figure 24.26).
Sliding clamp - a protein dimer that encircles the DNA strand and helps hold the DNA polymerase to the DNA strand.
RNA primer - a preexisting nucleic acid strand of RNA on which DNA replication is continued. The initiation of DNA synthesis requires a preexisting nucleic acid strand, so RNA primers are frequently used for this purpose. RNA primers are made by the primase enzyme.
Okazaki fragment - short discontinuous stretches of DNA arising from replication on the lagging strand. Okazaki fragments are named for the biochemists who discovered them.
DNA polymerase I and DNA ligase - the two enzymes that assemble short Okazaki fragments into a single continuous strand. DNA polymerase I has a catalytic activity that can remove RNA primers then replace them with DNA. DNA ligase catalyzes the covalent joining of the individual pieces of the lagging strand.
Leading strand - the strand of DNA at a replication fork that replicates continuously.
Lagging Strand - the strand of DNA at a replication fork that replicates in pieces (Okazaki fragments).
2. Primase
3. Helicase
4. Rotating SSB
