Reaction Replication fork

FIGURE 25-37 Models for recombinational DNA repair of stalled replication forks. The replication fork collapses on encountering a DNA lesion (left) or strand break (right). Recombination enzymes promote the DNA strand transfers needed to repair the branched DNA structure at the replication fork. A lesion in a single-strand gap is repaired in a reaction requiring the RecF, RecO, and RecR proteins. Double-strand breaks are repaired in a pathway requiring the RecBCD enzyme. Both pathways require RecA. Recombination intermediates... 

Re combinational DNA repair of a circular bacterial chromosome, while essential, sometimes generates deleterious byproducts. The resolution of a Holliday junction at a replication fork by a nuclease such as RuvC, followed by completion of replication, can give rise to one of two products the usual two monomeric chromosomes or a contiguous dimeric chromosome (Fig. 25-41). In the latter case, the covalently linked chromosomes cannot be segregated to daughter cells at cell division and the dividing cells become stuck. A specialized site-specific recombination system in E. coli, the XerCD system, converts the dimeric chromosomes to monomeric chromosomes so that cell division can proceed. The reaction is a site-specific deletion reaction (Fig. 25-39b). This is another example of the close coordination between DNA recombination processes and other aspects of DNA metabolism. 

In this review we summarize the general architecture of DNA polymerases and the chemistry of the DNA polymerase and 3 -5 exonuclease activities (see also DNA replication). The ultimate function of DNA polymerases is the duplication of genetic material, and therefore, we also describe how Pol III functions at a replication fork. Lastly, we present a brief overview of the different repair reactions in which the remaining DNA polymerases act. 

Polymerase I plays an essential role in the replication process in E. coli, but it is not responsible for the overall polymerization of the replicating strands. The enzyme that accomplishes this is a less abundant enzyme, polymerase III (pol III). (A DNA polymerase II has also been isolated from E. coli, but it probably plays no role in DNA synthesis.) Pol III catalyzes the same polymerization reaction as pot I but has certain distinguishing features. It is a very complex enzyme and is associated with eight other proteins to form the pol III holoenzyme. (The term holoenzyme refers to an enzyme that contains several different subunits and retains some activity even when one or more subunits is missing.) Pol III is similar to pol I in that it has a requirement for a template and a primer but its substrate specificity is much more limited. For a template pol III cannot act at a nick nor can it unwind a helix and carry out strand displacement. The latter deficiency means that an auxiliary system is needed to unwind the helix ahead of a replication fork. Pol III, like pol I, possesses a 3 5 exonuclease activity, which performs the major editing function in DNA replication. Polymerase III also has a y exonuclease activity, but this activity does not seem to play a role in replication. 

All reactions involved in nucleic acid synthesis are catalyzed by enzymes. The synthesis of DNA takes place in a region of the molecule where the strands have started to separate, called a replication fork. Because a nucleic acid can be synthesized only in the 5 ---> 3 direction, only the daughter strand on the left in Figure 27.11 is synthesized continuously in a single piece (because it is synthesized in the 5 - 3 direction). The other daughter strand needs to grow in the 3 --------- 5 direction, so it is... 

Summarize the reactions and identify the proteins at the replication fork that carry out DNA replication. 

When strand breaks remain open at a lesion site, or when non-repaired damage blocks the progress of a DNA rephcation fork to produce a daughter strand gap, a complex cascade of reactions is triggered to stop the cell cycle machinery and recruit repair factors. When, after replication, a second identical DNA copy is available, homologous recombination (HR) seems to be preferred otherwise cells rely on non-homologous end joining (NHEJ), which is more error-prone [17]. 

The DNA replication complex requires a variety of proteins to facilitate fork movement. Which answer best describes the minimum set of proteins required for E. coli DNA replication in an vitro reaction ... 

---