DNA strands separate at the replication fork

KEY TERMS:

• A replication fork (Growing point) is the point at which strands of parental duplex DNA are separated so that replication can proceed. A complex of proteins including DNA polymerase is found at the fork.
• A DNA polymerase is an enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). Any particular enzyme may be involved in repair or replication (or both).
• RNA polymerases are enzymes that synthesize RNA using a DNA template (formally described as DNA-dependent RNA polymerases).
• A deoxyribonuclease (DNAase) is an enzyme that attacks bonds in DNA. It may cut only one strand or both strands.
• Ribonucleases (RNAase) are enzymes that cleave RNA. They may be specific for single-stranded or for double-stranded RNA, and may be either endonucleases or exonucleases.
• Exonucleases cleave nucleotides one at a time from the end of a polynucleotide chain; they may be specific for either the 5 or 3 end of DNA or RNA.
• Endonucleases cleave bonds within a nucleic acid chain; they may be specific for RNA or for single-stranded or double-stranded DNA. 

KEY CONCEPTS:

• Replication of DNA is undertaken by a complex of enzymes that separate the parental strands and synthesize the daughter strands.
• The replication fork is the point at which the parental strands are separated.
• The enzymes that synthesize DNA are called DNA polymerases; the enzymes that synthesize RNA are RNA polymerases.
• Nucleases are enzymes that degrade nucleic acids; they include DNAases and RNAases, and can be divided into endonucleases and exonucleases.

Replication requires the two strands of the parental duplex to separate. However, the disruption of structure is only transient and is reversed as the daughter duplex is formed. Only a small stretch of the duplex DNA is separated into single strands at any moment.

The helical structure of a molecule of DNA engaged in replication is illustrated in Figure 1.13. The nonreplicated region consists of the parental duplex, opening into the replicated region where the two daughter duplexes have formed. The double helical structure is disrupted at the junction between the two regions, which is called the replication fork. Replication involves movement of the replication fork along the parental DNA, so there is a continuous unwinding of the parental strands and rewinding into daughter duplexes.

The synthesis of nucleic acids is catalyzed by specific enzymes, which recognize the template and undertake the task of catalyzing the addition of subunits to the polynucleotide chain that is being synthesized. The enzymes are named according to the type of chain that is synthesized: DNA polymerases synthesize DNA, and RNA polymerases synthesize RNA.

Degradation of nucleic acids also requires specific enzymes: deoxyribonucleases (DNAases) degrade DNA, and ribonucleases (RNAases) degrade RNA. The nucleases fall into the general classes of exonucleases and endonucleases: 

• Endonucleases cut individual bonds within RNA or DNA molecules, generating discrete fragments. Some DNAases cleave both strands of a duplex DNA at the target site, while others cleave only one of the two strands. Endonucleases are involved in cutting reactions, as shown in Figure 1.14.

• Exonucleases remove residues one at a time from the end of the molecule, generating mononucleotides. They always function on a single nucleic acid strand, and each exonuclease proceeds in a specific direction, that is, starting at either a 5 or at a 3 end and proceeding toward the other end. They are involved in trimming reactions, as shown in Figure 1.15.