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Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002.

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Biochemistry. 5th edition.

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Chapter 27DNA Replication, Recombination, and Repair

Perhaps the most exciting aspect of the structure of DNA deduced by Watson and Crick was, as expressed in their words, that the “specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” A double helix separated into two single strands can be replicated because each strand serves as a template on which its complementary strand can be assembled (Figure 27.1). Although this notion of how DNA is replicated is absolutely correct, the doublehelical structure of DNA poses a number of challenges to replication, as does the need for extremely faithful copying of the genetic information.

Figure 27.1. DNA Replication.

Figure 27.1

DNA Replication. The double-helical structure immediately suggests how DNA is replicated.

1.

The two strands of the double helix have a tremendous affinity for one another, created by the cooperative effects of the many hydrogen bonds that hold adjacent base pairs together. Thus, a mechanism is required for separating the strands in a local region to provide access to the bases that act as templates. Specific proteins melt the double helix at specific sites to initiate DNA replication, and other enzymes, termed helicases, use the free energy of ATP hydrolysis to move this melted region along the double helix as replication progresses.

2.

The DNA helix must be unwound to separate the two strands. The local unwinding in one region leads to stressful overwinding in surrounding regions (Figure 27.2). Enzymes termed topoisomerases introduce supercoils that release the strain caused by overwinding.

3.

DNA replication must be highly accurate. As noted in Chapter 5, the free energies associated with base pairing within the double helix suggest that approximately 1 in 104 bases incorporated will be incorrect. Yet, DNA replication has an error rate estimated to be 1 per 1010 nucleotides. As we shall see, additional mechanisms allow proofreading of the newly formed double helix.

4.

DNA replication must be very rapid, given the sizes of the genomes and the rates of cell division. The E. coli genome contains 4.8 million base pairs and is copied in less than 40 minutes. Thus, 2000 bases are incorporated per second. We shall examine some of the properties of the macromolecular machines that replicate DNA with such high accuracy and speed.

5.

The enzymes that copy DNA polymerize nucleotides in the 5′ → 3′ direction. The two polynucleotide strands of DNA run in opposite directions, yet both strands appear to grow in the same direction (Figure 27.3). Further analysis reveals that one strand is synthesized in a continuous fashion, whereas the opposite strand is synthesized in fragments in a discontinuous fashion. The synthesis of each fragment must be initiated in an independent manner, and then the fragments must be linked together. The DNA replication apparatus includes enzymes for these priming and ligation reactions.

6.

The replication machinery alone cannot replicate the ends of linear DNA molecules, so a mechanism is required to prevent the loss of sequence information with each replication. Specialized structures called telomeres are added by another enzyme to maintain the information content at chromosome ends.

7.

Most components of the DNA replication machinery serve to preserve the integrity of a DNA sequence to the maximum possible extent, yet a variety of biological processes require DNA formed by the exchange of material between two parent molecules. These processes range from the development of diverse antibody sequences in the immune system (Chapter 33) to the integration of viral genomes into host DNA. Specific enzymes, termed recombinases, facilitate these rearrangements.

8.

After replication, ultraviolet light and a range of chemical species can damage DNA in a variety of ways. All organisms have enzymes for detecting and repairing harmful DNA modifications. Agents that introduce chemical lesions into DNA are key factors in the development of cancer, as are defects in the repair systems that correct these lesions.

Figure 27.2. Consequences of Strand Separation.

Figure 27.2

Consequences of Strand Separation. DNA must be locally unwound to expose single-stranded templates for replication. This unwinding puts a strain on the molecule by causing the overwinding of nearby regions.

Figure 27.3. DNA Replication At Low Resolution.

Figure 27.3

DNA Replication At Low Resolution. On cursory examination, both strands of a DNA template appear to replicate continuously in the same direction.

We begin with a review of the structural properties of the DNA double helix.

Faithful copying is essential to the storage of genetic information.

Figure

Faithful copying is essential to the storage of genetic information. With the precision of a diligent monk copying an illuminated manuscript, a DNA polymerase (below) copies DNA strands, preserving the precise sequence of bases with very few errors. [(Left) The (more...)

  • 27.1. DNA Can Assume a Variety of Structural Forms
  • 27.2. DNA Polymerases Require a Template and a Primer
  • 27.3. Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures
  • 27.4. DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites
  • 27.5. Double-Stranded DNA Molecules with Similar Sequences Sometimes Recombine
  • 27.6. Mutations Involve Changes in the Base Sequence of DNA
  • Summary
  • Problems
  • Selected Readings

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2002, W. H. Freeman and Company.
Bookshelf ID: NBK21202

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