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DNA Replication, Repair,and Recombination

The ability of a cell to maintain order in a chaotic environment dependson the accurate duplication of the vast quantity of genetic informationcarried in its DNA. This duplication process, called

DNA replication

,must occur before a cell can produce two genetically identical daughtercells. Maintaining order in a cell also requires the continual surveillanceand repair of its genetic information, as DNA is subject to damage by chemicals and radiation from the environment, and by accidents andreactive molecules that occur inside the cell. As we shall see in thischapter, each cell contains elaborate machinery for accurately copying its store of genetic information, as well as specialized enzymes forrepairing DNA when it is damaged. These enzymes catalyze some of themost rapid and accurate processes that take place within cells, and theiractions reflect the elegance and efficiency of cellular chemistry.Despite these systems for protecting the genetic instructions fromcopying errors and accidental damage, permanent changes, or

muta-tions,

sometimes do occur. Mutations in the DNA often affect the infor-mation it encodes. Occasionally, this can benefit the organism in whicha mutation occurs: for example, mutations can make bacteria resistantto antibiotics that are used to kill them. Indeed, the accumulation of changes in DNA over millions of years provides the variety in geneticmaterial that makes one species distinct from another, as we discuss inChapter 9. Mutations also produce the smaller variations that underliethe differences between individuals of the same species that we can eas-ily see in humans and other animals (Figure 6–1).However, mutations are often detrimental: in humans, mutationsare responsible for thousands of inherited diseases, and mutations thatarise in the cells of the body throughout the lifetime of an individualmay also cause disease, most notably the many types of cancer. Thussurvival of a cell or organism can depend on preventing changes to itsDNA. Without the cellular systems that are continually monitoring andrepairing damage to DNA, it is questionable whether life could exist atall.In this chapter, we begin by reviewing the cellular mechanisms—DNA replication and repair—that are responsible for keeping mutationsto a minimum. Finally, we consider some of the intriguing ways in which cells alter their genetic information, including

DNA recombina-tion

and the movement of the special DNA sequences in our chromo-somes called

transposable elements

DNA Replication

Base-Pairing Enables DNA ReplicationDNA Synthesis Begins at Replication OriginsNew DNA Synthesis Occurs at ReplicationForksThe Replication Fork Is AsymmetricalDNA Polymerase Is Self-correctingShort Lengths of RNA Act as Primers for DNA SynthesisProteins at a Replication Fork Cooperate toForm a Replication MachineTelomerase Replicates the Ends ofEucaryotic ChromosomesDNA Replication Is Relatively Well Understood

DNA Repair

Mutations Can Have Severe Consequencesfor an Organism A DNA Mismatch Repair System RemovesReplication Errors That Escape theReplication MachineDNA Is Continually Suffering Damage in CellsThe Stability of Genes Depends on DNA RepairThe High Fidelity of DNA Maintenance AllowsClosely Related Species to Have Proteinswith Very Similar Sequences

DNA Recombination

Homologous Recombination Results in anExact Exchange of Genetic InformationRecombination Can Also Occur BetweenNonhomologous DNA SequencesMobile Genetic Elements Encode theComponents They Need for Movement A Large Fraction of the Human Genome IsComposed of Two Families of TransposableSequences Viruses Are Fully Mobile Genetic ElementsThat Can Escape from CellsRetroviruses Reverse the Normal Flow ofGenetic Information

DNA Replication

At each cell division, a cell must copy its genome with extraordinary accuracy. In this section, we explore how the cell achieves this precision, while duplicating DNA at rates as high as 1000 nucleotides per second.

Base-Pairing Enables DNA Replication

In the preceding chapter, we saw that each strand of the DNA doublehelix contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. Each strand can there-fore act as a

template

, or mold, for the synthesis of a new complemen-tary strand (Figure 6–2). In other words, if we designate the two DNA strands as S and S

, strand S can serve as a template for making a new strand S

, while strand S

can serve as a template for making a new strand S (Figure 6–3). Thus, the genetic information in DNA can beaccurately copied by the beautifully simple process in which strand Sseparates from strand S

, and each separated strand then serves as atemplate for the production of a new complementary partner strandthat is identical to its former partner.The ability of each strand of a DNA molecule to act as a template forproducing a complementary strand enables a cell to copy, or

replicate,

its genes before passing them on to its descendants. But the task is awe-inspiring, as it can involve copying billions of nucleotide pairs every time a cell divides. The copying must be carried out with speed andaccuracy: in about 8 hours, a dividing animal cell will copy the equiva-

Chapter 6: DNA Replication, Repair, and Recombination

6:2

Figure 6–1Hereditary information is passed faithfully from onegeneration to the next.

Changes in the DNA, however, can producethe variations that underlie the differences between individuals of thesame species—or, over time, the differences between one species andanother. In this family photo, the children resemble one another andtheir parents more closely than they resemble other people becausethey inherit their particular genes from their parents. The cat sharesmany features with humans, but during the millions of years of evolution that have separated humans and cats, we both haveaccumulated many hereditary changes that now make us quitedifferent species. The chicken is an even more distant relative.

Figure 6–2A DNA strand can serve as atemplate.

Preferential binding occursbetween pairs of nucleotides (A with T, andG with C) that can form base pairs. Thisenables each strand to act as a templatefor forming its complementary strand.

Figure 6–3DNA acts as a template for its own duplication.

Because thenucleotide A will successfully pair only with T, and G with C, each strand of DNAcan serve as a template to specify the sequence of nucleotides in its complementarystrand. In this way, double-helical DNA can be copied precisely. Keep in mind thatalthough they are colored differently here, the template strands

(orange)

and thenew strands

(red)

are chemically identical.

parent DNA double helixtemplate S strandtemplate S

strandnew S

strandnew S strand5

S strandS

strand

lent of 1000 books like this one and, on average, get no more than a sin-gle letter or two wrong. This feat is performed by a cluster of proteinsthat together form a “replication machine.” DNA replication producestwo complete double helices from the original DNA molecule, each new DNA helix identical (except for rare errors) in nucleotide sequence tothe parental DNA double helix (see Figure 6–3). Because each parentalstrand serves as the template for one new strand, each of the daughterDNA double helices ends up with one of the original (old) strands plusone strand that is completely new; this style of replication is said to besemiconservative (Figure 6–4).

DNA Synthesis Begins at Replication Origins

The DNA double helix is normally very stable: the two DNA strands arelocked together firmly by the large numbers of hydrogen bondsbetween the bases on both strands (see Figure 5–2). As a result, only temperatures approaching those of boiling water provide enough ther-mal energy to separate these strands. In order to be used as a template,however, the double helix must first be opened up and the two strandsseparated to expose unpaired bases. How does this occur at the tem-peratures found in living cells?The process of DNA replication is begun by initiator proteins thatbind to the DNA and pry the two strands apart, breaking the hydrogenbonds between the bases (Figure 6–5). Although the hydrogen bondscollectively make the DNA helix very stable, individually each hydrogenbond is weak (Chapter 2). Separating a short length of DNA does nottherefore require a large energy input and can occur with the assistanceof these proteins at normal temperatures.The positions at which the DNA is first opened are called

replica-tion origins

, and they are marked by a particular sequence of nucleotides. In simple cells like those of bacteria or yeast, replicationorigins span approximately 100 base pairs; they are composed of DNA sequences that attract the initiator proteins, as well as stretches of DNA that are especially easy to open. We saw in Chapter 5 that an A-T basepair is held together by fewer hydrogen bonds than is a G-C base pair.Therefore, DNA rich in A-T base pairs is relatively easy to pull apart, and A-T–rich stretches of DNA are typically found at replication origins. A bacterial genome, which is typically contained in a circular DNA molecule of several million nucleotide pairs, has a single origin of repli-cation. The human genome, which is very much larger, has approxi-mately 10,000 such origins. In humans, beginning DNA replication atmany places at once allows a cell to replicate its DNA relatively quickly.In How We Know, pp.



–



, we discuss experiments that reveal the loca-tions of the replication origins in an organism’s genome.Once an initiator protein binds to DNA at the replication origin andlocally opens up the double helix, it attracts a group of proteins thatcarry out DNA replication. This group operates as a

protein machine

, with each member carrying out a specific function. We will introduceeach of these proteins shortly, after we consider the overall process of DNA replication.

6:3

DNA Replication

Figure 6–4In each round of replication, each of the two strands ofDNA is used as a template for the formation of a complementaryDNA strand.

The original strands, therefore, remain intact throughmany cell generations. DNA replication is “semiconservative” becauseeach daughter DNA double helix is composed of one conserved strandand one newly synthesized strand.

REPLICATIONREPLICATIONREPLICATION

Figure 6–5A DNA double helix is openedat its replication origin.

Replicationinitiator proteins recognize sequences of DNA at replication origins and locally pryapart the two strands of the double helix.The exposed single strands can then serveas templates for copying the DNA.

replication origindouble-helicalDNAdouble helix openedwith the aid ofinitiator proteinssingle-stranded DNA templatesready for DNA synthesis5