Principles of Biology contents 45 DNA Replication16) 45-DNA... · 2016. 11. 17. · models for DNA replication — the conservative model and the dispersive model. Figure 1 illustrates

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45 DNA Replication

During DNA replication, a cell uses a variety of proteins to create a new copy of itsgenome.

DNA replication is a set of timed processes involving many different proteins and requiring lots of energy.How do our cells manage to replicate 3 billion base pairs without significant error?© 2011 Nature Education All rights reserved.

Topics Covered in this Module Semi-Conservative DNA ReplicationOverall Principles of DNA ReplicationProofreading and RepairEukaryotic DNA Replication

Major Objectives of this Module Describe DNA replication as being semi-conservative, and explain the difference between the semi-conservativemodel and the conservative and dispersive models.Explain the experimental setup, results, and conclusions of the Meselson-Stahl experiment.Explain the mechanisms by which DNA replication is initiated and the leading and lagging strands are synthesized,and how these processes differ in prokaryotes and eukaryotes.Describe how errors occur during replication, how they are repaired, and the consequences of failure to repair sucherrors.Explain how telomeres are replicated in eukaryotic cells.


45 DNA Replication

Figure 1: Possible mechanisms for DNA replication.

© 2013 Nature Education All rights reserved. Figure Detail

Watson and Crick proposed that DNA replication is semi-conservative,rather than conservative or dispersive.

Could a person retype an essay that is 3 billion letters long without making asingle typo? Most likely not. Every time a human cell divides, variousproteins in the cell function to copy the 3 billion nucleotides in the DNA in thecorrect sequence so that both cells have virtually the same copy of thegenome.

Semi-Conservative DNA ReplicationAfter James Watson and Francis Crick elucidated DNA's double helicalstructure, they also realized that the complementary strands could have afunctional importance in DNA replication. Scientists knew that cells neededto be able to copy genetic material when they divided, but they didn't knowhow DNA was copied. Watson and Crick proposed that the two strands in theparental DNA molecule separate, allowing each strand to act as a templatefor the daughter DNA molecules. Their model of DNA replication is thesemi-conservative model, where each daughter DNA molecule containsone intact strand of the parental DNA molecule and one intact, newlysynthesized molecule of DNA.

Watson and Crick did not have any experimental evidence to support thesemi-conservative model. Other scientists proposed two other possiblemodels for DNA replication — the conservative model and the dispersivemodel. Figure 1 illustrates the differences between the three proposedmechanisms of DNA replication.

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Compare the DNA molecules produced after the first and second rounds of replication foreach model. What are you able to predict about the DNA produced after each round ofreplication based on each model?

How do scientists now know that Watson and Crick’s semi-conservativemodel was correct? Matthew Meselson and Franklin Stahl designed anexperiment to determine the mechanism of DNA replication. They reasonedthat they could determine the method of replication by tracing the origins ofreplicated DNA. Meselson and Stahl predicted the following:

If the replication method were conservative, one round of replicationwould yield a DNA molecule that contained two strands of parentalDNA, and a second DNA molecule that contained two new strands.If the replication method were semi-conservative, one round ofreplication would yield two DNA molecules that each contained onestrand of parental DNA and one strand of new DNA.If the replication method were dispersive, one round of replicationwould yield two DNA molecules with each strand containing mixturesof fragments of both original and newly synthesized DNA.

Once Meselson and Stahl knew what the possible outcomes of DNAreplication would be, they were left with another question: How could they tellthe difference between the parental DNA and the new DNA? They were ableto solve this problem by developing a way to tag the DNA strands using thetwo stable isotopes of nitrogen, the lighter 14N, which is most common, andthe heavier 15N, which is rare in nature. By following the tagged DNAthrough two rounds of replication, they were able to distinguish between thethree models. Figure 2 shows their experimental design.

Meselson and Stahl's experiment confirmed that DNA replication follows thesemi-conservative model. According to this model, each strand of theparental DNA molecule serves as a template to produce a newcomplementary daughter strand. The resulting DNA molecule contains oneparental strand and one new daughter strand.

Although Meselson and Stahl performed this experiment over fifty years ago,the experiment has a modern quality. They developed alternative hypothesesbased on the different models proposed, and then determined whichhypotheses were supported, and which were not. Furthermore, the materialsthey used are still in wide use today. Most significantly, the simplicity andelegance of their experimental design make their experiment a timelessclassic.

Meselson and Stahl used Biomarkers and Gradient Centrifugation intheir Experimental Setup

Figure 2: The Meselson and Stahl experiment.Matthew Meselson and Franklin Stahl used isotopes of nitrogen asbiomarkers to distinguish between parental and daughter DNA strands. Indoing so, they determined that DNA replication proceeds according to thesemi-conservative model.

© 2014 Nature Education All rights reserved. Transcript

BIOSKILL

Semi-Conservative DNA Replication

Overall Principles of DNA Replication

Proofreading and Repair

Eukaryotic DNA Replication

Summary

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Can we expand the genetic code?Converting nonsense codons into sensecodons by targeted pseudouridylation.

The role of cyclin D1 in DNA repairlinked to cancer growthA function for cyclin D1 in DNA repairuncovered by protein interactome analysesin human cancers.


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Classic paper: How scientistsdiscovered the enzyme that turnsRNA into DNA (1970)RNA-dependent DNA polymerase in virionsof RNA tumour viruses.


45 DNA Replication

Figure 3: The prokaryotic replication bubble.

© 2013 Nature Education All rights reserved.

In E. coli and other bacteria, the DNA double helix separates at the origin ofreplication (yellow star), creating a replication bubble. Synthesis of thenew strands proceeds in both directions away from the origin ofreplication, forming a replication bubble, and the places where the twostrands separate are called the replication forks. As replication proceeds,the replication bubble gets larger, so that eventually the replication forksmeet at the DNA replication terminus (red star), and the two newchromosomes separate.

Overall Principles of DNA ReplicationIn theory, the idea of replicating DNA seems relatively easy; make acomplementary copy of a strand of DNA and put the two strands together.However, many intermediate steps have to take place for this to occur.Various proteins must first separate the double helix and then add the correctbases to the new strand.

Scientists have studied the prokaryotic mechanism of DNA replicationand outlined it in detail.The replication of Escherichia coli DNA is the most widely studied and bestunderstood. E. coli DNA is contained within a single, circular chromosome.The replication process does not begin at any random spot along the DNAmolecule. It begins at a certain sequence of nucleotides, the origin ofreplication. Each bacterial chromosome contains a single origin ofreplication. The hydrogen bonds between the two complementary DNAstrands break more easily at the origin so that the double helix can beopened in both directions starting from this point. The opening of the doublehelix creates two replication forks, which form a replication bubble (Figure3). Replication proceeds in both directions away from the origin ofreplication, expanding the replication bubble. Eventually, the two replicationforks meet at the DNA replication terminus opposite the origin of replication,and the result is two separate and complete circular chromosomes.

DNA replication proceeds according to base-pairing rules.DNA replication requires a template strand, which the proteins involved in

Figure 4: Adding nucleotides duringDNA replication.

© 2012 Nature Education All rightsreserved.

The enzyme DNA polymerase addsnucleotides to the 3′ end of each strandof DNA. Newly added nucleotides havebases that are complementary to thoseon the template strand.

replication use to determine which nucleotides to add to the growingdaughter strand. Nucleotides are added to the daughter strand according tobase-pairing rules. For example, if the template strand contains thesequence 3′–CTA–5′, then the daughter strand will contain the correspondingsequence 5′–GAT–3′. These complementary base pairs are joined byhydrogen bonds. During DNA synthesis, nucleotides are added to the 3′ endof the growing daughter strand — the end at which the DNA strand has afree hydroxyl (–OH) group on the 3′ carbon of the sugar (Figure 4).

Several proteins make up the molecular machinery responsible forunwinding the DNA double helix during the initiation of replication (Figure 5).First, proteins recognize and bind to the origin of replication sequence toseparate the two DNA strands and form two replication forks. Then, DNAhelicase binds to each replication fork of the double helix and continues tobreak the hydrogen bonds between the two strands. This allows the DNA tounwind into two separate strands at the replication fork. Single-strandDNA-binding (SSB) proteins prevent the separated strands from rejoiningby binding to the separated strands and stabilizing them. Topoisomerase isa protein that binds to the double helix ahead of the replication fork andrelieves the torsional strain placed on the double helix as it unravels.

Figure 5: Initiation of replication.


During the initiation of DNA replication, proteins bind to the origin ofreplication and separate the strands of the double helix there. DNAhelicase then unwinds the double helix and continues to break thehydrogen bonds that hold the two parental strands together. Single-strandDNA-binding (SSB) proteins bind to the separated strands of DNA toprevent spontaneous hydrogen bonding of the single strands.Topoisomerase stabilizes the region directly ahead of the replication forkby breaking the strands, turning them, and rejoining them to relieve thetorsional (twisting) strain created by the unwinding of the double helix.

DNA synthesis always proceeds in the 5′ to 3′ direction. The first hurdle isDNA polymerase specificity. The enzyme only continues synthesis from analready established 3′ hydroxyl (–OH) group on a nucleotide, meaning thatDNA can only be extended from an existing nucleotide — it cannot besynthesized from scratch. This obstacle is overcome by the enzyme DNAprimase. At the start of DNA replication, DNA primase synthesizes a short,temporary RNA primer on each DNA template strand. Like DNA polymerase,DNA primase requires a template, but unlike DNA polymerase, DNA primasedoes not need the 3′–OH group of the previous nucleotide to catalyze thereaction. After a short RNA primer sequence has been created on the DNAtemplate strand, the DNA primase falls off. From here, DNA polymeraseuses the 3′–OH of the RNA primer to continue synthesizing the new daughterstrand (Figure 6).

Figure 6: An overview of DNA replication in E. coli.


Synthesis of the leading and lagging strands of DNA involves coordinationof multiple proteins.

The enzyme DNA polymerase III recognizes the primer and addsnucleotides to the 3′ end of the primer, creating a growing daughter strand.However, both strands of the parental DNA serve as templates, and the DNApolymerase III enzymes that construct each daughter strand are connectedin a single complex at the replication fork. This means that both DNApolymerase III molecules must move towards the replication fork.

If both DNA polymerase III molecules move in the same direction, how dothey both synthesize antiparallel strands in the 5′ to 3′ direction? Synthesis ofeach of the two daughter strands occurs in a slightly different manner.Assembly of the leading strand occurs continuously, because the 3′ end ofthe growing strand faces the replication fork. In the leading strand, an RNAprimer is added near the origin of replication, and then DNA polymerase IIIadds nucleotides in a continuous fashion as the replication fork moves alongthe opening double helix.

However, the process is more complicated in the lagging strand. In thelagging strand, the 3′ end of the growing strand faces away from thereplication fork. The DNA polymerase complex moves in the same overalldirection as the DNA helicase. This means that DNA polymerase III cannotsimply continue adding nucleotides in a continuous strand for the laggingstrand, because doing so would require constantly moving away from thereplication fork. So, how does DNA polymerase III move from the 5′ to 3′direction while still moving towards the replication fork? The DNApolymerase must periodically detach from the lagging strand template, movecloser to the replication fork, and reattach to the template. Before the DNApolymerase reattaches to the template, DNA primase must add a new RNAprimer to the template for lagging strand synthesis. As a result, the laggingstrand is formed in a series of discontinuous fragments of 1,000–2,000nucleotides. These fragments are named Okazaki fragments, after theJapanese scientists who discovered this process.

Each Okazaki fragment is completed when DNA polymerase III runs into theRNA primer of the previous Okazaki fragment. How are the Okazaki

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© 2014 Nature Education All rights reserved. Transcript

fragments linked together to form a continuous strand of DNA? Uponcompletion of each Okazaki fragment, DNA polymerase I uses the 3′–OHend of each Okazaki fragment as a starting point to extend the fragment,replacing the RNA primer of the previous fragment with the correspondingDNA nucleotides. Removal of the primers results in gaps in the sugar-phosphate backbone of the new strand. Another enzyme, DNA ligase, joinsthese gaps in the backbone to form a single, continuous strand. This sameprocess also replaces the RNA primer used to initiate synthesis of theleading strand.

Test Yourself

Why must the lagging strand be produced in discontinuous Okazaki fragments?

Click on Figure 7 to see an animation of DNA replication.

Figure 7: DNA replication in E. coli.During the process of DNA replication, DNA helicase and other proteinsunwind and stabilize the template strands so that DNA polymerase III andother proteins can synthesize the daughter strands.





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45 DNA Replication

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Proofreading and RepairWhat happens to DNA that has been damaged or incorrectly replicated?DNA polymerases not only synthesize the new DNA strands, but they alsoproofread their own work. If they find a nucleotide that is incorrectly basepaired, they remove and replace the nucleotide. If an error in base pairingslips by the polymerases, the daughter strand may be repaired by theprocess of mismatch repair. In this process, enzymes cut out the incorrectnucleotide from the daughter strand and replace it with the appropriatenucleotide according to base-pairing rules.

What if more than one nucleotide is incorrectly paired? While mismatchrepair corrects errors in mismatched base pairs, it cannot repair other morebulky types of DNA lesions. DNA containing bulky lesions may undergonucleotide excision repair. Nucleotide excision repair is used to replaceportions of DNA chemically damaged by environmental effects, such asexposure to ultraviolet radiation from the Sun, or certain chemicals. Duringthis process, enzymes known as nucleases make incisions on either side ofthe lesion, a DNA polymerase replaces the damaged DNA with newnucleotides, and DNA ligase reconnects the newly replaced DNA fragmentwith the existing strand. DNA damage also occurs after replication, andthese same repair mechanisms help to prevent the damaged sequence frombecoming a permanent mutation.

Are all mistakes detected and repaired? Some errors in the DNA sequencemay go unrepaired. When the strand containing the error is replicated, theerror is passed on to the daughter DNA and becomes a permanent mutation.Some mutations are neutral and do not interfere with a cell's normalfunctions. Other errors in DNA replication may lead to diseases, such ascancer, or other deleterious effects. In fact, however, these mutations arealso essential for organisms to change and adapt as their surroundingenvironment changes. Even though mutations in DNA replication arerelatively rare, and the vast majority of them are either neutral or deleterious,some of those mutations can lead to an ever so slight change to an organismthat creates variation among individuals in a population. This variation is thensubject to fundamental evolutionary processes such as natural selection andgenetic drift and can ultimately lead to the formation of new species.

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What repair mechanisms does the cell use when it detects damage to its DNA?





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45 DNA Replication

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Eukaryotic DNA ReplicationDNA replication in eukaryotes involves mechanisms similar to the one in E. coli and other bacteria. However, there aresome key differences. Like many other eukaryotes, human DNA contains billions of base pairs and may have thousandsof origins of replication. In most eukaryotes, chromosomes are linear, and multiple replication bubbles at different stages inthe replication process are located along the chromosomes. The linear nature of eukaryotic DNA presents a challenge nottypically found in bacterial DNA replication; DNA polymerase III cannot add the final sequence of DNA to the 5′ end of thelagging daughter strand.

Test Yourself

If the final sequence of DNA cannot be added to the 5′ end of the lagging daughter strandduring replication, how would you expect this to affect the length of a molecule of DNA witheach round of replication?

In the circular DNA of prokaryotes, there is no end, so this is not a problem.However, in linear eukaryotic DNA, a solution is required or geneticinformation would be lost with each round of replication. For this reason,eukaryotic chromosomal DNA has special sequences at their ends calledtelomeres. Telomeres contain repeating sequences of bases that do notcode for proteins; they serve to protect the genetic information contained atthe ends of eukaryotic chromosomes.

Telomerase is an enzyme that contains its own RNA template, which is usedto lengthen the telomere of the lagging strand DNA template. Lengtheningthis DNA provides a region for DNA primase to create an RNA primer,allowing the DNA at the end of the chromosome to be replicated without lossof genetic information. How does telomerase work? Review Figure 8 to findout.

Figure 8: Replication of telomeres in eukaryotes.

© 2014 Nature Education All rights reserved.

During DNA replication, DNA polymerase can copy the leading strandcompletely (1, lower panel), but replicating the lagging strand of DNArequires a RNA primer at the very end of the chromosome (1, upperpanel). After degradation of the RNA primer, some DNA is left as a singlestrand (2) and will be lost during subsequent cell divisions. To protectagainst the loss of genetic information, the enzyme telomerase, whichcontains an internal strand of RNA, extends the end of the parental DNAstrand using the RNA as a template (3). Finally, RNA primase synthesizesa new primer complementary to this extension, which allows the DNA atthe end of the chromosome to be replicated faithfully (4).

Future perspectives.DNA replication in eukaryotic organisms is not as well understood as it is inprokaryotic organisms. Although the basic semi-conservative mechanismhas been maintained, there are some important differences. For example, atleast fifteen DNA polymerases have been discovered in eukaryotes, andthey are different from those in E. coli. Scientists still do not fully understandthe roles of the eukaryote polymerases, and they may not have evenidentified all of them yet.


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45 DNA Replication

OBJECTIVE Describe DNA replication as being semi-conservative, andexplain the difference between the semi-conservative modeland the conservative and dispersive models.

Watson and Crick proposed that the mechanism of DNA replication issemi-conservative, with each new DNA molecule containing one intact, newlysynthesized daughter strand and one intact original parental strand. Thealternative models proposed for DNA replication were the conservative anddispersive models. In the conservative model, the whole DNA double helixserves as a template and remains intact such that the original double-stranded DNA molecule and an entirely new double-stranded daughtermolecule exist after replication. In the dispersive model, the parental DNAmolecule is broken into fragments, which are replicated; the strand of thenew DNA molecule contains portions of both the parental strand and thedaughter strand in both strands.

OBJECTIVE Explain the experimental setup, results, and conclusions ofthe Meselson-Stahl experiment.

The Meselson-Stahl experiment provided evidence to support thesemi-conservative model. In this experiment, E. coli was first grown in thepresence of 15N isotopes and then switched to a medium containing 14N.This meant that virtually all DNA originally contained heavy nitrogen, and anynewly synthesized DNA would contain light nitrogen. DNA was collected fromtwo generations of E. coli grown in the 14N media and centrifuged in a densitygradient. After the first generation, the results showed a band thatcorresponded to DNA containing equal amounts of 14N and 15N. The secondgeneration showed two bands — one for DNA containing equal amounts of14N and 15N, and one for DNA containing only 14N. These results supportedthe semi-conservative model.

OBJECTIVE Explain the mechanisms by which DNA replication is initiatedand the leading and lagging strands are synthesized, andhow these processes differ in prokaryotes and eukaryotes.

DNA replication starts at the origin of replication, where proteins initially openthe DNA helix. DNA helicase then unwinds the DNA and continues to breakhydrogen bonds at the replication forks. Single-strand DNA-binding proteinskeep the strands from rejoining, and topoisomerase relieves the torsionalstrain in the unwound portion of the double helix. DNA primase adds an initialRNA primer to the template, after which DNA polymerase III begins addingnucleotides to the 3′ end. The leading strand is synthesized continuously inthe 5′ to 3′ direction. The lagging strand is discontinuously synthesized asOkazaki fragments starting with RNA primers. The RNA primers are removedby DNA polymerase I and simultaneously replaced with DNA (also in the 5′ to3′ direction). DNA ligase joins the backbone of the fragments to form acomplete, continuous strand. Prokaryotic chromosomes are circular andhave only one origin of replication, whereas eukaryotic chromosomes arelinear and may have thousands of origins of replication.

OBJECTIVE Describe how errors occur during replication, how they arerepaired, and the consequences of failure to repair sucherrors.

Errors may occur during replication when an incorrect base is added to thedaughter strand. DNA polymerase proofreads the added bases and has theability to replace incorrectly incorporated ones by itself. If an error in base

Summary

pairing slips by the polymerases, the daughter strand may be repaired bymismatch repair. In this process, enzymes cut out the incorrect nucleotidefrom the daughter strand and replace it with the appropriate nucleotide.Nucleases may also cut out bulky DNA lesions, after which a DNApolymerase replaces the fragment with the correct sequence by nucleotideexcision repair. Some of these errors, however, escape both proofreadingand repair mechanisms and can become mutations. Most mutations eitherhave no influence on the survival of an organism or are deleterious, causingharm. However, a small proportion of mutations cause a slight change in anorganism that is then subject to fundamental evolutionary processes, such asnatural selection and genetic drift; thus, a mutation can lead to a population'straits changing through time and ultimately lead to the formation of newspecies.

OBJECTIVE Explain how telomeres are replicated in eukaryotic cells.Linear eukaryotic chromosomes contain non-coding repetitive DNAsequences at their ends called telomeres. Telomerases lengthen the parentalstrand using an RNA template so that the lagging strand may be replicatedcompletely during DNA replication.

DNA helicaseA protein that binds to double-stranded DNA and breaks the hydrogen bondsbetween the two strands.

DNA ligaseAn enzyme involved in sealing gaps in the sugar-phosphate backbone of DNA bycatalyzing the formation of a phosphodiester bond.

DNA polymerase IAn enzyme that replaces RNA primers at the beginning of Okazaki fragments bysimultaneously removing the primers and replacing then with the correspondingDNA nucleotides.

DNA polymerase IIIThe primary DNA-synthesizing enzyme in E. coli; recognizes the RNA primer andadds DNA nucleotides to the 3′ end of the primer.

lagging strandThe strand of DNA that is replicated in the direction opposite to the movement ofthe replication fork; replicated discontinuously as a series of Okazaki fragments,each 1,000-2,000 nucleotides in length.

leading strandThe strand of DNA that is replicated in the same direction as the movement of thereplication fork; replicated continuously as the double helix opens.

mismatch repairThe process by which enzymes cut out an incorrectly base-paired nucleotide fromDNA and replace it with the appropriate nucleotide according to base-pairingrules.

nucleaseAn enzyme involved in removing corrupted sections of DNA during nucleotideexcision repair.

nucleotide excision repairA process in which proteins remove sections of DNA containing large, bulkylesions and replace these regions with new nucleotides using the undamagedDNA as a template.

Okazaki fragmentFragments of DNA formed during DNA replication on the lagging strand; must beconnected together with DNA ligase to complete replication of strand.

origin of replicationA sequence of nucleotides where DNA replication begins. In eukaryotes, there are

Key Terms


multiple origins of replication; in prokaryotes, there is typically only one.

replication forkDuring DNA replication, the region at which the double helix becomes separatedby DNA helicase.

semi-conservative modelThe model of DNA replication where each of the two daughter DNA moleculescontains one intact strand of the parental DNA molecule and one continuousnewly synthesized strand of DNA.

single-strand DNA-binding (SSB) proteinsA stabilizing protein involved in DNA replication that prevents the separated DNAstrands from re-joining or re-coiling during the replication process.

telomeraseAn enzyme that uses an RNA template to lengthen the telomere of the DNAtemplate strand.

telomeresSpecial end sequences containing repeating sequences of bases that serve toprotect the genetic information contained at the ends of eukaryotic chromosomes.

topoisomeraseA protein that binds to the double helix ahead of the replication fork and relievestorsional strain in the DNA caused by overwinding or underwinding.





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45 DNA Replication

1.

dispersiveconservativesemi-conservativesemi-dispersiveNone of the answers are correct.

In which model of DNA replication does the parent DNA molecule break intofragments that are copied?

2.

They needed to ensure that all newly synthesized DNA would contain the samemarker.The E. coli would only reproduce in media containing 14N.14N caused a higher rate of mutation in E. coli.They needed to be able to separate the parental and newly synthesized DNAthrough differential centrifugation, and only DNA containing the lighter isotopewould form a band.None of the answers are correct.

Why did Meselson and Stahl transfer E. coli from media containing 15N to mediacontaining 14N?

3.

helicaseprimasetopoisomeraseDNA polymerase INone of the answers are correct.

Which protein is responsible for synthesizing the new DNA strand duringreplication in prokaryotes?

4.

It replaces RNA nucleotides with DNA nucleotides.It adds nucleotides to the growing DNA strand.It synthesizes the RNA primers.It proofreads the DNA strand and corrects errors in base pairings.None of the answers are correct.

What is the role of DNA polymerase I in the replication of E. coli DNA?

5.

Helicase separates the strands of DNA.Nucleases cut the DNA strands apart.Primase begins to synthesize Okazaki fragments.DNA polymerase begins synthesizing the new DNA strand immediately.None of the answers are correct.

What happens at the origin of replication?

6.

Eukaryotic DNA replication does not require the replication of telomeres.Eukaryotic DNA requires the use of RNA primers.Eukaryotic DNA replication is faster.

What is one way that the replication of eukaryotic DNA generally differs from thereplication of prokaryotic DNA?

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There is no leading strand in eukaryotic DNA replication.Replication shortens the lagging strand in eukaryotic DNA.

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Principles of Biology contents 45 DNA Replication16) 45-DNA... · 2016. 11. 17. · models for DNA replication — the conservative model and the dispersive model. Figure 1 illustrates