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

Transcription

1 Principles of Biology contents 45 DNA Replication During DNA replication, a cell uses a variety of proteins to create a new copy of its genome. 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 Replication Overall Principles of DNA Replication Proofreading and Repair Eukaryotic DNA Replication Major Objectives of this Module Describe DNA replication as being semi-conservative, and explain the difference between the semi-conservative model 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 such errors. Explain how telomeres are replicated in eukaryotic cells. page 229 of pages left in this module

2 Principles of Biology contents 45 DNA Replication Could a person retype an essay that is 3 billion letters long without making a single typo? Most likely not. Every time a human cell divides, various proteins in the cell function to copy the 3 billion nucleotides in the DNA in the correct sequence so that both cells have virtually the same copy of the genome. Semi-Conservative DNA Replication After James Watson and Francis Crick elucidated DNA's double helical structure, they also realized that the complementary strands could have a functional importance in DNA replication. Scientists knew that cells needed to be able to copy genetic material when they divided, but they didn't know how DNA was copied. Watson and Crick proposed that the two strands in the parental DNA molecule separate, allowing each strand to act as a template for the daughter DNA molecules. Their model of DNA replication is the semi-conservative model, where each daughter DNA molecule contains one intact strand of the parental DNA molecule and one intact, newly synthesized molecule of DNA. Watson and Crick did not have any experimental evidence to support the semi-conservative model. Other scientists proposed two other possible models for DNA replication the conservative model and the dispersive model. Figure 1 illustrates the differences between the three proposed mechanisms of DNA replication. Figure 1: Possible mechanisms for DNA replication. Watson and Crick proposed that DNA replication is semi-conservative, rather than conservative or dispersive Nature Education All rights reserved. Figure Detail

3 Test Yourself Compare the DNA molecules produced after the first and second rounds of replication for each model. What are you able to predict about the DNA produced after each round of replication based on each model? Submit How do scientists now know that Watson and Crick s semi-conservative model was correct? Matthew Meselson and Franklin Stahl designed an experiment to determine the mechanism of DNA replication. They reasoned that they could determine the method of replication by tracing the origins of replicated DNA. Meselson and Stahl predicted the following: If the replication method were conservative, one round of replication would yield a DNA molecule that contained two strands of parental DNA, and a second DNA molecule that contained two new strands. If the replication method were semi-conservative, one round of replication would yield two DNA molecules that each contained one strand of parental DNA and one strand of new DNA. If the replication method were dispersive, one round of replication would yield two DNA molecules with each strand containing mixtures of fragments of both original and newly synthesized DNA. Once Meselson and Stahl knew what the possible outcomes of DNA replication would be, they were left with another question: How could they tell the difference between the parental DNA and the new DNA? They were able to solve this problem by developing a way to tag the DNA strands using the two stable isotopes of nitrogen, the lighter 14 N, which is most common, and the heavier 15 N, which is rare in nature. By following the tagged DNA through two rounds of replication, they were able to distinguish between the three models. Figure 2 shows their experimental design. Meselson and Stahl's experiment confirmed that DNA replication follows the semi-conservative model. According to this model, each strand of the parental DNA molecule serves as a template to produce a new complementary daughter strand. The resulting DNA molecule contains one parental 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 hypotheses based on the different models proposed, and then determined which hypotheses were supported, and which were not. Furthermore, the materials they used are still in wide use today. Most significantly, the simplicity and elegance of their experimental design make their experiment a timeless classic. BIOSKILL Meselson and Stahl used Biomarkers and Gradient Centrifugation in their Experimental Setup Figure 2: The Meselson and Stahl experiment. Matthew Meselson and Franklin Stahl used isotopes of nitrogen as biomarkers to distinguish between parental and daughter DNA strands. In doing so, they determined that DNA replication proceeds according to the semi-conservative model.

4 2014 Nature Education All rights reserved. Transcript BIOSKILL IN THIS MODULE Semi-Conservative DNA Replication Overall Principles of DNA Replication Proofreading and Repair Eukaryotic DNA Replication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Synthetic Biology: Making Life from Bits and Pieces Scientists are combining biology and engineering to change the world. PRIMARY LITERATURE Can we expand the genetic code? Converting nonsense codons into sense codons by targeted pseudouridylation. The role of cyclin D1 in DNA repair linked to cancer growth A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers.

5 Classic paper: How scientists discovered the enzyme that turns RNA into DNA (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. page 230 of pages left in this module

6 Principles of Biology contents 45 DNA Replication Overall Principles of DNA Replication In theory, the idea of replicating DNA seems relatively easy; make a complementary 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 correct bases to the new strand. Scientists have studied the prokaryotic mechanism of DNA replication and outlined it in detail. The replication of Escherichia coli DNA is the most widely studied and best understood. E. coli DNA is contained within a single, circular chromosome. The replication process does not begin at any random spot along the DNA molecule. It begins at a certain sequence of nucleotides, the origin of replication. Each bacterial chromosome contains a single origin of replication. The hydrogen bonds between the two complementary DNA strands break more easily at the origin so that the double helix can be opened in both directions starting from this point. The opening of the double helix creates two replication forks, which form a replication bubble (Figure 3). Replication proceeds in both directions away from the origin of replication, expanding the replication bubble. Eventually, the two replication forks meet at the DNA replication terminus opposite the origin of replication, and the result is two separate and complete circular chromosomes. Figure 3: The prokaryotic replication bubble. In E. coli and other bacteria, the DNA double helix separates at the origin of replication (yellow star), creating a replication bubble. Synthesis of the new strands proceeds in both directions away from the origin of replication, forming a replication bubble, and the places where the two strands separate are called the replication forks. As replication proceeds, the replication bubble gets larger, so that eventually the replication forks meet at the DNA replication terminus (red star), and the two new chromosomes separate Nature Education All rights reserved. DNA replication proceeds according to base-pairing rules. DNA replication requires a template strand, which the proteins involved in

7 replication use to determine which nucleotides to add to the growing daughter strand. Nucleotides are added to the daughter strand according to base-pairing rules. For example, if the template strand contains the sequence 3 CTA 5, then the daughter strand will contain the corresponding sequence 5 GAT 3. These complementary base pairs are joined by hydrogen bonds. During DNA synthesis, nucleotides are added to the 3 end of the growing daughter strand the end at which the DNA strand has a free hydroxyl ( OH) group on the 3 carbon of the sugar (Figure 4). Figure 4: Adding nucleotides during DNA replication. The enzyme DNA polymerase adds nucleotides to the 3 end of each strand of DNA. Newly added nucleotides have bases that are complementary to those on the template strand Nature Education All rights reserved. Several proteins make up the molecular machinery responsible for unwinding the DNA double helix during the initiation of replication (Figure 5). First, proteins recognize and bind to the origin of replication sequence to separate the two DNA strands and form two replication forks. Then, DNA helicase binds to each replication fork of the double helix and continues to break the hydrogen bonds between the two strands. This allows the DNA to unwind into two separate strands at the replication fork. Single-strand DNA-binding (SSB) proteins prevent the separated strands from rejoining by binding to the separated strands and stabilizing them. Topoisomerase is a protein that binds to the double helix ahead of the replication fork and relieves the torsional strain placed on the double helix as it unravels.

8 Figure 5: Initiation of replication. During the initiation of DNA replication, proteins bind to the origin of replication and separate the strands of the double helix there. DNA helicase then unwinds the double helix and continues to break the hydrogen bonds that hold the two parental strands together. Single-strand DNA-binding (SSB) proteins bind to the separated strands of DNA to prevent spontaneous hydrogen bonding of the single strands. Topoisomerase stabilizes the region directly ahead of the replication fork by breaking the strands, turning them, and rejoining them to relieve the torsional (twisting) strain created by the unwinding of the double helix Nature Education All rights reserved. Figure Detail DNA synthesis always proceeds in the 5 to 3 direction. The first hurdle is DNA polymerase specificity. The enzyme only continues synthesis from an already established 3 hydroxyl ( OH) group on a nucleotide, meaning that DNA can only be extended from an existing nucleotide it cannot be synthesized from scratch. This obstacle is overcome by the enzyme DNA primase. 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 primase does not need the 3 OH group of the previous nucleotide to catalyze the reaction. After a short RNA primer sequence has been created on the DNA template strand, the DNA primase falls off. From here, DNA polymerase uses the 3 OH of the RNA primer to continue synthesizing the new daughter strand (Figure 6).

9 Figure 6: An overview of DNA replication in E. coli. Synthesis of the leading and lagging strands of DNA involves coordination of multiple proteins Nature Education All rights reserved. Figure Detail The enzyme DNA polymerase III recognizes the primer and adds nucleotides to the 3 end of the primer, creating a growing daughter strand. However, both strands of the parental DNA serve as templates, and the DNA polymerase III enzymes that construct each daughter strand are connected in a single complex at the replication fork. This means that both DNA polymerase III molecules must move towards the replication fork. If both DNA polymerase III molecules move in the same direction, how do they both synthesize antiparallel strands in the 5 to 3 direction? Synthesis of each of the two daughter strands occurs in a slightly different manner. Assembly of the leading strand occurs continuously, because the 3 end of the growing strand faces the replication fork. In the leading strand, an RNA primer is added near the origin of replication, and then DNA polymerase III adds nucleotides in a continuous fashion as the replication fork moves along the opening double helix. However, the process is more complicated in the lagging strand. In the lagging strand, the 3 end of the growing strand faces away from the replication fork. The DNA polymerase complex moves in the same overall direction as the DNA helicase. This means that DNA polymerase III cannot simply continue adding nucleotides in a continuous strand for the lagging strand, because doing so would require constantly moving away from the replication fork. So, how does DNA polymerase III move from the 5 to 3 direction while still moving towards the replication fork? The DNA polymerase must periodically detach from the lagging strand template, move closer to the replication fork, and reattach to the template. Before the DNA polymerase reattaches to the template, DNA primase must add a new RNA primer to the template for lagging strand synthesis. As a result, the lagging strand is formed in a series of discontinuous fragments of 1,000 2,000 nucleotides. These fragments are named Okazaki fragments, after the Japanese scientists who discovered this process. Each Okazaki fragment is completed when DNA polymerase III runs into the RNA primer of the previous Okazaki fragment. How are the Okazaki

10 fragments linked together to form a continuous strand of DNA? Upon completion of each Okazaki fragment, DNA polymerase I uses the 3 OH end of each Okazaki fragment as a starting point to extend the fragment, replacing the RNA primer of the previous fragment with the corresponding DNA nucleotides. Removal of the primers results in gaps in the sugarphosphate backbone of the new strand. Another enzyme, DNA ligase, joins these gaps in the backbone to form a single, continuous strand. This same process also replaces the RNA primer used to initiate synthesis of the leading strand. Test Yourself Why must the lagging strand be produced in discontinuous Okazaki fragments? Submit 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 proteins unwind and stabilize the template strands so that DNA polymerase III and other proteins can synthesize the daughter strands Nature Education All rights reserved. Transcript IN THIS MODULE Semi-Conservative DNA Replication Overall Principles of DNA Replication Proofreading and Repair Eukaryotic DNA Replication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER?

11 Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Synthetic Biology: Making Life from Bits and Pieces Scientists are combining biology and engineering to change the world. PRIMARY LITERATURE Can we expand the genetic code? Converting nonsense codons into sense codons by targeted pseudouridylation. The role of cyclin D1 in DNA repair linked to cancer growth A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Classic paper: How scientists discovered the enzyme that turns RNA into DNA (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. page 231 of pages left in this module

12 Principles of Biology contents 45 DNA Replication Proofreading and Repair What happens to DNA that has been damaged or incorrectly replicated? DNA polymerases not only synthesize the new DNA strands, but they also proofread their own work. If they find a nucleotide that is incorrectly base paired, they remove and replace the nucleotide. If an error in base pairing slips by the polymerases, the daughter strand may be repaired by the process of mismatch repair. In this process, enzymes cut out the incorrect nucleotide from the daughter strand and replace it with the appropriate nucleotide according to base-pairing rules. What if more than one nucleotide is incorrectly paired? While mismatch repair corrects errors in mismatched base pairs, it cannot repair other more bulky types of DNA lesions. DNA containing bulky lesions may undergo nucleotide excision repair. Nucleotide excision repair is used to replace portions of DNA chemically damaged by environmental effects, such as exposure to ultraviolet radiation from the Sun, or certain chemicals. During this process, enzymes known as nucleases make incisions on either side of the lesion, a DNA polymerase replaces the damaged DNA with new nucleotides, and DNA ligase reconnects the newly replaced DNA fragment with the existing strand. DNA damage also occurs after replication, and these same repair mechanisms help to prevent the damaged sequence from becoming a permanent mutation. Are all mistakes detected and repaired? Some errors in the DNA sequence may go unrepaired. When the strand containing the error is replicated, the error is passed on to the daughter DNA and becomes a permanent mutation. Some mutations are neutral and do not interfere with a cell's normal functions. Other errors in DNA replication may lead to diseases, such as cancer, or other deleterious effects. In fact, however, these mutations are also essential for organisms to change and adapt as their surrounding environment changes. Even though mutations in DNA replication are relatively 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 organism that creates variation among individuals in a population. This variation is then subject to fundamental evolutionary processes such as natural selection and genetic drift and can ultimately lead to the formation of new species. Test Yourself What repair mechanisms does the cell use when it detects damage to its DNA? Submit IN THIS MODULE Semi-Conservative DNA Replication Overall Principles of DNA Replication Proofreading and Repair Eukaryotic DNA Replication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER?

13 Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Synthetic Biology: Making Life from Bits and Pieces Scientists are combining biology and engineering to change the world. PRIMARY LITERATURE Can we expand the genetic code? Converting nonsense codons into sense codons by targeted pseudouridylation. The role of cyclin D1 in DNA repair linked to cancer growth A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Classic paper: How scientists discovered the enzyme that turns RNA into DNA (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. page 232 of pages left in this module

14 Principles of Biology contents 45 DNA Replication Eukaryotic DNA Replication DNA replication in eukaryotes involves mechanisms similar to the one in E. coli and other bacteria. However, there are some key differences. Like many other eukaryotes, human DNA contains billions of base pairs and may have thousands of origins of replication. In most eukaryotes, chromosomes are linear, and multiple replication bubbles at different stages in the replication process are located along the chromosomes. The linear nature of eukaryotic DNA presents a challenge not typically found in bacterial DNA replication; DNA polymerase III cannot add the final sequence of DNA to the 5 end of the lagging daughter strand. Test Yourself If the final sequence of DNA cannot be added to the 5 end of the lagging daughter strand during replication, how would you expect this to affect the length of a molecule of DNA with each round of replication? Submit 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 genetic information would be lost with each round of replication. For this reason, eukaryotic chromosomal DNA has special sequences at their ends called telomeres. Telomeres contain repeating sequences of bases that do not code for proteins; they serve to protect the genetic information contained at the ends of eukaryotic chromosomes. Telomerase is an enzyme that contains its own RNA template, which is used to lengthen the telomere of the lagging strand DNA template. Lengthening this 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 loss of genetic information. How does telomerase work? Review Figure 8 to find out.

15 Figure 8: Replication of telomeres in eukaryotes. During DNA replication, DNA polymerase can copy the leading strand completely (1, lower panel), but replicating the lagging strand of DNA requires a RNA primer at the very end of the chromosome (1, upper panel). After degradation of the RNA primer, some DNA is left as a single strand (2) and will be lost during subsequent cell divisions. To protect against the loss of genetic information, the enzyme telomerase, which contains an internal strand of RNA, extends the end of the parental DNA strand using the RNA as a template (3). Finally, RNA primase synthesizes a new primer complementary to this extension, which allows the DNA at the end of the chromosome to be replicated faithfully (4) Nature Education All rights reserved. Future perspectives. DNA replication in eukaryotic organisms is not as well understood as it is in prokaryotic organisms. Although the basic semi-conservative mechanism has been maintained, there are some important differences. For example, at least fifteen DNA polymerases have been discovered in eukaryotes, and they are different from those in E. coli. Scientists still do not fully understand the roles of the eukaryote polymerases, and they may not have even identified all of them yet. IN THIS MODULE Semi-Conservative DNA Replication

16 Overall Principles of DNA Replication Proofreading and Repair Eukaryotic DNA Replication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Synthetic Biology: Making Life from Bits and Pieces Scientists are combining biology and engineering to change the world. PRIMARY LITERATURE Can we expand the genetic code? Converting nonsense codons into sense codons by targeted pseudouridylation. The role of cyclin D1 in DNA repair linked to cancer growth A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Classic paper: How scientists discovered the enzyme that turns RNA into DNA (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. page 233 of pages left in this module

17 Principles of Biology contents 45 DNA Replication Summary OBJECTIVE Describe DNA replication as being semi-conservative, and explain the difference between the semi-conservative model and the conservative and dispersive models. Watson and Crick proposed that the mechanism of DNA replication is semi-conservative, with each new DNA molecule containing one intact, newly synthesized daughter strand and one intact original parental strand. The alternative models proposed for DNA replication were the conservative and dispersive models. In the conservative model, the whole DNA double helix serves as a template and remains intact such that the original doublestranded DNA molecule and an entirely new double-stranded daughter molecule exist after replication. In the dispersive model, the parental DNA molecule is broken into fragments, which are replicated; the strand of the new DNA molecule contains portions of both the parental strand and the daughter strand in both strands. OBJECTIVE Explain the experimental setup, results, and conclusions of the Meselson-Stahl experiment. The Meselson-Stahl experiment provided evidence to support the semi-conservative model. In this experiment, E. coli was first grown in the presence of 15 N isotopes and then switched to a medium containing 14 N. This meant that virtually all DNA originally contained heavy nitrogen, and any newly synthesized DNA would contain light nitrogen. DNA was collected from two generations of E. coli grown in the 14 N media and centrifuged in a density gradient. After the first generation, the results showed a band that corresponded to DNA containing equal amounts of 14 N and 15 N. The second generation showed two bands one for DNA containing equal amounts of 14 N and 15 N, and one for DNA containing only 14 N. These results supported the semi-conservative model. OBJECTIVE 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. DNA replication starts at the origin of replication, where proteins initially open the DNA helix. DNA helicase then unwinds the DNA and continues to break hydrogen bonds at the replication forks. Single-strand DNA-binding proteins keep the strands from rejoining, and topoisomerase relieves the torsional strain in the unwound portion of the double helix. DNA primase adds an initial RNA primer to the template, after which DNA polymerase III begins adding nucleotides to the 3 end. The leading strand is synthesized continuously in the 5 to 3 direction. The lagging strand is discontinuously synthesized as Okazaki fragments starting with RNA primers. The RNA primers are removed by DNA polymerase I and simultaneously replaced with DNA (also in the 5 to 3 direction). DNA ligase joins the backbone of the fragments to form a complete, continuous strand. Prokaryotic chromosomes are circular and have only one origin of replication, whereas eukaryotic chromosomes are linear and may have thousands of origins of replication. OBJECTIVE Describe how errors occur during replication, how they are repaired, and the consequences of failure to repair such errors. Errors may occur during replication when an incorrect base is added to the daughter strand. DNA polymerase proofreads the added bases and has the ability to replace incorrectly incorporated ones by itself. If an error in base

18 pairing slips by the polymerases, the daughter strand may be repaired by mismatch repair. In this process, enzymes cut out the incorrect nucleotide from the daughter strand and replace it with the appropriate nucleotide. Nucleases may also cut out bulky DNA lesions, after which a DNA polymerase replaces the fragment with the correct sequence by nucleotide excision repair. Some of these errors, however, escape both proofreading and repair mechanisms and can become mutations. Most mutations either have no influence on the survival of an organism or are deleterious, causing harm. However, a small proportion of mutations cause a slight change in an organism that is then subject to fundamental evolutionary processes, such as natural selection and genetic drift; thus, a mutation can lead to a population's traits changing through time and ultimately lead to the formation of new species. OBJECTIVE Explain how telomeres are replicated in eukaryotic cells. Linear eukaryotic chromosomes contain non-coding repetitive DNA sequences at their ends called telomeres. Telomerases lengthen the parental strand using an RNA template so that the lagging strand may be replicated completely during DNA replication. Key Terms DNA helicase A protein that binds to double-stranded DNA and breaks the hydrogen bonds between the two strands. DNA ligase An enzyme involved in sealing gaps in the sugar-phosphate backbone of DNA by catalyzing the formation of a phosphodiester bond. DNA polymerase I An enzyme that replaces RNA primers at the beginning of Okazaki fragments by simultaneously removing the primers and replacing then with the corresponding DNA nucleotides. DNA polymerase III The primary DNA-synthesizing enzyme in E. coli; recognizes the RNA primer and adds DNA nucleotides to the 3 end of the primer. lagging strand The strand of DNA that is replicated in the direction opposite to the movement of the replication fork; replicated discontinuously as a series of Okazaki fragments, each 1,000-2,000 nucleotides in length. leading strand The strand of DNA that is replicated in the same direction as the movement of the replication fork; replicated continuously as the double helix opens. mismatch repair The process by which enzymes cut out an incorrectly base-paired nucleotide from DNA and replace it with the appropriate nucleotide according to base-pairing rules. nuclease An enzyme involved in removing corrupted sections of DNA during nucleotide excision repair. nucleotide excision repair A process in which proteins remove sections of DNA containing large, bulky lesions and replace these regions with new nucleotides using the undamaged DNA as a template. Okazaki fragment Fragments of DNA formed during DNA replication on the lagging strand; must be connected together with DNA ligase to complete replication of strand. origin of replication A sequence of nucleotides where DNA replication begins. In eukaryotes, there are

19 multiple origins of replication; in prokaryotes, there is typically only one. replication fork During DNA replication, the region at which the double helix becomes separated by DNA helicase. semi-conservative model The model of DNA replication where each of the two daughter DNA molecules contains one intact strand of the parental DNA molecule and one continuous newly synthesized strand of DNA. single-strand DNA-binding (SSB) proteins A stabilizing protein involved in DNA replication that prevents the separated DNA strands from re-joining or re-coiling during the replication process. telomerase An enzyme that uses an RNA template to lengthen the telomere of the DNA template strand. telomeres Special end sequences containing repeating sequences of bases that serve to protect the genetic information contained at the ends of eukaryotic chromosomes. topoisomerase A protein that binds to the double helix ahead of the replication fork and relieves torsional strain in the DNA caused by overwinding or underwinding. IN THIS MODULE Semi-Conservative DNA Replication Overall Principles of DNA Replication Proofreading and Repair Eukaryotic DNA Replication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Synthetic Biology: Making Life from Bits and Pieces Scientists are combining biology and engineering to change the world. PRIMARY LITERATURE Can we expand the genetic code? Converting nonsense codons into sense codons by targeted pseudouridylation. The role of cyclin D1 in DNA repair linked to cancer growth A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Classic paper: How scientists discovered the enzyme that turns RNA into DNA (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. page 234 of pages left in this module

20 Principles of Biology contents 45 DNA Replication Test Your Knowledge 1. In which model of DNA replication does the parent DNA molecule break into fragments that are copied? dispersive conservative semi-conservative semi-dispersive None of the answers are correct. 2. Why did Meselson and Stahl transfer E. coli from media containing 15 N to media containing 14 N? They needed to ensure that all newly synthesized DNA would contain the same marker. The E. coli would only reproduce in media containing 14 N. 14 N caused a higher rate of mutation in E. coli. They needed to be able to separate the parental and newly synthesized DNA through differential centrifugation, and only DNA containing the lighter isotope would form a band. None of the answers are correct. 3. Which protein is responsible for synthesizing the new DNA strand during replication in prokaryotes? helicase primase topoisomerase DNA polymerase I None of the answers are correct. 4. What is the role of DNA polymerase I in the replication of E. coli DNA? 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. 5. What happens at the origin of replication? 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. 6. What is one way that the replication of eukaryotic DNA generally differs from the replication of prokaryotic DNA? Eukaryotic DNA replication does not require the replication of telomeres. Eukaryotic DNA requires the use of RNA primers. Eukaryotic DNA replication is faster.

21 There is no leading strand in eukaryotic DNA replication. Replication shortens the lagging strand in eukaryotic DNA. Submit IN THIS MODULE Semi-Conservative DNA Replication Overall Principles of DNA Replication Proofreading and Repair Eukaryotic DNA Replication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Synthetic Biology: Making Life from Bits and Pieces Scientists are combining biology and engineering to change the world. PRIMARY LITERATURE Can we expand the genetic code? Converting nonsense codons into sense codons by targeted pseudouridylation. The role of cyclin D1 in DNA repair linked to cancer growth A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Classic paper: How scientists discovered the enzyme that turns RNA into DNA (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. page 235 of 989