Becker's World of the Cell, Tenth Edition - Chapter 17 PDF

Becker’s World of the Cell Tenth Edition Chapter 17 DNA Replication, Repair, and Recombination Lectures by Anna Hegsted, Simon Fraser University Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Replication, Repair, and Recombination • Cells must be able to accurately reproduce, o...

Becker’s World of the Cell Tenth Edition Chapter 17 DNA Replication, Repair, and Recombination Lectures by Anna Hegsted, Simon Fraser University Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Replication, Repair, and Recombination • Cells must be able to accurately reproduce, or replicate, their genetic material at each cell division. • Without accurate replication, the genetic material of resulting cells would be riddled with errors. • Cells must also repair damage to their genetic material. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 17.1 DNA Replication • All DNA in the nucleus of a parent cell must be duplicated and carefully distributed to the daughter cells. • The division process involves nuclear division (mitosis) and division of the cytoplasm (cytokinesis). • Chromosomes that have duplicated and are attached are sister chromatids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Separation of Sister Chromatids • The microtubules of the mitotic spindle separate the sister chromatids. • Each is now a full-fledged chromosome, and they move to opposite poles of the cell. • New nuclear envelopes form around the two sets of daughter chromosomes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Eukaryotic Cell Cycle Figure 17.1 The Eukaryotic Cell Cycle. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Synthesis Occurs During S Phase • The events of mitosis (known as M phase) are only one phase of the cell cycle. • Cells spend most of their time between divisions, called interphase. • During interphase, the amount of nuclear DNA doubles during a specific time named S phase. • A time gap called G1 phase separates S phase from the previous M phase and a second gap, G2 phase, separates S phase from the next M phase. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Replication Is Semiconservative • The Watson and Crick model of DNA structure suggested a mechanism for how the base-paired structure could duplicate itself. • Their key suggestion was that one of the two strands of each new D NA molecule was derived from the parent molecule and the other strand was newly synthesized. • This is called semiconservative replication. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Watson–Crick Model of DNA Replication Figure 17.2 The Watson–Crick Model of DNA Replication. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Two Other Models for DNA Replication • In the conservative model of DNA replication, the parent molecule is intact, and a second, completely new, copy is made. • In the dispersive model, each strand of the double helix is a mixture of old and newly synthesized segments. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Alternative Models for DNA Replication Figure 17.3 Alternative Models for DNA Replication Copyright © 2022 Pearson Education, Inc. All Rights Reserved Demonstration of Semiconservative Replication • Matthew Meselson and Franklin Stahl (with Jerome Vinograd) showed that replication is semiconservative by using 14N and 15N to distinguish newly formed DNA strands from old strands. • Bacterial cells were grown in 15N medium for many generations to incorporate heavy nitrogen into their DNA, then transferred to 14N medium. • The strands were distinguished by equilibrium density centrifugation. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Results of the Experiment • After one cycle of replication in the 14N medium, a band was observed intermediate between the heavy and light strands. • If the hybrid DNA was heated to separate the strands, one strand was “heavy,” and the other was “light”. • These results are consistent with semiconservative replication. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Semiconservative Replication of Density-Labeled DNA Figure 17.4 Semiconservative Replication of Density-Labeled DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Additional Experimental Results • After two cycles of replication, Meselson and Stahl observed two bands, one at the hybrid density and one entirely made of 14N-D NA. • Additional experiments used cells from bean roots and newly synthesized DNA labeled with 3H-thymidine. • These also support semiconservative replication. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Evidence for Semi-Conservative Replication in Eukaryotes Figure 17.5 Evidence for Semi-Conservative Replication in Eukaryotes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Replication Is Usually Bidirectional • DNA replication is especially well understood in Escherichia coli. • Replication is very similar in prokaryotes and eukaryotes. • Early experiments to directly visualize DNA replication were carried out by John Cairns, using 3H-thymidine to label E. coli DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication Forks • Cairns visualized the circular chromosomes by autoradiography; he observed replication forks. • These are formed where replication begins and then proceeds in bidirectional fashion away from the origin. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Bacterial Replication • Replication forks move away from the origin, unwind the DNA, and copy both strands as they proceed. • This is called theta (Θ) replication and is observed in replication of circular DNA molecules. • The two copies of the replicating chromosome bind to the plasma membrane at their origins; when replication is complete, the cell divides by binary fission. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication of Circular DNA Figure 17.6 Replication of Circular DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Eukaryotic DNA Replication • In eukaryotes, replication of linear chromosomes is initiated at multiple sites, creating replication units called replicons. • The DNA of a typical chromosome may contain several thousand replicons, each 50,000 to 300,000 bp in length. • At each origin of replication, two replication forks synthesize DNA in opposite directions, forming a “replication bubble”. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Multiple Replicons in Eukaryotic DNA Figure 17.7 Multiple Replicons in Eukaryotic DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication Initiates at Specialized DNA Elements • The site where DNA replication initiates, in bacteria or eukaryotes, is known as an origin of replication. • This sequence in E. coli is AT rich, about 245 bp in length and a characteristic set of tandem repeats. • The sequence varies among bacterial species but contains recognizable, similar sequences. • Conserved sequences are called consensus sequences. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Origins of Replication in a Bacterium and a Eukaryote Figure 17.8 Origins of Replication in a Bacterium and a Eukaryote. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication Origins in S. cerevisiae • In budding yeast (Saccharomyces cerevisiae), the replication origin is called the autonomously replicating sequence (ARS). • These elements are 100–150 bp long and contain a common 11 nucleotide core sequence, largely AT base pairs • Replication origins of multicellular eukaryotes are generally larger and more variable in sequence than the ARS in S. cerevisiae. However, they also contain regions that are AT-rich. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication Initiation in Bacteria • In E. coli, three enzymes, DnaA, DnaB, and DnaC, bind or iC and initiate replication. • DnaA binding to the 9-mer of oriC results in unwinding of D NA at the 13-mer sites. • To stabilize the single strands of DNA, SSB (single stranded binding protein) binds to the unwound regions. • DnaB is a DNA helicase, which unwinds the DNA strands as replication proceeds. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Initiation of Replication in Bacteria and Eukaryotes Figure 17.9 Initiation of Replication in Bacteria and Eukaryotes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication Initiation in Eukaryotes (1 of 2) • Origins of replication recruit proteins that initiate the unwinding and replication of DNA: • A multisubunit protein complex called the origin recognition complex (ORC) binds the replication origin. • The minichromosome maintenance (MCM) proteins bind the origin. These include DNA helicases. • The helicase loaders recruit the MCM proteins and mediate the binding of MCM proteins to the ORC. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication Initiation in Eukaryotes (2 of 2) • At this point, all the DNA-bound proteins make up the prereplication complex. • The formation of this complex is called licensing. Only licensed origins can replicate. • Replication does not occur until more proteins, including the enzymes for DNA synthesis are added. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replicons Are Not All Fired at the Same Time • Certain clusters of replicons replicate early during S phase, whereas others replicate later. • This is demonstrated by incubating cells during S phase with 5-bromodeoxyuridine (BrdU), which is incorporated into DNA in place of thymidine. • Active genes are replicated early during S phase, whereas inactive genes are replicated later. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Polymerases Catalyze the Elongation of DNA Chains • DNA polymerase is an enzyme that can copy DNA molecules. • Incoming nucleotides are added to the 3′ hydroxyl end of the growing DNA chain, so elongation occurs in the 5′ → 3′ direction. • Several other forms of DNA polymerase have been identified; the original is now called DNA polymerase Ⅰ. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Directionality of DNA Synthesis Figure 17.10 The Directionality of DNA Synthesis. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Polymerases • Arthur Kornberg discovered the first DNA polymerase (called DNA polymerase I). • Soon after, several other DNA polymerases were discovered, including bacterial DNA polymerases II, III, and IV. • DNA polymerase III appears to be the only polymerase fast enough to account for DNA replication in cells (about 50,000 bp/minute). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Some Important DNA Replication Proteins in Bacteria and Eukaryotes (1 of 3) Table 17.1 Some Important D N A Replication Proteins in Bacteria and Eukaryotes Protein Cell Type Main Activities and/or Functions Initiator proteins Both Bind to origin of replication and initiate unwinding of DNA double helix DNA polymerase I Bacteria DNA synthesis; 3′ → 5′ exonuclease (for proofreading); 5′ → 3′ exonuclease; removes and replaces RNA primers used in DNA replication (also functions in excision repair of damaged DNA) DNA polymerase III Bacteria DNA synthesis; 3′ → 5′ exonuclease (for proofreading); used in synthesis of both DNA strands DNA polymerase α (alpha) Eukaryotes Nuclear DNA synthesis; forms complex with primase and begins DNA synthesis at the 3′ end of RNA primers for both leading and lagging strands (also functions in DNA repair) DNA polymerase γ (gamma) Eukaryotes Mitochondrial DNA synthesis DNA polymerase δ (delta) Eukaryotes Nuclear DNA synthesis; 3′ → 5′ exonuclease (for proofreading); involved in lagging and leading strand synthesis (also functions in DNA repair) Copyright © 2022 Pearson Education, Inc. All Rights Reserved Some Important DNA Replication Proteins in Bacteria and Eukaryotes (2 of 3) Table 17.1 Some Important D N A Replication Proteins in Bacteria and Eukaryotes (Continued) Protein Cell Type Main Activities and/or Functions DNA polymerase ε (epsilon) Eukaryotes Nuclear DNA synthesis; 3′ → 5′ exonuclease (for proofreading); thought to be involved in leading and lagging strand synthesis (also functions in DNA repair) Primase Both RNA synthesis; makes RNA oligonucleotides that are used as primers for DNA synthesis DNA helicase Both Unwinds double-stranded DNA Sliding clamp (PCNA in eukaryotes) Both Binds core polymerase subunit and keeps it on DNA Single-stranded DNAbinding protein (SSBs in bacteria) Both Binds to single-stranded DNA; stabilizes strands of unwound DNA in an extended configuration that facilitates access by other proteins DNA topoisomerase (type I and type II) Both Makes single-strand cuts (type I) or double-strand cuts (type II) in DNA; induces and/or relaxes DNA supercoiling; can serve as a swivel to prevent overwinding ahead of the DNA replication fork; can separate linked DNA circles at the end of DNA replication Copyright © 2022 Pearson Education, Inc. All Rights Reserved Some Important DNA Replication Proteins in Bacteria and Eukaryotes (3 of 3) Table 17.1 Some Important D N A Replication Proteins in Bacteria and Eukaryotes (Continued) Protein Cell Type Main Activities and/or Functions DNA gyrase Bacteria Type II DNA topoisomerase that serves as a swivel to relax supercoiling ahead of the DNA replication fork in E. coli DNA ligase Both Makes covalent bonds to join together adjacent DNA strands, including the Okazaki fragments in lagging strand D NA synthesis and the new and old DNA segments in excision repair of DNA Telomerase Eukaryotes Using an integral RNA molecule as template, synthesizes D NA for extension of telomeres (sequences at ends of chromosomal DNA) RNA endonuclease (R Nase H), RNA exonuclease (FEN1) Eukaryotes RNase H recognizes RNA/DNA strands and nicks them; FE N1 then digests the RNA Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Polymerase III Is the Main Enzyme Responsible for DNA Replication in Bacteria (1 of 2) • Temperature-sensitive mutants were used to determine whether DNA polymerase III is the main enzyme for DNA replication. • Temperature-sensitive mutants are strains where a protein functions properly at normal temperatures but cannot function at altered temperatures. • In a bacterial strain with temperature-sensitive DNA polymerase III, it was found that at high temperatures, the bacterium cannot replicate the DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Polymerase III Is the Main Enzyme Responsible for DNA Replication in Bacteria (2 of 2) • DNA polymerase III is not the only enzyme needed for DNA replication, DNA polymerase I is also needed. • The other bacterial DNA polymerases (II, IV, and V) are all associated with DNA repair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Eukaryotic DNA Polymerases • Eukaryotic cells contain more than a dozen types of DNA polymerases. • DNA polymerase α, δ, and ε: are involved in nuclear DNA replication. • DNA γ polymerase is only present in the mitochondria and is the main polymerase for mitochondrial DNA replication. • Most other Eukaryotic DNA polymerases function in DNA repair or replication of damaged regions. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Is Synthesized as Discontinuous Segments That Are Joined Together by DNA Ligase • DNA polymerase only synthesizes 5′ → 3′. • The leading strand is synthesized as a continuous chain because it is growing in the 5′ → 3′ direction. • The lagging strand, which must grow 3′ → 5′, is synthesized in discontinuous short fragments called Okazaki fragments. • Okazaki fragments are then joined by DNA ligase to make a continuous 3′ → 5′ stand. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Okazaki’s Experiments • Reiji Okazaki isolated DNA from bacteria that were briefly exposed to a radioactive substrate incorporated into newly made DNA. • Much of the radioactivity was located in small fragments about 1000 nucleotides long. • With longer labeling, the radioactivity became associated with longer molecules. • This conversion did not take place in bacteria lacking DNA ligase. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Okazaki’s Observations Illustrate How Lagging Strand Synthesis Occurs • DNA synthesis from the lagging strand is synthesized in Okazaki fragments. • These are then joined by DNA ligase to form a continuous new 3′ → 5′ DNA strand. • Okazaki fragments are 1000–2000 nucleotides long in bacteria and viruses, but about one-tenth this length in eukaryotic cells. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Directions for DNA Synthesis at a Replication Fork Figure 17.11 Directions for DNA Synthesis at a Replication Fork. Copyright © 2022 Pearson Education, Inc. All Rights Reserved In Bacteria, Proofreading Is Performed by the 3′→ 5′ Exonuclease Activity of DNA Polymerase • About 1 of every 100,000 nucleotides incorporated during DNA replication is incorrect. • Such mistakes are usually fixed by a proofreading mechanism that uses DNA polymerase. • Almost all DNA polymerases have a 3′ → 5′ exonuclease activity. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Proofreading • Exonucleases degrade nucleic acids from the ends of the molecules (no internal cuts). • Endonucleases make internal cuts in nucleic acid molecules. • The exonuclease activity of DNA polymerase allows it to remove incorrectly base-paired nucleotides and incorporate the correct base. • This makes the error rate only a few per billion base pairs. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Proofreading by 3′ → 5′ Exonuclease Figure 17.12 Proofreading by 3′ → 5′ Exonuclease. Copyright © 2022 Pearson Education, Inc. All Rights Reserved RNA Primers Initiate DNA Replication (1 of 2) • DNA polymerase can add nucleotides only to the 3′ end of an existing nucleotide chain. • Researchers implicated RNA in the initiation process based on several observations: 1. Okazaki fragments usually have short stretches of RNA at their 5′ ends. 2. DNA polymerase can add nucleotides to RNA chains as well as DNA chains. Copyright © 2022 Pearson Education, Inc. All Rights Reserved RNA Primers Initiate DNA Replication (2 of 2) • Researchers implicated RNA in the initiation process based on several observations (continued): 3. Cells contain an enzyme called primase that synthesizes short (~10 bases) chains of RNA using DNA as a template. 4. Primase can initiate RNA synthesis without a preexisting chain to add to by joining two nucleotides together. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Synthesis Requires RNA Primers • The observations led to the conclusion that DNA synthesis is initiated by the formation of short RNA primers. • In E. coli, primase is inactive unless accompanied by six other proteins, forming a complex called a primosome. • In eukaryotes, primase is tightly bound to DNA polymerase α. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Role of RNA Primers in DNA Replication: Step 1 (1 of 3) 1. RNA primers are synthesized by primase which uses a single DNA strand as a template. • Primase is an RNA polymerase only used during replication. • RNA polymerases can initiate the synthesis of a polynucleotide. They do not need a primer (DNA polymerase cannot do this). Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Role of RNA Primers in DNA Replication: Step 2 (2 of 3) 2. Once an RNA primer is synthesized, DNA synthesis can proceed. • DNA polymerase adds nucleotides starting at the hydroxyl group on the 3′ end of the primer. • On the leading strand, initiation using an RNA primer only occurs once. • On the lagging strand, each Okazaki fragment has an RNA primer. DNA polymerase then adds nucleotides until it reaches the next fragment. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Role of RNA Primers in DNA Replication: Step 3 and 4 (3 of 3) 3. The RNA primer is removed, and DNA nucleotides are polymerized to fill its place. • In E. coli this removal is done by the 5′ → 3′ exonuclease ability of DNA polymerase I. (This is different than the 3′ → 5′ exonuclease ability used to proofread.) 4. Adjacent fragments are joined by DNA ligase. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Role of RNA Primers in DNA Replication Figure 17.13 The Role of RNA Primers in DNA Replication. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The DNA Double Helix Must Be Locally Unwound During Replication • During DNA replication, the two strands of the double helix must unwind at each replication fork. • Three classes of proteins facilitate the unwinding: DNA helicases, topoisomerases, and single-stranded DNA binding proteins. • DNA helicases are responsible for unwinding the DNA, using energy from ATP hydrolysis. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Helicases • The DNA double helix is unwound ahead of the replication fork, the helicases break the hydrogen bonds as they go. • In E. coli, at least two different helicases are involved; one attaches to the lagging strand and moves 5′ → 3′, whereas the other attaches to the leading strand and moves 3′ → 5′. • Both are part of the primosome. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Single-Stranded DNA Binding Protein • Once strand separation has begun, molecules of SSB (single-stranded DNA binding protein) move in quickly and attach to the exposed single strands. • They keep the DNA unwound and accessible to the replication machinery. • When a segment of DNA has been replicated, the SSB molecules fall off and are recycled. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Topoisomerases • The unwinding of the helix would create too much supercoiling if not for topoisomerases. • These enzymes create swivel points in the DNA molecule by making and then quickly sealing double-stranded or singlestranded breaks. • Of the ~10 topoisomerases in E. coli, the key enzyme for DNA replication is gyrase. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Proteins Involved in Unwinding DNA at the Replication Fork Figure 17.14 Proteins Involved in Unwinding DNA at the Replication Fork. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Unwinding and DNA Synthesis Are Coordinated on Both Strands Via the Replisome • Starting at the origin of replication, the machinery at the replication fork adds proteins required for synthesizing DNA. • These are DNA helicase, DNA gyrase, SSB, primase, DNA polymerase, and DNA ligase. • The proteins involved in replication are closely associated in a large complex called a replisome. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Replisome (1 of 2) • The replisome is about the size of a ribosome. • The activity and movement of the replisome is powered by nucleoside triphosphate hydrolysis. • As the replisome moves along the DNA, it must accommodate the fact that DNA is being produced on both leading and lagging strands. Copyright © 2022 Pearson Education, Inc. All Rights Reserved A Summary of DNA Replication in Bacteria Figure 17.15 A Summary of DNA Replication in Bacteria. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Trombone Model • A key element of the replisome is the folding of the lagging strand template into a loop. • This model for how the replisome works is called the trombone model. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Trombone Model: The Holoenzyme • The replisome relies on the assembly a protein complex called the holoenzyme, which includes the clamp loader, the sliding clamp, and DNA polymerase linked together by tau protein. • The clamp loader protein feeds the sliding clamp protein onto the DNA. • The sliding clamp protein is ring-shaped that fits around the DNA and allows the polymerase to remain on the DNA strand. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Trombone Model: Leading and Lagging Strands • The leading and lagging strands differ regarding how long the sliding clamp and associated polymerase remain attached. • It can remain associated with the leading strand throughout replication. • On the lagging strand, as each Okazaki fragment is completed, the polymerase detaches, and the sliding clamp must be reloaded. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Replisome (2 of 2) Figure 17.16 The Replisome. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Eukaryotes Disassemble and Reassemble Nucleosomes as Replication Proceeds • Eukaryotes have much of the same replication machinery found in prokaryotes. • A DNA clamp protein acts along with DNA polymerase; one example is proliferating nuclear cell antigen (PCNA). • To remove the RNA primer, eukaryotes use RNAse H, an RNA endonuclease to nick the backbone of the RNA-DNA hybrid. • An RNA exonuclease, FEN1, removes the RNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Replication Factories and Chromatin Remodeling • Studies addressing how many origins of replication can be coordinated suggest that immobile structures called replication factories synthesize DNA as chromatin fibers are fed through them. • Unfolding chromatin fibers ahead of the replication fork is facilitated by chromatin remodeling proteins that loosen nucleosome packing. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Chromatin Remodeling Proteins • After a stretch of DNA is replicated, nucleosomes are reassembled on the newly formed strands. • Nucleosome assembly protein-1 (Nap-1) and chromatin assembly factor-1 (CAF-1) are examples of chromatin assembly proteins. • The dynamic disassembly/reassembly allows nucleosome association with DNA throughout the replication process. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Nucleosomes Are Disassembled and Reassembled During Replication in Eukaryotes Figure 17.17 Nucleosomes Are Disassembled and Reassembled During Replication in Eukaryotes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Telomeres Solve the DNA EndReplication Problem • Linear DNA molecules have a problem in completing DNA replication on the lagging strand because primers are required. • Each round of replication would end with the loss of some nucleotides from the ends of each linear molecule. • Eukaryotes solve this problems with telomeres, highly repeated sequences at the ends of chromosomes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The End-Replication Problem Figure 17.18 The End-Replication Problem. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Telomeres and Telomerase • Human telomeres have 100 to 1500 copies of TTAGGG at the ends of chromosomes. • These noncoding sequences ensure that the cell will not lose important genetic information if DNA molecules shorten during replication. • A DNA polymerase called telomerase can catalyze the addition of repeats to chromosome ends. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Telomerase Function • Telomerase is composed of protein and RNA. • In the protozoan Tetrahymena, the RNA component of the telomerase (3′—AACCCC—5′) is complementary to the telomere repeat sequence (5′—TTGGGG—3′). • This enzyme-bound RNA acts as a template for adding the DNA repeat sequence to the telomere ends. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Extension of Telomeres by Telomerase Figure 17.19 The Extension of Telomeres by Telomerase. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Protecting Chromosome Ends • After telomeres are lengthened by telomerase, telomere capping proteins bind to the exposed 3′ end to protect from degradation. • In many eukaryotes, the 3′ ends of the DNA also loop back and base-pair with the opposite strand to form a protective closed loop. • In multicellular organisms, telomerase function is restricted to germ cells and a few other types of actively proliferating cells. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Telomeres and Cell Culture • In primary cultured cells, the absence of telomerase limits the number of times the cells can be passaged. • This limit is known as the Hayflick limit. • Shortened telomeric DNA signals the beginning of a cell destruction pathway that ends in apoptosis. • Cell lines can be immortalized and circumvent the Hayflick limit if they produce telomerase. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Importance of Telomeres During Cellular Aging Figure 17.20 The Importance of Telomeres During Cellular Aging. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Telomeres, Aging, and Disease (1 of 2) • Immortalized cell lines, such as HeLa cells, produce telomerase and can be passaged indefinitely. • Cell death triggered by a lifetime of telomere shortening is thought to contribute to some of the degenerative diseases associated with human aging. • Scientists speculate that telomerase-based therapy may one day be used to combat symptoms of human aging. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Telomeres, Aging, and Disease (2 of 2) • Telomerase has been detected in almost all types of human cancers. • Proteins that bind the tandem repeat DNA in telomeres recruit telomere capping proteins to protect the singlestranded DNA at the ends from damage. • Patients with Werner syndrome lack a telomere cap protein (WRN) and exhibit premature signs of aging. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 17.2 DNA Damage and Repair • DNA must be accurately passed on to daughter cells. • In addition to ensuring that replication is faithful, this also means that DNA alterations must be repaired. • DNA alterations, or mutations, can arise spontaneously or through exposure to environmental agents. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Mutations Can Occur Spontaneously During Replication • During DNA replication, some types of mutations occur through 1. Spontaneous mispairing of bases due to transient formation of tautomers 2. Slippage during replication 3. Spontaneous damage to individual bases Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Tautomers • Mispairing of DNA nucleotides due to presence of tautomers is the most common form of spontaneous replication error. • Tautomers are rare, alternate resonance structures of nitrogenous bases. • In this form, a base can pair in a nonstandard way in a process known as a tautomeric shift. • The result is a new daughter strand that carries an incorrect base at that position. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Tautomers and DNA Mismatch Figure 17.21 Tautomers and DNA Mismatch. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Trinucleotide Repeats • Spontaneous replication errors can occur in regions with repetitive DNA. • One example involves trinucleotide repeats, which are susceptible to strand slippage. • In this process, DNA polymerase replicates a short stretch of DNA twice. • Several well-characterized human diseases, trinucleotide repeat disorders, involve accumulation of various trinucleotide repeats. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Trinucleotide Repeat Expansion Figure 17.22 Trinucleotide Repeat Expansion. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Human Trinucleotide Repeat Disorders Table 17.2 Human Trinucleotide Repeat Disorders* Copyright © 2022 Pearson Education, Inc. All Rights Reserved Chemical Modifications • Another reaction that can occur spontaneously involves chemical modification of bases. • Depurination, the loss of a purine base, and deamination, the removal of a base’s amino group, are the most common. • A human cell may undergo thousands of depurinations each day, and about 100 deaminations. • Failure to repair these can lead to base changes in the DNA sequence. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Two Common Types of DNA Damage Figure 17.23 Two Common Types of DNA Damage. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Mutagens Can Induce Mutations • DNA damage can be caused by mutation-causing agents, mutagens. • Environmental mutagens fall into two categories: chemicals and radiation. • Mutation can also be induced by mobile genetic elements, such as found in viruses, or transposable elements (transposons). • Mutagenic chemicals alter DNA structure through a variety of mechanisms. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Damage by Chemical Mutagens • Base analogues resemble nitrogenous bases and are incorporated into DNA. • Base-modifying agents react chemically with DNA bases to alter their structures, forming DNA adducts. • Intercalating agents insert themselves between adjacent bases, distorting DNA structure. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Base Analogues • Base analogues, structurally similar to one of the DNA nucleotides, can be incorporated into a DNA molecule during replication. • An example is 5-bromodeoxyuridine (BrdU) with pairing properties similar to thymine. • The bromine group allows for a tautomeric shift, allowing it to pair with guanine. • In the next round of replication, the AT pairing will be replaced with a GC pairing. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Base-Modifying Agents • Several mutagens act by chemically modifying a base that will then mispair at the next replication. • Ethyl methansulfonate (EMS) adds ethyl groups to bases, while nitrosoguanidine adds methyl groups. • Nitrous acid (HNO2) dramatically increases the likelihood of deamination. • Other agents add bulky DNA adducts to DNA. • Aflatoxin B1 attaches to guanine, leading to depurination. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Intercalating Agents • Intercalating agents (such as proflavin, acridine orange, benzo(a)pyrene) insert into the DNA double helix. • They alter the shape of the double helix, leading to small nicks in the DNA. • When repaired, there may be additions or deletions of nucleotides. • Ethidium bromide is a common fluorescent dye (and intercalating agent) used for gel electrophoresis of DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Two Types of Chemical Mutagens Figure 17.24 Two Types of Chemical Mutagens. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Radiation • Ultraviolet radiation alters DNA by triggering pyrimidine dimer formation—covalent bonds between adjacent pyrimidine bases. • X-rays and related types of radiation, called ionizing radiation, remove electrons from molecules and generate highly reactive intermediates that damage DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Pyrimidine Dimer Formation Figure 17.25 Pyrimidine Dimer Formation. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Repair Systems Correct Many Kinds of DNA Damage • A variety of mechanisms have evolved for DNA repair. • The strategies depend on how severe the damage is and whether or not the cell is undergoing division. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Light-Dependent Repair • Pyrimidine dimers can be directly repaired in a lightdependent process called photoactive repair. • It depends on the enzyme photolyase, which catalyzes breakage of bonds between thymine dimers. • The energy for this repair is provided by visible light. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Base Excision Repair (1 of 2) • Excision repair pathways are classified into two types: base excision repair and nucleotide excision repair. • Base excision repair corrects single damaged bases. • For example, deaminated bases are detected by DNA glycosylases, which recognize and remove the base by cleaving the bond between the base and the sugar. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Base Excision Repair (2 of 2) • The sugar with the missing base is then recognized by a repair endonuclease (AP endonuclease) that detects depurination. • It breaks the phosphodiester backbone to one side of the sugar, and a second enzyme removes the sugar. • DNA polymerase then synthesizes the correct new base, and DNA ligase seals the nick in the DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Base Excision Repair-Thymine and Uracil • DNA uses thymine, but RNA uses uracil. Both pair with adenine. • When deamination converts cytosine to uracil and is detected, the uracil can be removed by uracil DNA glycosylate, a DNA repair enzyme. • This repair pathway would not work if DNA used uracil as one of the four bases. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Base Excision Repair Figure 17.26 Base Excision Repair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Nucleotide Excision Repair • Nucleotide excision repair (NER) uses proteins that detect distortions in the DNA helix and recruit NER endonuclease (or excinuclease) that cuts the DNA backbone on either side of the lesion. • Helicase unwinds the DNA between the nicks and frees it from the DNA. • DNA polymerase and ligase complete the repair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Nucleotide Excision Repair in Bacteria Figure 17.27 Nucleotide Excision Repair in Bacteria. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The NER System Is Versatile • The nucleotide excision repair system detects and corrects many types of DNA damage. • Sometimes it is recruited to regions where transcription is stalled because of DNA damage; this is called transcription-coupled repair. • People with xeroderma pigmentosum must stay out of the sun because of mutations that prevent them from carrying out NER. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Mismatch Repair • Errors remaining after DNA replication are repaired by mismatch repair, in which abnormal nucleotides are removed and replaced. • E. coli has nearly 100 genes that code for proteins involved in this process. • Excision repair works by a basic three-step process. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Methylation in Mismatch Repair • DNA methylation does not occur immediately after DNA replication. • Therefore, mismatch repair systems can distinguish the original DNA (methylated) from the newly made strand (unmethylated). • The incorrect nucleotide in the newly made strand is excised and replaced. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Process of Mismatch Repair 1. A protein known as MutS detects the mismatch. 2. A repair endonuclease called MutH introduces a nick in the unmethylated strand. 3. An exonuclease removes the incorrect nucleotides from the nicked strand, and these are replaced with the correct sequence. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Mismatch Repair in Bacteria Figure 17.28 Mismatch Repair in Bacteria. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Error-Prone Repair: Translesion Synthesis • Sometimes, DNA damage is too severe for the preceding types of repair. • Bacteria and eukaryotes have evolved mechanisms that serve as a last-ditch effort to repair DNA. • In E. coli, this process involves the SOS system, activated when a replication fork stalls due to damage of the DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The SOS System in E. coli • The DNA in front of the stalled DNA polymerase continues to be unwound. • A protein called RecA joins SSB on this single strand. • RecA leads to expression of special DNA polymerases called bypass polymerases. • These continue the DNA replication despite the damage. • Once the damage is passed, DNA polymerase III can resume the replication. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Translesion Synthesis • In eukaryotes, specialized bypass polymerases carry out translesion synthesis. • Though it is sometimes prone to error, this type of synthesis can sometimes produce new strands from which the damage has been eliminated. • For example, polymerase η can catalyze synthesis across a thymine dimer, correctly inserting two new adenines in the new strand. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Double-Strand Break Repair • When double-strand breaks cleave DNA into two fragments, it is difficult for the repair system to identify and rejoin the correct broken ends without loss of nucleotides. • Two pathways are used: nonhomologous end-joining and recombination when a homologous region is available as a template. • Generation and repair of double stranded breaks is the foundation upon which CRISPR genome editing is built. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Nonhomologous End-Joining (NHEJ) • Nonhomologous end-joining (NHEJ) uses a set of proteins that bind to ends of broken DNA fragments and join them together. • This is error-prone because nucleotides can be lost from the broken ends, and there is no way to ensure the correct DNA fragments are joined. • This process is used only when the existing DNA sequence cannot be used as a template for repair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Process of Nonhomologous EndJoining 1. A double-stranded break in the DNA is caused by X-rays or oxidative damage. 2. It is detected by Ku70 and Ku80 proteins, which bind one another and fit over the broken DNA ends. 3. The ends of the break are trimmed by nucleases. 4. The break is sealed by DNA ligase IV. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Nonhomologous End-Joining (NHEJ) Figure 17.29 Nonhomologous End-Joining (NHEJ). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Synthesis-Dependent Strand Annealing (SDSA) • Synthesis-dependent strand annealing (SDSA) depends on the fact that once DNA synthesis is complete, each chromosome has two sister chromatids. • Thus, if one chromatid incurs a double-strand break, there is a second intact copy of the same DNA available to guide repair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Process of Synthesis-Dependent Strand Annealing (1 of 2) • SDSA begins with trimming of the break by nucleases and recruitment of the Rad51 protein to strands at the break. • Strands search for homologous sequences on the sister chromatid during a process called strand invasion. • The invading strand displaced the DNA of the sister chromatid, creating a D loop. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Process of Synthesis-Dependent Strand Annealing (2 of 2) • The D loop structure allows replication of the single strand from the broken DNA. • Bits of repaired DNA then dissociate from the D loop and are ligated to the broken chromatid, leading to its repair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Homologous Recombination • Homologous recombination involves the process of crossing over, genetic exchange between DNA molecules with extensive sequence similarity. • If the DNA molecule from one chromosome is broken, the homologue is available as a template to guide accurate repair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Process of Homologous Recombination • The break in the DNA is detected and the ends trimmed. • As with SDSA, strand invasion occurs, but involving both strands. • DNA synthesis fills in DNA on both strands using the intact pieces of DNA as a template. • The result is a Holliday junction, a crossed structure, which is resolved to generate two separate stands of repaired DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Result of Homologous Recombination • One possible result is permanent exchange of DNA between the broken DNA of one homologue and the intact DNA of the other (crossing over). • The other possibility is repair of the DNA without exchange. • In this case, the repaired chromosome has the same sequence as the undamaged one (even if they started as two different alleles). • This process is known as gene conversion. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Repair Using Homologous Sequences Figure 17.30 DNA Repair Using Homologous Sequences. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 17.3 Homologous Recombination and Mobile Genetic Elements • A widespread exchange of chromatin occurs during the process of meiosis. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Homologous Recombination Is Initiated by Double-Stranded Breaks in DNA • Homologous recombination is more complicated than a simple breakage-and-exchange model. • This model has been superseded by a model involving double-stranded breaks in the DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Double-Strand Breaks and Formation of Crossovers: Step 1 (1 of 5) 1. In eukaryotes, recombination begins with an asymmetrical cleavage of one chromatid by dimeric protein Spo11. • Spo11 recruits two proteins to trim single strands. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Double-Strand Breaks and Formation of Crossovers: Steps 2 and 3 (2 of 5) 2. Rad51 stabilizes single-stranded DNA and joins the trimmed region to engage in strand exchange. • Rad51 performs this same stabilizing function in DNA repair. 3. Once the single stranded DNA is stabilized, it can invade a complementary region on a piece of homologous DNA. • One of the two strands is displaced to form a D loop. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Double-Strand Breaks and Formation of Crossovers: Step 4 (3 of 5) 4. The invading strand pairs with the complementary DNA in the D loop. • The Holliday junction is an interim structure where a single strand of DNA from each double helix has crossed over and joined the opposite double helix. • The Holliday junction has been verified by electron microscopy. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Double-Strand Breaks and Formation of Crossovers: Step 5 (4 of 5) 5. DNA synthesis leads to strand extension which displaces the D loop. This allows it to pair with more singlestranded DNA. • This involves more recombination proteins such as Rad52 and Rad59. • This process can rapidly increase the length of the single-stranded DNA exchanged. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Double-Strand Breaks and Formation of Crossovers: Step 6 and 7 (5 of 5) 6. Gaps in the single-stranded DNA are repaired with DNA polymerase and ligase. 7. The 3′ end of the invading strand connects with the 5′ end of the original strand. This leads to a double Holliday structure. Copyright © 2022 Pearson Education, Inc. All Rights Reserved A Model for Homologous Recombination via Double-Strand Breaks Figure 17.31 A Model for Homologous Recombination via Double-Strand Breaks. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Holliday Junction Resolution • Holliday junctions are transitory structures that must be resolved (and the homologous chromosomes disconnected) before cell division. • The junction can be cleaved, or resolved, in either of two ways: – Same-sense resolution – Opposite-sense resolution Copyright © 2022 Pearson Education, Inc. All Rights Reserved Holliday Junction Resolution: SameSense and Opposite-Sense Resolution • If the junction is resolved via same-sense resolution, crossing over does not occur. • The DNA molecules have a noncomplementary region near the site of the Holliday junction. • Opposite-sense resolution results in crossing over (chromosomal DNA beyond the point where recombination occurred will be completely exchanged between the two chromosomes). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Holliday Junction Resolution: Heteroduplex Regions • However the Holliday junction is resolved, there will be DNA where the two strands paired are derived from different chromosomes, known as heteroduplex regions. • Heteroduplex regions often contain single-base mismatches. • These mismatches are repaired using a mismatch repair system, but the strand picked for repair is random. This can lead to gene conversion during meiosis. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Resolution of Holliday Junctions During Recombination Figure 17.32 Resolution of Holliday Junctions During Recombination. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Transposons Are Mobile Genetic Elements • Recombination is one way organisms maintain genetic diversity. • Another type of genetic exchange involves mobile genetic elements, called transposable elements or transposons. • The first evidence for such movable genetic elements came from pioneering work by the maize (corn) geneticist Barbara McClintock in the 1940s and 1950s. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Movement of Transposons • Transposon movement does not require sequence similarity with the insertion site. • Transposons encode all or many of the components they need to move within a genome. • DNA-only transposons act only through DNA and the proteins they encode. • Retrotransposons act through an RNA intermediate step. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Transposons Differ Based on Their Autonomy and Mechanism of Movement • Autonomous transposable elements encode their own transposase (enzyme required for movement). • Nonautonomous transposable elements lack a fundamental transposase gene and need the help of other autonomous elements to move. • This process is sometimes referred to as “mobilizing” the element. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Two Mechanisms of Transposition for DNA-Only Transposons • In replicative transposition, the transposon is copied from the current site and the new copy inserted at the new site (a “copy-and-paste” mechanism). • In conservative transposition, the transposon is excised from the original site and moves to a new site in the genome (a “cut-and-paste” mechanism). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Two Types of Transposition Figure 17.33 Two Types of Transposition. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Bacterial Transposons Can Be Composite or Noncomposite • Composite transposons carry IS (insertion-sequence) elements. • Different IS elements vary in length and structure, but all encode transposases and begin and end with short inverted repeats. • Noncomposite transposons do not rely on IS elements. • Instead, they have short, inverted repeat sequences at their ends and a transposase gene in the middle. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Types of Transposable Elements in Bacteria Figure 17.34 Types of Transposable Elements in Bacteria. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Mechanism of Insertion at a New Location • When a transposase gene is used to produce transposase enzyme, the transposon can move to a new site. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Steps of Transposon Movement • Transposase makes a staggered cut in the DNA at the new insertion site. • The transposon inserts between the staggered ends. • The DNA repair machinery of the bacterium seals the remaining single-stranded gaps. • The result is two duplicate sequences on either side of the inserted transposition, called target site duplication. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Target Site Duplication During Transposon Insertion Figure 17.35 Target Site Duplication During Transposon Insertion. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Eukaryotes Also Have DNA-Only Transposons • Other eukaryotes (besides maize) have DNA-only transposons. • One of the best studies is the P element of the fruit fly, Drosophila. • When P elements insert into genes at random, they can disrupt the function of the gene, a process called transposon tagging. • Similar transposons have been found in Caenorhabditis elegans. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Retrotransposons • Retrotransposons are a special type of transposable element that use reverse transcription to carry out movement. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Retrotransposon Movement (1 of 2) • Transposition begins with transcription of the retrotransposon DNA followed by translation of the resulting RN A. • This produces a protein with reverse transcriptase and endonuclease activities. • The retrotransposon RNA and protein then bind chromosomal DNA in a new location. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Retrotransposon Movement (2 of 2) • The endonuclease cuts one of the DNA strands. • The reverse transcriptase uses the retrotransposon RNA as a template to make a DNA copy that is then integrated into the target site. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Alu Sequences • Retrotransposons can attain high copy numbers within a genome despite transposing rarely. • Alu sequences are 300 bp long and do not encode a reverse transcriptase. • But using reverse transposase from elsewhere in the genome, they have increased their copy number in humans and other primates. • In the human genome, about 1 million Alu sequences represent about 11% of the total DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved L1 Element • The L1 element is a retrotransposon responsible for about 17% of human DNA. • It encodes its own transcriptase and endonuclease. • It is not clear why genomes contain large amounts of retrotransposon sequences. • They may contribute to evolutionary flexibility and variability. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Movement of Retrotransposons Figure 17.36 Movement of Retrotransposons. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright This work is protected by United States copyright laws and is provided solely for the use of instructors in teaching their courses and assessing student learning. Dissemination or sale of any part of this work (including on the World Wide Web) will destroy the integrity of the work and is not permitted. The work and materials from it should never be made available to students except by instructors using the accompanying text in their classes. All recipients of this work are expected to abide by these restrictions and to honor the intended pedagogical purposes and the needs of other instructors who rely on these materials. Copyright © 2022 Pearson Education, Inc. All Rights Reserved