1. Paul D. Adams University of Arkansas Mary K. Campbell Shawn O. Farrell http://academic.cengage.com/chemistry/campbell Chapter Ten Biosynthesis of Nucleic Acids: Replication

2. Replication of DNA Naturally occurring DNA exists in single-stranded and double-stranded forms, both of which can exist in linear and circular forms Difficult to generalize about all cases of DNA replication We will study the replication of circular double- stranded DNA and then of linear double-stranded DNA most of the details we discuss were first investigated in prokaryotes, particularly E. coli

3. Flow of Genetic Information in the Cell Mechanisms by which information is transferred in the cell is based on “Central Dogma”

4. Prokaryotic Replication Challenges in duplication of circular double-stranded DNA achievement of continuous unwinding and separation of the two DNA strands arotection of unwound portions from attack by nucleases that attack single-stranded DNA synthesis of the DNA template from one 5’ -> 3’ strand and one 3’ -> 5’ strand efficient protection from errors in replication

5. Prokaryotic Replication (Cont’d) Replication involves separation of the two original strands and synthesis of two new daughter strands using the original strands as templates Semiconservative replication:Semiconservative replication: each daughter strand contains one template strand and one newly synthesized strand Incorporation of isotopic label as sole nitrogen source ( 15 NH 4 Cl) Observed that 15 N-DNA has a higher density than 14 N-DNA, and the two can be separated by density-gradient ultracentrifugation

6. Which Direction does Replication go? origin of replicationDNA double helix unwinds at a specific point called an origin of replication bidirectionalPolynucleotide chains are synthesized in both directions from the origin of replication; DNA replication is bidirectional in most organisms replication forksAt each origin of replication, there are two replication forks, points at which new polynucleotide chains are formed There is one origin of replication and two replication forks in the circular DNA of prokaryotes In replication of a eukaryotic chromosome, there are several origins of replication and two replication forks at each origin

7. DNA Polymerase DNA is synthesized from its 5’ -> 3’ end (from the 3’ -> 5’ direction of the template) leading strandthe leading strand is synthesized continuously in the 5’ -> 3’ direction toward the replication fork lagging strand Okazaki fragments)the lagging strand is synthesized semidiscontinuously (Okazaki fragments) also in the 5’ -> 3’ direction, but away from the replication fork DNA ligaselagging strand fragments are joined by the enzyme DNA ligase

8. DNA Polymerase Reaction The 3’-OH group at the end of the growing DNA chain acts as a nucleophile. The phosphorus adjacent to the sugar is attacked, and then added to the growing chain.

9. Properties of DNA Polymerases DNA polymeraseThere are at least five types of DNA polymerase (Pol) in E coli, three of which have been studied extensively

10. Function of DNA Polymerase DNA polymerase function has the following requirements: all four deoxyribonucleoside triphosphates: dTTP, dATP, dGTP, and dCTP Mg 2+ an RNA primer - a short strand of RNA to which the growing polynucleotide chain is covalently bonded in the early stages of replication DNA-Pol I: repair and patching of DNA DNA-Pol III: responsible for the polymerization of the newly formed DNA strand DNA-Pol II, IV, and V: proofreading and repair enzymes

11. Supercoiling and Replication DNA gyraseDNA gyrase (class II topoisomerase) catalyzes reaction involving relaxed circular DNA: creates a nick in relaxed circular DNA a slight unwinding at the point of the nick introduces supercoiling the nick is resealed The energy required for this process is supplied by the hydrolysis of ATP to ADP and P i

12. Replication with Supercoiled DNA Replication of supercoiled circular DNA DNA gyrase has different role here. ItDNA gyrase has different role here. It introduces a nick in supercoiled DNA a swivel point is created at the site of the nick the gyrase opens and reseals the swivel point in advance of the replication fork the newly synthesized DNA automatically assumes the supercoiled form because it does not have the nick at the swivel point helicasehelicase, a helix-destabilizing protein, promotes unwinding by binding at the replication fork single-stranded binding (SSB) protein stabilizes single-stranded regions by binding tightly to them

13. Primase Reaction The primase reaction RNA serves as a primer in DNA replication primer activity first observed in-vivo. Primase -Primase - catalyzes the copying of a short stretch of the DNA template strand to produce RNA primer sequence Synthesis and linking of new DNA strands begun by DNA polymerase III the newly formed DNA is linked to the 3’-OH of the RNA primer as the replication fork moves away, the RNA primer is removed by DNA polymerase I

14. Replication Fork General Features

15. Summary of DNA Replication in Prokaryotes DNA synthesis is bidirectional DNA synthesis is in the 5’ -> 3’ direction the leading strand is formed continuously the lagging strand is formed as a series of Okazaki fragments which are later joined Five DNA polymerases have been found to exist in E. coli Pol I is involved in synthesis and repair Pol II, IV, and V are for repair under unique conditions Pol III is primarily responsible for new synthesis

16. Summary of DNA Replication in Prokaryotes Unwinding DNA gyrase introduces a swivel point in advance of the replication fork a helicase binds at the replication fork and promotes unwinding single-stranded binding (SSB) protein protects exposed regions of single-stranded DNA Primase catalyzes the synthesis of RNA primer Synthesis catalyzed by Pol III primer removed by Pol I DNA ligase seals remaining nicks

17. Proofreading and Repair DNA replication takes place only once each generation in each cell Errors in replication (mutations) occur spontaneously only once in every 10 9 to 10 10 base pairs Can be lethal to organisms Proofreading - the removal of incorrect nucleotides immediately after they are added to the growing DNA during replication (Figure 10.10) Errors in hydrogen bonding lead to errors in a growing DNA chain once in every 10 4 to 10 5 base pairs

18. Proofreading Improves Replication Fidelity Cut-and-patchCut-and-patch catalyzed by Pol I: cutting is removal of the RNA primer and patching is incorporation of the required deoxynucleotides Nick translationNick translation: Pol I removes RNA primer or DNA mistakes as it moves along the DNA and then fills in behind it with its polymerase activity Mismatch repair:Mismatch repair: enzymes recognize that two bases are incorrectly paired, the area of mismatch is removed, and the area replicated again Base excision repair:Base excision repair: a damaged base is removed by DNA glycosylase leaving an AP site; the sugar and phosphate are removed along with several more bases, and then Pol I fills the gap

19. DNA Polymerase Repair

20. Mismatch Repair in Prokaryotes Mechanisms of mismatch repair encompass:

21. Eukaryotic Replication Not as understood as prokaryotic. Due in no small part to higher level of complexity. Cell growth and division divided into phases: M, G 1, S, and G 2

22. Eukaryotic Replication Best understood model for control of eukaryotic replication is from yeast. DNA replication initiated by chromosomes that have reached the G 1 phase

23. Eukaryotic DNA Polymerase At least 15 different polymerases are present in eukaryotes (5 have been studied more extensively)

24. Structure of the PCNA Homotrimer PCNA is the eukaryotic equivalent of the part of Pol III that functions as a sliding clamp (  ).

25. The Eukaryotic Replication Fork The general features of DNA replication in eukaryotes are similar to those in prokaryotes. Differences summarized in Table 10.5.

26. Telomerase and Cancer (Biochemical Connections) Replication of linear DNA molecules poses particular problems at the ends of the molecules Ends of eukaryotic chromosomes called telomeres Telomere- series of repeated DNA sequences See figures on p. 282-283