DNA replication (Lecture 28,29)

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1 DNA replication (Lecture 28,29) 1. DNA replication and the cell cycle 2. DNA is Reproduced by Semiconservative Replication 2.1 Conservation of the Original Helix 2.2 The Meselson-Stahl Experiment 2.3 Semiconservative Replication in Eukaryotes 2.4 Origins, Forks and Units of Replication 3. Enzymes involved in DNA Synthesis in Bacteria 3.1 DNA Polymerase I 3.2 Synthesis of Biologically Active DNA 3.3 DNA Polymerase II and III. DNA is hereditary material In 1928, Frederick Griffith showed that genetic material is a specific molecule. Two distinguishable strains of Spreptococcus pneumoniae (a bacterium that causes pneumonia in mammals): with smooth colonies (S) and rough colonies (R). Cells of the smooth strain were encapsulated with a polysaccharide coat and cells of the rough strain were not. These alternative phenotypes were inherited Transformation of bacteria Griffith discovered that (a) the S strain of the bacterium Streptococcus pneumoniae, which was protected from a mouse's defensive system by a capsule, was pathogenic; (b) the R strain, a mutant lacking the capsule, was nonpathogenic; (c) heat-killed S cells were harmless; but (d) a mixture of heat-killed S cells and live R cells caused pneumonia and death. (e) Live S bacteria could be retrieved from the dead mice injected with the mixture. Griffith concluded that molecules from the dead S cells had genetically transformed some of the living R bacteria into S bacteria. In 1944, Oswald Avery, Maclyn McCarty and Colin MacLeod discovered that the transforming agent had to be DNA More evidence came from studies of bacteriophages viruses that infect bacteria The Hershey-Chase experiment Viral proteins, labeled with radioactive sulfur, remained outside the host cell during infection. 32P labeled viral DNA entered the bacterial cell Additional evidence that DNA is genetic material A eukaryotic cell doubles its DNA content prior to mitosis During mitosis, the doubled DNA is equally divided between two daughter cells

2 An organism s diploid cells have twice the DNA as its haploid gametes In 1947, Erwin Chargaff analyzed the DNA content of different organisms: DNA composition is species-specific The amount and ratios of nitrogenous bases vary from one species to another The number of adenine (A) residues approximated the number of thymines (T), same was true for guanines (G) and cytosines (C). The A=T and G=C equalities became known later as Chargraff s rules. Watson and Crick building models to confirm to x-ray data DNA is helix with a uniform width of 2 nm. Purine and pyrimidine bases are stacked.34 nm apart The helix makes one full turn every 3.4 nm along its length There are ten layers of nitrogenous base pairs in each turn of the helix To be consistent with a 2 nm width, a purine on one strand must pair (by hydrogen bonding) with a pyrimidine on the other antiparallel helix Base structure dictates which pair of bases can hydrogen bonds Consistence of base-pairing rule It explains Chargraff s rules It suggests the general mechanism of replication It dictates the combination of complementary base pairs and places no restriction on the linear sequence along the length of a DNA strand. Watson and Crick s model of replication Upon the replication of double-helix each of the two daughter molecules will have one old strand (parental) and one newly made strand. Such a process is called semiconservative replication. Alternative models Conservative replication: complementary chains are synthesized as for semiconservative, but the two newly created strands then come together and the parental strand reassociate. The original helix is conserved Dispersive replication: the parental strands cleave during replication and the DNA is then dispersed into two new double-helices. Each strand consists of both old and new DNA original helix is not conserved. Summary of Meselson-Stahl experiment The replication in bacteria is semiconservative The conservative model could be ruled out after the first round of replication, since the only one intermediate bend was present Dispersive model was ruled out by two major observations: when the hybrid molecule was heat denatured after the first round of replication, the density of the single strands corresponded to either 15N- or 14N-profile but not an intermediate;

3 - the second round of replication resulted in the presence of two bends in semiconservative (intermediate and 14N forms) and would result in one shifted bend in dispersive model. Semiconservative Replication in Eukaryotes 1957 J.H. Taylor, P. Woods, W. Hughes presented the evidence that semiconservative replication occurs in eukaryotes. Origins, Forks and Units of Replication DNA replication is initiated at origin. At the point of origin the strands of the helix unwound, creating a replication fork. The unit of DNA in which an individual act of replication occurs is called the replicon. Beside an origin, a replicon can contain a terminus a place where replication ends Is the a single origin or replication can start at several places? Does replication proceed in one direction (unidirectional) or in both (bidirectional)? Replication starts at several places and is bidirectional. The two strands of DNA are antiparallel The problem of antiparallel DNA strands is solved by the continuous synthesis of one strand (leading strand) and discontinuous synthesis of the complementary strand (lagging strand) Synthesis of leading and lagging strands Leading strand the DNA strand which is synthesized as a single polymer in the 5 3 direction towards the replication fork. Lagging strand the DNA strand that is discontinuously synthesized against the overall direction of replication. Priming DNA synthesis Primer short RNA segment that is complementary to a DNA segment and that is necessary to begin DNA replication. Steps of DNA replication 1. Double helix unwinds, providing single-stranded DNA templates. This is done with the help of helicases and single-strand binding proteins. 2. Synthesis of leading strand. Priming (done with the help of primase) Elongation (DNA polymerase) Replacement of RNA primer by DNA (DNA polymerase) 3. Synthesis of lagging strand Priming for Okazaki fragment (primase) Elongation of fragment (DNA polymerase)

4 Replacement of RNA primer (DNA polymerase) Joining of fragments (DNA ligase) DNA polymerase I 1957 Arthur Kornberg isolated an enzyme (DNA polymerase I) from E. coli that was able to direct DNA synthesis in vitro. Major requirements for in vitro DNA synthesis were: 1. All four deoxyribonucleoside triphosphates (datp, dctp, dgtp, dttp = dntp). 2. Template DNA DNA Polymerases II and III 1969 Peter DeLucia and John Cairns discovered a mutant strain of E. coli that was deficient in polymerase I activity. Observation: the mutant strain duplicated its DNA and reproduced itself but cells are highly deficient in DNA repair (UV-sensitive). Conclusions: 1. At least one more enzyme is able to replicate E. coli DNA. 2. DNA polymerase I may serve a secondary (at least for replication) function which is associated with DNA fidelity. Two other unique DNA polymerases have been isolated Properties of Three Bacterial DNA Polymerases I II III Initiation of chain synthesis polymerization exonuclease activity exonuclease activity Molecules of polymerase/cell 400? 15 Role of the polymerases in vivo Polymerase I : - removes the RNA primer; - fills the gaps that naturally occur as primers are removed; - has proofreading function. Polymerase II: -is involved in UV-damaged DNA repair; -has proofreading function. Polymerase III: -is the most replication relevant polymerase; -has proofreading function.

5 Features of eukaryotic replication 1. Eukaryotes have times larger chromosomes 2. Rates of DNA replication in eukaryotes is 1000 fold slower (in E. coli chromosome replicates 40 min) 3. Tight control over replication (S phase lasts 9 hrs) 4. Multiple origins of replications, autonomously replicating sequences (ARS). Summary 1. DNA replication is semiconservative 2. Ones replication has started it continues until the entire genome has been duplicated 3. It starts at origin. An origin fires ones and only ones during the cell cycle. 4. It is bidirectional 5. At the place of the replication start (origin) helix unwinds and creates two replicational forks 6. Enzymes that synthesise new strands are called polymerases and have complex structure and function including proofreading activity. Reading CH. 16 ( )

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