BIOL 302 Lecture 5Outline of Last LectureI. Discovery that DNA was genetic materiala. James Watson and Francis Crickb. Rosalind Franklinc. Fred GriffithII. DNA structurea. Chromosomes, chromatidb. Nucleotide building blocksc. Hydrogen bondsd. Double helixe. Hershey & Chasef. Genes, genomeIII. DNA packinga. Chromatinb. Nucleosomesc. Genesd. Histone molecules, histone modificationOutline of Current Lecture I. DNA duplicationa. Semiconservative replicationb. Replication forkc. DNA polymerased. Lagging strand, leading strandII. DNA synthesisa. Telomeresb. Sickle cell anemiaIII. DNA mismatch repairThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.a. Depurinationb. Deaminationc. MutationsIV. Basic DNA repairCurrent LectureCh 6. DNA Replication, Repair, and RecombinationHereditary info is passed faithfully from one generation to the next- DNA replication: accurate duplication of the genetic info carried in its DNA, occurs beforea cell can produce two genetically identical daughter cells.- Mutations: permanent changes of DNA caused by copying errors and accidental damage.- Differences in DNA: can produce the variations that underlie the differences between individuals of the same species or, over time, the differences between on species and another (EVOLUTION)DNA acts as a template for its own duplication- Both S strand and its complementary S’ strand can serve as a template to specify the sequence of the nucleotides in its complementary strand. - This complementarity allows for the double helical DNA to be copied precisely.- The copy must be carried out with speed and accuracy (in about 8 hours, a dividing animal cell will copy the equivalent of 1000 books like ECB and get no more than a letter or two wrong)- This is performed by a cluster of proteins that together form a replication machine.Each of the two strands of DNA is used as a template for the formation of a complementary DNA strand. This is referred to as semiconservative replication.- Semiconservative replication: each parent strand serves as template for one new strand, and thereby each daughter DNA double helix is composed of one of the original strands plus one strand that is completely new. To initiate DNA replication, A DNA double helix is opened at its replication origin- Replication initiator proteins: recognize specific sequences of DNA at replication origins and locally pry/pull apart the two strands of the double helix by breaking the hydrogen bonds that hold the base pairs together.- The exposed single strands can then serve as templates for copying the DNA.Origins of replication create a “replication fork” which is due to the antiparallel nature of the DNA double helix (think about polarity of the DNA molecule moving 5’ to 3’ in opposite directions. Replication forks move away in opposite directions from multiple replication origins in a eukaryotic chromosome.DNA is synthesized in the 5’ to 3’ direction- Addition of a deoxyribonucleotide to the 3’ hydroxyl end of a polynucleotide chain is the fundamental reaction by which DNA is synthesized.- The new DNA chain is thereby synthesized in the 5’ to 3’ direction- The nucleotides enter the reaction as nucleoside triphosphates (5 C sugar attached to nitrogenous base and 3 phosphate groups)- Base pairing between the incoming deoxyribonucleotide and the template strand guidesthe formation of a new strand of DNA that is complementary in nucleotide sequence to the template chain- The enzyme DNA polymerase catalyzes the addition of nucleotides to the free 3’ hydroxyl on the growing DNA strand- Breakage of a phosphoanhydride bond (bond b/w phosphate groups on the nucleoside tri-phosphate) in the incoming nucleoside triphosphate releases a large amount of free energy and thus provide the energy for the polymerization rxn. DNA replication forks are asymmetrical. - DNA polymerase enzyme acts on both strands of the DNA double helix. - DNA polymerase can only catalyze the addition of incoming nucleotides in one direction (5’ to 3’, adding nucleotides to the free 3’ end of the molecule) - Since DNA pol can only move in one direction, but the strands are moving in opposite directions, we encounter a problem within the cell. - This asymmetrical characteristic establishes a discontinuity in the replication of the parental strands, creating a leading and lagging strand. This is due to the fact that DNA isreplicated in 5’ to 3’ direction. o Bc both new strands are synthesized in the 5’ to 3’ direction, the lagging strand ofDNA must be made initially as a series of short DNA strands called Okazaki fragments that later joined together. o The DNA strand that is synthesized discontinuously in this way is called the lagging strand, the other strand, which is synthesized continuously is called the leading strand. DNA polymerase proofreads its own work- If an incorrect nucleotide is added to a growing strand, the DNA polymerase will cleave itfrom the strand and replace it with a correct nucleotide before continuing.- First, the DNA polymerase carefully monitors the base pairing b/w each incoming nucleotide and the template strand. Only when the match is correct does DNA polymerase catalyze the nucleotide addition reaction.- Second, when DNA polymerase make a rare mistake and add the wrong nucleotide, it can correct the error through an activity called proofreading. - DNA polymerase contains separate sites for DNA synthesis and proofreading- A need for proofreading explains why DNAs are synthesized only in the 5’ to 3’ directiono In the hypothetical 3’ to 5’ polymerization scheme, proofreading would remove an incorrect nucleotide, which would then block addition of the correct nucleotide and thereby prevent further chain elongationo Growth in the 5’ to 3’ direction allows the chain to continue to be elongated when an incorrect nucleotide has been added and then removed by proofreading.On the lagging strand, DNA is synthesized in fragments- DNA polymerase cannot start a completely new DNA strand- In eukaryotes, RNA primers are made at intervals of about 200 nucleotides on the lagging strand by primase (an RNA polymerase), and each RNA primer is about 10 nucleotides long.- Primers are removed by nucleases that recognize an RNA strand in an RNA/DNA helix and degrade it; this leaves