BIOLOGY 172 1st Edition Lecture 5 Outline of Last Lecture I. Four Levels of Protein StructureII. Macromolecules: Proteins and Nucleic AcidsIII. DNA ReplicationOutline of Current Lecture I. MacromoleculesII. DNA ReplicationCurrent LectureDNA Strands and the Macromolecules within them: Bases pair as complements for DNA and RNA.Hydrogen bonding between G and C happens more than between A and T, therefore G and C pairs are harder to break apart and they are more stable.Erwin Chargaff: He found that pairs would have the same amounts as each other in DNA strands. There are equivalent amounts of A and T. There are equivalent amounts of G and C. Forces that stabilize DNA: Phosphodiester bonds. Hydrogen bonds.Base stacking.Heat will break DNA double helix to a single strand. This is partly because heat breaks hydrogen bonds.These 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.Double stranded DNA- measure the absorbency. How much Absorbance a DNA strand has is different from double to single stranded DNA.Hydrogen bonds melt when you add head, so the double bonds break away. A and T would meltthe fastest because it only has two hydrogen bonds. High GC content would need more energy/heat to break it apart. If the temperature began to cool, they could find their complimentary base pairing and realign.DNA forms a template for its own synthesis: Each DNA strand serves as a template for new strands. Then the info is copied and synthesized (those first strands serve as the template for new complementary copies… you have one old, and one new strand!)DNA replication: Light Blue: the solid replication indicated is the leading strand. The lagging strand is in light blue, but is the “broken” half. Bacterial and viral DNA with 1 point of origin. Between the two forks of replication, there’s a bubble where the chain grows from 5’ to 3’. Always extending onto the 3’ because the 5’ leads.Eukaryotic chromosomes with 100’s to 1000’s of origins. From a replication fork, replication proceeds in both directions in Eukaryotes.During replication: H-bonds between strands are broken and the helix is untwisted.Features of DNA replication: I. New Nucleotides are added to an existing chain, by making Phosphodiester bonds. The breaking of high-energy phosphate bonds drives this reaction.II. Requires a template- DNA.III. Requires dNTPS.IV. Catalyzed (or started) by DNA polymerase. (this makes replication GO)V. Proceeds in 5’ to 3’ direction, adding to 3’ side.DNA polymerase requires: a template, a 3’ OH (hydroxyl from a primer), and dNTPs.*Know the proteins in the chart below!Proteins that bind to origin region pull apart the DNA to get to the bases.Helicase unwinds, at the front of the replication fork. It breaks all hydrogen bonds between bases. Helicase is the zipper that unzips the attached parts! It keeps them separated- so that DNA doesnot come back together.New strand5 endPhosphateBaseSugarTemplate strand3 end5 end3 end5 end3 end5 end3 endNucleosidetriphosphateCoil pulled to open… the bubble has knots around it. Topoisomerase: relieves the knotting/twisted strain in front of and behind the bubble.Dna polymerase cannot start synthesizing until Primase places the RNA primer.DNA polymerase 3: for synthesizing the DNA.Sliding clamp: holds DNA polymerase in place…keeps the DNA polymerase on the DNA.Dna polymerase 1: removes the RNA and helps keep the new strands stable. DNA ligase: works on lagging strand, all the different fragments are sealed by ligase so you have a continuous strand at the end.DNA polymerase III-responsible for chromosomal replication (all leading strand most of the lagging strand)Helicase (above) unwinds in a  direction.DNA polymerase on a lagging strand extends each primer.Topoisomerase is working ahead of the fork.DNA is negatively charged (because it’s slightly acidic), so the sliding clamp must also have a negative charge so it does not get attached along the strand!Be able to label all the parts on the following diagram:Okazaki fragments: lagging strand. Primer laid down, DNA polymerase 3 extends the lagging strand, then bumps into the next primer and stops. Ligase puts together the fragments.Synthesis of the Leading Strand:DNA is opened, unwound, and primed.Once primer is laid down, an H-O group is generated.Helicase continues to unwind the DNA.Synthesis begins:Sliding clamp holds DNA in place, while DNA polymerase works from 5’ to 3’.Primase is constantly needed on the lagging strand so that it can be extended and eventually put together completely. It needs to be “reprimed.”Leading strands extended/unwound further:Primer generates a 3’ H-O group. Then needs to be extended and reprimed.Synthesis of the Lagging Strand:Primase synthesizes RNA primer.DNA Polymerase 3 works in a 5’ to 3’ direction, synthesizing the first Okazaki fragment ofthe lagging strand.DNA Polymerase 1 removes ribonucleotides of the primer, and replaces them with deoxyribonucleotides in 5’ to 3’ direction.DNA ligase closes the gap in the sugar-phosphate backbone. Ligase seals the fragments together, so phosphate and H-O are put together.LIGASE sealing two