Bio 118 1st Edition Lecture 14 Outline of Last Lecture I. Photosynthesisa. Two Linked Sets of Reactionsb. Nature of Light Energyc. Photosynthetic Pigments Absorb Lightd. Role of Carotenoids and Other Accessory Pigmentse. Resonance f. Reaction Centerg. Two Types of Reaction Centersh. Electrons Participate in Redox Reactions i. Chemiosmosis and Photophosphorylationj. Oxygenic Photosynthesisk. How Does Photosystem 1 Work?l. Summary of Photosystemsm. The Z Schemen. The Calvin Cycle and Carbon Fixationo. The Calvin Cyclep. The Importance of Rubiscoq. Connection to Global Warming 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.Outline of Current Lecture I. DNA’s Primary StructureII. DNA Has DirectionalityIII. DNA’s Secondary StructureIV. DNA Strands Are Templates for DNA SynthesisV. How Do the New DNA Strands Form?VI. A Comprehensive Model for DNA SynthesisVII. Characteristics of DNA PolymerasesVIII. How Does Replication Get Started?IX. How is the Helix Opened & Stabilized?X. How is the Leading Strand Synthesized?XI. PrimaseXII. The Lagging StrandXIII. How is the Lagging Strand Synthesized?XIV. The Discontinuous Replication HypothesisXV. The Discovery of Okazaki FragmentsXVI. DNA Synthesis Enzymes Are Well-OrganizedXVII. Replicating the Ends of Linear ChromosomesXVIII. Repairing Mistakes & DNA DamageXIX. If DNA is Damaged, How is It Detected?XX. What if DNA Polymerase Misses an Error?XXI. Repairing Damaged DNAXXII. Nucleoside Excision Repair SystemCurrent LectureDNA’s Primary Structure- Has 2 major componentso Backbone: Made of the sugar and phosphate groups of deoxyribonucleotideso Series of nitrogen containing bases that project from the backboneDNA Has Directionality- One end has an exposed hydroxyl group on the 3’ carbon of deoxyribose- Other end has an exposed phosphate group on the 5’ carbonDNA’s Secondary Structure- Watson & Crick proposed 2 DNA strands line up in the opposite direction to each other antiparallel fashion- Antiparallel strands twist to form a double helix- Secondary structure is stabilized by complementary base pairing o A(denine)T(hymine)o G(uanine)C(ytosine)DNA Strands are Templates for DNA Synthesis- Watson & Crick suggested the existing strands of DNA served as a template for the production of new strands- Bases were added to new strands according to complementary base pairingHow Do New DNA Strands Form? Three Possibilities:- 3 alternative hypotheses for how the old and new DNA strands interact during replicationo Semiconservative replication Parental DNA strands separate each used as template for synthesis of new strand Daughter molecules each consist of one old and one new strando Conservative replication Parental molecule serves as template for synthesis of entirely new moleculeo Dispersive replication The parent molecule cut into sections Daughter molecules contain old DNA interspersed with newly synthesizedDNAComprehensive Model for DNA Synthesis- Meselson & Stahl’s Key Experiment:o Showed that each parental DNA strand is copied in its entirety; semi-conservativereplicationo Did not illustrate a mechanism for this processo DNA polymerase is the enzyme that catalyzes DNA synthesiso Discovery of DNA polymerase cleared the way for understanding DNA replication reactionsCharacteristics of DNA Polymerases- Critical characteristic of DNA polymerases can only work in one direction- DNA polymerases can add deoxyribonucleotides to only the 3’ end of a growing DNA chain- DNA synthesis always proceeds in the 5’3’ direction- DNA polymerization is exergonic because monomers that act as substrates in reaction (deoxyribonucleoside triphosphates) have high potential energy because of their 3 closely packed phosphate groups How Does Replication Get Started?- A replication bubble forms in a chromosome that is actively being replicated Grows as DNA proceeds - Synthesis is bidirectional replication process begins at a single location in bacterial chromosomes (origin of replication)- Eukaryotes also have bidirectional replication but synthesis does not start at end of chromosomes, but has multiple origins of replications & replication ubbles- Replication fork is the T-shaped region where the DNA is split into 2 separate strandsHow Is The Helix Opened and Stabilized?- Several proteins are responsible for opening and stabilizing the double helix:o Enzyme helicase catalyzes the breaking of hydrogen bonds between the 2 DNA strands to separate themo Single strand DNA binding proteins (SSBPs) attach to separated strands to prevent from closingo Enzyme topoisomerase cuts & rejoins the DNA downstream of the replication fork, relieving tension in the helix due to the unwindingHow is the Leading Strand Synthesized?- DNA polymerase requires a free 3’ hydroxyl (OH) group to commence & there isn’t one available therefore it requires a primer to start replication- A few nucleotides possessing free 3’ hydroxyl groups bond to the template strand is the primer made of RNAo Provides a free 3’ hydroxyl group that can combine with incoming dNTP to form phosphodiester bond later RNA segment removedPrimase- A type of RNA polymerase that synthesizes a short RNA segment that serves as primer- DNA Polymerase 3 then adds bases to the 3’ end of the primer creates the leading strand- Then leads into the replication fork- Synthesized continuously in the 5’3’ directionThe Lagging Strand- The other DNA strand- Synthesized discontinuously in the direction away from the replication fork because DNAsynthesis must proceed in 5’3’ directionHow is the Lagging Strand Synthesized?- Synthesis starts when primase synthesizes a short stretch of RNA again acting as a primer- DNA polymerase 3 then adds bases to the 3’ end of the primer- DNA polymerase moves away from replication fork as helicase continues to open the replication fork, exposing DNADiscontinuation Replication Hypothesis- Once primase synthesizes an RNA primer on the lagging strand, DNA polymerase might synthesize short fragments of DNA along lagging strand- These fragments would later be linked together to form a continuous whole strand- Tested by Okazaki & colleaguesDiscovery of Okazaki Fragments- Lagging strand is synthesized as short discontinuous fragments called Okazaki fragments- DNA polymerase 1 then removes the RNA primer at the
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