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AP Biology, Chapter 16 The Molecular Basis of Inheritance Life’s Operating Instructions 16.1 DNA is the genetic material Intro The Search for the Genetic Material: Science Inquiry Intro 1. Explain why researchers originally thought protein was the genetic material. Chromosomes were known to be composed of DNA and protein Hypothesized characteristics of the genetic material Had to be specific in determining traits Had to be heterogeneous for transmitting a variety of traits Characteristics of protein Enzymes, at least were know to be very specific in function ` Proteins were known to come in many forms Evidence That DNA Can Transform Bacteria 2. Summarize the experiments performed by scientists that provided evidence that DNA can transform bacteria. Frederick Griffith Transformed Pneumococcus Experimental: heat-killed smooth + live rough killed Controls Live smooth killed Live rough didn't Heat-killed smooth didn't Heat-killed rough didn't Conclusion: a substance transferred the smooth trait Oswald Avery, Maclyn McCarty, and Colin MacLeod Purified components of the smooth bacteria Only DNA could transform Evidence That Viral DNA Can Program Cells 3. Summarize the experiment that provided evidence that viral DNA can program cells. Alfred Hershey and Martha Chase System: T2 bacteriophage of E. coli Differential labeling T2 grown in radioactive sulfur had labeled protein T2 grown in radioactive phosphorus had labeled DNA Experiment Infect A short time later knock phage off with a blender Centrifuge to separate knocked off phage and host cells Results Radioactive protein stayed on the outside of the host Radioactive DNA entered the host Conclusion: DNA carried traits for viral replication Additional Evidence That DNA is the Genetic Material 4. Summarize the findings of Chargaff that provided evidence that DNA is the genetic material. Erwin Chargaff Analyzed DNA from a variety of organisms Results Amounts of ATGC varied But A=T and G=C Conclusion: DNA not so simple, specifically varies by species Building a Structural Model of DNA: Scientific Inquiry 5. Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain the significance of the research of Rosalind Franklin. Known covalent structure Sugar-phosphate backbone One nitrogen base attached to each sugar From Rosalind Franklin's X-ray crystallography Helix Constant width of 2 nm One turn every 3.4 nm Bases spaced every 0.34 nm Open questions Number of strands Bases outside or inside Watson and Crick built models Two strands Hydrophobic bases inside Strands run in opposite directions; 3'5' and 5'3' AT and GC pairs give a constant 2 nm width Also satisfies Chargaff's rule (equilvalencies) 6. Describe the structure of DNA. Explain the "base-pairing rule" and describe its significance. Double stranded helix Sugar-phosphate backbones AT and GC pairs held by hydrogen bonds Opposing sequences are complementary; given one the other 16.2 Many proteins work together in DNA replication and repair Intro The Basic Principle: Base Pairing to a Template Strand 5. Describe the semiconservative model of replication and the significance of the experiments by Matthew Meselson and Franklin Stahl. Three models Conservative: original DNA stays intact Dispersive: original is spread at each replication Semiconservative: half of the original makes half of the new DNAs Experiment Completely label DNA with heavy 15N Switch to light 14N medium Grow, sample, purify DNA, determine density in an ultracentrifuge Results Original heavy band is replaced by a half-heavy band Half-heavy band then splits off an equal light band Interpretation: semi-conservative DNA Replication: A Closer Look Intro Getting Started 6. Describe the process of DNA replication. Note the structure of the many origins of replication and replication forks and explain the role of DNA polymerase. DNA sequences where replication begins = origins of replication Appear as a bubble in EM Origin is essential for DNA to be copied Replication forks are at the ends of the bubbles Steps Helicases unwind the original double helix Single-stranded binding proteins stabilize the unwound parental DNA Matching bases line up The leading strand is synthesized continuously, 5'3' The lagging strand is synthesized in pieces, 3'5' DNA polymerase checks for the correct base and covalently attaches them Synthesizing a New DNA Strand 7. Explain what energy source drives the polymerization of DNA. Nucleotide precursors are their triphosphates: dGTP, dTTP, dATP, dCTP Like ATP, their carry energy Antiparallel Elongation 8. Define "antiparallel" and explain why continuous synthesis of both strand is not possible. Nucleotides are added onto the 3' end of the growing strand The 5'3' strand can be continuously synthesized New nucleotides matching 3'5' original strand cannot be added onto the 5' end The DNA Replication Complex 9. Distinguish between the leading strand and the lagging strand. Leading strand (new with 3' end toward the fork) No problem 3 phosphates on 5' end of d_TP react with the 3' hydroxyl Catalyzed by DNA polymerase Lagging strand (new with 5' end toward fork) 10. Explain how the lagging strand is synthesized and even though DNA polymerase can add nucleotides only to the 3' end. Primase makes a series of short RNA primers DNA polymerase adds DNA bases onto the primer's 3' end The short DNA sections are Okazaki fragments DNA polymerase removes primers and fills in the gaps Fragments are joined by DNA ligase 11. Explain the roles of DNA ligase, primer, primase, helicase, and the singlestrand binding protein. DNA ligase heals single-stranded breaks Primers are short, temporary sequences that allow DNA polymerase to work Primase is an RNA polymerase that makes short primers Helicase breaks the sugar-phosphate backbone and allows unwinding Single-strand binding protein stabilizes the separated strands Proofreading and Repairing DNA 12. Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair. DNA polymerase recognizes non-AT,GC pairs Backs up removing them Reverses and resumes adding bases Mismatch repair enzymes Recognize damaged bases in DNA Cut the sugar-phosphate backbone Nuclease removes nucleotides in the damaged area DNA polymerase fills in the gap Ligase heals the sugar-phosphate backbone Evolutionary Significance of Altered DNA Nucleotides 13. How would organisms and species be affected if DNA was either replicated too accurately or not accurately enough? Too accurately No new traits Species wouldn’t be able to generate new adaptations Not accurately enough Cells resulting from mitosis would be too different Traits would change too fast for evolution to have an effect Replicating the Ends of DNA Molecules 14. Describe the structure and function of telomeres. Explain the significance of telomerase to healthy and cancerous cells. Telomeres are chromosome ends; a 3' and a 5' end Leading strand cannot be completed, primer remains Telomeres shorten with each replication Contain repeated TTAGGG = extra DNA We can lose some at each replication without effect As we age the telomeres get shorter Telomerase has built-in primer, can add more TTAGGG Present in germ cell lines And present in cancer cells 16.3 A chromosome consists of a DNA molecule packed together with proteins 15. Compare the structure and organization of prokaryotic and eukaryotic genomes. Prokaryotes Several million base pairs Circular chromosome Attached proteins control and pack it Eukaryotes Billions of base pairs 2 to hundreds of linear chromosomes Larger amounts of protein control and pack it 16. Describe the current model for progressive levels of DNA packing. Mitotic chromosomes Nucleosomes are the 11 nm beads on a string Folded into a 30-nm chromatin fiber 30-nm fibers form looped domains attached to protein scaffold Looped domains coil and fold Interphase Same up to looped domains Looped domains attached to inside surface of nuclear envelope 17. Explain how histones influence folding in eukaryotic DNA. Nucleosomes = DNA wound around clusters of 8 histones with space in between Add histone H1, nucleosomes fold into a 30-nm chromatin fiber 18. Distinguish between heterochromatin and euchromatin. More condensed, non-transcribed = heterochromatin Less condensed, transcribed = euchromatin