AP Biology, Chapter 16
The Molecular Basis of Inheritance

Summary
Introduction

DNA AS THE GENETIC MATERIAL
	Introduction
	The search for the genetic material led to DNA: science as a process
		1. Explain why researchers originally thought protein was the genetic material.
			a. Chromosomes were known to be composed of DNA and protein
			b. Hypothesized characteristics of the genetic material
				i. Had to be specific in determining traits
				ii. Had to be heterogeneous for transmitting a variety of traits
			c. Characteristics of protein
				i. Enzymes, at least were know to be very specific in function
`				ii. Proteins were known to come in many forms
		2. Summarize the experiments performed by scientists that provided evidence that DNA 
		is the genetic material.
			a. Frederick Griffith
				i. Transformed Pneumococcus
				ii. Experimental: heat-killed smooth + live rough  killed
				iii. Controls
					.Live smooth  killed
					.Live rough   didn't
					.Heat-killed smooth   didn't
					.Heat-killed rough   didn't
				iv. Conclusion: a substance transferred the smooth trait			
			b. Oswald Avery, Maclyn McCarty, and Colin MacLeod
				i. Purified components of the smooth bacteria
				ii. Only DNA could transform
			c. Alfred Hershey and Martha Chase
				i. System: T2 bacteriophage of E. coli
				ii. Differential labeling 
					.T2 grown in radioactive sulfur had labeled protein
					.T2 grown in radioactive phosphorus had labeled DNA
				iii. Experiment
					.Infect
					.A short time later knock phage off with a blender
					.Centrifuge to separate knocked off phage and host cells
				iv. Results
					.Radioactive protein stayed on the outside of the host
					. Radioactive DNA entered the host
				v. Conclusion: DNA carried traits for viral replication
			d. Erwin Chargaff
				i. Analyzed DNA from a variety of organisms
				ii. Results
					.Amounts of ATGC varied
					.But A=T and G=C
				iii. Conclusion: DNA not so simple, specifically varies by species
	Watson and Crick discovered the double helix by building models to conform to X-ray 
	data: science as a process
		3. 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.
			a. Known covalent structure
				.Sugar-phosphate backbone
				.One nitrogen base attached to each sugar
			b. 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
			c. Open questions
				.Number of strands
				.Bases outside or inside
			d. 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)
		4. Describe the structure of DNA. Explain the "base-pairing rule" and describe its 
		significance.
			a. Double stranded helix
			b. Sugar-phosphate backbones
			c. AT and GC pairs held by hydrogen bonds
			d. Opposing sequences are complementary; given one  the other

DNA REPLICATION AND REPAIR
	Introduction
	During DNA replication, base pairing enables existing DNA strands to serve as 
	templates for new complementary strands
		5. Describe the semiconservative model of replication and the significance of the 
		experiments by Matthew Meselson and Franklin Stahl.
			a. Three models
				i. Conservative: original DNA stays intact
				ii. Dispersive: original is spread at each replication
				iii. Semiconservative: half of the original makes half of the new DNAs
			b. Experiment
				i. Completely label DNA with heavy 15N
				ii. Switch to light 14N medium
				iii. Grow, sample, purify DNA, determine density in an ultracentrifuge
			c. Results
				i. Original heavy band is replaced by a half-heavy band
				i. Half-heavy band then splits off an equal light band
			d. Interpretation: semi-conservative  
	A large team of enzymes and other proteins carries out DNA replication
		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.
			a. DNA sequences where replication begins = origins of replication
				i. Appear as a bubble in EM
				ii. Origin is essential for DNA to be copied
				iii. Replication forks are at the ends of the bubbles
			b. Steps
				i. Helicases unwind the original double helix
				ii. Single-stranded binding proteins stabilize the unwound parental DNA
				iii. Matching bases line up
				iii. The leading strand is synthesized continuously, 5'3'
				iv. The lagging strand is synthesized in pieces, 3'5'
				v. DNA polymerase checks for the correct base and covalently attaches 
				them
		7. Explain what energy source drives the polymerization of DNA.
			a. Nucleotide precursors are their triphosphates: dGTP, dTTP, dATP, dCTP
			b. Like ATP, their carry energy 	
		8. Define "antiparallel" and explain why continuous synthesis of both strand is not 
		possible.
			a. Nucleotides are added onto the 3' end of the growing strand
			b. The 5'3' strand can be continuously synthesized
			c. New nucleotides matching 3'5' original strand cannot be added onto the 5' 
			end
		9. Distinguish between the leading strand and the lagging strand.
			a. Leading strand (new with 3' end toward the fork)
				i. No problem
				ii. 3 phosphates on 5' end of d_TP react with the 3' hydroxyl
				ii. Catalyzed by DNA polymerase
			b. 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.
			a. Primase makes a series of short RNA primers
			b. DNA polymerase adds DNA bases onto the primer's 3' end
			c. The short DNA sections are Okazaki fragments
			d. DNA polymerase removes primers and fills in the gaps
			e. Fragments are joined by DNA ligase
		11. Explain the roles of DNA ligase, primer, primase, helicase, and the single-strand 
		binding protein.
			a. DNA ligase heals single-stranded breaks
			b. Primers are short, temporary sequences that allow DNA polymerase to work
			c. Primase is an RNA polymerase that makes short primers
			d. Helicase breaks the sugar-phosphate backbone and allows unwinding
			e. Single-strand binding protein stabilizes the separated strands
	Enzymes proofread DNA during its replication and repair damage in existing DNA
		12. Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA 
		proofreading and repair.
			a. DNA polymerase recognizes non-AT,GC pairs
				i. Backs up removing them
				ii. Reverses and resumes adding bases
			b. Mismatch repair enzymes
				i. Recognize damaged bases in DNA
				ii. Cut the sugar-phosphate backbone
			c. Nuclease removes nucleotides in the damaged area
				i. DNA polymerase fills in the gap
				ii. ligase heals the sugar-phosphate backbone
	The ends of DNA molecules pose a special problem
		13. Describe the structure and function of telomeres. Explain the significance of 
		telomerase to healthy and cancerous cells.
			a. Telomeres are chromosome ends; a 3' and a 5' end
				i. Leading strand cannot be completed, primer remains
				ii. Telomeres shorten with each replication
			b. Contain repeated TTAGGG = extra DNA
				i. We can lose some at each replication without effect
				ii. As we age the telomeres get shorter
			c. Telomerase has built-in primer, can add more TTAGGG
				i. Present in germ cell lines
				ii. And present in cancer cells