Understanding DNA Structure and Replication

1. Hello!

3. What is a virus that infects bacteria called? Who actually took the X-ray diffraction photo of DNA’s structure? What are the bonds between nitrogenous bases? What does the “semiconservative model” describe? What does “topoisomerase” do? Chapter 16 sec 1 & 2 RQ bacteriophage Rosalind Franklin Hydrogen bonds DNA replication Relieves the strain of replicating DNA molecules; breaks, swivels, and rejoins DNA strands

4. Why researchers originally thought protein was the genetic material. • Proteins are macromolecules with great heterogeneity and functional specificity • Little was known about nucleic acids • The physical and chemical properties of DNA seemed too uniform to account for the multitude of inherited traits 

5. The experiment that led to the discovery that DNA was the genetic material in cells. • Frederick Griffith in 1928 • Trying to find a vaccine to fight pneumonia • Experimented with the two strains of pneumococcus; smooth & rough • Smooth caused the disease, rough did not • When dead S strain was mixed with live R, the mice DID die, indicating an acquired ability 

7. Transformation and viruses and their effects on bacteria. • Change in phenotype due to the assimilation of external genetic material by a cell • Viruses can inject their information into cells and cause drastic changes in behavior 

8. Hershey & Chase experiment

9. The three components of a nucleotide. • Pentose (5-C sugar) 2. Phosphate 3. Nitrogenous base 

10. Pyrimidines 6 membered ring of carbon and nitrogen C – cytosine T – thymine (DNA) U – uracil (RNA) Purines 5 membered ring with 6 membered ring A – adenine G – guanine  The nitrogenous bases found in DNA; pyrimidines and purines.

12. How Watson and Crick deduced the structure of DNA and what evidence they used. • Built models to conform to x-ray data - sugar phosphate backbone - nitrogenous base interior 

14. The “base-pairing rule” and it’s significance. • A – T : 2 hydrogen bonds • G – C : 3 hydrogen bonds • Suggests the mechanisms for DNA replication • Dictates combination of complementary pairs 

15. The structure of DNA and the kind of chemical bond that holds the two strands together. • Hydrogen bonds hold the nitrogen bases together • Van der Waals forces help keep helix spiral shape • Covalent bonds link the sugar-phosphate backbone 

16. Semiconservative replication and the Meselson-Stahl experiment.

19. Chapter 6 Sections 2 & 3 RQ A primer • What does primase synthesize? • Okazaki fragments make up which replicating strand? • _____ are special nucleotide sequences found at the ends of eukaryotic chromosomal DNA molecules. • Which proteins make up almost half of chromatin? • The less compacted, more dispersed, “true chromatin” is called _______. lagging Telomeres histones euchromatin

20. The process of DNA replication and the role of helicase, single strand binding protein, DNA polymerase, ligase, and primase. • The helical molecule untwists while it copies its 2 antiparallel strands simultaneously • Very rapid – 50 nucleotides are copied per second • Very accurate – one in ten billion nucleotides are incorrect • Helicase  catalyzes the unwinding of the parental double helix to expose the template • Single strand binding protein  keeps the separated strands apart and stabilizes the unwound DNA • Topoisomerase – relieves twisting strain • Polymerase and ligase  catalyze the filling-in process • Primase  the enzymes that polymerize the short segments of RNA (primers) to get the DNA replication started 

25. The energy source that drives the endergonic synthesis of DNA. • It is the hydrolysis of nucleoside triphosphates, which are nucleotides with a triphosphate covalently linked to the 5’ carbon of the pentose • Exergonic hydrolysis of this phosphate bond drives the endergonic synthesis of DNA  it provides the required energy to form the new covalent linkages between nucleotides 

27. Antiparallel DNA strands and why continuous synthesis of both is not possible. • Antiparallel  the sugar-phosphate backbones of the 2 complementary DNA strands run in opposite directions • DNA can only elongate in the 5’ to 3’ direction due to polarity issues - 3’ end has a hydroxyl group - 5’ end has a phosphate 

28. The leading strand and the lagging strand. • Leading  continuous DNA synthesis, it is synthesized as a single polymer in the 5’ to 3’ direction towards the replication fork • Lagging  the DNA strand that is discontinuously synthesized against the overall direction of replication 

29. The lagging strand is synthesized when DNA polymerase can add nucleotides only to the 3’ end. • The lagging strand is produced as a series of Okazaki fragments in the 5’  3’ direction • Fragments are ligated by DNA ligase which catalyzes the formation of a covalent bond between the 3’ end of each fragment to the 5’ end of the chain 

30. The role of DNA polymerase, ligase, and repair enzymes in DNA proofreading and repair. • DNA polymerases and ligase catalyze the filling-in process of the new DNA strands • Repair enzymes excise ( remove) the damaged segments and the gap is filled in by the correct nucleotides  Pictures 

34. the role of telomeres in solving the end-replication problem with the lagging DNA strand. • Telomere  series of short tandem repeats at the ends of eukaryotic chromosomes; prevents chromosomes from shortening with each replication cycle • Telomerase  enzyme that periodically restores this repetitive sequence to the ends of DNA molecules 

37. Prokaryotic Usually circular Smaller Found in the nucleoid region Less elaborately structured and folded Eukaryotic Complexed with a large amount of protein to form chromatin Highly extended and tangled during interphase Found in the nucleus  prokaryotic and eukaryotic genomes.

39. the current model for progressive levels of DNA packing. • Nucleosome  basic unit of DNA packing [formed from DNA wound around a protein core that consists of 2 copies each of the 4 types of histone (H2A, H2B, H3, H4)] • A 5th histone (H1) attaches near the bead when the chromatin undergoes the next level of packing • 30 nm chromatin fiber  next level of packing; coil with 6 nucleosomes per turn • the 30 nm chromatin forms looped domains, which are attached to a nonhistone protein scaffold (contains 20,000 – 100,000 base pairs) • Looped domains attach to the inside of the nuclear envelope 

43. how histones influence folding in eukaryotic DNA. • Histones  small proteins rich in basic amino acids that bind to DNA, forming chromatin • Contain a high proportion of positively charged amino acids which bind tightly to the negatively charged DNA 

44. Heterochromatin Chromatin that remains highly condensed during interphase and is NOT actively transcribed Euchromatin Chromatin that is less condensed during interphase and IS actively transcribed Becomes highly condensed during mitosis  heterochromatin and euchromatin.