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Nucleotides and DNA Structure

Nucleotides and DNA Structure. C483 Spring 2013. 1. Purine(s) which are found mainly in both deoxyribonucleotides and ribonucleotides are A) thymine and cytosine. B) cytosine and uracil. C) cytosine. D) guanine and cytosine. E) adenine and guanine.

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Nucleotides and DNA Structure

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  1. Nucleotides and DNA Structure C483 Spring 2013

  2. 1. Purine(s) which are found mainly in both deoxyribonucleotides and ribonucleotides are A) thymine and cytosine. B) cytosine and uracil. C) cytosine. D) guanine and cytosine. E) adenine and guanine. 2. The abbreviation dGp indicates A) 5' deoxyguanylate. B) 3' deoxyguanylate. C) 3', 5' deoxyguanylate. D) 5', 3'deoxyguanylate. E) dGMP 3. Much of the stability of the double stranded helical DNA structure is the result of A) hydrogen bonding between purines. B) the phosphodiester backbone. C) Ionic nucleobase attraction. D) the stacking interactions between base pairs.

  3. All five histones are rich in ________ amino acid residues whose positive charges allow binding to the sugar-phosphate backbone of DNA. A) lysine and alanine B) lysine and arginine C) leucine and alanine D) leucine and arginine Which does not apply to most bacterial DNA? A) Circular. B) Relaxed. C) Not packed into nucleosomes. D) Supercoiled. Which best describes the structure of a nucleosome core particle? A) A histone octamer with DNA threaded through its center. B) About 50 bp of DNA associated with one histone H1 molecule. C) One nucleosome plus one histone H1 and linker DNA. D) A histone octamer wrapped approximately two times around with DNA.

  4. Nucleic Acid Structure • Nucleobase • Nucleoside • Nucleotide • Nucleic acid • Chromatin • Chromosome

  5. Base Structure • Purines and pyrimidines • Aromatic • Tautomers • H-bonding

  6. Nucleosides • Ribonucleosides and deoxyribonucleoside • Purine = osine; pyrimidine = idine (watch cytosine)

  7. Nucleotides • Phosphorylated on 2’, 3’, or 5’ • 5’ unless noted • Draw these: • dA • ADP • ppAp • ApAp • pA is normally called _______ or _______________

  8. Polynucleotides • Phosphate diesters • polyanion • directionality • 5’  3’ • Abbreviation is pdApdGpdTpdC • tetranucleotide

  9. Double Stranded DNA • Chargaff’ Rule: %A =%T and %G = %C • (C + G) not necessarily equal to (A + T)

  10. Complementary Base Pairs Mismatching may occur with tautomers

  11. Antiparallel • Inaccuracy of two-dimensional drawing: bases are perpendicular to the paper • “ladder” • H-bonding

  12. Helix • Maximization of base pair stacking • More compact • Major and minor groove • How do we explain major/minor grooves?

  13. Major/Minor Groove • Many pictures show ladder with backbone at 180o • Actually a distorted ladder with poles closer to each other, on one side

  14. Weak Forces Stabilize Double Helix • Stacking interactions (vdW forces) • Hydrogen bonding • Hydrophobic effect • Charge-charge

  15. Denaturation • Melting point • Melting curve • UV-absorption • cooperative

  16. A/T Rich and G/C Rich strands • GC rich strands harder to denature due to STACKING (not H-bonds) • Cooperativity due to initial unstacking, which exposes bases to water, which destabilizes H-bonds, which leads to further denaturation

  17. Supercoiling • Bacterial DNA • Closed, circular DNA • Topology and topoisomerases

  18. Eukaryotic DNA • Chromatin • 8000x packing ratio • Nucleosomes (10x) • 30nm chromatin fiber (4x) • RNA/Protein scaffold holds loops (200x condensation of DNA length

  19. Nucleosomes • Beads on string • Histones form octamer • Core particle

  20. Unpacking • Histones serve as negative supercoiling • Histone acyltransferases (HATS) • Necessary for expression

  21. Chromosome • Scaffold of RNA and protein • 30nm fibers are looped many times • Picture of histone-depleted chromosome: DNA strands have fallen off of scaffold

  22. Answers • E • B • D • B • B • D

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