1. DNA & RNA Structure Fig 1.9

2. Deoxyribonucleic acid (DNA) is the genetic material -Stores genetic information in the form of a code: a linear sequence of nucleotides. - Replicated by copying the strands using each as a template for the production of the complementary strand.

3. 3 Ways of Depicting DNA Structure

4. Nucleosides (of DNA) – Precursors to Nucleotides Nucleoside = base + sugar Sugar = deoxyribose; 5 carbons, no OH on the 2nd (or 2’) carbon; base is attached to carbon 1

5. The 4 Nucleotides (precursors) of DNA γ β α

6. Ribose replaces deoxyribose; uracil replaces thymine RNA

7. e.g., AMP is a ribonucleotide, dAMP is a deoxyribonucleotide

8. In DNA and RNA, nucleotides are held together by phosphodiester bonds.

9. Stem-loops are common elements of secondary RNA structure. Stem loop Stems are double- stranded regions of RNA that are A-form helices. They usually follow Watson-Crick base pairing rules (U replaces T), but other pairs occur (G – U is common). (DNA is typically a B- form helix). Higher Order RNA Structure

10. Secondary structure diagramTertiary structure diagram Cr.LSU rRNA intron Tetrahymena rRNA intron

11. What chemical forces hold (or drive) the DNA strands together? (also applies to double-stranded regions of RNA)

12. 1. Hydrogen bonds between bases Also important that the purine- pyrimidine base pairs are of similar size.

13. 2. DNA strands also held together by base stacking: Van der Waals interactions between successive (or neighbor) base-pairs 3. Double-stranded helix structure also promoted by having phosphates on outside, interact with H 2 O and counter ions (K +, Mg 2+, etc.) Evidence: Compounds that interfere with Hydrogen bonds (urea, formamide) don’t separate strands by themselves, still requires heat

14. Double-stranded (DS) DNA statistics (B-form) 1.Helix is right handed 2.10 base-pairs/turn 3.3.4 nm (34 angstroms)/turn 4.Helix has a major groove and a minor groove.

15. 3 Ways of Depicting DNA Structure

16. 1 0 10

17. Molecular Visualization: www.umass.edu/microbio/chime/ DNA Structure: www.umass.edu/molvis/tutorials/dna/

18. Study Helix Stability with Melting Curves DNA melting curve of Streptococcus DNA. When DNA melts, the 2 strands come apart, and its absorbance in the UV region increases. T m = temp. at which 50% of DNA is melted.

19. Re-Annealing or Hybridization Works with: DNA - DNA DNA - RNA RNA - RNA Basis of many techniques in molecular biology.

20. Base composition (G-C content) determines melting temperature: varies among organisms

21. Separation of nuclear (nuc) and mitochondrial (mt) DNA on a CsCl-ethidium bromide gradient – visualized with long- wave UV light. G-C content also determines density of DNA (g/cc)