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Nucleotides and Nucleic Acids - Lehninger Chapter8

Nucleotides and Nucleic Acids - Lehninger Chapter8. 8.1 Basics 8.2 Structure 8.3 Chemistry 8.4 Nucleotide Function . 8.1 Basics. Building Blocks Canonical and Minor Bases Phosphodiester bonds Naming and Drawing Base Stacking and Pairing. Building Blocks.

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Nucleotides and Nucleic Acids - Lehninger Chapter8

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  1. Nucleotides and Nucleic Acids - Lehninger Chapter8 • 8.1 Basics • 8.2 Structure • 8.3 Chemistry • 8.4 Nucleotide Function

  2. 8.1 Basics • Building Blocks • Canonical and Minor Bases • Phosphodiester bonds • Naming and Drawing • Base Stacking and Pairing

  3. Building Blocks • Nucleotides = Base + Sugar + Phosphate • Nucleosides = Base + Sugar • Nitrogen Bases • Purines (5 + 6 membered rings) – numbering • Adenine Guanine • Pyrimidines (6 membered ring) – numbering • Thymine Cytosine Uracil • Pentose Sugars (numbering) • – Ribose • – Deoxy Ribose

  4. Ribose

  5. Sugar “Pucker”

  6. Canonical and Minor Bases • DNA A, G, C, T • RNA A, G, C, U • Modified bases • Methylation in DNA • Lots of Mods in RNA

  7. Purines

  8. Pyrimidines

  9. Phosphodiester bonds • Formed by Polymerase and Ligase activities • C-5' OH carries the phosphate in nucleotides • C5' - O - P - O - C3' • Phosphate pKa ~ 0 • Natural Oligonucleotides have 5' P and 3' 0H • Base hydrolysis due to ionizaiton of 2' OH in RNA

  10. Oligonucleotide naming / drawing conventions • 5’ - Left to Right - 3’ • pACGTOH • ACGT

  11. Base Stacking and Base Pairing • Bases are very nearly planar • Aromaticity => large absorbance at 260nm • Epsilon 260 ≈ 10,000 (M-1 cm-1 ) • The A260 ≈ 50 μg /ml for DS DNA • The A260 ≈ 40 μg /ml for SS DNA or RNA • Flat surfaces are hydrophobic • Dipole-Dipole and Van Der Waals interactions also stabilize stacked structures • Bases have hydrogen bond donors and acceptors • H-bonding potential satisfied in paired structures

  12. 8.2 Structure • DNA contains genetic Information • Distinctive base composition foretells base pairing patterns • Double helical structures • Local structures • mRNAs - little structure • Stable RNAs - complex structures

  13. DNA contains genetic Information • Purified DNA can "transform" Bacteria • Avery, MacLeod & McCarty transferred the virulence trait to pneumococci • The genetic material contains 32P (DNA) and not 35S (protein – C, M) • Hershey and Chase grew bacteriophage on either 32P or 35S • Bacteriophage infection resulted in transfer of 32 P and not 35S

  14. Distinctive Base composition foretell base pairing patterns • Hydrolysis of DNA and analysis of base composition • Same for different individuals of a given species • Same over time • Same in different tissues • %A = %T and %G = %C (Chargaff's Rules) • Amino acid compositions vary under all three conditions • No quantitative relationships in AA composition

  15. Structural Basis of Chargaff’s Rules Two Strands have complementary sequences 2 logical operations to obtain complementary strand 5' to 3' 1. Reverse: Rewrite the sequence, back to front 2. Complement: Swap A with T, C with G

  16. Double helical structures • Potentially Right or Left Handed • Actually Mostly Right Handed • Potentially Parallel or Anti-parallel • Actually anti-parallel • Sugar Pucker + 6 rotatable bonds gives 3 families • A, B, Z structures • http://www.olemiss.edu/depts/chemistry/courses/chem471_10/ABZ_DNA.kin • KING 3D display software: • http://kinemage.biochem.duke.edu/software/king.php

  17. B-DNA

  18. Semi-conservative Replication

  19. DNA Backbone Flexibility Multiple Degrees of Rotational Freedom

  20. Glycosidic Bond Configurations

  21. 3 Canonical Helical DNA Structures

  22. A, B and Z DNA A form – favored by RNA B form – Standard DNA double helix under physiological conditions Z form – laboratory anomaly, Left Handed Requires Alt. GC High Salt/ Charge neutralization • A, B & Z DNA Kinemages

  23. Local structures • Palindromes – Inverted repeats • Not quite the same as (Madam I’m Adam) • Symmetrical Sequence Elements Match Symmetry of Protein Homo-Oligomers • Symmetry often incomplete/imperfect • Direct Repeats • Hairpin and Cruciform Structures

  24. Hoogstein Pairing in Base Triples

  25. Messenger RNAs • Contain protein coding information • ATG start codon to UAA, UAG, UGA Stop Codon • A cistron is the unit of RNA that encodes one polypeptide chain • Prokaryotic mRNAs are poly-cistronic • Eukaryotic mRNAs are mono-cistronic • Base pairing/3D structure is the exception • Can be used to regulate RNA stability termination, RNA editng, RNA splicing

  26. GG[GACU] code for Glycine UGG codes for Tryptophan UGA, UAG, UAA are stop codons AG[CU] and UC[GACU] code for Serine The Genetic Code

  27. mRNA coding patterns

  28. Stable RNAs with complex structures

  29. RNA Helices are short, bulges, loops

  30. RNA Secondary Structure Maps Calculated from helix thermodynamic parameters Loop entropy considerations

  31. tRNA-Phe 2° Structure

  32. tRNA - the prototype structure

  33. tRNA Phe Kinemage http://www.olemiss.edu/depts/chemistry/courses/chem471/6tna.kin

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