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Understanding Nucleotides and Nucleic Acids Chemistry

Explore the basics, structure, and chemistry of nucleotides and nucleic acids. Discover how nucleotides are building blocks with base, sugar, and phosphate components. Learn about the formation of phosphodiester bonds, base stacking, and base pairing. Understand the genetic information encoded in DNA and RNA, as well as the importance of complementary base sequences. Delve into the chemical properties of nucleotides, including denaturation, hybridization, and sequencing techniques. Enhance your knowledge of Chargaff's rules, DNA replication, and the genetic code.

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Understanding Nucleotides and Nucleic Acids Chemistry

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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 • 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. Purines

  6. Pyrimidines

  7. 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

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

  9. Base Stacking and Base Pairing • Bases are very nearly planar • Aromaticity => large absorbance at 260nm • 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. B-DNA

  16. Semi-conservative Replication

  17. DNA Backbone Flexibility Multiple Degrees of Rotational Freedom

  18. Glycosidic Bond Configurations

  19. 3 Canonical Helical DNA Structures

  20. 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

  21. 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

  22. Hoogstein Pairing in Base Triples

  23. 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

  24. 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

  25. mRNA coding patterns

  26. Stable RNAs with complex structures

  27. RNA Helices are short, bulges, loops

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

  29. tRNA-Phe 2° Structure

  30. tRNA - the prototype structure

  31. 8.3 Chemistry • Denaturation and reannealing • Hybridization • Spontaneous Chemical Reactions • Methylation • Sequencing • Chemical Synthesis

  32. Denaturation and reannealing

  33. Tm (transition midpoint) as a function of base composition Salt dependence is more dramatic

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