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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 • 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 • 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
Canonical and Minor Bases • DNA A, G, C, T • RNA A, G, C, U • Modified bases • Methylation in DNA • Lots of Mods in RNA
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
Oligonucleotide naming / drawing conventions • 5’ - Left to Right - 3’ • pACGTOH • ACGT
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
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
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
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
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
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
DNA Backbone Flexibility Multiple Degrees of Rotational Freedom
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
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
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
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
RNA Secondary Structure Maps Calculated from helix thermodynamic parameters Loop entropy considerations
tRNA Phe Kinemage http://www.olemiss.edu/depts/chemistry/courses/chem471/6tna.kin