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)
ౠౠRibose Deoxy Ribose

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Ribose .

Sugar ³Pucker´ .

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

Purines .

Pyrimidines .

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

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3¶ ± pACGTOH ± ACGT .Oligonucleotide naming / drawing conventions ± 5¶ .Left to Right .

000 (M-1 cm-1 ) ± The A260 § 50 g /ml for DS DNA ± The A260 § 40 g /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 .Base Stacking and Base Pairing ± Bases are very nearly planar ± Aromaticity => large absorbance at 260nm ± Epsilon 260 § 10.

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2 Structure ± DNA contains genetic Information ± Distinctive base composition foretells base pairing patterns ± Double helical structures ± Local structures ± mRNAs .complex structures .8.little structure ± Stable RNAs .

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

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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 .

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

php .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. Z structures ‡ http://www. B.biochem.duke.kin ± KING 3D display software: ‡ http://kinemage.edu/depts/chemistry/courses/chem47 1_10/ABZ_DNA.olemiss.edu/software/king.

B-DNA .

Semiconservative Replication .

DNA Backbone Flexibility ‡ Multiple Degrees of Rotational Freedom .

Glycosidic Bond Configurations .

3 Canonical Helical DNA Structures .

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

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 .

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Hoogstein Pairing in Base Triples .

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RNA editng. UAG. RNA splicing .Messenger RNAs ‡ Contain protein coding information ± ATG start codon to UAA. 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.

UAG. UAA are stop codons AG[CU] and UC[GACU] code for Serine .The Genetic Code G G A C U G glu ala val A C U met A arg asp lys thr ile A C U G G ser asn gln C arg his pro leu A C U leu G A trp U cys tyr ser phe C U gly ‡ ‡ ‡ ‡ GG[GACU] code for Glycine UGG codes for Tryptophan UGA.

mRNA coding patterns .

Stable RNAs with complex structures .

loops .RNA Helices are short. bulges.

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

tRNA-Phe 2r Structure .

tRNA - the prototype structure

tRNA Phe Kinemage
‡ http://www.olemi ss.edu/depts/chem istry/courses/che m471/6tna.kin

8.3 Chemistry
± Denaturation and reannealing ± Hybridization ± Spontaneous Chemical Reactions ± Methylation ± Sequencing ± Chemical Synthesis

Denaturation and reannealing .

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

± PCR. DNA sequencing .Hybridization ‡ DNA sequences can spontaneously reanneal and form helices ‡ Basis for many of molecular biology techniques.

Spontaneous Chemical Reactions .

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Pyrimidine Dimers .

Keto ± Enol Tautomerization .

Methylation Reactions .

DNA Polymerase Mechanism .

Di-deoxy NTPs ± Chain terminators .

Sanger Sequencing .

Dye-Terminator (one-tube rxns) .

1038/nbt1486 .Next-generation DNA sequencing ‡ Millions of DNA fragments isolated. 1135 1145 (2008) Published online: 9 October 2008 doi:10. amplified by PCR and monitored in parallel ‡ ‡ ‡ Jay Shendure & Hanlee Ji Nature Biotechnology 26.

DNA Solid-Phase Synthesis .

4 Nucleotide Function ± Energetic Intermediates ± Adenine Enzyme Cofactors ± Regulatory Molecules .8.

Nucleotides .

Phospho-Anhydrides and Phosphate Esters ± High Energy Bonds .

fatty acid synthesis and oxidation .Co-Enzyme A ± Carrier for Acetyl units in intermediary metabolism.

+/NADH. NAD +/NADPH NADP and FAD/FADH2 ‡ Redox Cofactors .

Regulatory/Signalling Molecules .

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