Lec2_web - Polynucleotide Structure - Its important to keep...

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Polynucleotide Structure - It’s important to keep in mind that the Function of a molecule is a direct consequence of Structure and Chemistry . - It’s important to keep in mind that these molecules are: 1. Three-dimensional 2. Dynamic and Flexible
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What do we mean by 5’ or 3’? - This refers to the free phosphate – at the 5’ or 3’ position of the ribose. Nomenclature: - By convention (unless otherwise indicated), a nucleic acid sequence is read from left to right, in a 5’ to 3’ direction. 5’ 3’
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5’-ATCGATCAAT-3’ ( Most Common ) pApCpGpU (Ribo) pdApdCpdGpdT (Deoxyribo) P 5’ 3’ 3’ 3’ A G C P P
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This does not give a real impression of a nucleic acid molecule. - That is, these examples list the primary (1 0 ) sequence, but say nothing about the real structure of the molecules. What about “Polymerized” Nucleotides? (Polynucleotide Structure) - Let’s first look at this in two dimensions.
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- The nucleotide unit is defined by the six single bonds and corresponding torsion angles – α through ζ . - The glycosidic bond and corresponding torsion angle χ gives seven bonds in the backbone with large rotations. - This results in a very flexible molecule. - The linkage is a 3’-5’ phosphodiester bond. - These features give a nucleic acid chain (polymer) great flexibility.
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1 2 3 4 5 α β γ δ 6 ε ζ Chain Direction nucleotide unit n (n-1) (n+1) χ
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1 2 3 4 5 α β γ δ 6 ε ζ χ
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One important point: - Since the pKa of oxygen on the α phosphate group is ~2, then it is ionized at physiological pH. - This results in a nucleotide unit that is negatively charged. As a result of their pseudoaromatic nature, the bases in the polymer tend to stack on top of each other when the polymer is in an aqueous environment. - Given the choice of being in a completely random coil, or an ordered helix, the bases maximize hydrophobic contacts and minimize contact with water.
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N N 1 2 3 4 5 6 O H O H N N 1 2 3 4 5 6 O H O H CH 3 N N 1 2 3 4 5 6 O NH 2 H U T C Q. Which base ring (purine or pyrimidine) would you predict is the poorest stacker? Q. Which pyrimidine would you predict is the poorest stacker? Why?
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A look in three-dimensions singlehelix.pdb
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A Historical Perspective 1869 – Miescher discovered “nuclein.” 1900 – general components of DNA, RNA and protein were known. Chromosomes must be composed of a polymer. 1944 – Avery showed that DNA was the genetic material. 1950 – Chargaff: DNA base composition varied from one species to another.
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Chargaff, continued. Bases were not in equal proportions. Purine = Pyrimidine G = C A = T Three research groups studied the structure. 1. Linus Pauling 2. Maurice Wilkins and Rosalind Franklin 3. James Watson and Francis Crick
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The x-ray diffraction data obtained by Wilkins and Franklin strongly suggested that the DNA was a helical structure. -
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This note was uploaded on 09/11/2008 for the course BCH 453 taught by Professor Clark during the Fall '08 term at N.C. State.

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Lec2_web - Polynucleotide Structure - Its important to keep...

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