7b. What is the charge at pH7aciated with each monophosphonucleotide at pH 7.4?

Question

7b. What is the charge at pH7aciated with each monophosphonucleotide at pH 7.4? Note that follows. You should refer te that the concentration is relatively low. each monopho is typical inside a cell, the structure of and AMP is as essentially as to your text for pictures of DNA. Note that a low pH means of H' is very high. A high pH means that the concentration of H NH2 pH = 2.0 2 OH Raise the pH by adding hydroxide ions. Lower the pH by adding protons. 2 H,O 2 H H2N pH7.4 O-P-O OH H Consider the following oligomers (short chains) of DNA. The 5' end has a phosphate group attached, whereas the 3' end is an -OH group. 7c. 5-TATGGGGCCT-3 5' -AGGTTGTGAGCCACAT-3 a piece of DNA that is 123 deoxynucleotides in length with an unknown sequence d. For "a", "b" and "c", assume that each exists as a double strand. Calculate the exact molecular weight for each double-strand piece of DNA, and estimate the total charge for each at pH 7.4. For "a", "b" and "c", calculate an estimated molecular weight for each double-strand piece of DNA by using the average molecular weight of a deoxynucleotide that you calculated, and estimate the total charge for each at pH 7.4 How do the exact and estimated values compare? How might you establish the mass and charge for a double-strand form of oligomer "d"? What is the mass/charge ratio for each oligomer?

Explanation / Answer

7 b) unbounded phosphate group carry -3 charge but once it forms bond with sugar residue the negative charges compensate because of involvement of that extra electron in bond formation.

at pH=2, monophosphatenucleotide carries neutral (0) charge as 2 oxygen get protonated and nutralize their extra eleltron and 3rd oxygen involves in forming phosphodiester bond with sugar.

at pH=7.4, monophosphatenucleotide carries negative charge with the magnitude of -2 as here the OH group get deprotonated leaving their electroton.

7 c) average molecular weight of nucleic acid is 327 for ssDNA, so for dsDNA the average molecular weigth for nucleic acid is 607 : from this the calculation is

c 1) (no. of nucleic acids* 607.4)+157 = ( here 157 is the mw of triphsphate at the end of strand)

23* 607.4+157 = 14,127 dalton

c 2)  (no. of nucleic acids* 607.4)+157  = 10* 607.4+157 = 6,221 dalton

c 3)  (no. of nucleic acids* 607.4)+157  = 16* 607.4+157 = 9,875 dalton

c 4)  (no. of nucleic acids* 607.4)+157  = 123* 607.4+157 = 74,867 dalton

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