I know that the 3' end of a polynucleotide has a free OH group. But what about the 5' end? On one of the handouts, you showed a tetranucleotide composed entirely of dNMPs (including the last nucleotide on the 5' end, which had one free phosphate). However, some of the problems (for instance, 6-5) seemed to indicate that this last nucleotide on the 5' end could also be a dNTP (a nucleotide with a free chain of three phosphates on its 5' end) attached by its 3' end to a long chain of dNMPs (which were made from dNTPs into dNMPs in the polymerization of the strand). Is there a "rule" regarding how many free phosphates are attached to the last nucleotide on the 5' end of a strand? Or does it depend. . .on what? Thanks.
If polynucleotide is made continuously, starting from the 5' end, it should have all P's (that came in with the first nucleotide) still left on the 5' end. However, because of the fine points of synthesis and/or modification, the 5' end may not retain all of those P's. Alternatively, the polynucleotide may be obtained from cutting up a longer chain -- in that case, the 5' end will only have (at most) 1 P. So it all depends, and that's why the problems are not all the same.