5. If T is in one strand of a DNA molecule and G is in the complementary strand, is there a problem? If you think that this situation may represent a problem (or potential problem) for a cell, then in no more than two sentences explain why it might be a problem. (4 points)
This mismatch is a potential problem to the cell, because it represents a potential mutation. If it is replicated before it is repaired, then one of the daughter DNA molecules will be mutant. Although the mismatch produces some distortion of the DNA double helix, that distortion by itself does not generate a problem. The distortion will not impede either RNA polymerase or DNA polymerase, because both polymerases unwind the DNA double helix as they proceed. At the moment when either the T or G would be used as template by a polymerase, it would be unwound (single-stranded) and would be used efficiently by the polymerase, because both T and G are normal nucleotides.
Note that, even though this mismatch can be converted to a mutation by replication, the mutation may not be harmful. Many mutations have no detectable phenotypic effect.
Also, please note that mismatches do not necessarily arise as a consequence of replication errors. The T-G mismatch can also be generated by spontaneous deamination of 5-methyl cytosine, which converts 5-methyl cytosine to thymidine.
Thus it is incorrect to assume, as many students did in answering this question, that T is the "correct" base and G is "incorrect." Unless one knows what the original DNA sequence was, there's no way to tell for sure which base is correct. Because cells frequently contain a DNA N-glycosylase specific for the T in T-G mismatches, it appears that cells make the assumption that, in the special case of T-G mismatches, the T is most likely to be the incorrect base.
6. List all of the repair pathways you can think of that are capable of repairing a situation where T is in one strand and G is in the complementary strand. For each pathway that you list, use a few words (no more than one sentence) to explain why you think this pathway is capable of repairing this situation. (4 points)
1. Mismatch repair-because this is a mismatch, and the enzymes of mismatch repair are designed to "correct" it. They do so by removing one of the mismatched bases and replacing it with the correct complement to the other base. Note that if this mismatch arose by 5-methyl-C deamination rather than as a replication error, the mismatch repair system will have no way to tell which is the correct base and may "repair" the mismatch incorrectly (to T-A rather than to C-G).
2. Base excision repair-because most cells contain a DNA N-glycosylase that removes the T in T-G mismatches. Subsequent removal of the AP site and fill-in synthesis leads to replacement of the T-G mismatch by a correct base-pair, C-G. Unless the T-G mismatch arose by 5-methyl C deamination, the C-G base pair may not be the correct one.
Thus, both mismatch repair and base excision repair will remove the mismatch and produce a "correct" base pair, but it may not be the original base pair.
Please note that nucleotide excision repair (NER) is incapable of dealing with a T-G mismatch. NER requires both distorted DNA structure (which the T-G mismatch provides) and altered DNA chemistry, which the T-G mismatch does not provide.
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