Question

Depurination HN 3. Hydrolysis of the N-glycosyl bond between deoxyribose and a purine base in DNA creates an apurinic (AP) site. An AP site creates a thermodynamic destabilization greater than that of any DNA base pair mismatch. HN 'N -O-P-O-CH2O Guanosine residue (in DNA) HH V a) Draw a G-C base pair. H b) See the figure to the right and speculate on some reasons why losing the purine base might be so much more destabilizing than a simple base pairing mismatch and describe some chemical consequences of this loss. HN 0-d= P-O-CH2O OH H2N IZ 0 KH H Η Ν Η Guanine H 4. Draw the structure of the amino acid tyrosine in its protonated and deprotonated states. Show, structurally, why Apurinic residue

I just need help with 3b. Thank you!

Answer 1

3b. In a situation where the DNA loses a purine base (depurination), there is creation of an Apurinic site. As shown in the figure, when there is depurination of a guanosine base in DNA, guanine and an Apurinic residue is formed. There is DNA strand separation seen in DNA replication. Each strand acts as template for synthesis of new strand. When depurination occur, the strand that still has the normal bases, will replicate normally. However, the strand that has the Apurinic site undergoes replication; it cannot provide a template for addition of complementary base on the newly synthesized strand. This leads to addition of in incorrect base which is mostly adenine in the newly synthesized strand. Thus, after DNA replication, two new ds DNA molecules are formed-one which is normal while the other molecule which is mutated. In the second round of DNA replication, the mutant strand with the new base is used as template to another new strand synthesis. As a result, there will be DNA strands formed which has a permanent mutation in them. Thus, half of the replicated DNA becomes mutated. However, if they persist, then they cause lethality. There will be deletion of that base and base- substitution errors. These mutations are propagated through the subsequent generations, giving disastrous consequences. Apurinic sites can only be removed by Apurinic endonucleases (AP endonuclease). Excision repair will try to remove these Apurinic sites, leading to base pair errors and therefore lead to lethal mutations in DNA.

When there is a simple base mismatch created, DNA polymerase 1 can excise the mismatched base as it has 3’ to 5’ proofreading and 3’ to 5’ exonuclease activity. The DNA polymerase can easily remove this mismatched base. In case the mismatched base survives the proof reading activity of DNA polymerase 1, DNA mismatch repair enzymes will remove these bases. Hence, it is very rare that simple base mismatch will be propagated through subsequent generations and are rarely permanent. If they still persist, base substitutions can occur, which may or may not alter protein function. Thus, simple mismatch repair is less destabilizing than the Apurinic site mutations in DNA.