Biochemistry 401 Lecture 36 Transcript 1 Biochemistry 401 Lecture 36 Today we re going to talk about what can go wrong and how to fix it Safeguarding the genome We re going to talk about mutations and repair of those mutations and then we re going to talk about recombination Some things do not belong together such as cytosine and adenine and guanine and thymine but sometimes mistakes happen and we re going to go over some of the things that can cause mistakes to happen that can give rise to mutations And so when problems occur with mismatching and mutations generally speaking it s all about that base hydrogen bond donors and acceptors Normally deoxyadenosine binds to deoxythymidine because of the patterns of hydrogen bond donors and acceptors and the same with deoxyguanosine and deoxycytidine These patterns of hydrogen bond donors and acceptors are complementary and so they bind to one another efficiently but when these patterns of hydrogen bond donors and acceptors are changed that s when problems occur In this diagram we ll take a look at deoxyadenosine and you can see that there s an amino group at position two This amino group has two hydrogen bond donors and one of them makes contact with the hydrogen bond acceptor oxygen in deoxythymidine It s a complementary pairing The same thing for that nitrogen at position one it s a hydrogen bond acceptor and so it accepts the hydrogen bond from the nitrogen at position three in deoxythymidine That is a hydrogen bond donor and so again that is complementary But when you change these patterns when you introduce a hydrogen bond donor where it doesn t belong or when you take one away this is what causes problems Some of the factors that change hydrogen bonding in deoxynucleotides are listed here There s tautomerization syn versus anti position of the base relative to the sugar water mediation this is when three s a crowd and the water molecule gets in between the two bases and forms its own hydrogen bonds between the bases That can be bad news Then there s oxidative deamination alkyation oxidative damage by reactive oxygen species there s dimerization and there s intercalation That s a pretty big list but let s look at them one at a time Sometimes deoxynucleotide bases can adopt alternate conformations by tautomerization and the change of conformation that we see here in adenine is caused by a migration of the hydrogen shown in red and a double bond There Biochemistry 401 Lecture 36 Transcript 2 was a double bond originally between the nitrogen at position one and the carbon at position six as shown in the diagram in the upper right This double bond has now formed an imino tautomer Because of this the nitrogen at position one is no longer a hydrogen bond acceptor it s a hydrogen bond donor and for this reason alanine in the tautomeric form can bind with cytosine because the pattern of hydrogen bond acceptor and donor is complementary And so tautomerization is the migration of a hydrogen atom or proton and concomitant switch of a single bond and an adjacent double bond In this diagram we see the predominant forms on the left and the more rare forms on the right and in each case whether we re going from an amino group to an imino group in adenine and cytosine or from a keto group to an enol group in guanine and thymine these changes in configuration cause differences in hydrogen bonding patterns Now are you going to have to know the difference between a regular adenine and its tautomer No you re not going to have to know those structural differences but you do need to know the concept and you do need to know what tautomerization is and why it can cause mutations in the DNA You also do need to know that the common forms for deoxyribonucleotide bases are in the amino form and the keto form and the rare forms are the imino and enol forms Base pairing can also occur because of differences in hydrogen bonding between the syn versus anti conformations of the bases with respect to the sugars Now purines once in a while can be in the syn conformation but most of the time purines are in the anti conformation This is normal Pyrimidines on the other hand are always in the anti position In the diagram above we see synguanosine and anti guanosine You can see that in the anti position the bases are extending toward the center of what would be a DNA helix whereas in the syn position the base lies over the ribose sugar In the panels on the bottom on the left we can see the normal hydrogen bonding between guanine and cytidine and on the right we can see the abnormal bonding between adenosine which has flipped into the syn conformation and guanosine which is in the normal anticonfiguration In these configurations the patterns of hydrogen bond donors and acceptors are such that adenine can bind with guanine Base pairings can also be disturbed when water gets into the center Here we see a water molecule in the center between a thymine and a cytidine and this is Biochemistry 401 Lecture 36 Transcript 3 shown by the purple arrow This disturbs the hydrogen bonding that would normally form and so thymine can now bind with cytidine rather than with adenine Chemical mutagens can also cause changes in hydrogen bonding patterns For instance an alkylating agent that adds a methyl group to the ketone in guanine can prevent the hydrogen bonding that would normally occur at that oxygen So we ve lost a hydrogen bond acceptor and because of this alkylation there s steric hindrance for the formation of a CG base pair and for this reason O6 methylguanine will sometimes pair with thymine One of the most well known alkylating cleaning is aflatoxin Aflatoxin is a toxin that s produced by a fungus that attacks peanuts This aflatoxin on its own can intercalate between base pairs but an enzyme in our liver does a really nasty trick When cytochrome P450 tries to detoxify aflatoxin B1 it actually forms an epoxide which is a highly reactive DNA modifying agent So this activated aflatoxin cannot only intercalate between base pairs that the epoxide can form an aflatoxin DNA adduct and this is what we see in the lower left of this diagram And so alkylating agents add carbon containing molecules as adducts where they shouldn t be Reactive oxygen species can also attack DNA bases In this case we ve oxidized the carbon at position eight to form 8 oxo guanine In so doing we ve added another hydrogen bond donor at nitrogen seven and so this base is a perfect complement to adenine Now
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