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Lecture 5

Cell Biology - Lecture 5 - Video 2.2 - Notes

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Boston University
CAS BI 203
Martin Steffen

Lesson 5 – Video 2b [00:00:00.00] 2014 [00:00:01.92] PROFESSOR: Hi. In this video, we'll talk about three different ways that the cell 2015 repairs damaged DNA. In method one, we'll talk about base excision repair. This is when a 2016 single base is affected. In this case, there's a type of damage called deamination. 2017 [00:00:19.30] This is when a C base within an amino group is deaminated. And then you have a 2018 base which has a carbonyl group in place of the nitrogen. And coincidentally, this base is uracil, 2019 the base that is in RNA. 2020 [00:00:38.77] Now, you'll remember that uracil acts the same, base pairs the same as a T. And so 2021 this seems to the DNA like a C to T mutation. But they're also special enzymes-- for instance, 2022 DNA glycosylase-- that recognizes that uracil is not to be incorporated into to DNA. It's an RNA 2023 nucleotide. 56 [00:01:07.32] And so it'll scan the genome for places where a 2024 U is present. When it finds it, it 2025 will excise the base, then cut the backbones of the sugar and phosphate groups, insert the correct 2026 base, which is done by DNA polymerase. And then DNA ligase will seal the nick. 2027 [00:01:34.01] There is another type of DNA damage called depurination, which happens to 2028 purines, which are G's or C's. And those effect the bond between the sugar and the base. And the 2029 bases will be lost. And so those types of mutations or DNA errors enter this flow chart at this 2030 position. 2031 [00:02:00.30] So these are both two very common kinds of mutations. And they are repaired 2032 effectively by the cell. However not perfectly, we can actually see evolutionarily that there are 2033 more C to T mutations then other types of base pair changes. So again, it's very common 2034 occurring event. And the cell catches most of them. 2035 [00:02:27.67] A second type of method is called nucleotide excision repair. In this case, two or 2036 more bases can be affected. And the type of damage shown here is a pyrimidine dimer, which is 2037 a more generic term for the type of damage we saw in the previous video, thymine dimers or 2038 thymidine dimers. So this is a pyrimidine dimer. Instead of TT, we have a CT base pair. 2039 [00:02:56.82] And once, again there are proteins which constantly scan and surveil the genome. 2040 When it finds this kind of an error, it will cleave the backbone at some distance from the lesion 2041 site, remove the entire piece of DNA using the enzyme DNA helicase. DNA polymerase will fill 2042 in the temple plate 3 ' to 5 ', and ligase will seal the final nick. So again, this is an efficient 2043 mechanism for repairing thymidine dimers. 2044 [00:03:37.51] So now we're going to ask, before we get to the third mechanism, we're going to 2045 ask the question, how does the cell know when it encounters a bubble or a mutation? How does it 2046 know which strand to repair? This picture is not very realistic, because really the bubble is on 2047 both sides. It implies that the correct base is a straight and normal backbone. And then because 2048 you have an incredible base, it bubbles out a little bit. 2049 [00:04:09.87] But obviously that's not the case. After replication, a T will be inserted next to the 2050 A. And a C will properly be inserted next to the G. And going on, you would have 50% mutated 2051 cells and 50% non-mutated cells. Now let's-- although we don't know how yet-- if the cell knows 2052 somehow that the A is the incorrect base, it can correct that. And then it can put 2 G's there. And 2053 now you'll have 100% correct, of the cells progeny will have the correct genome. 2054 [00:05:00.68] But think about the consequences if the incorrect base is repaired, if the G is cut 2055 out and it gets converted to a T. Now you have 100% of the progeny cells having the mutation 2056 incorporated. So how does the cell figure out which is the proper base to go at that position? 2057 [00:05:25.76] The answer is quite ingenious. And what the cell does-- which gets it right most of 2058 the time, but not every time-- is it will, once it finds a mismatch, here, it will scan in both 2059 directions, looking for the closest to nick in the backbone of the strand. The cell then assumes 2060 that this is the most recently synthesized strand, the other strand with no nicks having stood the 2061 test of time, per se. 57 [00:06:01.63] And so it will decide to cut out the region of the 2062 DNA that has the pre- existing 2063 nick. And it will repair that-- again, with I should draw it like that-- with a polymerase, and then 2064 ligase sealing the final nick. As you might guess, this all happens relatively quickly, right after 2065 DNA synthesis. 2066 [00:06:29.73] Because if a different enzyme happens to notice there's a nick present in the DNA, 2067 it will repair that not knowing that there's a bulge there. So after synthesis, the DNA is basically 2068 a ticking time bomb, where the cell has to repair this bulge before another enzyme fixes this 2069 nick, if it's going to use this mechanism for picking out which
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