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‘Humpty Dumpty sat on a wall.

..’ We all know what happens next, right? In this lesson, learn what happens when DNA is broken into pieces and how our cells try to put them back together again.

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Double-Strand Breaks

In this chapter, we’ve been learning a lot about what kinds of things can happen that mess up a cell’s DNA. We’ve learned about mutagens and the mutations, or changes in DNA sequences, that they cause. We’ve also learned that DNA can be physically damaged.

As you can imagine, one of the worst things that can happen to DNA is that it can be broken into pieces. This can sometimes happen because of accidents during DNA replication in our cells. Another cause is ionizing radiation, a kind of radiation that can break the covalent bonds that make up the backbone of DNA.

If only one of the two strands of a DNA molecule is broken, it’s not such a big deal. An enzyme called ligase can swoop in and glue the broken strand back together. But what happens if both DNA strands are broken? This is called a double-strand break, and it’s much more difficult to fix because now the fragments of DNA have completely separated from each other.And what if a long DNA molecule got many double-strand breaks? You thought Humpty Dumpty was in a tough situation, but this is much worse. We could have tons of little DNA fragments on our hands. How on Earth does a cell find the fragments and seal their ends back together? And how does it know in which order to put the pieces back together? In this lesson, we’ll learn about two ways that cells can deal with double-strand breaks.

Homologous Recombination

The first way that we’ll learn about is called homologous recombination.

In this strategy, cells use the sister chromatid or homologous chromosome as a template to repair a double-strand break. Let’s back up for a minute. What’s a sister chromatid? What’s a homologous chromosome? Both contain sequences that are homologous, or very similar to, the broken chromosome; hence the name homologous recombination.Sister chromatids are kind of like a photocopy of a chromosome. Sister chromatids are the exact copies of chromosomes that are made when a cell replicates its DNA. When you see a cartoon of a chromosome that looks like an X, what you are looking at is two sister chromatids that are stuck together at the middle.

This happens in the beginning of mitosis or meiosis, and then the sister chromatids are pulled apart into their soon-to-be new cells, remember?On the other hand, homologous chromosomes are the two different, say, chromosome 17’s that you have. One came from your mother, and one came from your father. They are very similar, because, hey, we’re all humans.

But they are not exact copies of each other. Just like your mom and dad are not the exact same person, to say the least!Okay, back to homologous recombination as a way to repair double-strand DNA breaks. Like I said before, in this process, cells use another nearby chromosome with the same or similar sequence as a template to repair the double-strand break.

Let’s say it’s a sister chromatid. The sister chromatid’s sequence is like a recipe that helps the cell fix the double-strand break without mixing up the DNA sequence.Here’s how it works. First, the broken pieces of DNA need to line up next to a sister chromatid or a homologous chromosome with the same sequence they have.

These DNA pieces have to line up nice and cozy so that they can interact. As you can see, matching the DNA sequences makes sure that the DNA fragments are lined up in the right order and position.Next, the broken ends will be trimmed down a bit by nucleases, which are enzymes that chew up DNA. Importantly, only one strand of each broken end will be trimmed. This leaves short so-called overhangs, which are single, unpaired strands that will be extended according to the sequence of the sister chromatid.The next thing that happens is called invasion of the single strands. They actually physically invade the intact sister chromatid.

Talk about getting into someone’s personal bubble! But the sister chromatid doesn’t get too annoyed because she knows how important her job is; namely, to provide the correct sequence for the broken strands to be extended.As you can see in this diagram, new DNA, shown as blue dotted lines, is forming on both broken strands, according to the sister chromatid’s sequence. It sure is great to have a sister. In this case, it means that the sequence on the repaired strand will be perfect, with no mistakes.Finally, this crisscrossed, jumbled-up mess needs to be resolved. Those crazy, four-legged crossed-over regions are called ‘Holliday junctions,’ named after the geneticist who came up with this theory of how homologous recombination works. They actually look like this! The Holliday junctions can simply be snipped, and the nicked single strands can be glued back together with the help of DNA ligase.

Good as new!

Non-Homologous End Joining

But what if there are no homologous chromosomes or sister chromatids available? What’s a cell to do? Don’t worry; there’s a second way that cells can fix double-strand breaks. It’s called non-homologous end joining. As you can tell by its name, there are no homologous or similar sequences involved.

This strategy is used when no sister chromatids are available. For example, in parts of the cell cycle when the DNA hasn’t been replicated yet and each chromosome is not sitting right next to its twin. Unfortunately, this means that there is no master copy of the correct sequence to help put the strands back together correctly, like there was in homologous recombination, so it’s easier to make mistakes. In non-homologous end joining, ends of DNA are recognized and resealed, but the process often causes deletions.Here’s how non-homologous end joining works. First, broken ends of DNA are recognized by protein complexes that specialize in that sort of thing. These protein complexes have nucleases to trim down single strands of the broken ends, similar to what happened in homologous recombination.

What’s different is that the goal here is to create short, one to six base pair regions that have complementary sequences and could base pair together.I bet you guys know that it would be very rare to find a long, perfectly matching complementary sequence somewhere else on a piece of DNA. After all, there’s a one in four chance that any of the DNA bases show up at any particular location. However, if the sequence doesn’t have to be very long, the chances increase a lot.In non-homologous end joining, these very short complementary sequences that are produced will be overlapped together.

Then, any small gaps in the DNA will be filled in by DNA polymerase, and the ends sealed by DNA ligase. Looks pretty good! So, what was the problem here? What was that about deletions?Where could a deletion come from here? Quite simply, the deletion came from trimming those ends back looking for short complementary sequences. It’s like if you broke a candy bar in half, but then trimmed the ends off of those halves and stuck the candy bar back together, it would be a bit shorter than it started off. Chocolate, uh, information was lost in that step, and you can bet the cell hopes that information wasn’t too important! If it was, the cell could die or even become cancerous. But most of the time, with our big genomes, a tiny loss of information won’t cause any major problems.

Lesson Summary

Today we’ve learned about two ways that cells can repair double-strand breaks, which are when both strands of a DNA molecule are broken.The first way is called homologous recombination. This is when cells use the sister chromatid or homologous chromosome as a template to repair a double-strand break. That sister chromatid or homologous chromosome sure comes in handy because it serves as a recipe to make sure that new DNA with the perfect sequence is added in to fix the break.

The second method is called non-homologous end joining, and cells use it when there are no sister chromatids or homologous chromosomes available. In this process, the ends of DNA are recognized and resealed, but the process often causes deletions.

Learning Outcomes

Once you are finished with this lesson you should be able to:

  • Name the two ways a cell can repair double-strand DNA breaks
  • Describe how a cell repairs with sister chromatids or homologous chromosomes
  • Explain how errors can occur during non-homologous end-joining

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