So, after having wandered around in the specifics of joining a various gene regions in gene rearrangement, let's back up, go down, and look at the whole antibody again in this context. So, here is the whole antibody and you can see that most of these antibody will be coded for by the constant regions, and in fact, the parts that are not coded for by the constant regions are mostly coded for by unrearranged parts of the V. So, let's go take a closer look at this complementarity determining region that is the specific loops, those six loops at the tip of each Y. This time, we're going to go take a closer look at the left arm. So, here we have in the lower part, the place where the V and J come together, and you can see that that junction will code for the third loop of this CDR. The first two loops here and here are coded for by sequences that are built into that V chain and are part of the instructions that are determined by whichever V you picked. The corresponding situation on the heavy chain works much the same way. When you pick out a V region, you pick out the instructions for the first two loops right here. The third loop in this case is even more variable because you picked up another region, the D region or diversity region in between two joining regions, or rather the joining region and the little silvery things here that show you how you are putting these together. So, in both cases, the third loop has a variability that comes from the processes we looked at in the previous video. But, on the heavy chain, this is what particularly long and variable and complicated loop because it essentially has two of these regions, and these regions have in addition to the P nucleotide addition, they also have some N nucleotide addition tossed in the middle of the joint. Now, so when we're looking at the overall variability of these CDRs, it comes from picking out different Vs, putting them with different J's, and doing funky things to the loop that puts the two of those together, and we're especially likely to do fun and games with the third loop of the heavy chain because we have to toss it in the D region and N nucleotide addition. So, between the combinatorial possibilities for these and Js and the additional fooling around that we do, putting in the ceiling up and joining of the third loop, you get an enormous number of possible types of CDRs, and it turns out, of course, that most of them will not be good for much of anything. Because you're making them at random. The other probability is that two-thirds of the time you're going to put things together at random, you're going to make a frame shift mutation. That is, you will put in one base too many or one base too few and you will set the rest of the molecule out of frame. This can produce garbage and in particular a frame shift mutation is likely to show up with a lot of stop codon, so you terminate pretty early and you have something that is, again, what's referred to as a non productive rearrangement. Even if the message is in phase, you can toss in something and produce a stop codon and that will stop the whole thing as well. Now, happily recall most, I mean, these cells are diploid and you have a gene from mom and a gene from dad on the heavy chain you can work with, and two from mom and dad that you can work with for the light chains. So, here is a picture of the genes on the light chain and you can see here we have incorporated between the J and the V some of the nucleotides of the palindromic region, that's the palindromic region only, of course. If this makes a productive rearrangement, then you will shut down any further rearrangements. That's what's called allelic exclusion. So, if this guy produces something that's in phase works, then you will put the light chain that it codes for on the antibody before you release it, and you'll make sure that the other genes that code for the light chain had been turned off. Okay. Now, for the heavy chain, again, here we have the palindromic regions on both sides of the D and notice I put a little red line in between, that's where you find the N nucleotide addition in here. So, that between the V and the J on the heavy chain, you not only have these little teeny instructions for three amino acids from the Ds, but you have the palindromic regions that were incorporated and also in the middle of those palindromic region some N nucleotides that may have been incorporated also in the process of rearrangement. So, and all of those things incidentally are in the third loop. The other two loops are coming out of instructions from the upstream parts of this, and are again, first synthesized, so it's the third loop that comes from this region. Sadly, even though you have several chances, only about eight percent of the cells go through this whole process able to make a good light and a good heavy chain. But, once you do that, you do the allelic exclusion and that's pretty much what the cell will make. There is one exception and that is if there is some kind of self-recognition going on and you got a cape chain here, you can sometimes open up the Lambda and try again. So, but on the other hand, there are other dangers in this too. One of the more common things that happens in all of these is that you keep dividing cells as they go through this process and the cells will break and rejoin the DNA and that gives you the opportunity for all kinds of disasters as you make these various kinds of chains. In particular, you're likely to perhaps damage the genes that prevent cells from becoming malignant, and one of the consequences of the enormous amount of cell division, rearrangement, DNA changes is that mutations happen and you can get leukemias, lymphomas, and other diseases of blood cells. So, here is a picture from a microscope of a normal blood field. You can see that this is probably a little more organized than normal, but mostly you have red blood cells. Here, you have a few platelets that looks like a neutrophil or two, maybe a monocyte and the macrophage, and that's what a normal blood smear looks like. You usually have to search around to find eosinophils and other blood types, but here we have something in leukemia and in this one, the monocytes, the lymphocytes, the macrophages, everything is dividing, and it's crowding out the red blood cells. So, in this case, what you've got are these very cells, in many cases the lymphocytes that had been rearranging the genes can turn cancerous because in the process they damage some of the genes' DNA that is used to control them. So, again, these mechanisms do have a price, but they're one of the things that keeps you healthy. So, in the next one, we're going to do a quick review of the isotype switching, and some of the other ways that we improve the functioning of an antibody.
