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Lecture 7

Cell Biology - Lecture 7 - Video 1 - Notes

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Boston University
CAS BI 203
Martin Steffen

Lesson 7 – Video 1 [00:00:00.00] 2725 [00:00:01.08] SPEAKER: Hi there. In today's series of videos, we're going to talk about gene 2726 specific transcription. In the previous class, we talked about general features of transcription and 2727 translation. What genes, in general, have to happen for genes to get turned on or off. But it's not 2728 enough to be able to turn genes on or off. You have to turn on selective genes when you want 2729 them, and keep others off when you need them to be off. 2730 [00:00:27.82] So this is about a higher level of control.And the very basic switch in that control 2731 is a DNAbinding protein binding to a DNAspecific sequence to turn a gene on that's right in 2732 that locality. Call this a lock and a key. The pieces have to fit perfectly. They're made to match 2733 each other.And that's how a gene can be activated. 2734 [00:00:56.12] We'll look at some of the molecular details, in terms of how proteins contact DNA, 2735 which I say is reading the code of the DNAin the major and minor grooves to recognize this is 2736 the gene that I'm supposed to turn on.And then lastly, in this video we'll talk extremely briefly 2737 about some different classes of DNAbinding proteins or transcription factors. 2738 [00:01:22.38] And this slide sort of highlights the point. Let's start with the carrot. Here we have 2739 a single cell with one nucleus, with one copy of the genome, and yet all the information is there 2740 so that it, over time, develops from a young embryo, young plant, finally to a mature carrot plant. 2741 This is a timed orchestration of turning genes on and off so they produce the proper proteins at 2742 the proper time, the proper molecules. They build the proper structures, and in the end, allow the 2743 life cycle to continue.And they have produced an adult functioning organism. 2744 [00:02:07.51] The frog and the cow examples focus in on the cloning techniques, and we'll 2745 discuss those later in the course. But it's the same thing as how do the various instructions that 2746 are contained in the DNAbe deployed in a time dependent manner to produce the final results of 2747 an adult organism? 2748 [00:02:31.52] So here we see a slide again. Six levels where genes can be controlled and their 2749 functions modulated so that you can have, in the end, an active protein doing a job that you want 2750 it to do. We'll talk mostly today about this very first step, transcriptional control. Because of its 2751 primacy, it's one of the best studied of these features.And it is, as you know, in essence, of your 2752 20,000 to 25,000 genes, which ones are we going to turn on at this particular time to perform the 76 next steps that we need to do in order to respond to the environment 2753 or carry out the plan that is 2754 inherent in our genome? 2755 [00:03:17.97] Once you've made the RNA, there's lots of other ways to influence this process of 2756 getting to the active protein, processing the RNA, transporting the RNA, binding to it, 2757 localization, making it free and available, or sequestering it from being used. There is control at 2758 how much protein is made for each mRNA, how actively or quickly the mRNA is degraded, how 2759 folded proteins' activity is controlled. Because an inactive verses an active protein can produce 2760 completely different results.And by the second part of this course, we will have discussed all of 2761 these in pretty decent detail. 2762 [00:04:10.55] OK, transcriptional control. Two basic components, a lock and key. The biological 2763 equivalents are a short stretch of a defined DNAsequence. This is the gatekeeper for a gene.And 2764 a gene regulatory protein that recognizes and binds to that sequence. This is the key that's sort of 2765 opening the lock or turning the gene on. 2766 [00:04:42.51] So how will the proteins read the sequence that is present? We know-- this is a 2767 picture from a previous slide-- how DNArecognizes itself.Aand T participate in hydrogen 2768 bonding.And T recognizes anAby two hydrogen bonds.And C recognizes G by three hydrogen 2769 bonds. But the protein is not able to recognize these bases based on this base pairing. It is in the 2770 center here of the DNAdouble helix, and they are occupied with each other. That is not 2771 available. 2772 [00:05:21.12] What is available to the proteins is the ends that are exposed in the major and 2773 minor grooves.And although it's poorly drawn, this is what-- the protein C is looking at the end-- 2774 this is what's in the major groove. Same here. Down here. This side is, in the way it's drawn in 2775 this book, which is this is a poor representation of the actual geometry, is what's seen in the 2776 minor groove. 2777 [00:05:56.14] So let's look here. Let's look at a particular slice, right here in the end on of a base 2778 pair. You could see hydrogens; carbons, the darker blue; nitrogens, the lighter blue; carbon, 2779 hydrogen, nitrogen, and oxygen.And this pattern, which we will schematize on the next slide, is 2780 how DNAbinding protein recognizes whether it is a G, a C, anA, or a T, at that location.And it 2781 has the ability to query several base pairs at a particular time. You'll see, because of the geometry 2782 of the double helix, because it is twisting, that it's going to be hard for a single protein, for 2783 instance, to recognize 20 consecutive bases. 2784 [00:06:58.64] Because of the approach, it might be able to recognize quite a few. But it might 2785 recognize five here, down here, and five here, just because that is the face of the DNA that is 2786 exposed to the protein. And here we make that clearer. This is drawn to better perspective.And 2787 it's color coded in a very convenient way. So let's imagine the protein is approaching this GC 2788 base pair from the major groove. It'll see a hydrogen, nitrogen, oxygen, a hydrogen, a hydrogen, 2789 and a hydrogen. 2790 [00:07:39.09] Also note that, if we go left to right, a GC base pair will look different to it than a 2791 CG base pair. So the proteins distinguish between these two binding situations. If we compare 77 the GC to theAT, we can see, for instance, that the G will see if it's 2792 looking at a G, it's going to 2793 see an oxygen here where it's seeing a hydrogen in sort of the complementary position. And th
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