Download L07v02 Trp part1a final export.stamped_doc

L07v02 Trp part1a final export
[00:00:00.00]
[00:00:01.67] SPEAKER: Hi. In this video, we'll continue our discussion on Gene Specific
Transcription. In particular, we're going to focus most of this lecture on the Trp repressor. Trp is
short for tryptophan, the amino acid. And we're going to talk about negative feedback, which
we've already seen with enzymes. And again, allostery is going to play the key role in terms of a
small molecule binding to a protein, changing its shape, which then changes the proteins
function.
[00:00:32.18] We'll look at more complex mechanisms of gene regulation. In particular, we'll
look at the way the cells decide which sugar to use. And then we'll look at some other complex
mechanisms. So here is the operon for tryptophan bio synthesis. There are five genes that make
five proteins that each play a different role in the bio synthesis of this amino acid; amino end,
alpha carbon, carboxylic end, and then the big side chain here.
[00:01:11.29] These five genes are coordinately regulated since this is an operon, it's a
polycistronic mRNA. They are all regulated by this promoter region. With the idea that if you
need to make one of these enzymes, you need to make all of them. Because there's not much use
in going part of the way to making the tryptophan molecule, but not completing the task.
[00:01:35.25] In this example, the cells default state is that the genes are turned on if the
promoter region is empty, RNA polymerase will bind to the promoter region, and start making
the mRNA tryptophan bio synthesis. Since tryptophan is going into every protein that's made, it's
important to have a lot of it. So the default decision for the cell is to have the gene turned on.
[00:02:03.14] But what happens when you have too much tryptophan when you've already made
a lot and you don't need more? In that case, tryptophan binds to the Trp repressor protein right
here. And will induce a confirmation, here it's rounded in a won't bind DNA. When the repressor
binds to the protein, it changes its conformation. It's now able to bind DNA in the place where
RNA polymerase normally binds and so that the genes are turned off.
[00:02:37.80] So this is a very simple example of negative feedback regulation. Here the default
state is, let's make more tryptophan. The negative feedback is, hey, we've got too much
tryptophan, stop for a little bit. And this all happens automatically since the molecule being made
is also the molecule that binds to the repressor to induce the conformational change.
[00:03:03.54] On this slide, we see a bit of the detail of the repressor bound to DNA. Let's look
first at the case where the genes are off, where the repressor is bound to DNA. You see this is a
symmetrical protein. You can see that helix is perfectly positioned to bind to the major groove
here. And a second helix is binding to a second major groove here. And the spacing between
these two arms is just appropriate for sitting down and having those both spaced properly. And
you can see the tryptophan here is sort of in a hinge region. And you can see that the binding
here can easily affect this angle here so that it's properly positioned for both sides to bind
simultaneously. In general, this probably doesn't have enough binding energy to bind with just
one of the two helices.
[00:03:59.06] In the case where tryptophan is not bound, we have a smaller angle here. A shorter
distance between these two arms, such that they will not sit down properly. Instead of sitting in
over here, it sits down to maybe here and here. And so it cannot bind to both the major groups.
[00:04:22.64] Again, this is just a consequence of having too much tryptophan in the cell or a
sufficient amount that you don't need to make more. It automatically will regulate this protein
and it will bind this, it'll prevent the genes from being made. Now I'd like to remind you about
what negative feedback regulation that we saw earlier in the class, where molecules were-- in
this case CTP was the molecule z, it binds to this enzyme complex here that converts b to x. And
because we have enough CTP, it will bind and prevent the conversion of b to x. So all the
molecules of intermediate molecules b will go on to make molecule c.
[00:05:14.82] In this case, we have negative feedback regulation of enzymatic activity. Down
here with the tryptophan repressor, we have negative feedback of genetic regulations. So same
principle, different mechanism of controlling the regulation of the enzymes that you need.
[00:05:38.81] In addition to repressors being used, soon people found activators for the protein.
And it can be modulated in just the same way as repressor. First of all, you might have some
repressor activators that bind without any ligands. Or you could also have ligands binding to
activators to induce a fit such that they can bind a promoter region. And because they provide
extra binding energy to the RNA polymerase, it can help recruit the RNA polymerase to this
promoter.
[00:06:11.32] Again, that would be simple thermodynamics. You have more positive interactions
building up, this is going to make an event happen more frequently. And just to give a specific
example, we'll talk about hormone receptors.
[00:06:29.26] In this case, it's glucocorticoid hormone. It could be estrogen or any number
others. A lot of them work by this mechanism. And here is the glucocorticoid receptor, when
this-- which is a protein internal to the cell in the cytoplasm, whenever glucocorticoid which
passes through the membrane binds to the protein, it induces a shape change. Now it interacts
with a protein that's there and the promoter region. And now it will encourage the polymerase to
sit down and you can have transcription of hundreds to thousands of genes.
[00:07:08.50] Hormone receptors in general influence the expression levels of lots of genes. And
although the book talks about genes expressed at low levels versus high levels, you can think of
it as turned off or turned on. I think this is a good place to pause our discussion. And we'll
resume in the next video with this slide, which is a little bit more involved than most. Thanks.