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>> Izzy: Dude, I like what you built there.

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What's it do?

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>> Dude: Oh...hi Iz.

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This is a cool bug.

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I made it using an electronics
building kit that Sally got me.

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She wanted to get me a genetics
kit but nothing's available yet.

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Eesh! I don't get it.

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Why is it so easy to turn on and off the
lights for this electronic bug but so hard

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to turn things on and off in biology?

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>> Izzy: What do you mean Dude?

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The arsenic sensor that we built in
bacteria a few years ago works pretty well.

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If there's arsenic in the water
being tested the sensor turns on.

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And when arsenic isn't in
the water, the sensor is off.

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And we built that sensor with
natural biological parts!

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>> Dude: So arsenic works like this switch?

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How is that possible?

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How does the cell know?

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>> Izzy: We used parts from the ArsR operon
to program arsenic-inducible expression.

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>> Dude: Hold up!

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Arsenic-inducible expression?

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What's that mean??

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All I know is that arsenic is toxic.

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Don't the cells just die when you poison them?

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>> Izzy: Cells have come up with
a bunch of clever ways to survive.

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In the case of arsenic, the cells
make a pump to get the poison

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out as soon as any comes inside the cell.

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>> Dude: That makes sense.

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So ass-er is the pump?

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And why did you call it inducible?

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>> Izzy: Dude, be careful how you
say it: the protein is called ArsR

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since it's the ARSenic Repressor protein.

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And ArsR isn't the pump.

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It just tells the cell when to make the pump.

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The operon has promoter, which is
where the cell's RNA polymerase binds.

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And at least three genes: the ArsR gene, which
encodes the repressor protein, the ArsB gene,

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which encodes the pump, and the ArsC gene,
which encodes an enzyme that reduces arsenic

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in the cell so it can be pumped out.

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Most of the time, the operon is turned "off"

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since the ArsR protein binds the DNA
near the promoter to stop transcription.

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But when arsenic comes into the
cell, it binds the ArsR protein.

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And when the repressor is bound to arsenic,
it can't bind the DNA so RNA polymerase can.

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That way the cell makes more
of the repressor, the pump,

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and the enzyme only when there's arsenic around.

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That's the inducible part.

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>> Dude: So why did you include the
whole operon in your arsenic sensor?

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It seems like you could just
include the ArsR gene

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and the promoter parts for
your arsenic sensor device?

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>> Izzy: Nice work.

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That's actually exactly what we did.

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We simplified the natural system
to only use the parts we wanted.

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So it looks like this...

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>> Dude: So you're arsenic
sensor works like this?

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>> Izzy: Dude, that's great but I
have two even simpler way to write it.

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This is called a truth table and
this is called a transfer curve.

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Both tell you that when arsenic levels
are low, the operon is mostly off

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and when arsenic levels are high, the operon
turns on and starts cranking out proteins.

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Earth to Dude...what are you doing?

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>> Dude: Well here's the thing Iz.

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I'm always looking for some way
to get Buddy's gas-o-matic module

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to turn off before he gets too big.

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I was hoping I could maybe switch this operon
around to get the truth table working like this.

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And get the transfer curve looking like this.

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>> Izzy: No problem!

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You're looking for a simple
digital device called an inverter.

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>> Dude: Oe-kaaay.

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Can we turn this operon into an inverter or do
I have to build something completely different?

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>> Izzy: There are already a few
transcription-based inverters in the registry,

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but I don't know if anyone's built
one using the arsenic repressor.

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Maybe you can be the first.

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Do you want to try?

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>> Dude: You bet!!

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But how?? What about this idea: lets take
this promoter that binds the "Ars R" protein

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and move it to the end of the operon.

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This way if I put my gas-o-matic device
after the promoter, then high production

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of the arsenic operon gives low
production of the gas-o-matic device.

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Input 1 Output 0...I think I nailed it!

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>> Izzy: Nice thinking Dude.

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Most of the Registry's transcriptional inverters
are of that form: DNA that encodes the repressor

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and then a promoter that's repressed by it.

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One thing to remember about transcriptional
inverters is that they're pretty slow to switch.

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It can take over an hour for the
inverter to change its output signal

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after it receives a change in input signal.

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>> Dude: Well that might be ok.

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It's not like Buddy grows super fast.

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>> Izzy: Well then maybe for your application
a transcriptional inverter is just fine,

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or maybe the registry has
one that will work better.

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>> Dude: Registry.

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Search Parts .Inverter.

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I like this number: Q04401.

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Hmm that's strange.

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The Registry says that BBa_Q04401 works

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but the transfer curve doesn't
look like what you've drawn.

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>> Izzy: Well, the transfer curve that I
drew is a perfect inverter transfer curve.

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But when you actually build the devices,
they aren't going to have perfect behavior.

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And that's as true in electrical
engineering and biological engineering.

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Devices won't switch from high to
low as sharply as what I've drawn.

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>> Dude: I'd really like a
sharper change than this though.

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Maybe I should just build the
ArsR inverter to try in Buddy?

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>> Izzy: I think it would be worth a
shot ...let's get the parts you'll need

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and we can start today...