BioBuilding: Synthetic Biology for Students: Circuit Rewrite

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Part II. Electronic vs Biological Circuits
In this activity, we'll explore signaling in the context of an electrical circuit. As you work through this exercise, consider how the lessons learned from experimenting with an electronic circuit would map to the engineering of biological systems. You will be given a kit to construct this circuit.



Safety
Safety for you: In this exercise, you'll be working with circuits connected to a battery. Although you are unlikely to seriously injure yourself, you should make a habit of unplugging / powering-off the circuit before you touch it.

Safety for the circuit components: In order to avoid frying your components, take note of which ones require power to be applied in one direction and not the other. Specifically, the OpAmp has one pin for + power and one pin for ground, and the diodes (photodiode and LED) must have their positive legs toward + power and their negative legs toward ground. Likewise, make sure not to connect your battery backwards. Applying power backwards can result in a dead component that looks just like a working one. 

System design
Edit diagram to show polarity of photodiode connection, change phrasing of "variable resistor", and have more boxes to show analogy with cellular system.

This system is a fairly simple one, consisting of only a few components. In contrast to the bacterial photography system in which the signal is propagated through protein activities, here signals are propagated as either voltage or current. As you can see in the schematic, the circuit contains the following parts: paragraph needs to be rewritten: describe analogy in more detail?


 * 1) [[Media:Photodiode SpecSheet.pdf| Photodiode]]: #LT959X-91-0125: a light sensor (analogous to the Cph8-OmpR signaling system). When light shines on the photodiode, its resistance decreases, and current flows through it.


 * 1) [[Media:OpAmpDataSheet.pdf| OpAmp]]: #AD8031ANZ: a signal propagator (analogous to the transcription/translation machinery that translates an OmpR signal into synthesis of LacZ). More generally, an OpAmp is a logic device that detects and amplifies a difference between the currents into its plus and minus inputs. With the addition of the feedback resistor connecting the output to the minus input, the OpAmp translates an incoming current signal into an outgoing voltage signal.


 * 1) Resistor: component which resists current flow by producing a voltage drop across it. The gain in this system is proportional to the resistance. Thus, by varying the resistance, we can vary the circuit's sensitivity to light. Would it make sense to mention Ohm's Law here? I'm not convinced that students will have heard of the concept of gain, and stating V=IR might clarify -- but not for HS freshmen who haven't taken physics.


 * 1) LED: a device with a detectable output (mimics LacZ). A voltage drop across its terminals turns the green-colored light on. (The small 820&Omega; resistor is placed in line with the LED to ensure that the voltage drop across the LED isn't too high, which can fry the LED. This small resistor has no direct analogue in the bacterial photography system.)

Move part numbers to teachers notes only.



Let's start building
INTRO TO BREADBOARDS

You will be building this circuit on a breadboard, which is a much cleaner way to construct circuits than just wiring everything together. Start by building a very simple, "Hello World" circuit to understand intuitively how breadboarding works. (If you have experience building circuits, feel free to skip this step.)

Image: What we want to build. +V|---|>|---v^v^v^---|GND

remember the LED is polarized, it only allows current through it one way, if you try to put current through it backwards it won't work. Need the resistor to take up some of the voltage drop. You could also put the resistor on the power side and the LED on the ground side.

Image: Connections on a breadboard with example wires.
 * Wires X and Y are connected
 * Wires Y and Z are not connected
 * Wire Z is connected to power
 * any other cases?

You want to deliver power from the battery to the rails on either side of the breadboard. Use the binding posts. (Why?) Make sure you get a good connection (sometimes the plastic insulation can block it).

Now plug in the LED and the resistor. Push in the wires firmly to make a good connection. You should see light. If not, something is broken.

STOPPED EDITING AT THIS POINT - THU NIGHT



The circuit has been constructed using a breadboard which is a convenient way to construct electrical circuits. The breadboard holes are connected beneath the plastic as shown in the photo. Take note of these connections because they'll affect how you will connect up components in this exercise.


 * 1) Power the breadboard by running a wire from the +V source (= the red terminal) to the + rail (= the red + connections at the "top" of the breadboard).


 * 1) Run the - rail (= the blue - at the "bottom" of the breadboard) to the black, ground terminal.


 * 1) Use a small wire to connect the A-E rails to +9V.


 * 1) Use a small wire to connect the F-J rails to ground.
 * 1) Position the OpAmp across the trench in the breadboard.


 * 1) Power the OpAmp by connecting it to the +9V and ground using the pin diagram that's in the spec sheet and is reproduced here. Note that the small dot on the corner of the OpAmp indicates pin #1.


 * 1) Connect the OpAmp's + input (pin 3) to ground.


 * 1) Connect the OpAmp's - input (pin 2) to the photodiode. NOTE: the photodiode is asymetric and must be inserted into the breadboard so that the leg under the "flat" edge is to ground. Leave some space between the photodiode input and the OpAmp so an additional resistor can be added to the circuit later.


 * 1) You'll make 2 connections to the OpAmp's output (pin 6)


 * 1) *The first connection from the OpAmp's output should be to the 820 ohm resistor and the LED. NOTE: the LED is asymmetric and must be inserted into the breadboard so that the leg under the "flat" edge is connected to the 820 ohm resistor and the round side is inserted into the +9V rail.


 * 1) *The second connection is to a wire that runs to a variable resistor (see the "finished circuit"). You will change the current into the OpAmp by varying the resistance through the circuit this point. You will start by putting no resistor in, where air serves as an infinitely large resistor.


 * 1) Double check your connections with the system diagram above before you power it up.


 * 1) To connect the 9V battery to the terminals, place the snap battery cover on the battery. Attach the alligator clip on the red battery lead to the red terminal of the breadboard, and the alligator clip on the black battery lead to the black terminal.

Resistance = infinite &Omega;
Air connects the OpAmp's pin 6 to pin 2


 * 1) What happens to the LED when you power up the circuit?


 * 1) What happens to the LED when you shine the flashlight on the photodiode?


 * 1) Can you shine the flashlight on the photodiode so that the LED holds steady at 1/2 its maximal light intensity?

The range of flashlight intensities that can hold the LED 1/2 lit is a measure of the "gain" in the system--where a narrow range of fully on to fully off is "digital" (switch-like) behavior, while a wide range of flashlight intensities that hold the LED 1/2 on is more "analog" (dial-like) behavior.


 * 1) Sketch a graph that has flashlight intensity on the x-axis and LED light intensity on the y-axis. At infinite resistance in place, is the circuit's behavior better described as a switch or a dial?

Resistance = 0&Omega;
Connect the OpAmp's pin 6 to pin 2 with a wire.


 * 1) What happens to the LED when you power up the circuit?


 * 1) What happens to the LED when you shine the flashlight on the photodiode?


 * 1) Can you shine the flashlight on the photodiode so that the LED holds steady at 1/2 its maximal light intensity?


 * 1) Add a line to your graph that has flashlight intensity on the x-axis and LED light intensity on the y-axis. With zero resistance in place, is the circuit's behavior better described as a switch or a dial?

Variable resistance
Connect the OpAmp's pin 6 to pin 2 with a 10 M&Omega; resistor.


 * 1) What happens to the LED when you power up the circuit?


 * 1) What happens to the LED when you shine the flashlight on the photodiode?


 * 1) Can you shine the flashlight on the photodiode so that the LED holds steady at 1/2 its maximal light intensity?


 * 1) Add one last line to your graph that has flashlight intensity on the x-axis and LED light intensity on the y-axis. Is this circuit's behavior better described as a switch or a dial?

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