SYNTHETIC BIOLOGY

Guillermo RODRIGO

Alfonso JARAMILLO

LOGIC GATES

NOT

AND

OR

NAND NOR

A O

0 1

1 0

A B O

0 0 0

0 1 0

1 0 0

1 1 1

A B O

0 0 0

0 1 1

1 0 1

1 1 1

INVERTER

• Biological Inverter:

High input concentration, low output concentration (vv)

• Digital gate: NOT

• True table

Chemical equations

PROBLEM 1

1.- Using chemical equations and kinetic constants, obtain differential equations. Which is the general expression of reaction velocity with R reactifs and P products of stechiometry n i?

2.- Using Simulink, implement the differential system.

3.- Obtain the concentrations when the drive (mRNA) is 1 between 10 and 20 (x100) s. Is it really a NOT gate?

4.- Try to modify some kinetic constant to reduce the delay.

PROBLEM 2

1.- Which biological circuit is designed by this DNA sequence (in parts)?

2.- Implement that with logic gates and use Simulink to show the protein concentrations.

Note: proteins are not the input/output of the subsystems, it is mRNA, namely, RNA Polymerase.

3.- Study the form of the curves and play with the time scale.

PROBLEM 2’ (version)

1.- Using the NOT gate, implement a NAND gate with Simulink.

2.- Implement the RS Latch with NAND gates and show the protein concentrations.

3.- What is your opinion of this sequence (in parts)?

PROBLEM 3

1.- Obtain the biologic circuit of the following genetic sequence.

2.- Obtain the logic circuit.

3.- Implement it with Simulink and show the graphics of the protein concentrations. What is happen?

4.- Try to solve this problem to obtain an oscillator. Can we lose the symmetric behavior?