Summary Lecture 3 Image by MIT OCW. L4: Cooperativity & introduction λ phage model λ phage model (Hasty et al.) as example for applying mass action law. A d k X nXP 2 DX t k P 2 DX 2 DX 2 DX 4 K 2 X 2 DX * 2 DX 3 K 2 XD 2 DX 2 K 2 XD 2 X 1 K 2X ??→? ++??→?+ ??→←+ ??→←+ ??→←+ ??→← OR2 OR3 λλ λλ λ λ OR2 OR3 λλ OR2 OR3 λλ λλ K 1 K 2 fast slow most important step in modeling !! most important step in modeling !! biology math 2 K 1 Kr d k γ r T d 0 p t nk α 2 K 4 K 2 σ 2 K 3 K 1 σ 1γx 4 x 2 σ 2 )x 1 σ(11 2 αx dt dx = = = = +? +++ = A d k X nXP 2 DX t k P 2 DX 2 DX 2 DX 4 K 2 X 2 DX * 2 DX 3 K 2 XD 2 DX 2 K 2 XD 2 X 1 K 2X ??→? ++??→?+ ??→←+ ??→←+ ??→←+ ??→← relative binding constants ~ synthesis/basal rate ~ degradation/basal rate mass action choose elegant (dimensionless, relative) variables ! graphical stability analysis How to experimentally verify these ideas ? Synthetic Biology Build your own designed network ‘from scratch’ and test your model Examples for synthetic genetic switches: Isaacs et al. Prediction and measurement of an autoregulatory genetic module. PNAS 100, 7714 (2003) Gardner et al. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 399 (2000) First a short intro on ‘Genetic Engineering’ Toolbox of the genetic engineer: 1. Restriction enzymes 2. Plasmids 3. PCR (Polymerase Chain Reaction) 4. Fluorescent proteins