-New bigger room: Rm. 4-163New bigger room: Rm. 4163- First PS will be posted tomorrow(d 10/06/09)(due 10/06/09)- Tomorrow’s recitation W 9/23/094-5 PM Rm. 26-204‘Basic MATLAB crash course’Basic MATLAB crash course1Review Lecture 3Equilibrium binding and cooperativityjP1jPS ↔+j1j−32Adair’s Equation:nnnn[S]...K2K1K...2[S]2K1K[S]1K1[S]...K2K1nK...3[S]3K2K13K2[S]2K12K[S]1Kr++++++++=21211][S][P]j[PjK =macroscopic association constantfor transitions between state j-1 and j2][S]1j[Pj−for transitions between state j1 and jNote #1 Detailed balancePP1P2...P1Pk+1k+2k+nPoP1P2...Pn-1Pnk-1k-2k-n]d[P]1[P1k][S][P1k]2[P2k][S]1[P2k]1d[P0]1[P1k][S]o[P1kdt]o[0=−++−==−++−==]2[P2k][S]1[P2k]1[P1k][S]o[P1k]2[P2k][S]1[P2kdt0−++−=−++−++etc.][S]1j[P]j[PjkjkjK−=−+≡3jjI Identical and independent binding sitesSk+k+SSk+k-k+k-SSk+k+K2KKK/2Kk/kSk-k-K1=2KK2=K/22K[S]2[S]22K2K[S]+K=k+/k-4use Adair: K[S]12K[S]2[S]2K2K[S]1[S]2K2K[S]r+=+++=II Non-identical and independent binding sitesSk+k+*SSk+k-k+k-*SSk+k+*K=k+/k-Sk-k-*[S]*KK[S]K*=k+*/k-*5Independent binding: [S]*K1[S]KK[S]1K[S]r+++=III Identical and interacting binding sitesSk+k+*SSk+k-k+k-*SSk+*k+K2KKK*/2Kk/kSk-*k-K1=2KK2=K*/2K=k+/k-K*=k+*/k-*2[S]*2KK2K[S]+6use Adair: 2[S]*KK2K[S]1[S]2KK2K[S]r+++=Cooperativity2[S]*KK2K[S]12[S]*2KK2K[S]r+++=2βx2x1βx)x(1Y+++=β = K*/Kx=K[S]β > 1: positive cooperativityβx K[S]β> 2: sigmoidal curveβ < 1: negative cooperativity(always: d2Y/dx2< 0)7Hill number for ‘real’ dimer8A (very) short intro on ‘Genetic Engineering’lb f h i iToolbox of the genetic engineer:1. Restriction enzymes2. Plasmids (and de novo DNA synthesis)3. PCR (Polymerase Chain Reaction)4Fl t ti4. Fluorescent proteins91. Restriction Enzymes10112 Plasmids2. Plasmids123. PCR134. Fluorescent proteins1415(courtesy of Nick Buchler)N. E Buchler, F. R. Cross , Molecular Systems Biology 5, doi:10.1038/msb.2009.30 (2009) 16(courtesy of Nick Buchler)17(courtesy of Nick Buchler)18(courtesy of Nick Buchler)19(courtesy of Nick Buchler)20(courtesy of Nick Buchler)21(courtesy of Nick Buchler)22(courtesy of Nick Buchler)23(courtesy of Nick Buchler)24(courtesy of Nick Buchler)25(courtesy of N. Buchler)26(courtesy of N.