From 822bd0b04d1cce54c2fff57c4b206c51d1dcb940 Mon Sep 17 00:00:00 2001 From: bnewbold Date: Tue, 22 Apr 2014 22:01:56 -0400 Subject: rename notes -> lectures --- lectures/lec06_intro1 | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 lectures/lec06_intro1 (limited to 'lectures/lec06_intro1') diff --git a/lectures/lec06_intro1 b/lectures/lec06_intro1 new file mode 100644 index 0000000..97b2f39 --- /dev/null +++ b/lectures/lec06_intro1 @@ -0,0 +1,44 @@ + +Background: + +Ligands are little molecules (which could be proteins or chemicals or whatever) +which bind to a larger biomolecule (eg, a protein or DNA) called the receptor. +"Receptor/ligand" binding affinity refers to how strongly different ligands +want to attach to different receptors. Both binding (association) and +un-binding (dissociation) is happening all the time, so you get a (dynamic, or +possibly steady state) distribution of binding probability. + +ref: https://en.wikipedia.org/wiki/Ligand_(biochemistry) + +ODEs (ordinary differential equations) are those involving only a single +independent variable; eg, solving for x in terms of t, only having derivatives +dx/dt, (d^2 x / d x^2), etc. the order of the ODE is the highest order of +derivative. + +PDEs (partial differential equations) are those involving multiple independent +variables, and thus partial derivatives. Eg, x in terms of t and r, having +derivatives del x / del t, del x / del r, and del^2 x / (del t * del r). + +ref: https://en.wikipedia.org/wiki/Differential_equation#Ordinary_and_partial +--------- + +Law of mass action: rate of a reaction involving two quantities is proportional +to the product of the densities of both. + +Michaelis-Menten: approximation to solution of enzyme-catalyzed reaction +equation: + + d [S] / dt = (max reaction rate) * [S] / (Km + [S]) + + [S] is concentration of substrate S + Km is Michaelis constant, which is a specific substrate concentration + + (max reaction rate) =~ k_2 [E]_total + Km =~ (k_-1 + k_2) / (k_1) + + all assuming that enzyme E catalizes S into P with rates k_n: + + -> k_1 + [E] + [S] [ES] -> k_2 [E] + [P] + <- k_-1 + -- cgit v1.2.3