Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online



Last Updated: 3/25/16

Learning Goals/Objectives for Chapter 5B:  After class and this reading, students will be able to

  • derive equations  from the equation for fractional saturation  Y = ([ML]/[M0] = [L]/(KD+ [L])  equations for 1/Y as a function of 1/[L] (double reciprocal plot), Y/[L] vs Y (bound/free vs bound or the Scatchard Plot) and draw a plot of Y vs log [L] (semilog plot)
  • draw error bars on the plots of Y vs L, 1/Y vs I/L, Y/L vs Y and Y vs log L.
  • explain from these derivative equations and graphs how to calculate determine Kd
  • describe appropriate methods to fit the data from these equations with special attention given to the effect of error bars in the experimental value of Y

B2.  Binding of Two Identical Ligands

Explore the interactive graphs below to see how binding of identical ligands to two independent sites with different affinity changes the nature of the binding graphs. The subtle changes in the graphs should make it clear that binding analyses should be done with a rigorous mathematical analysis fitting of data to the simplest hyperbolic model before moving on to more complex models.

Hyperbolic Graph for Two Independent Binding Sites 

WolframWolfram Mathematica CDF Player - Fractional Saturation of Sites (0-1)for Binding of L to 2 Independet Sites - Hyperbolic Plot (free plugin required)

SageMathLogoInteractive SageMath Graph: Fractional Saturation of Sites for binding of L to 2 Independent sites


Double Reciprocal Graph for Two Binding Sites 

WolframWolfram Mathematica CDF Player - Fraction Saturation of Sites (0-1) for Binding of L to 2 Sities - Double Reciprocal Plot.  (Note that 1/Y max is 1 at the y intercept)

Scatchard Graph for Two Binding Sites 


WolframWolfram Mathematica CDF Player - Semilog Plot for binding of ligand to 2 independent sites

SageMathLogoInteractive SageMath Graph: Semilog Plot for binding of ligand to 2 independent sites


Return to Chapter 5B: Mathematical Analyses of Binding Graphs Sections

Return to Biochemistry Online Table of Contents

Archived version of full Chapter 5B:  Mathematical Analyses of Binding Graphs


Creative Commons License
Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.