  Biology is perhaps the most complex of the sciences, given the incredible
variety of chemical species that are interconnected in spatial and temporal
pathways that are daunting to understand. Their interconnections lead to
emergent properties such as memory, consciousness, and recognition of self and
non-self. To understand how these interconnected reactions lead to cellular
life characterized by activation, inhibition, regulation, homeostasis, and
adaptation, computational analyses and simulations are essential, a fact
recognized by the biological communities. At the same time, students struggle
to understand and apply binding and kinetic analyses for the simplest reactions
such as the irreversible first-order conversion of a single reactant to a
product. This likely results from cognitive difficulties in combining
structural, chemical, mathematical, and textual descriptions of binding and
catalytic reactions. To help students better understand dynamic reactions and
their analyses, we have introduced two kinds of interactive graphs and
simulations into the online educational resource, Fundamentals of Biochemistry,
a multivolume biochemistry textbook that is part of the LibreText collection.
One type is available for simple binding and kinetic reactions. The other
displays progress curves (concentrations vs time) for both simple reactions and
more complex metabolic and signal transduction pathways, including those
available through databases using systems biology markup language (SBML) files.
Users can move sliders to change dissociation and kinetic constants as well as
initial concentrations and see instantaneous changes in the graphs. They can
also export data into a spreadsheet for further processing, such as producing
derivative Lineweaver-Burk and traditional Michaelis-Menten graphs of initial
velocity (v0) vs substrate concentration.
