CBEMS 115 Kinetics of Biochemical Networks (2015-2016)

CBEMS 115 Kinetics of Biochemical Networks

(Not required for any major.)
Catalog Data:

CBEMS 115 Kinetics of Biochemical Networks (Credit Units: 4) Principles from statistical mechanics, thermodynamics, and chemical kinetics applied to biochemical systems, from fundamental processes such as receptor-ligand binding and enzyme catalysis, to complex cellular functions including signal transduction and gene regulation. Upper-division students only. Concurrent with CBEMS 215. (Design units: 0)

Required Textbook:
Recommended Textbook:


Elizabeth Louise Read
Relationship to Student Outcomes
No student outcomes specified.
Course Learning Outcomes. Students will:

1. Be able to model cellular processes using kinetic and thermodynamic approaches.

2. Be familiar with recent experimental literature on quantitative models of gene regulation and signaling network.

3. Understand the role of stochastic processes in biology, and the application of the chemical Master Equation to such processes.

Prerequisites by Topic

CBEMS 45C (thermodynamics) and Math 3D (differential) equations.

Lecture Topics:
  • Introduction: central dogma of biology
  • Overview of biological macromolecules and intermolecular forces
  • What is systems biology, what is quantitative biology
  • Statistical thermodynamics in biology
  • Thermodynamic driving forces
  • Thermodynamic models of ligand receptor binding
  • Chemical kinetics and equilibrium in biology
  • Michaelis-menten enzyme kinetics
  • Ultrasensitivity, digital behaviors and hysteresis
  • Information processing in biological systems
  • Network motifs in gene regulation
  • Natural and synthetic genetic switches
  • Oscillatory systems: circadian clocks, the repressilator
  • Cell signaling network: robustness and adaptation
  • Stochastic processes: cell fate decisions
  • Chemical Master Equation and Gillespie algorithm
Class Schedule:

Meets for 3 hours of lecture each week for 10 weeks.

Computer Usage:


Laboratory Projects:


Professional Component


Design Content Description
Laboratory Portion:
Grading Criteria:
  • Homework Problems: 35%
  • Class Participation: 30%
  • Final Presentation: 35%
  • Total: 100%
Estimated ABET Category Content:

Mathematics and Basic Science: 0.0 credit units

Computing: 0.0 credit units

Engineering Topics: 0.0 credit units

Engineering Science: 0.0 credit units

Engineering Design: 0.0 credit units

August 6, 2014
Senate Approved:
March 11, 2014
Approved Effective:
2014 Fall Qtr