1. Electron Transport Markus Krummenacker Bioinformatics Research Group SRI International kr@ai.sri.com

2. SRI International Bioinformatics What is the Electron Transport System ? The overall purpose of the electron transport system is to re-generate ATP using energy contained in high-energy electrons. Gradually extract energy from high-energy electrons in a series of redox steps. This energy is used to pump protons across the membrane, creating an electrochemical gradient. The proton gradient drives ATP synthase. The electron transport system consists of a series of membrane-associated electron carriers and membrane-associated enzyme systems.

3. SRI International Bioinformatics Theme: Q-Loop Membrane-localized quino redox cofactors

4. SRI International Bioinformatics Internal Representation ETRs are |Composite-Reactions| Slots similar to pathways refer to sub-reactions Involve 2 |Redox-Half-Reactions| RHRs contain explicit electrons, which can not occur freely Therefore, 2 RHRs are paired up, connected by the electrons The electrons are not visible outside of the ETR The LEFT and RIGHT substrates of the ETR are computed from the RHRs Additional vectoral proton transport can be added as another sub-reaction

5. SRI International Bioinformatics Redox Half Reactions They are the building blocks for ETRs STD-REDUCTION-POTENTIAL slot, units of V Always written in direction: Ox. + e- --> Red. This allows redox potentials to be compared, to derive reaction directionality Compartments are important, even for PROTON Convention: e- has no compartment Convention: Quino factors (in |Membrane-Electron- Carriers|) have no explicit compartment, and are always presumed to reside in the membrane

6. SRI International Bioinformatics Reaction Editor Support First, the appropriate Redox Half Reactions need to be created In a second step, an ETR can be constructed by selecting: a Quino Half Reaction a Non-Quino Half Reaction optionally, a vectoral proton transport reaction