Electron Transfer Reactions and Pathways

1. Electron Transfer Reactions and Pathways Markus Krummenacker Bioinformatics Research Group SRI International kr@ai.sri.com

2. What is an Electron Transfer System? • The overall purpose of an electron transfer system is to create a proton gradient which will be used to re-generate ATP. • 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 generation by ATP synthase. • An electron transfer system consists of a series of membrane-associated electron carriers and membrane-associated enzyme systems.

3. Electron Transfer Pathways(version 12.5 and higher)

4. Internal Representation • ETRs are |Composite-Reactions| • Slots similar to pathways refer to sub-reactions • Involve two |Redox-Half-Reactions| • RHRs contain explicit electrons, which can not occur freely • Therefore, two 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. 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. 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 • If desired, an Electron Transfer Pathway can be created from two ETRs