Metabolism & Biogeochemical Cycling

Electron transport chain (ETC)

Collection of electron carriers embedded in a membrane that transfer electrons through redox reactions to generate a proton motive force (PMF)

ETC location in prokaryotes

Plasma membrane in bacteria and archaea

ETC location in eukaryotes

Inner mitochondrial membrane

Prokaryotic respiratory systems

Flexible, modular systems that may have branched chains, different carriers, and variable lengths

ETC organization

Carriers are organized by increasing reduction potential; the first carrier has the most negative potential and the terminal electron acceptor has the most positive

Purpose of an ETC

Generate a proton motive force by coupling energy released from electron transfer to proton pumping

Electron donor in an ETC

Donates electrons to the first ETC complex and has a lower reduction potential than the electron acceptor

Terminal electron acceptor

Final molecule that receives electrons from an ETC; has the highest reduction potential in the chain

ETC and ATP synthase

ATP synthase is separate from the ETC and uses the PMF generated by the ETC to produce ATP

ETC steps

1. Electron donor releases electrons. 2. Electrons move through carriers, releasing energy. 3. Energy pumps protons outward. 4. Electrons reach the terminal acceptor. 5. Protons flow back through ATP synthase, producing ATP

Proton motive force (PMF)

Electrochemical gradient created by a higher proton concentration and charge difference across a membrane

Proton pumping

Movement of protons from the cytoplasm across the membrane using energy released during exergonic redox reactions

PMF functions

Drives ATP synthesis, flagellar rotation, and secondary active transport

Redox potential (E0)

Measure in volts of a molecule's tendency to donate or accept electrons under standard conditions

More negative reduction potential

Greater tendency to donate electrons; characteristic of reducing agents

More positive reduction potential

Greater tendency to accept electrons; characteristic of oxidizing agents

Reducing agent

Electron donor that becomes oxidized when it transfers electrons

Oxidizing agent

Electron acceptor that becomes reduced when it receives electrons

Delta E0

Reduction potential of the electron acceptor minus reduction potential of the electron donor

Redox energy yield

The greater the difference between acceptor and donor reduction potentials, the more negative the delta G and the more energy released

Electron transfer direction

Electrons generally move from carriers with more negative reduction potentials toward carriers with more positive reduction potentials

NADH oxidation

NADH → NAD+ + H+ + 2e-

Oxygen reduction

½O2 + 2H+ + 2e- → H2O

NAD+/NADH

Electron carrier pair used in cellular metabolism; NADH carries high-energy electrons

NADP+/NADPH

Electron carrier pair especially important for supplying reducing power to biosynthetic reactions

FAD/FADH2

Electron carrier pair that transfers electrons to metabolic pathways and respiratory chains

Cytochromes

ETC proteins containing heme groups that use iron to transfer electrons

Ubiquinones

Non-protein, lipid-soluble electron carriers, such as coenzyme Q, with hydrophobic tails that move horizontally within the membrane

Bacterial ETC characteristics

May resemble mitochondrial ETCs or differ from them; can be branched, shorter, and use different carriers

Why bacterial ETCs may generate less ATP

The PMF also powers processes such as flagellar rotation and secondary active transport

Aerobic respiration

Uses oxygen (O2) as the terminal electron acceptor

Anaerobic respiration

Uses terminal electron acceptors other than oxygen, such as nitrate, sulfate, CO2, ferric iron, or selenate

Aerobic vs. anaerobic ETC energy

Oxygen has a more positive reduction potential than alternative acceptors, usually producing a larger delta E0 and greater energy yield

Chemotrophy

Obtaining energy from chemical compounds rather than light

Chemoorganotrophs

Organisms that oxidize organic compounds, such as glucose, to obtain energy

Chemoorganic respiration

Harvesting energy by oxidizing organic substrates and transferring electrons to respiratory pathways

Substrate-level phosphorylation

Direct production of ATP during metabolic reactions, including glycolysis and the TCA cycle

NADH and FADH2 in respiration

Carry electrons generated during metabolism to membrane-bound ETCs, where most respiratory ATP is produced

Aerobic respiration

Respiration using oxygen as the terminal electron acceptor; generally produces the highest energy yield because oxygen has the most positive reduction potential

Organisms capable of aerobic respiration

Obligate aerobes, facultative anaerobes, and microaerophiles

Factors affecting ATP yield

PMF use, biosynthesis, environmental conditions, and ETC structure

ATP yield per NADH

Approximately 2.5 ATP through oxidative phosphorylation

ATP yield per FADH2

Approximately 1.5 ATP through oxidative phosphorylation

Oxidative phosphorylation example

10 NADH produce 25 ATP and 2 FADH2 produce 3 ATP, totaling 28 ATP

Anaerobic respiration

Respiration using an electron acceptor other than oxygen; generally yields less energy than aerobic respiration

Nitrate respiration

Uses nitrate (NO3−) as the terminal electron acceptor; found in organisms such as enteric bacteria

Sulfur respiration

Uses sulfur compounds as electron acceptors; examples include Desulfuromonas and Thermoproteus

Ferric iron respiration

Uses ferric iron (Fe3+) as an electron acceptor; examples include Pseudomonas, Bacillus, and Geobacter

Organisms capable of anaerobic respiration

May include facultative anaerobes and obligate anaerobes; aerotolerant anaerobes do not use oxygen for respiration

Facultative anaerobes

Can grow with or without oxygen and generally grow faster with oxygen because aerobic respiration produces more ATP

Metabolic flexibility

Ability to switch metabolic pathways or electron donors and acceptors as conditions change

E. coli metabolic flexibility

Can use multiple electron donors and acceptors in different ETCs

Chemolithotrophs

Organisms that obtain electrons from inorganic compounds to feed respiratory ETCs

Chemolithotroph energy metabolism

Generally do not use sugars, glycolysis, or the TCA cycle to obtain energy from organic carbon; they oxidize inorganic electron donors instead

Chemolithotroph electron carriers

Because they oxidize inorganic substrates rather than organic fuels through conventional pathways, their reducing equivalents are generated differently and may require reverse electron flow

Chemolithotroph energy yield

Often lower than glucose oxidation because many inorganic electron donors provide less favorable energy yields

Energy from glucose oxidation

Complete oxidation of glucose to CO2 releases approximately 686 kcal/mol of free energy (delta G ≈ −686 kcal/mol)

Ecologically important chemolithotrophs

Hydrogen oxidizers, sulfur oxidizers, and nitrifying bacteria

Chemolithotroph metabolic flexibility

Some can switch between chemolithotrophic and chemoorganotrophic metabolism or between autotrophy and heterotrophy

Chemolithoautotrophs

Use inorganic electron donors for energy and fix CO2 into organic carbon

Calvin cycle in chemolithoautotrophs

Fixes CO2 into organic molecules and requires ATP and NAD(P)H

Reverse electron flow

Uses energy from the PMF to drive electrons toward carriers such as NAD(P)+, producing NAD(P)H for anabolic reactions

Phototrophy

Conversion of light energy into chemical energy that powers cellular functions

Phototrophy vs. photosynthesis

Phototrophy captures light energy; photosynthesis combines light-energy capture with carbon fixation

Photosynthesis

Uses light-derived chemical energy to fix CO2 into organic carbon

Phototrophic strategies

Oxygenic phototrophy, anoxygenic phototrophy, and archaerhodopsin-based phototrophy

Oxygenic phototrophy

Light-driven electron transport that uses water as an electron donor and releases oxygen

Organisms performing oxygenic phototrophy

Cyanobacteria and photosynthetic eukaryotes

Oxygenic phototrophy in eukaryotes

Produces ATP and NADPH primarily to power Calvin cycle carbon fixation

Oxygenic phototrophy in cyanobacteria

Produces ATP and NADPH for carbon fixation and other cellular energy needs

Oxygenic phototrophy and autotrophy

The oxygenic phototrophs described in these notes are autotrophs that fix CO2 using the Calvin cycle

Photosystem II (PSII)

Contains light-absorbing pigments, including chlorophyll, and receives replacement electrons from water

Photosystem I (PSI)

Absorbs another photon to re-energize electrons so they can reduce NADP+

Oxygenic phototrophy steps

1. Water donates electrons to PSII. 2. Light excites electrons. 3. Electrons travel through the ETC and generate a PMF. 4. PSI absorbs light to re-energize electrons. 5. Electrons reduce NADP+ to NADPH

NADP+ in oxygenic phototrophy

Terminal electron acceptor of the light-driven pathway that forms NADPH for biosynthesis

Photophosphorylation

Production of ATP using a proton motive force generated by light-driven processes

Anoxygenic phototrophy

Light-driven energy generation that does not use water as an electron donor and therefore does not produce oxygen

Organisms performing anoxygenic phototrophy

Green bacteria, purple bacteria, and heliobacteria

Bacteriochlorophyll

Light-absorbing pigment used by many anoxygenic phototrophs

Anoxygenic photosystems

Typically use one photosystem, unlike the two photosystems in oxygenic phototrophy

Anoxygenic phototrophy and autotrophy

Some anoxygenic phototrophs fix CO2, but others are heterotrophs and do not use the Calvin cycle

Cyclic electron flow in anoxygenic phototrophy

Excited electrons travel through carriers to generate a PMF and then return to the photosystem for repeated use

Noncyclic electron flow in anoxygenic phototrophy

Electrons leave cyclic transport to generate reducing equivalents such as NADH; replacement electrons must come from an external donor

Electron donors in anoxygenic phototrophy

Must be supplied by a source other than water when electrons are diverted to produce reducing equivalents; hydrogen sulfide is one example

Anoxygenic phototrophy steps

1. Light excites an electron in the photosystem. 2. The electron travels through the ETC, generating a PMF for ATP production. 3. The electron may return to the photosystem and repeat the cycle

Archaerhodopsin-based phototrophy

Light-driven proton pumping by a membrane protein without an ETC

Archaerhodopsin

Integral membrane protein containing a retinal chromophore that absorbs light and undergoes a shape change to pump a proton across the membrane

Archaerhodopsin mechanism

Light triggers retinal photoisomerization and a conformational change that pumps a proton from the cell into the external space

Archaerhodopsin energy production

Creates a PMF that ATP synthase uses to produce ATP through photophosphorylation

Photoheterotrophs

Use light for energy but rely on preformed organic compounds as carbon sources because they lack carbon-fixation pathways

Purple non-sulfur bacteria

Example of metabolically flexible organisms that may use photoheterotrophy

Two processes sustaining ecosystems

Energy flow and nutrient cycling

Energy flow in ecosystems

Energy enters mainly as sunlight and eventually dissipates as heat

Nutrient cycling

Atoms repeatedly move between living organisms and nonliving parts of ecosystems

Decomposition

Breakdown of dead organic matter, allowing nutrients to return to the environment

Microbial decomposers

Microbes that break down dead organic matter and recycle nutrients

Mineralization

Conversion of organic matter into inorganic forms that return elements to the nutrient pool

Microbial environmental impacts

Microbial metabolism changes atmospheric conditions, aquatic systems, and soil chemistry

Environmental redox potential (Eh)

Measure of the tendency of an environment to support oxidation or reduction; influences available electron acceptors and donors

Eh and terminal electron acceptors

Environmental redox conditions help determine which oxidized compounds are available for respiration