Microbial Metabolism & Photosynthesis: Pathways, ETC, and Calvin Cycle

Chemoorganotrophic fermentation

Uses an endogenous electron acceptor (an intermediate of the pathway used to oxidize the organic energy source such as pyruvate). Does NOT involve an electron transport chain nor generation of a proton motive force.

Glycolysis (EMP)

Essential catabolism of glucose involving 10 distinct reactions divided into 2 stages.

Role of oxygen in aerobic respiration

Acts as the terminal electron acceptor.

Reduced form between NAD+ and NADH

NADH.

When reduced, NAD accepts

One proton and two electrons.

Catabolic pathways function

Break down larger molecules to release energy.

ATP provides energy by

Breaking phosphodiester bonds.

Assembly of DNA energized by

ATP hydrolysis with release of pyrophosphate.

Products of EMP pathway

2 ATP, 2 NADH, 2 pyruvate.

ATP Synthase

Harvests energy from PMF to synthesize ATP; 10 H⁺ per NADH (= 3 ATP) and 6 H⁺ per FADH₂ (= 2 ATP).

Theoretical vs Actual Yield of ATP

Depends on growth conditions and ETC type; anaerobic glycolysis yields 2 ATP.

Mycobacterium tuberculosis

Most lethal infectious disease; grows inside macrophages; uses the glyoxylate bypass to divert carbon for biosynthesis.

Fermentation

Completion of glucose catabolism; produces no extra ATP beyond glycolysis.

Fermentation byproducts

Alcohols, carboxylates, H₂, CO₂ (energy stored in ATP).

Homolactic fermentation

Produces 2 lactic acid molecules.

Ethanolic fermentation

Produces 2 ethanol + 2 CO₂.

Heterolactic fermentation

Produces 1 lactic acid, 1 ethanol, 1 CO₂.

Mixed-acid fermentation

Produces acetate, formate, lactate, succinate + ethanol, H₂, CO₂.

Electron Transport Chain (ETC)

Series of e⁻ carriers transferring electrons from NADH/FADH₂ to O₂ or another acceptor.

Flow of electrons in ETC

From more negative to more positive reduction potentials.

Oxidative phosphorylation

ATP synthesized as a result of electron transport driven by oxidation of energy source.

Anaerobic respiration

Uses metals or oxidized ions of N or S as terminal acceptors; occurs where O₂ is scarce (wetlands, gut).

Dissimilatory nitrate reduction

Nitrate used as terminal electron acceptor, unavailable for assimilation.

Denitrification

Reduction of nitrate to N₂ gas; causes loss of soil fertility.

ETS Summary

Membrane-embedded proteins transfer e⁻ to terminal acceptor; generate PMF; carriers contain metal ions or conjugated rings.

Where does all NADH/FADH₂ go

10 NADH + 2 FADH₂ per glucose; 2 from EMP, 2 from transition, 6 + 2 from TCA.

TCA Cycle Summary

2 CO₂ via decarboxylation; 3 NADH, 1 FADH₂, 1 ATP by substrate-level phosphorylation.

TCA function

Originally evolved to aid in amino acid production (links 2-oxoglutarate→glutamate, oxaloacetate→aspartate, citrate→fatty acids).

Phototrophy definition

Use of photons to excite electrons and pump protons.

Light absorption mechanism

Excites electrons to higher orbitals then returns to ground state.

Rhodopsin-based phototrophy

Single membrane protein around retinal molecule; functions as proton pump.

Peak absorption of rhodopsin

500-550 nm (green); reflects red, blue, purple.

Antenna complex function

Organizes light-harvesting arrays and transfers energy to reaction center.

Reaction center complex

Photosystems I and II absorb light and separate electrons from chlorophyll.

Photoexcitation

Light raises electrons to higher energy state.

Photoionization

Light causes electron separation.

Photolysis

Light splits molecules.

Photosynthesis

Photolysis combined with CO₂ fixation and biosynthesis.

Oxygenic photosynthesis (non-cyclic)

Produces ATP + NADPH and O₂; cyclic flow only makes ATP.

Proton potential in cytoplasm

More negative inside (stroma).

Cyanobacteria

Oxygen-producing bacteria with chlorophyll; split H₂O and release electrons for ETS.

Chlorophylls absorb light

Chromophore is light-absorbing e⁻ carrier; absorbs red/blue/purple, reflects green.

Nitrifying bacteria

Oxidize ammonia to nitrate.

Rhodobacter (purple sulfur bacteria)

Contain bacteriochlorophyll; absorb far-red and UV light missed by cyanobacteria.

Photosynthetic ETC types

Anaerobic Photosystem I, Anaerobic Photosystem II, Oxygenic Z pathway.

Calvin Cycle (CBB) stages

1) Carbon fixation 2) Reduction 3) Regeneration.

Light-independent reactions location

Cytoplasm of bacteria.

Carbon fixation step

Rubisco fixes CO₂ to RuBP (ribulose 1,5-bisphosphate).

Carbon reduction step

6 ATP + NADPH convert 3-PGA to G3P → glucose.

Regeneration step

G3P regenerates RuBP (uses 3 ATP) to continue cycle.