Phototrophy, Chemolithotrophy & Major Biosyntheses
2 sub-topics · Pages 403–437
1. Introduction
Phototrophic and chemolithotrophic microorganisms drive primary production in ecosystems beyond the reach of organic carbon — deep-sea vents, stratified lake chemoclines, and sunlit anaerobic zones. Oxygenic photosynthesis (cyanobacteria, algae, plants) uses water as electron donor, releasing O₂; anoxygenic photosynthesis (purple and green sulfur bacteria) uses H₂S, H₂, or organic acids, producing no O₂. Understanding these pathways reveals the full scope of life's energy strategies.
✏️ Fill in the Blank
1. In oxygenic photosynthesis the two photosystems involved are Photosystem _______ and Photosystem II.
Show Answer
I2. The photosynthetic pigment found in purple bacteria and green bacteria (not found in plants) is called _______.
Show Answer
Bacteriochlorophyll3. Halobacterium salinarium uses a membrane protein called _______ to harvest light energy without chlorophyll, pumping protons across the membrane.
Show Answer
Bacteriorhodopsin4. The two photosystems in oxygenic photosynthesis are Photosystem I (PSI) and Photosystem _______.
Show Answer
II (PSII)5. The biosynthesis of fatty acids uses repeated additions of _______ units derived from malonyl-ACP.
Show Answer
Two-carbon (C2 / acetyl)🔘 Multiple Choice
1. Nitrogenase, the enzyme that catalyses N₂ fixation, is irreversibly inhibited by:
Show Answer
Correct: C) O₂2. In the Z-scheme of oxygenic photosynthesis, water is split at Photosystem II to provide electrons. The oxidising agent responsible for this splitting is:
Show Answer
Correct: B) The oxygen-evolving complex (Mn cluster)3. Reverse electron transport in chemolithotrophs is energetically costly. What is the source of energy that drives electrons 'uphill' to reduce NAD⁺?
Show Answer
Correct: B) The proton-motive force generated by chemiosmosis4. Bacteriorhodopsin found in Halobacterium differs from chlorophyll-based photosystems in that it:
Show Answer
Correct: B) Is a light-driven proton pump that generates PMF without an electron transport chain5. Purple sulfur bacteria (e.g., Chromatium) use H₂S as an electron donor in photosynthesis. What compound accumulates as a by-product in their cells?
Show Answer
Correct: C) Elemental sulfur (S⁰) stored as intracellular granules6. Purple sulfur bacteria (e.g., Chromatium) are classified as:
Show Answer
Correct: B) Anoxygenic photolithotrophs using H₂S as electron donor7. Which molecule donates electrons to reduce ferredoxin in PSI?
Show Answer
Correct: B) Plastocyanin / cytochrome c5538. Aerobic anoxygenic phototrophic bacteria (AAP) differ from purple bacteria in that they:
Show Answer
Correct: B) Use bacteriochlorophyll but require O₂ and cannot grow solely by photosynthesis💬 Open-Ended Questions
1. Compare oxygenic and anoxygenic photosynthesis: electron donors, photosystems involved, end products, and example organisms.
Hint / Guidance
Oxygenic: H₂O as electron donor; PS I and PS II (Z-scheme); O₂ produced; cyanobacteria, algae, plants. Anoxygenic: H₂S, H₂, Fe²⁺, or organic acids as donors; single photosystem (type I or II); no O₂; purple sulfur bacteria (Chromatium — type II RC), green sulfur bacteria (Chlorobium — type I RC), purple non-sulfur bacteria (Rhodobacter).2. What is reverse electron transport in chemolithotrophs? Why is it necessary, and in what types of organisms does it occur?
Hint / Guidance
Chemolithotrophs oxidise inorganic compounds (NH₃ at E₀'=+0.34 V, Fe²⁺ at +0.77 V) via ETC → ATP. Problem: NAD⁺/NADH E₀'= -0.32 V; inorganic donors with positive E₀' cannot reduce NAD⁺ directly. Solution: reverse electron transport — PMF drives electrons backward up ETC from donor to NAD⁺. Energetically expensive; organisms (Nitrosomonas, Nitrobacter, Thiobacillus ferrooxidans) grow very slowly.3. Explain how nitrogen fixation is regulated at both the enzyme level and the gene expression level in free-living diazotrophs such as Azotobacter and Klebsiella.
Hint / Guidance
Enzyme level: nitrogenase O₂-inhibited; reversibly inhibited by NH₄⁺ via DraT/DraG ADP-ribosylation of Fe protein. O₂ protection in Azotobacter: high respiration scavenges O₂; conformational protection. Gene level: nif genes regulated by NifA activator (σ⁵⁴-dependent); NifA activity inhibited by O₂ (via NifL) and NH₄⁺ (via PII/NtrC cascade sensing 2-OG:glutamine ratio). Nitrogenase synthesised only when O₂ low and combined N limiting.4. What are chlorosomes, and how do they give green sulfur bacteria a competitive advantage in low-light environments?
Hint / Guidance
Chlorosomes: large oblong antenna complexes containing BChl c/d/e self-assembled without protein scaffold (~10,000–250,000 BChl). Advantage: enormous light-harvesting area enables photosynthesis at ~1 µmol photons m⁻²s⁻¹. Ecological: Chlorobium thrives in anoxic hypolimnion below cyanobacteria; utilises far-red wavelengths (715–750 nm).5. Describe the roles of different microbial groups in key transformations of the nitrogen cycle, including nitrification, denitrification, and anammox.
Hint / Guidance
N₂ fixation: Rhizobium, Azotobacter, Cyanobacteria; N₂→NH₃ via nitrogenase. Ammonification: decomposers; organic N→NH₄⁺. Nitrification: Nitrosomonas NH₃→NO₂⁻; Nitrobacter NO₂⁻→NO₃⁻; comammox Nitrospira NH₃→NO₃⁻. Denitrification: Pseudomonas, Paracoccus; NO₃⁻→N₂ anaerobically. Anammox: Candidatus Brocadia (Planctomycetes); NH₄⁺+NO₂⁻→N₂; used in sustainable wastewater treatment.6. How is glutamate synthesised in bacteria and why is it the central amino group donor for biosynthesis of other amino acids?
Hint / Guidance
GS-GOGAT pathway: (1) Glutamine synthetase (GS): glutamate + NH₄⁺ + ATP → glutamine; (2) Glutamate synthase (GOGAT): glutamine + α-ketoglutarate + NADPH → 2 glutamate. Glutamate = primary nitrogen-containing product; donates amino group to other amino acids via transamination (aminotransferases, PLP-dependent): α-ketoglutarate + amino acid ↔ glutamate + α-keto acid. Also: glutamate → glutamine (N donor for purine/pyrimidine/histidine/arginine biosynthesis). At low NH₄⁺: GS-GOGAT; at high NH₄⁺: glutamate dehydrogenase (direct reductive amination).7. What is the role of ferredoxin in microbial metabolism? In how many different metabolic contexts can it function?
Hint / Guidance
Ferredoxin (Fd): small iron-sulfur protein (2Fe-2S or 4Fe-4S); very low reduction potential (E₀' ≈ -0.39V); shuttles electrons. Contexts: (1) Photosynthesis (PSI) — accepts electrons, reduces NADP⁺; (2) Nitrogen fixation — reduces nitrogenase; (3) Pyruvate:Fd oxidoreductase — replaces pyruvate dehydrogenase in anaerobes; (4) H₂ production (hydrogenase) — Fd re-oxidised by proton reduction; (5) Carbon fixation (Fd-dependent GOGAT, reverse TCA cycle); (6) Steroid/antibiotic biosynthesis (electron donor to cytochrome P450). Fd's extremely low E₀' makes it versatile reductant.2. The Energetics of Chemolithotrophy
Chemolithotrophs extract energy from inorganic electron donors — ammonia, nitrite, hydrogen sulfide, ferrous iron, or molecular hydrogen. While electron transport from these donors generates a proton-motive force and ATP, many donors have reduction potentials too positive to reduce NAD⁺ directly (E₀' = −0.32 V). Consequently, these organisms must drive reverse electron transport — spending PMF to push electrons thermodynamically 'uphill' to NADH — making them slow-growing but ecologically indispensable engineers of the nitrogen and sulfur cycles.
✏️ Fill in the Blank
1. The enzyme responsible for fixing atmospheric N₂ into ammonia is _______.
Show Answer
Nitrogenase2. In the Calvin cycle, the enzyme that catalyses the primary CO₂ fixation step (carboxylation of RuBP) is _______.
Show Answer
RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase)3. Bacteriorhodopsin is a light-driven _______ pump found in halophilic Archaea.
Show Answer
Proton🔘 Multiple Choice
1. Anoxygenic photosynthesis differs from oxygenic photosynthesis in that it:
Show Answer
Correct: B) Uses electron donors other than water and does not produce O₂2. Heterocysts in cyanobacteria are specialised cells that:
Show Answer
Correct: B) Provide a micro-anaerobic environment that protects nitrogenase from oxygen3. Chemolithotrophs like Nitrosomonas europaea oxidise ammonia as their energy source. What is the final electron acceptor in their respiratory chain?
Show Answer
Correct: C) O₂4. Green sulfur bacteria (Chlorobium) differ from purple sulfur bacteria in that they:
Show Answer
Correct: B) Have a type I reaction centre and large chlorosome antenna complexes enabling growth at very low light intensities5. Nitrogen fixation (N₂ → 2NH₃) requires substantial energy. Which of the following correctly represents the approximate ATP cost per N₂ fixed?
Show Answer
Correct: C) 16 ATP6. The Calvin cycle (reductive pentose phosphate cycle) requires both ATP and NADPH. In autotrophic bacteria growing without photosynthesis (e.g., Thiobacillus), these are generated by:
Show Answer
Correct: B) Oxidation of inorganic compounds via ETC and reverse electron transport7. In the Z-scheme of oxygenic photosynthesis, the ultimate source of electrons for NADP⁺ reduction is:
Show Answer
Correct: C) Water (H₂O)8. The biosynthesis of purines and pyrimidines begins with:
Show Answer
Correct: B) Ribose-5-phosphate (purines) or aspartate + carbamoyl phosphate (pyrimidines)9. The FASII bacterial fatty acid synthesis pathway differs from eukaryotic FAS in that:
Show Answer
Correct: B) Bacterial enzymes are separate dissociable proteins (type II FAS) making it a target for antibiotics💬 Open-Ended Questions
1. Explain how heterocysts in cyanobacteria allow N₂ fixation to occur in an aerobic environment. Include structural adaptations and metabolic exchange with vegetative cells.
Hint / Guidance
Heterocyst differentiation triggered by N-limitation. Structural: glycolipid + polysaccharide outer layer limits O₂ diffusion; absence of PS II eliminates internal O₂ source; elevated cytochrome oxidase respiration scavenges O₂. Metabolic exchange: vegetative cells supply sucrose → heterocyst; heterocyst exports glutamine (amide N) back. Non-heterocyst cyanobacteria (Trichodesmium) fix N₂ during low-photosynthesis periods when O₂ is low.2. Describe the Calvin cycle for CO₂ fixation. How many turns are required to produce one G3P, and what are the ATP and NADPH requirements?
Hint / Guidance
Three stages: (1) Carboxylation: RuBisCO catalyses CO₂ + RuBP → 2×3-PGA. (2) Reduction: 3-PGA + ATP → 1,3-bisphosphoglycerate; NADPH → G3P. (3) Regeneration: 5 G3P → 3 RuBP using 3 ATP. Net: 3 CO₂ per G3P. ATP cost: 9 ATP; NADPH cost: 6 NADPH per G3P. Glucose synthesis: 6 CO₂, 18 ATP, 12 NADPH.3. Purple non-sulfur bacteria (e.g., Rhodobacter sphaeroides) are metabolically versatile. List their different modes of energy metabolism and the conditions that favour each.
Hint / Guidance
(1) Photoautotrophy: light + CO₂ + H₂; anaerobic. (2) Photoheterotrophy: light + organic carbon; anaerobic; most common. (3) Aerobic dark respiration: darkness + O₂; BChl synthesis repressed. (4) Chemolithotrophy: H₂ oxidation; dark, microaerobic. O₂ represses photosynthetic genes (AppA/PpsR); light stimulates BChl synthesis anaerobically.4. Describe three alternative carbon fixation pathways used by bacteria other than the Calvin cycle. For each, state the organisms and key enzymes.
Hint / Guidance
(1) Reductive TCA cycle: CO₂ fixed via reverse TCA; ATP-citrate lyase key enzyme; Chlorobium, Thermoproteus. (2) 3-Hydroxypropionate bicycle: acetyl-CoA/propionyl-CoA carboxylase; Chloroflexus aurantiacus. (3) Wood-Ljungdahl pathway: CO₂ → CO (CODH) + CH₃-THF → acetyl-CoA; acetogens (Moorella), methanogens, sulfate-reducers. Wood-Ljungdahl most energy-efficient (net 1 ATP to fix 2 CO₂).5. Explain why photosynthetic organisms require both a light-dependent stage and a Calvin cycle. What would happen if only one stage existed?
Hint / Guidance
Light reactions: photons → ATP + NADPH. Calvin cycle: ATP + NADPH → CO₂ fixed into organic molecules. Without Calvin cycle: ATP/NADPH accumulate, ADP/NADP⁺ depleted → photosystems halt; no stable energy storage. Without light reactions: no ATP/NADPH; Calvin cycle cannot proceed; organism dies. Together: transient photon energy converted into stable chemical bonds.6. Explain how cyclic and non-cyclic photophosphorylation differ in terms of electron flow and the products generated.
Hint / Guidance
Non-cyclic (Z-scheme): electrons from H₂O → PSII (P680) → plastoquinone → cytb6f → plastocyanin → PSI (P700) → ferredoxin → NADP⁺ reductase → NADPH; products: NADPH + ATP (via PMF from cytb6f). Cyclic: electrons from PSI (P700) → ferredoxin → cytb6f → plastocyanin → back to PSI; no NADPH produced; generates only ATP; balances ATP/NADPH ratio. Cyclic is used when ATP demand exceeds NADPH demand (e.g., CO₂ fixation requires 3 ATP:2 NADPH per CO₂ — balanced by mix of both).7. Describe the biosynthesis of peptidoglycan and explain at which steps different antibiotic classes act.
Hint / Guidance
Steps: (1) Cytoplasm: UDP-GlcNAc + UDP-MurNAc synthesised; pentapeptide attached to MurNAc via Mur ligases; (2) Membrane: lipid I (MurNAc-pentapeptide + undecaprenyl-PP) then lipid II (+ GlcNAc) formed; (3) Flipped to periplasm by MurJ flippase; (4) Transglycosylation: strands polymerised; (5) Transpeptidation: cross-linking by PBPs. Antibiotic targets: Fosfomycin — inhibits MurA (step 1); D-cycloserine — inhibits D-Ala-D-Ala ligase; Bacitracin — inhibits undecaprenyl-PP recycling (step 2); Vancomycin — binds D-Ala-D-Ala terminus (block steps 4/5); β-lactams — acylate PBP transpeptidase (step 5).8. Explain how the type and amount of lipids in a bacterial membrane change in response to temperature, and what this means for membrane function (homeoviscous adaptation).