Why this mattersThis process IS the microalgae industry
Chloroplast · inputs and outputs
The engine of the industry
What photosynthesis actually is
Photosynthesis is the process by which algae (and plants) use the energy in sunlight to convert carbon dioxide and water into sugar — and release oxygen as a byproduct. It is the single most important biological process on Earth. It is also the engine that powers every commercial product in the microalgae industry.
Here is the full equation, which you are now equipped to read properly after Weeks 3–4:
The photosynthesis equation — fully readable
6 CO₂ + 6 H₂O + light energy → C₆H₁₂O₆ + 6 O₂
Carbon dioxide + Water + Sunlight → Glucose (sugar) + Oxygen released
Six carbon atoms from the air. Twelve hydrogen atoms and six oxygen atoms from water. Energy from sunlight to stick them together. The result: glucose — a six-carbon sugar, the cell's primary fuel — and six molecules of oxygen, expelled into the atmosphere as waste. The oxygen you are breathing right now is, in large part, the "exhaust" of photosynthesis.
But that equation, elegant as it is, hides enormous complexity inside the arrow. The real story — what actually happens step by step inside the chloroplast — is where the commercial insights live. That complexity is what we unpack over these three weeks.
The three-week structure
Week 5 covers the setting — the chloroplast, its anatomy, and how pigments capture light. Week 6 is the Light Reactions — what happens first, when sunlight hits. Week 7 is the Calvin Cycle — how CO₂ is turned into sugar, and how algae divert that sugar into fats and pigments worth thousands of dollars per kilogram.
Week 5 · Part 1 of 3
The chloroplast — anatomy of the solar factory
Photosynthesis does not happen in the whole cell. It happens inside a specific organelle — the chloroplast. You met it briefly in Week 1. Now we go inside it properly.
The chloroplast is enclosed by two membranes (an outer and an inner layer). Inside is a fluid called the stroma. Floating in the stroma are stacked, flattened membrane sacs called thylakoids — and where the thylakoids stack up like piles of coins, those stacks are called grana (singular: granum).
Chloroplast anatomy — where each phase of photosynthesis happens
Phase 1 location
Thylakoid membranes
This is where the Light Reactions happen. The thylakoid membrane is embedded with protein complexes that capture sunlight and use it to split water and generate energy carriers. The hollow space inside each thylakoid (the lumen) accumulates protons that drive energy production.
Phase 2 location
Stroma (the fluid)
This is where the Calvin Cycle happens. The stroma is a thick fluid containing enzymes — particularly RuBisCO, the most abundant protein on Earth — that use the energy from the Light Reactions to grab CO₂ from the air and build sugar molecules from it.
Pigments — how light is captured
Before sunlight can power chemistry, it must be absorbed. This is the job of pigments — coloured molecules embedded in the thylakoid membrane. Different pigments absorb different wavelengths (colours) of light. This is why algae can appear green, red, blue-green, or orange depending on which pigments dominate.
Chlorophyll a
Absorbs: Red + Blue light
The primary pigment. Present in all photosynthetic organisms. Reflects green — which is why almost all photosynthetic things look green. The core molecule that actually converts light energy into chemical energy.
Chlorophyll b
Absorbs: Blue + Orange light
The accessory chlorophyll. Expands the range of light the cell can use. Passes captured energy to chlorophyll a. Found mainly in green algae and plants.
Carotenoids
Absorbs: Blue + Green light
Includes beta-carotene, zeaxanthin, fucoxanthin. Accessory pigments — widen the light spectrum captured. Also protect the cell from excess light damage (photoprotection). Beta-carotene from Dunaliella: ~$300–800/kg.
Phycocyanin
Absorbs: Orange-red light
The brilliant blue pigment of Spirulina. A protein-pigment complex found only in cyanobacteria and red algae. Exceptionally effective at capturing light in the orange spectrum. Used as a natural blue food colourant: $500–1,500/kg.
Astaxanthin
Absorbs: Blue-green light
Technically a carotenoid, but its primary role in Haematococcus is photoprotection — a molecular sunscreen. Accumulated when light is too intense. The red colour visible when cultures are stressed. $2,000–5,000/kg.
The commercial insight hiding in pigments
Every pigment is simultaneously a photosynthesis tool and a potential commercial product. The cell makes these molecules to run its own energy system — but we harvest them as high-value ingredients. This is why understanding photosynthesis directly unlocks understanding of the most valuable products in the industry. Astaxanthin, phycocyanin, beta-carotene, fucoxanthin — all exist because algae need them to capture and manage light.
Week 6 · Part 2 of 3
The Light Reactions — capturing sunlight
Photosynthesis happens in two distinct stages. The first stage — the Light Reactions — happens in the thylakoid membranes and requires direct sunlight. The second stage — the Calvin Cycle — happens in the stroma and does not directly need light. Think of it as a two-department factory: the first department captures energy, the second department uses it.
⚡ Light Reactions (thylakoid membrane)
🔄 Calvin Cycle (stroma)
The Light Reactions are all about capturing energy from photons and converting it into two chemical "batteries" — NADPH and ATP — that the Calvin Cycle will spend. A precise sequence of four steps:
1
Light hits Photosystem II — water is split
Sunlight strikes a cluster of pigment molecules called Photosystem II (confusingly named — it acts first). The energy from the photon excites electrons to a higher energy state. The cell immediately replaces those lost electrons by splitting water molecules: H₂O → 2H⁺ + 2e⁻ + ½O₂. The oxygen is released as a gas — this is where the oxygen in air comes from.
Analogy: sunlight charges a battery. To recharge the battery, the cell breaks apart water and steals its electrons. The leftover oxygen is exhaust.
The excited electrons from Photosystem II pass through a series of protein complexes embedded in the thylakoid membrane — the electron transport chain. As electrons move "downhill" from one protein to the next, they release energy at each step. This energy is used to pump protons (H⁺) from the stroma into the thylakoid interior, creating a concentration gradient — more protons inside than outside.
Analogy: like water building up behind a dam. The proton gradient is stored potential energy, ready to be released when the dam opens.
Output: Proton gradient across thylakoid membrane
3
ATP synthase — the spinning turbine makes ATP
The protons rush back from inside the thylakoid to the stroma through a protein called ATP synthase — the cell's molecular turbine. The flow of protons physically spins part of the protein, and that rotation drives the assembly of ATP (adenosine triphosphate) from ADP and a phosphate group. ATP is the universal energy currency of the cell — a charged battery that the Calvin Cycle will spend.
Analogy: the proton gradient is the water behind the dam. ATP synthase is the turbine. The spinning produces electricity — except in biology, "electricity" is ATP.
Output: ATP — the cell's energy currency ⚡
4
Photosystem I — electrons are re-energised, NADPH is made
After passing through the electron transport chain, the electrons (now lower energy) reach Photosystem I. A second hit of sunlight re-energises them. These re-excited electrons are then used to reduce NADP⁺ into NADPH — a second charged molecule that carries high-energy electrons. NADPH is the other "battery" the Calvin Cycle needs. Together, ATP and NADPH are the complete output of the Light Reactions.
Analogy: NADPH is a charged power pack — it carries high-energy electrons that will be used to "glue" carbon atoms together in the next stage.
Output: NADPH — the electron carrier 🔋
Summary of Light Reactions
Inputs: Sunlight + Water + NADP⁺ + ADP Outputs: O₂ (released to air) + ATP (energy currency) + NADPH (electron carrier)
The Light Reactions produce no sugar. They only produce the energy carriers that will be used to make sugar in the Calvin Cycle. Think of them as the power plant supplying electricity to the manufacturing floor.
The Calvin Cycle happens in the stroma — the fluid inside the chloroplast. It uses the ATP and NADPH produced by the Light Reactions to fix CO₂ from the air into sugar. It runs continuously as long as ATP and NADPH are available. Three phases, cycling round and round:
1
Carbon fixation — CO₂ is grabbed from the air
An enzyme called RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) — the most abundant protein on Earth, found in every plant and algae — grabs a CO₂ molecule from the surrounding air and attaches it to a 5-carbon molecule already inside the cycle (RuBP). This creates an unstable 6-carbon compound that immediately splits into two 3-carbon molecules called 3-PGA. This step is called "carbon fixation" — atmospheric CO₂ is now chemically locked into the cell's organic chemistry for the first time.
Analogy: RuBisCO is a molecular fishing hook that grabs invisible CO₂ out of the air and reels it into the cell's chemistry permanently.
CO₂ + RuBP (5C) → 2× 3-PGA (3C each) · RuBisCO is the enzyme
2
Reduction — ATP and NADPH power the build
The two 3-PGA molecules are now "reduced" — meaning electrons (from NADPH) and energy (from ATP) are used to transform them into a higher-energy 3-carbon molecule called G3P (glyceraldehyde-3-phosphate). G3P is the first true sugar — a 3-carbon carbohydrate. This step directly consumes the ATP and NADPH generated in the Light Reactions. This is the moment that light energy becomes chemical energy locked in a sugar molecule.
Analogy: ATP and NADPH are the tools and power. RuBisCO caught the carbon; now these tools shape it into something useful — like rough stone being carved into a finished brick.
Output: G3P — glyceraldehyde-3-phosphate — the first sugar 🍬
3
Regeneration — RuBP is rebuilt to keep the cycle going
Most of the G3P molecules produced are not used to make glucose immediately. Most are used to regenerate RuBP — the 5-carbon CO₂ acceptor that started the cycle. This requires more ATP. By regenerating RuBP, the cycle can keep running, continuously pulling CO₂ from the air. For every 3 CO₂ molecules fixed, one G3P is the net gain — which can be used to build glucose and other molecules. Two G3P molecules combine to make one glucose (C₆H₁₂O₆).
Analogy: the cycle is a factory assembly line that rebuilds its own tools on every pass. Most of the product goes back into keeping the line running; only the surplus is sent to the warehouse as finished goods.
Net: 1 glucose from 6 turns of the cycle · 6 CO₂ fixed · 18 ATP + 12 NADPH consumed
The Calvin Cycle is the manufacturing floor. The Light Reactions are the power plant. One cannot run without the other. Together, they convert atmospheric carbon into biological molecules — which is the foundation of every product on your microalgae commercial map.
Week 7 · Part 3 of 3
From sugar to everything — the commercial connections
Glucose is not the end of the story. It is the beginning of the industry. The cell takes that glucose and uses it as raw material to build everything else — fats, proteins, pigments, and the complex molecules that make microalgae commercially remarkable. Understanding this routing is what makes you a sophisticated observer of the algae industry.
How glucose becomes every commercial product — the metabolic routing map
The stress trigger — how producers hijack the cell's response
Under normal, comfortable growing conditions, algae prioritise growth — they make more cells. They use glucose to build proteins (for enzymes and structure) and nucleic acids (for DNA when dividing). Lipid and pigment production is modest.
But under stress — too much light, not enough nitrogen, salinity changes, temperature extremes — the cell shifts its priorities dramatically. It can no longer divide rapidly, so it stops investing in growth. Instead, it builds up reserves and protective molecules:
Haematococcus pluvialis
Eukaryote · Green alga
Normal: ~1–5% astaxanthin
Stressed: ~3–5% (up to 7%)
Trigger: High light + N starvation
Astaxanthin ~$3,500/kg
Nannochloropsis sp.
Eukaryote · Microalga
Normal: ~15% EPA
Stressed: ~30–40% total lipid
Trigger: N starvation + high light
EPA omega-3 ~$100–300/kg
Dunaliella salina
Eukaryote · Halophyte
Normal: ~0.2% β-carotene
Stressed: up to 10% of dry weight
Trigger: High salinity + intense sun
β-Carotene ~$300–800/kg
Spirulina platensis
Prokaryote · Cyanobacterium
Normal: ~60–70% protein
Optimal: Maximum growth, no stress
Trigger: Comfortable conditions
Protein + Phycocyanin
Schizochytrium sp.
Eukaryote · Thraustochytrid
Mode: Heterotrophic (no light)
DHA: ~35–50% of oil
Trigger: Sugar feed in fermenter
DHA ~$100–200/kg
The three levers producers control
Commercial algae producers are essentially manipulating three variables of photosynthesis to push cells toward producing more of the target molecule:
☀️
Light intensity
Too little: slow photosynthesis, low productivity. Too much: photoinhibition (damages the photosystems), triggers stress pigments. Optimal range is species-specific. Getting this right is the primary engineering challenge of outdoor ponds.
Haematococcus: high light → astaxanthin trigger
💨
CO₂ supply
Atmospheric CO₂ (~0.04%) is often the limiting factor for fast-growing algae. Injecting CO₂ — sometimes from industrial flue gas — dramatically increases photosynthetic rate and productivity. This is why algae can be used for carbon capture: they actively consume CO₂ as food.
Optimal: 1–5% CO₂ in air supply
🌡️
Temperature
Enzyme reactions (especially RuBisCO in the Calvin Cycle) have an optimal temperature range — typically 20–35°C for most commercial species. Below: enzymes are sluggish. Above: they denature. Temperature stress also triggers lipid remodelling — cells change fatty acid composition.
Most species: 20–30°C optimum
🧪
Nitrogen availability
Nitrogen is needed to make protein (and chlorophyll, which contains N). Deplete nitrogen and the cell cannot grow — but it keeps running photosynthesis, diverting glucose into lipids and protective pigments. The classic two-phase strategy: grow fast in full N, then starve to accumulate product.
N-starvation → lipid/pigment accumulation
🫧
Mixing and gas exchange
Algae cells near the surface get too much light; cells at the bottom get too little. Good mixing cycles cells through the light gradient. It also removes O₂ (which inhibits photosynthesis at high concentrations) and replenishes CO₂. Mixing design is central to reactor engineering.
Key for productivity and O₂ removal
🔬
Genetic engineering
Modifying the genes for specific enzymes in the metabolic routing map. Overexpress the gene for a key enzyme in astaxanthin synthesis → more astaxanthin without stress. Knock out genes for competing pathways → more product diverted to the target molecule. CRISPR is making this faster and cheaper.
Phase 3 topic — the future of the field
The master insight of weeks 5–7
Photosynthesis is not just one process — it is two linked stages, each with distinct inputs, outputs, and locations within the chloroplast. The Light Reactions harvest solar energy; the Calvin Cycle fixes carbon into sugar. Everything the algae industry sells is downstream of that sugar: lipids, proteins, pigments, and pharmaceuticals are all metabolic derivatives of glucose. Controlling photosynthesis — its rate, its duration, and where the cell routes its glucose — is the core technical act of commercial algae production. Every cultivation decision, every bioreactor design choice, every genetic engineering target ultimately traces back to manipulating this single process.
Quick-reference summary
Concept
Definition
Commercial relevance
Light Reactions
Stage 1: sunlight splits water, makes ATP + NADPH, releases O₂. Happens in thylakoid membrane.
O₂ released is half Earth's atmospheric oxygen. ATP/NADPH power all downstream biosynthesis.
Calvin Cycle
Stage 2: CO₂ fixed by RuBisCO into G3P (sugar) using ATP + NADPH. Happens in stroma.
Fixes atmospheric CO₂ into carbon chains that become every commercial product.
ATP
Adenosine triphosphate — the cell's universal energy currency. Made by ATP synthase spinning on a proton gradient.
Powers every biosynthetic reaction — making protein, fat, pigment all cost ATP.
RuBisCO
The enzyme that grabs CO₂ from air. Most abundant protein on Earth. Slow but essential.
Rate-limiting step for algae productivity. Engineering faster RuBisCO is a major research goal.
Pigments
Light-absorbing molecules in thylakoids: chlorophylls, carotenoids, phycocyanin. Each absorbs specific wavelengths.
Pigments themselves are the highest-value products: astaxanthin, phycocyanin, beta-carotene, fucoxanthin.
Stress response
Under N-starvation or high light, algae divert glucose to lipids and protective pigments instead of growth.
Carotenoids (esp. astaxanthin) protect cells from excess light by dissipating energy as heat.
Explains why Haematococcus turns red under stress — the astaxanthin accumulation is visible and harvest-signalling.
Self-check — end of week 7
These questions require connecting photosynthesis biology to commercial reasoning. Attempt each before revealing.
1. A producer wants to maximise astaxanthin yield from Haematococcus. They run the culture in two phases. What does phase 1 optimise for, and what does phase 2 optimise for — and why must they be separate?
Phase 1 (growth phase): optimise for maximum cell division. High nitrogen, ideal light, ideal CO₂ and temperature. The Calvin Cycle is running fast, glucose goes into protein and DNA for rapid reproduction. Astaxanthin is low, but cell numbers are high. Phase 2 (stress phase): nitrogen is cut off, light intensity is raised. Cells can no longer divide — they have no nitrogen for protein synthesis. But photosynthesis continues. The glucose surplus is diverted into astaxanthin (a lipid-based carotenoid) as a photoprotectant against the high light. Astaxanthin accumulates rapidly. They must be separate because the stress that triggers astaxanthin production also stops growth — you cannot have both simultaneously. You build your cell population first, then stress them all at once to maximise total astaxanthin output from the large biomass.
2. CO₂ is a greenhouse gas that causes climate change. Yet microalgae companies sometimes claim their algae "capture" CO₂. Explain in photosynthesis terms whether this claim is valid — and what condition must be true for it to represent a genuine net capture.
The claim is mechanistically valid: RuBisCO in the Calvin Cycle physically grabs CO₂ from the surrounding environment and incorporates it into sugar molecules. The carbon is then "fixed" inside the algae's biomolecules. If that biomass is then sold as food, nutraceuticals, or materials — and the product's carbon is not immediately released back as CO₂ (e.g. by burning) — then there is a genuine net capture over the lifetime of the product. However, if the algae are used to make biodiesel which is burned, the CO₂ is immediately re-released. The production process also uses energy — if that energy is fossil-fuel derived, the net CO₂ balance may be neutral or even positive. True net capture requires: renewable energy for cultivation + long-lived product (food/materials, not fuel) + the CO₂ source being atmospheric or from otherwise-emitted industrial exhaust. This is what a proper life-cycle analysis (Phase 4 of this curriculum) measures.
3. Schizochytrium produces DHA without any light at all — it grows in fermenters on sugar in complete darkness. Does it perform photosynthesis? Where does its DHA come from?
No — Schizochytrium is heterotrophic, meaning it gets its energy and carbon from an external organic source (glucose fed in the fermenter), not from sunlight. It does not perform photosynthesis. It makes DHA through fatty acid synthesis pathways powered by the energy it extracts from glucose via cellular respiration (in its mitochondria). The metabolic routing is the same — glucose → lipid synthesis — but the glucose comes from outside (fed sugar) rather than from CO₂ fixed by photosynthesis. This is actually a commercial advantage: fermenters are cheap and controllable, you avoid the light engineering challenges of photobioreactors, and you can achieve very high cell densities. The trade-off: you need to buy or make glucose feedstock, which has its own cost and carbon footprint. Most of the world's infant formula DHA (e.g. life'sDHA by DSM) comes from Schizochytrium grown this way.
4. O₂ at high concentrations actually inhibits photosynthesis — called photooxidative inhibition. Why would this be a problem in a sealed photobioreactor but not in an open pond?
In an open raceway pond, O₂ produced by photosynthesis diffuses freely into the surrounding atmosphere — the gas exchange is unrestricted, so O₂ never builds up to inhibitory levels. In a sealed photobioreactor (tubular or flat-panel), the culture is enclosed and O₂ has nowhere to escape. As algae photosynthesize, O₂ accumulates inside the reactor. At high concentrations, O₂ competes with CO₂ at the RuBisCO enzyme (a reaction called photorespiration), reducing the efficiency of carbon fixation. It also generates reactive oxygen species that damage the photosystems. This is why photobioreactor design must include effective gas stripping — bubbling gas through the culture or using degassing columns to physically remove O₂. O₂ accumulation is one of the primary engineering problems of closed bioreactor systems and is a major contributor to their higher cost versus open ponds.
5. The planet Venus has CO₂ in its atmosphere. Mars has CO₂ and water ice. Could photosynthesis theoretically work there — and if you were designing an algae-based life support system for a Mars mission, what would you need to engineer?
The raw inputs for photosynthesis — CO₂, H₂O, and light — do technically exist on Mars. CO₂ is 95% of the Martian atmosphere. Water ice exists. Sunlight reaches the surface (at about 43% the intensity of Earth). So in principle the inputs are present. The engineering challenges are severe: (1) Light: Mars receives less than half Earth's solar intensity — algae would need to be optimised for low-light photosynthesis, or artificial lighting would supplement. (2) Temperature: Mars surface averages −60°C, far below any known photosynthetic optimum. Cold-adapted (psychrophilic) strains would be needed, or the habitat must be heated. (3) Pressure: Mars atmospheric pressure is less than 1% of Earth's — algae must be grown in a pressurised enclosure. (4) CO₂ concentration: the 95% CO₂ atmosphere would actually be too high (toxic at those concentrations) — it would need to be diluted. (5) UV radiation: Mars has no ozone layer — UV would destroy unprotected cells. This is exactly what NASA and ESA are researching in projects like MELiSSA — you will cover this in Phase 5.
Coming up — Week 8–9
How cells eat and produce energy — cellular respiration
Photosynthesis makes sugar. Cellular respiration burns it. Understanding both processes — and how algae balance them — explains why cultivation conditions at night matter, why temperature at night affects productivity, and how the cell's energy economy works as a complete system.