Across the chain · topic 3 of 5
Science
The chemistry, biology and physics behind coffee: what happens inside the fruit, the seed and the cup, and how we know.
- PlantCoffee cherry anatomyThe layers of the coffee fruit, from the outer skin to the seed, and why each one matters for processing.Source-checked
- PlantSeed anatomy and storageThe coffee seed as a living seed – embryo, endosperm and silverskin inside the parchment – and why it survives partial drying but not cold storage when dry, so coffee diversity is kept in field genebanks.Source-checked
- PlantGermination and seedlingsHow a coffee seed takes up water, weakens the endosperm in front of its root, pushes out a radicle and lifts its seed leaves above the soil – and why this takes weeks rather than days.Source-checked
- PlantFlowering and pollinationHow the coffee plant forms flower buds, why they wait for rain after a dry spell, how long a flower lasts, and how arabica pollinates itself while canephora needs pollen from another plant – and what bees add.Source-checked
- PlantFruit developmentHow a fertilised coffee flower becomes a ripe cherry – the growth phases, how long each species takes, why the fruit turns red or yellow, and when the size of the bean is decided.Source-checked
- PlantPeaberries and bean shapesMost coffee fruits hold two flat-sided seeds, but some hold one round seed (a peaberry), three seeds or two seeds locked in one shell. What causes each shape, how often it occurs and how it is sorted.Source-checked
- PlantThe coffee genus (Coffea)Coffea is a genus of 133 known wild species in Africa, Madagascar, Asia and Australasia. Two of them make almost all the world’s coffee, and most of the rest are threatened.Source-checked
- PlantArabica and robusta comparedHow the two commercial coffee species differ as plants, in their climate needs, in the shape of the bean and in what the seed holds, and how a laboratory tells them apart in green coffee, roast coffee and blends.Source-checked
- PlantEugenioides, arabica’s other parentA wild coffee species of the East African highlands and one of the two parents of arabica, the one that passed on its plastids. In one study its seeds held about a fifth of the caffeine of canephora.Source-checked
- PlantStenophylla and other wild relativesWild coffee species beyond arabica and robusta, such as stenophylla and two East African species, carry heat tolerance and distinct flavours that breeders may need. Most wild species are threatened, and many are held in no genebank.Source-checked
- PlantPolyploidy and the arabica genomeArabica coffee carries the full chromosome sets of two species, Coffea canephora and Coffea eugenioides. This double genome explains why arabica pollinates itself, how it is inherited and why its age is hard to date.Source-checked
- PlantThe arabica bottleneckCultivated arabica is one of the least genetically diverse crops. How a single hybrid origin, self-pollination and a few founding plants narrowed it, and what that means for disease and breeding.Source-checked
- PlantThe Timor HybridA natural cross of arabica and robusta found on the island of Timor. It carries robusta genes against coffee leaf rust and is the parent of the Catimor and Sarchimor groups of varieties.Source-checked
- PlantF1 hybridsFirst-generation crosses between genetically distant arabica parents, often a cultivated line and a wild Ethiopian accession. They outyield pure lines, but their seed does not breed true, so most are cloned.Source-checked
- PlantBranching and fruiting woodHow a coffee plant is built – one upright stem, pairs of horizontal side branches – and why its flowers and fruit form on young wood, so that the crop moves up and out every year.Source-checked
- FarmShade and agroforestryWhy coffee is grown under trees or in full sun, how shade is measured, and what shade trees change for microclimate, yield, bean size, pests, water and biodiversity.Source-checked
- FarmCoffee leaf rustThe fungal disease that strips coffee trees of their leaves. How Hemileia vastatrix infects, why it spread from Ceylon to Hawaii, how resistance genes and races interact, and how producers control it.Source-checked
- FarmCoffee berry diseaseThe fungal disease that attacks green arabica berries on the tree. How Colletotrichum kahawae infects, why wet highlands in Africa suffer most, how resistant varieties were bred, and why other regions guard against it.Source-checked
- FarmCoffee berry borerThe small beetle that breeds inside the coffee seed. How Hypothenemus hampei lives and spreads, why warming lifts it to higher farms, what it does to weight and grade, and how producers and mills keep it down.Source-checked
- ProcessAnaerobic fermentationFermenting whole cherries or pulped coffee in closed, oxygen-poor vessels before drying. It changes the acids, alcohols and aroma of the coffee, and it carries its own risks for the seed and the cup.Source-checked
- ProcessStarter cultures and co-fermentationSteering coffee fermentation by adding selected yeasts or bacteria, or by fermenting the coffee with fruit, spices or other ingredients – how strains are chosen, what trials found, and what competition rules allow.Source-checked
- ProcessMucilageThe sticky, pectin-rich inner layer of the coffee fruit that clings to the parchment – removed in washed coffee, kept in honey and pulped-natural coffee, and the main food for fermentation.Source-checked
- ProcessMicroorganisms in coffee processingThe bacteria, yeasts and moulds that grow on coffee cherries and seeds after harvest, what each group does, and how processing method, place and starter cultures shape them.Source-checked
- ProcessMoisture and water activityHow much water a coffee seed holds (moisture content) and how freely that water can act (water activity) – the two numbers that decide when coffee is dry, safe from mould and stable in storage.Source-checked
- ProcessThe living seed during processingThe coffee seed is still alive when it is picked. Processing switches on germination and drought-stress metabolism inside it, and heat or storage can kill it – changes that leave traces in green coffee chemistry and quality.Source-checked
- ProcessCherry-to-green conversionHow much green coffee a harvest gives – the mass lost at each step from fresh cherry to green coffee, the moisture behind it, and the conversion factors producers and traders use to calculate it.Source-checked
- ProcessOchratoxin AOchratoxin A (OTA) is a mould toxin that can form in coffee on the farm, during drying and in storage. This entry covers the moulds that make it, where it forms, how roasting and brewing change it, how it is tested and the EU limits.Source-checked
- RoastRoastingDry heat that turns dense, green coffee seeds into brittle, porous, brown beans – forming aroma, taste and colour, driving off water and building up carbon dioxide.Source-checked
- RoastGreen coffee compositionWhat green coffee is made of – carbohydrates, proteins and amino acids, lipids, acids, alkaloids, minerals and water – how arabica and robusta differ, and which constituents the roast turns into flavour and colour.Source-checked
- RoastPreheating and chargeThe first step of a roast – heating the empty roaster to a steady state, then charging the green coffee. What charge temperature means, why the probe reading drops to a turning point, and what studies show.Source-checked
- RoastDrying phaseThe first stage of a roast, from charge to the visible yellowing of the beans – water heats up and evaporates, the bean starts to swell, and much of the heat goes into warming and evaporating that water.Source-checked
- RoastBrowning phaseThe stretch of a roast between yellowing and first crack, often called the Maillard phase – when the bean darkens fastest, loses most of its sucrose, forms new acids and aroma, and builds up the gas that ends in first crack.Source-checked
- RoastFirst crackThe first audible cracking of the beans during a roast – what breaks inside the bean, how it sounds, which temperatures are reported, whether heat is released, and why roasters time development and roast degree from it.Source-checked
- RoastDevelopment timeThe time from first crack to the end of the roast – how it is measured, what the development time ratio is, and what studies found when only this phase was changed at the same roast colour.Source-checked
- RoastSecond crackThe second, snapping series of cracks heard when a roast is taken dark – what breaks in the bean, why oil reaches the surface, how flavour and chemistry change, and the smoke and gas that come with it.Source-checked
- RoastRoast profilesThe time–temperature curve of a roast – what the probes really measure, how rate of rise, turning point, first crack and development time are read, how roasters steer the curve, and what research says about profiles and flavour.Source-checked
- RoastRate of riseHow fast the bean-probe temperature climbs during a roast – how software calculates it, why it usually falls, why it describes the probe as much as the beans, and what studies have measured.Source-checked
- RoastTurning pointThe lowest bean-probe reading after the charge, where the curve stops falling and starts to climb. Why it is a feature of the probe rather than the beans, what moves it, and what it can and cannot tell a roaster.Source-checked
- RoastHeat transferHow heat moves from the burner to the bean and into it – conduction, convection and radiation in a roaster, how roaster designs shift the balance, and why the slow flow of heat inside the bean matters for even roasting.Source-checked
- RoastGlass–rubber transitionHow the material of the coffee bean switches between a rigid, glassy state and a soft, rubbery one, how water and heat drive the change, and what it means for swelling in the roaster, grinding and storage.Source-checked
- RoastPorosity and cell structureHow roasting turns the dense, thick-walled cells of green coffee into a swollen, porous structure – and why those pores decide how a bean holds gas, sweats oil, grinds and extracts.Source-checked
- RoastWater in roastingWhere the water in a roast comes from and where it goes – the green coffee's own moisture, water formed by reactions, the heat needed to evaporate it, the steam that swells the bean, and the little that is left at the end.Source-checked
- RoastEndothermic and exothermic phasesWhy a roast first soaks up heat and later starts to release heat of its own – what calorimetry and models show, why nobody agrees where the switch happens, and what it means for heat control and cooling.Source-checked
- RoastBean size and densityHow large and how dense green coffee beans are, how both are measured, and what they mean for roasting – heat uptake, evenness, and the swelling that lowers density as the roast goes on.Source-checked
- RoastMaillard reactionThe chain of reactions between sugars and amino acids that browns roasting coffee and forms much of its aroma – running through the whole roast, at rates that change with temperature, time and roast degree.Source-checked
- RoastStrecker degradationA branch of the Maillard network in which amino acids react with sugar-derived dicarbonyls during roasting, giving malty, potato-like and honey-like aldehydes, carbon dioxide and building blocks for pyrazines.Source-checked
- RoastCaramelisationThe breakdown of sugars by heat alone, without amino acids. In roasting coffee it runs alongside the Maillard reaction, shares many of its products, and leaves almost no sugar behind.Source-checked
- RoastChlorogenic acidsThe family of phenolic acids that makes up a large share of green coffee – how roasting breaks them down into bitter lactones, phenols and melanoidin material, and why their loss tracks roast degree.Source-checked
- RoastMelanoidinsThe brown, high-molecular-weight compounds that form late in roasting and give roasted coffee its colour – built on polysaccharides and protein, with chlorogenic acids worked in, and still without a known structure.Source-checked
- RoastAcids in coffeeThe acids behind coffee's sourness – which ones the green bean brings, which form or break down during roasting, how acidity is measured, and why the cup's acidity is not the taste of any single acid.Source-checked
- RoastCaffeine and roast degreeWhether light or dark roasts hold more caffeine – what roasting does to caffeine in the bean, why the answer depends on counting per bean, per gram or per scoop, and what reaches the cup.Source-checked
- RoastCarbohydrates and bodyHalf of green coffee is carbohydrate, mostly cell-wall polysaccharides. Roasting burns off the sugar and breaks part of the polysaccharides down; what dissolves helps shape viscosity, crema and, by most accounts, body.Source-checked
- RoastCoffee oilThe fat of the coffee bean – what it is made of, where it sits in the cell, why it reaches the surface of dark and ageing beans, how much of it ends up in each brew, and how its oxidation makes coffee stale.Source-checked
- RoastRoast gases and CO₂The gases a coffee bean forms while it roasts – mostly carbon dioxide, plus water vapour, carbon monoxide and aroma compounds – which reactions make them, how much leaves in the roaster and how much stays trapped.Source-checked
- RoastRoasting contaminantsUnwanted compounds that form in coffee during roasting – acrylamide, furan and methylfurans, and traces of polycyclic aromatic hydrocarbons – how roast degree shifts them and what food authorities say and require.Source-checked
- RoastRoast degree and colourHow far a coffee has been roasted, and how it is measured – mostly as colour, by reflected light on ground coffee – with the scales in use, why they do not convert, and what colour does and does not tell.Source-checked
- RoastRoast lossThe weight green coffee loses in the roaster, as a share of its starting weight – mostly water, plus carbon dioxide, other volatiles and chaff. A roast-degree index next to colour, and the step from green to roasted cost.Source-checked
- RoastRoast defectsFlaws the roast itself puts into coffee – underdeveloped, baked, over-roasted, scorched, tipped, faced, cratered or uneven beans – how each looks, what causes it in the roaster, how it affects flavour and how to catch it.Source-checked
- RoastDrum roastersThe most widespread batch coffee roaster – a heated, rotating drum through which hot air is drawn. How it is built, how heat reaches the beans, what the burner, airflow and drum speed controls do, and how batch size changes bean motion.Source-checked
- RoastFluid-bed roastersHot-air roasters with no moving parts in the roasting chamber – a stream of hot air lifts, mixes and heats the beans, mainly by convection. Common in research, in sample roasting and in some industrial designs.Source-checked
- RoastFreshness and storageWhat happens to roasted coffee, whole and ground, between the roaster and the cup – gas loss, aroma loss and oxidation – what speeds it up, and how roasteries, cafés and homes slow it down.Source-checked
- RoastDegassingThe gas that roasting traps inside coffee – mostly carbon dioxide, with some carbon monoxide – where it is held, how it escapes by flow and diffusion, what speeds it up, how it is measured, and what it means for packing, brewing and safety.Source-checked
- RoastDecaffeinationHow caffeine is taken out of green coffee before roasting – with organic solvents, water or carbon dioxide – what else leaves the bean, what the law calls decaffeinated, and how decaf roasts differently.Source-checked
- BrewWhat extraction isHow water takes coffee out of the grounds – what dissolves and what is only carried along, how broken and intact cells give up their contents, and why the brew changes as extraction goes on.Source-checked
- BrewExtraction yield and TDSHow strong a coffee is (total dissolved solids) and how much of the grounds ended up in it (extraction yield) – the two numbers behind the brewing control chart, how to measure them and what they say about flavour.Source-checked
- BrewExtraction variablesThe settings a brewer controls – grind, contact time, flow, temperature, ratio, pressure, the coffee and the water – what each does to extraction yield and strength, and how they interact.Source-checked
- BrewCO₂ and the bloomWhat happens to the carbon dioxide left in ground coffee when hot water reaches it – the bloom in filter brewing and the crema on espresso – how much gas remains at brewing time, and what is known about its effect on extraction.Source-checked
- BrewBrew temperatureHow hot the water is when it meets the coffee – the ranges that standards specify, what heat does to the speed and end point of extraction, where heat is lost, and why water boils below 100 °C at altitude.Source-checked
- BrewBrew ratio and strengthHow much coffee is used for how much water, how that ratio is written, and how it sets the strength of the cup – with the published specifications and what sensory studies say about strength and liking.Source-checked
- BrewBrewing control chartThe chart that plots brew strength against extraction yield, with brew ratios as diagonal lines and target boxes for filter coffee – where it came from, which targets exist and what sensory research since 2020 has found.Source-checked
- BrewWater for coffeeWhy brewing water matters, where its minerals come from, how hardness and alkalinity shape flavour and machines, which targets are published, and how water is measured and treated.Source-checked
- BrewHardness and alkalinityWhat total, carbonate and non-carbonate hardness and alkalinity mean, how the carbonate system ties them to pH, how alkalinity buffers coffee acids, and how both values are measured and reported.Source-checked
- BrewWater minerals and flavourWhat studies have measured about how the minerals in brewing water change coffee – alkalinity lowers perceived acidity, while the effects of hardness, magnesium and sodium are smaller or unsettled.Source-checked
- BrewMeasuring waterHow to find out what is in your brewing water – drop tests for hardness and alkalinity, conductivity meters, chlorine tests, water reports and bottle labels – and what each method can and cannot tell you.Source-checked
- BrewWater treatmentHow filters, ion exchangers, reverse osmosis and added salts change brewing water – what each removes or adds, which suits which tap water, and how to keep a treatment system clean and working.Source-checked
- BrewGrindingWhy roasted coffee is ground before brewing – it breaks open cells and shortens the paths that solubles must travel – and what grind size, freshness, heat, moisture and static change in the cup.Source-checked
- BrewGrinder types and burrsHow coffee grinders break beans – blades, conical burrs, flat burrs and industrial roller mills – and how the shape, gap, wear and temperature of the grinding parts change particle sizes, fines, heat and retention.Source-checked
- BrewParticle size and finesGround coffee is a mix of sizes, usually with two peaks – small cell fragments called fines and much larger particles. This spread shapes how fast coffee extracts and how easily water flows through the bed.Source-checked
- BrewPour-over and immersionHow the main non-espresso brew methods work – percolation, where fresh water flows through the grounds, and immersion, where all the water steeps with all the coffee – and what each device changes.Source-checked
- BrewPour-over techniqueHow a manual pour-over works step by step – ratio, grind, water temperature, bloom, pouring and drawdown – how filter and dripper shape change the cup, and how to adjust the grind, with published example values.Source-checked
- BrewCold brewCoffee extracted with water at room temperature or colder over hours instead of minutes – how immersion and slow-drip methods work, what low temperature changes in the cup, and how cold brew is kept safe.Source-checked
- BrewMoka potA stove-top coffee maker in which heated air and vapour in a closed lower chamber push water up through a bed of ground coffee into an upper chamber, at far lower pressure than an espresso machine.Source-checked
- BrewEspressoA small, concentrated coffee made by forcing hot water at high pressure through a compacted bed of ground coffee. It carries dissolved solids, oil droplets, fine particles and a foam, the crema.Source-checked
- BrewHow an espresso machine worksAn espresso machine heats water, pressurises it to about 9 bar, spreads it over a compacted bed of fine coffee and ends the shot. The entry covers how pumps, boilers, groups and levers do these jobs and how the coffee bed resists the water.Source-checked
- BrewEspresso recipes and ratiosHow an espresso recipe is written – dose, beverage mass, ratio, time, temperature and pressure – what each setting does to strength, extraction and flavour, and how baristas calculate and adjust a shot.Source-checked
- BrewPuck preparationHow ground coffee is dosed, distributed and tamped into an espresso basket. The aim is an even bed, so that water passes through all of it instead of channelling through a few paths.Source-checked
- CupHow we taste coffeeHow taste, smell by two routes, and touch combine into the single impression we call flavour – and why cuppers smell, slurp and wait in a fixed order, and why people perceive the same cup differently.Source-checked
- CupThe aroma of coffeeMore than a thousand volatile compounds have been found in roasted coffee, yet a few dozen key odorants carry its smell. How they form in roasting, how they are lost, and how chemists find them with the human nose.Source-checked
- CupBody and mouthfeelHow coffee feels in the mouth – thickness, oiliness, smoothness, grit and the drying sensation of astringency – what in the cup causes it, how brew method and filter change it, and how cuppers and laboratories measure it.Source-checked
- CupCrossmodal effectsHow one sense changes what another reports – why the colour, shape and feel of a cup, a label, a sound or a smell can shift how sweet, sour or good the same coffee seems, and why cuppers taste blind.Source-checked
- CupFlavour languageHow the coffee trade puts flavour into words – the World Coffee Research Sensory Lexicon, the Coffee Taster’s Flavor Wheel built from it, and the tick lists of the SCA cupping form – and where shared words fall short.Source-checked
- CupCuppingThe coffee trade’s standard tasting method – coffee steeped in bowls, smelled, slurped and judged – and how the SCA’s 2024 Coffee Value Assessment separates describing a coffee from scoring it.Source-checked
- CupSensory science methodsHow sensory scientists test coffee beyond cupping – difference tests such as the triangle test, trained descriptive panels, consumer liking scales, and the coding, serving order and statistics that make results trustworthy.Source-checked
- CupCaffeineThe bitter purine alkaloid that makes coffee stimulating – where it sits in the plant, how much reaches the cup and why that varies so much, what it does in the body, how it is broken down, and the official safe-intake advice.Source-checked
- CupWhat’s in a cup of coffeeA cup of black coffee is almost all water. The rest – about 1–2% in filter coffee – holds caffeine, chlorogenic acids, melanoidins, minerals and traces of niacin. What the published figures say per cup, and what they mean.Source-checked
- CupBioactive compoundsCaffeine, chlorogenic acids, trigonelline, diterpenes, melanoidins and minerals in a cup of coffee – how much a cup holds, where the body takes them up, and what has been measured in people.Source-checked
- CupCoffee and digestionWhat studies show about coffee and the digestive tract – stomach acid, reflux, the gallbladder, the colon and gut microbes – which effects were measured in people, which are associations, and what “low-acid” claims measure.Source-checked
- CupContaminants and food safetyThe food-safety picture of coffee from farm to cup – mould toxins, pesticide residues, roasting contaminants, metals from machines, microbes in cold brew and fraud – and the limits EU and Swiss food law set.Source-checked
- CupCoffee and long-term healthWhat large reviews, genetic studies, trials and health authorities report about habitual coffee drinking and mortality, heart disease, diabetes, liver disease, cancer and more – and why most of it shows association, not cause.Source-checked
- CupHow to read coffee health newsA sourced checklist for judging a coffee-and-health headline – the type of study behind it, relative versus absolute risk, what a “cup” means, confounding, missing studies, funding and press-release spin.Source-checked
- CupServing temperatureHow hot coffee is served and drunk, how the flavour changes as a cup cools, how fast it cools, and what burn research and the World Health Organization’s cancer agency say about very hot drinks.Source-checked
- CupCups and vesselsWhat the cup does to coffee once it is poured – how lids, volume and the cup wall change cooling, how the shape of the opening changes aroma, what the cupping standard specifies, and the food-contact rules for cup materials.Source-checked
Each entry lives in its own stage and is listed here because it is tagged science.