So then…if amylase (the enzyme that breaks flour’s carbohydrate molecules down into simple sugars) is abundant in packaged flour, where does it come from? Well, amylase occurs naturally in wheat berries, especially when they germinate (or malt). Every wheat berry is essentially a seed, you see, containing an embryo (the germ) and its food supply, the comparatively large and carbohydrate-laden endosperm (both of which are contained within a hard protective shell, the bran). When the wheat berry germinates, the embryo begins producing a variety of enzymes. Some help break down cell walls so the shoot can form and exit the kernel. Others, like amylase, break down the long-chain carbohydrates (the amylose and amylopectin) into the smaller sugars that the shoot uses to fuel its growth. For plants run on simple sugars too, you see. Long-chain carbohydrate molecules are simply energy storage devices.
So then flour is made of malted wheat berries! Er, no actually. Malted wheat makes very poor baking flour for a variety of reasons. Being partly digested, it’s lower in many nutrients compared to unsprouted grain, it’s darker in color, and is inclined to spoilage because it becomes infested with a variety of microbes. It also performs unevenly, since the level of enzyme activity is highly variable from berry to berry.
So then where does the amylase come from? The answer is that it’s added into commercially made flour at the mill, usually in the form of ground malted wheat or barley (the stuff we typically know as “malt”). It’s a technique that millers have employed for centuries to improve the baking properties of flour, though it’s increasingly being replaced by laboratory-produced amylase, so-called “fungal amylase”, which is made by (you guessed it) a fungus called Aspergillus oryzae. Practically speaking, it’s no different from grain amylase, save to say it’s purer, more consistent and easier to blend in.