Understanding the science behind making bread can help you control the quality of your bread or adjust the recipe for different circumstances. Below, we’ve detailed exactly what is happening in every step of the process to help you get that better scientific understanding. From the initial mixing of ingredients to the final rise in the oven, each stage plays a crucial role in shaping the perfect loaf.

INGREDIENT PREPERATION

STARCH: The Role of Starch Damage in Flour

When flour is milled, around 12% of its starch granules become damaged, creating cracks on their surfaces. These cracks are important for baking because they allow access during the mixing process to enzymes like amylase and starch molecules that contain amylose and amylopectin. Before milling, these components are locked away, but the cracks make them available for the baking process to begin. The damage will affect the amount of water a dough will require, how long the dough will need to mix, and even the browning of the crust.

YEAST: Activation Begins

Active dry yeast is desiccated and coated in dead cells to form granules, which is why this commercial yeast needs to be reactivated by blooming in lukewarm water (40–43 °C / 104–109 °F). Activation is not required for instant yeast because it is made with a fast-acting strain of S. cerevisiae, and the noodle-shaped granules are finer than those of active dry yeast. The surface layer of dead cells is also more porous than that of active dry yeast, which allows the granules to rehydrate more rapidly. Compared with the active dry form, the instant variety produces more gas during fermentation. You can also build a preferment like a poolish or levain where the yeast will be actively bubbling away before you use it in the mixing process.

GLUTEN: Flour’s Protein Content

Flour made from bread wheat contains proteins called glutenin and gliadin. These proteins form gluten when hydrated, which will begin to develop during the mixing process. Gluten gives body and structure to dough, holding all the components in place (especially if the dough contains inclusions). It’s what makes bread pleasantly chewy and springy. The more gluten a flour can produce, the more able the dough is to hold gas bubbles, and those gas bubbles are what gives bread an open crumb.

MIXING

STARCH: Enzymatic Breakdown

Before flour and water (and other ingredients) become bread, some of their chemical components need to be broken down. Enzymes in grain play that scissor-like role and create the chemical reactions that make turning flour into bread possible. They snip glucose bonds to make food for the yeast, to help the flour absorb water, aid gluten development, and to produce other chemical reactions.

The enzymes’ job is essentially to break things down. In bread, four of the grain’s natural enzymes are key:

1. Amylase breaks down amylose and amylopectin, which makes food for the yeasts.
2. Pentosanase breaks down pentosan, which affects the dough’s ability to absorb water.
3. Protease breaks down protein, which can make the dough more extensible.
4. Lipoxidase breaks down lipids (fats), which affects the color of the crumb.

During mixing, water and amylase enter damaged starch granules through cracks. The granules become hydrated, and the enzymes break down starch molecules into sugars. Intact starch granules are broken down much more slowly. Since yeast can feed only on simple sugars, not on floury starch, fermentation wouldn’t happen without enzymes performing their chain-cutting act.

You can learn more about using added enzymes for customizations in our blog about adjusting the extensibility of pizza dough.

YEAST: Aerobic Fermentation and Cell Division

During the stage that bakers refer to as fermentation—from the time the dough is mixed to just before baking—yeasts swing between their two metabolic modes each time their environ­ment changes. As a baker kneads and degasses the dough, more oxygen flows into it, so the yeasts can respire for a while. They then switch back to fer­menting as the oxygen gets used up and more fer­mentable sugars become available. Specifically, two important processes kick off in dough once commercial yeast is activated during mixing (this also occurs in preferments as they ripen):

1. Aerobic fermentation
   • Mixing disperses yeast cells and air throughout the dough. Using available oxygen to metabolize sugar, the cells respire, which rapidly produces water and large quantities of CO₂.
2. Cell division
   • Under aerobic conditions, the yeast buds and creates more yeast cells.

GLUTEN: Gluten Development Begins

When flour is mixed with water and the gluten-forming proteins in the flour (glutenin and gliadin) are hydrated, they then almost immediately bind and form gluten. Your mixing method matters but not because it is necessary to develop gluten; you can develop gluten with minimal mixing.

The point of mixing is that it can speed up the process, which has practical importance to bakers. Using an electric mixer can make many breads feasible that would otherwise be difficult to mix by hand, like challah.

The amount of water in the mix influences this process. The more water you add, the more extensible the dough will be, which can make it harder to handle. The stiffer the dough, the stronger it will be. Often, the area in between those extremes is the best. The amount of water also has a direct effect on both enzymatic activity and fermentation: more water means increased activity and vice versa.

BULK FERMENT

STARCH: The Enzymatic Breakdown Continues

Enzymes in flour continue to break down starch, providing fuel for the yeasts’ activity.

YEAST: Bulk Fermentation

Yeast, along with bacteria, uses dough as food and the medium in which they grow. When oxygen is present and sugars are in short supply, yeast expels carbon dioxide (CO₂) and water in a process known as respiration.

Respiration continues, but the oxygen supply is depleted quickly, so yeast cells begin a shift to anaerobic fermentation. The cells produce ethanol, aromatic compounds, and CO₂, all of which gather into tiny air bubbles made during mixing.

The yeast can switch back and forth between those modes depending on the dough’s environment or perform both simultaneously (see Modernist Bread Vol 2:270). The CO₂ produced by the yeast dissolves into the aqueous phase of the dough, as in a carbonated drink, and then migrates to join the air bubbles in the dough that were formed during mixing. As fermentation proceeds, the bubbles grow.

GLUTEN: Gluten Matrix

As the gluten further develops through the bread-making process, the chains become more numerous and elongated, and they organize into a crosslinked net that is both extensible and elastic. That rubbery framework will give the dough structure and allow it to expand as the yeast creates gas. Proteases (protein-snipping enzymes) cut the gluten strands into smaller pieces that are able to make additional connections. Chains of gluten grow longer and stronger as more and more molecules stick together. The long chains form a flexible, weblike matrix that traps bubbles full of CO₂, air, ethanol, and other compounds.

SHAPING

STARCH: Enzymatic Breakdown Continues

The starch in the flour progressively transforms while bread is being shaped by further breaking down and making itself available to the yeast and other ingredients in the dough matrix.

YEAST: Redistribution

Like with folding during bulk fermentation, shaping equalizes the temperature of the dough throughout its entire mass, redistributing simple sugars and making them more readily available for yeasts to eat during final proofing. It also restarts the fermentation process, releasing carbon dioxide, which helps to strengthen the dough, and gives the carbon dioxide and water vapor more “housing” to create larger bubbles throughout the dough.

GLUTEN: Matrix Grows

The gluten matrix continues to grow larger and stronger as dough is stretched and handled during the shaping process. When dough is properly and evenly shaped, the gluten strands have been realigned to support expansion as the dough rises during final proofing and the early stages of baking. In fact, shaped doughs will expand more in the oven than unshaped doughs.

FINAL PROOF

STARCH: Enzymatic Breakdown Continues

Water and amylase continue to break the amylose and amylopectin in the starch molecules down into simple sugars.

YEAST: Fermentation

Final proofing replaces gas that is depleted through the dividing and shaping process with new carbon dioxide and ethanol from the yeast, continuing the fermentation process that began when the dough was mixed. While fermentation continues, the baker can regulate proofing time by adjusting the temperature. Different environmental factors and ingredients affect the final proofing time. The type of yeast (commercial yeast versus levain) and its percentage in the dough will make a difference. Generally, the higher the ambient temperature (up to a certain point), the faster the fermentation.

GLUTEN: The Matrix Grows

The new gas produced at this step expands the dough’s existing bubbles and (depending on the dough) creates an open crumb that is soft and pleasant to eat. The baker’s role in this process is to provide an appropriate environment for the dough, to protect it as it develops, and then determine when final proofing is complete. Calling proof is a part of the bread-making craft that’s hard to teach—even experienced bakers find it can be one of their most difficult tasks. Success stems from a hands-on familiarity with the feel of a properly proofed dough and an understanding of its fermentation process.

BAKE

STARCH: Browning and Gelatinization

When the dough is placed into the oven, starch begins to transform. Two important changes take place:

1. Browning

As the surface of the dough dries out from the heat, a crust begins to form. When the surface temperature exceeds roughly 130°C / 265°F, Maillard reactions start to occur rapidly. Sugars react chemically with amino acids and other protein fragments to produce brown pigments, complex flavor compounds, and a stiff, brittle surface—all crucial elements in a good crust.

2. Gelatinization

By the time the core temperature of the bread reaches between 91 and 93°C / 195 and 200°F, the crumb structure is set, but the color of the crust should (with a few exceptions) be the determining factor for when to remove it from the oven.

If you examine flour under a microscope, you’ll see individual granules that are crystalline, looking something like river stones. In the heat of the oven, the granules (now hydrated with water) burst or solubilize, releasing their contents. Now, instead of individual grains, you have an interconnected mass that is a gel.

This process is called gelatinization.

As the dough heats up, the surfaces of starch granules crack. Between 55° and 65°C / 131° and 149°F, they swell with water, causing amylose molecules within the starch to start seeping out. Between 60 °C and 80 °C / 140°F and 176°F, the expelled molecules form a set gel.

Proteins are coagulating at the same time, and together the coagulated proteins and interconnected starch gel control the formation of the crumb.

YEAST: Oven Spring

Oven spring is what bakers call the rapid rising of bread during the initial baking in the oven, making the volume of the loaf expand. Yeast cells help fuel oven spring. When the loaf goes into the oven, the yeast cells are still alive. At first, they respond to their warming surroundings by making even more carbon dioxide and alcohol (which promptly evaporates). This continues until the temperature gets too hot for the yeast to function, around 50°C / 122°F, which is when the microbes begin to die.

At the same time, the warming environment causes water and dissolved CO₂ in the dough to start to, respectively, evaporate and revert to a gaseous form. This adds to the pressure and the rise of the dough. As the dough continues to bake in the oven, warming bubbles take on more carbon dioxide (CO2) from yeast, more CO₂ from dough, and more water vapor from dough. The number of molecules of these substances in the bubbles increases. These gases naturally take up more volume (or exert more pressure) the hotter they are. The CO₂, water vapor, and air all expand thermally as the temperature goes up. Oven spring comes to a halt when dough starts to lose most of its stretchiness.

GLUTEN: Stretching

The gluten matrix stretches to accommodate increasing gas pressure in the bubbles caused by the expansion of CO2 and the vaporization of water as the bread rises. The gas pressure grows inside the bubbles, and since dough is stretchy, the bubbles inflate, and the dough rises. Eventually, these balloon-like cells stretch to the breaking point. Holes burst open in the walls between the bubbles, joining them together into a spongy, open-cell foam. The stronger and more elastic the dough, the bigger the bubbles can grow inside the loaf before they burst. In the heat of the oven, the proteins coagulate, forming a solid network of irreversibly bonded proteins and starches gelatinize to set the structure of the crumb.

COOL

STARCH: Retrogradation

After the bread is removed from the oven, the temperature of the crust and crumb begins to fall. While the center will continue to bake a little longer, vapor is escaping from the crumb, out through the crust, and the once-pressurized loaf begins to equilibrate. As the vapor pressure drops, air is forced into the loaf and the crumb structure begins to solidify. This is why it’s important to let bread rest and cool after you pull it out of the oven.

When the bread is cool, the gelatinized starch slowly begins to recrystallize, also known as retrogradation. Essentially, the starch is trying to return to its native state, the way it was before it was doused in water and subjected to intense heat. Water begins to migrate out of the granules, and the molecules restructure into more organized chains. This process is what gives the crumb of stale bread such a brittle, crumbly texture.

YEAST: Flavor Loss

Aromatic compounds, produced by yeast and the Maillard reaction, contribute to the bread’s freshly baked flavor. Over time, they dissipate, changing the bread’s taste and aroma.

GLUTEN: Migration

Water travels back into the gluten matrix and/or escapes from the bread as the bread cools. The bread dries as more water is lost as it ages. The bread will begin to stale as the starch continues to retrograde and moisture from the crumb migrates into the crust.

Mastering the process of bread making means understanding the step-by-step transformations from mixing to baking. It’s not just about mixing ingredients but knowing how they chemically react and change. Each stage, from breaking down starches to fermenting yeast and forming gluten, plays a vital role in creating the perfect loaf. Now you’ll know the science behind the baking process the next time you bite into a slice of homemade bread.

Want to further your bread education? Learn more with Modernist Bread at Home. We also have free email courses at the Modernist Bread School.