Proteins: An Introduction

Proteins are one of the most important molecules in baking. They form the scaffolds of our treats and break down other molecules in our batters and doughs. Proteins are the reason our baked goods solidify in the oven, the reason we boil custards, and the reason we add acid to meringues. In the next few posts, we’ll explore what proteins are, what they do, and how we bake with them.

Proteins are essential to life.

Proteins are one of four classes of large molecules essential to life. The others are nucleic acids (such as DNA), lipids (fats, like butter and oil), and carbohydrates (like sugar and starch). In living organisms, proteins serve a diverse range of functions. They provide structure for cells, convert food into energy, and make more proteins. In baking, we often talk about proteins when we work with flour and eggs, but proteins are present in all ingredients that came from living things.

Proteins can be responsible for such a wide variety of tasks in the biological world because they can take on a vast array of shapes. Just as there are different tools for each task in the kitchen, protein shapes are uniquely suited to their purpose. When we bake, we reshape proteins so that they hold air, form scaffolding, or stop breaking down molecules we need. To better understand how we modify protein structure to suit our needs in the kitchen, let’s first discuss how it forms naturally.

Proteins are like folded strings of beads.

Proteins are strings of amino acids that fold into three-dimensional shapes.

Scientists think of proteins as molecular strings of dozens to millions of beads called amino acids. Living organisms make their proteins from twenty amino acids, which we can represent with twenty different colors of beads. Chemically, amino acids differ only in a region called the R group or side chain (see the pink areas in the figure below), and it is the composition of the R group that determines how an amino acid interacts with its environment. Within our protein string, these interactions are like detailed rules about which bead colors must touch and which must be as far away from each other as possible. We’ll discuss those rules in much more detail in the next post, but even with the limited colors and rules shown in the illustration above, the protein string folds into a three-dimensional structure. This isn’t shown in the illustration, but amino acids also interact with other molecules in their environment such as water, gases, or fats. The ultimate shape of a protein is the result of a delicate yet stable balance between its amino acids and the molecules that surround it.

Chemical structures of six amino acids with their R groups highlighted in pink.

In living organisms, proteins can be quite large and complex, so they are folded into shape by special chaperone proteins as they are synthesized in the cell. These shapes are adapted to the specific conditions inside an organism—typically watery, not too acidic or alkaline, and warm. In the kitchen, we dump these folded proteins into a new environment. There might be a little less water than they’re used to, or it might be acidic or cold. The same rules for folding apply, but the amino acids rearrange themselves to fulfill as many of those rules as possible in this new environment. Some amino acids separate while others form new bonds, and the protein loses its native shape in a process called denaturation. Denatured proteins will not regain their original structure. Even if they return to their native environment, there are no chaperones to help them into shape. But denatured proteins can take on new shapes together. This is where a baker’s magic begins.

Proteins unfold into new shapes.

Consider the process of cooking an egg white. We start with a liquid white full of individual folded proteins. It’s translucent because the proteins are spaced out far enough for light to pass between them (same goes for meat). As we apply heat, we break the bonds between amino acids and the protein strings denature. But the amino acids form new bonds with each other across separate proteins. This process is called coagulation. As the proteins coagulate, they come closer together, trapping other molecules such as water in between and solidifying the egg white. Light can no longer pass between the proteins, so the egg white turns opaque. If we continue to cook the egg, the bonds between the amino acids tighten, pulling the protein strings closer together and squeezing out water molecules. Overcooking brings the proteins too close together and removes too much water, resulting in a tough, leathery egg white.

Other things that denature proteins include acid and air. The Peruvian dish ceviche, for example, marinades seafood in citrus juices. The acid denatures the proteins just as heat would, resulting in seafood with coagulated proteins that tastes cooked even though it was never heated.

Coagulated proteins provide structure.

In most baked goods, coagulated proteins from eggs and flour provide structure. When we mix these ingredients into a batter, we begin to denature those proteins. And as the batter heats up in the oven, the proteins coagulate, forming a network that spans the entire mass of the product. The network tightens and squeezes out water until the protein structure is dry and rigid and the product is solid. Overcooking, of course, removes too much water and results in a dry product.

Structural proteins such as glutenin from flour are typically fibrous. Because fibrous proteins are already long in their native structure, it’s easy for them to form an extended network as they denature and coagulate along their lengths. In contrast, globular proteins such as gliadin are more spherical, and their roles once denatured are variable. In gluten, for example, gliadin functions mainly as a lubricant that allows glutenin to stretch. However, enzymes, which are globular proteins that speed up chemical reactions, lose their efficacy when they are denatured.

Denatured enzymes are inactive.

Enzymes are a type of protein found in all living things. In food, we find them in eggs, flour, dairy, fruits, vegetables, and grains. They speed up the chemical reactions of processes like metabolism to rates that can sustain life. Enzymes continue their work for as long as they can, sometimes into the kitchen. Depending on the recipe, this could be beneficial or detrimental. In bread, for example, amylases break starches down into sugars that yeast can eat during rises. Eggs also contain amylases. If the amylases in a custard are not deactivated, they break down the starch and thin the custard within hours. Thus, it is important to boil custards after adding eggs to inactivate amylases and keep the custard thick.

Heat inactivates enzymes because their efficiency is dependent upon their structure. Biologists called this the lock and key model, where enzymes were the locks and molecules were the keys. Though outdated, the concept is useful. When the correct keys fit into the correct lock, the enzyme helps the molecules react together. Crucially, the lock must maintain its shape for the keys to fit. If the enzyme is denatured, its activity ceases. Many food products are subjected to heat to inactivate unwanted enzymes at some point in their processing. Rolled oats, for example, are steamed in part to denature and inactivate lipases that would otherwise break down oils and produce rancid flavors.

Proteins are one of the most important building blocks of our baked goods. Without them, our baked goods would not have structure, and many crucial chemical processes would not occur. In the next post, we’ll discuss the most common changes we effect in the kitchen to denature proteins. Ultimately, we’ll have a better understanding of what happens to proteins throughout the baking process.


Corriher, S. O. Bakewise; Scribner: New York, 2008.

Figoni, P. How Baking Works, 3rd ed.; John Wiley & Sons, Inc.: Hoboken, 2011.

Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, 6th ed.; Freeman, W. H. & Company: New York, 2012.

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