Proteins in the Kitchen

Updated January 2022.

In the last post, we described proteins as strings of amino acid beads that we reshape when we bake. In this post, we’ll discuss how we manipulate some of the most important factors in protein shape such as water availability, mixing, acidity, salt, and temperature, and we’ll explore the chemical effects of these changes.

Different protein shapes are stable under different conditions.

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

Let’s start with a quick recap from the introduction: proteins are strings of amino acid beads. Different colors of beads represent slight molecular variations in a region called the R group that determine what the beads can or can’t touch. These could be other amino acids or other molecules nearby. When the beads arrange themselves according to these rules, the protein takes on a three-dimensional shape. The shape a protein adopts in a living organism is its native state. When we move the protein into a new environment, like a mixing bowl, we surround it with lots of new molecules. The same rules are still in play, but because the neighboring molecules have changed, the beads have to rearrange themselves in order to fulfill the rules as much as possible. Thus, the protein loses its native shape (it’s denatured) and takes on a new one.

Some of the most common changes we force upon proteins in the kitchen are in water availability, motion, acidity, salt, and temperature. So let’s discuss each of these in turn: what they’re like in a protein’s native environment, how they’re different in our kitchens, and how they ultimately denature a protein.

Water anchors some amino acids and repels others.

Water is crucial to protein stability. There are seven amino acids that love to interact with water, which scientists call hydrophilic or “water-loving.” In a living cell, proteins are surrounded by water molecules, so they fold these hydrophilic amino acids to the outside of the protein where they can easily interact with water. The water molecules essentially serve as little anchors for these amino acids and keep them in the same positions relative to each other. The opposite of the hydrophilic amino acids are the hydrophobic (“water-fearing”) ones, of which there are eight. As the name suggests, hydrophobic amino acids dislike interacting with water, and they fold to the inside of a protein to avoid it.

An amino acid’s structure determines its attraction to water.

The propensity of these amino acids (or of any molecule) to interact with water is based on their electric properties. As shown below, water is a molecule of H2O: two atoms of hydrogen bonded to one molecule of oxygen. Think of the atoms like kids who are fighting for toys. The toys represent electrons, which are negatively charged particles that the atoms must share. In the case of a water molecule, the kids are not equal in strength. Oxygen is much stronger than the two hydrogens, and he will hold on to the toys for most of time. The hydrogens might wrest one from him every so often, but oxygen wins it back. Because of this disparity in strength, the oxygen atom carries the electrons’ negative charge most of the time, and it develops a partial negative charge. The hydrogens are, for the most part, left without the electrons, so they develop partial positive charges. These partial charges result from the unequal sharing of electrons in what scientists call a polar molecule, one in which the atoms are unequal in electron-grabbing strength. In the figure below, the “delta” (δ) symbol represents partial charges.

Water molecules contain an oxygen atom (O) bonded to two hydrogen atoms (H). The oxygen holds the electrons (e) and acquires a partial negative (δ) charge. The hydrogens acquire a partial positive (δ+) charge. In ice, water molecules form a hydrogen-bonded lattice.

Just as the north and south poles on a magnet attract, positive and negative electric charges attract. The partial negative charge on a water molecule’s oxygen attracts positive charges. The partial positive charge on the hydrogens attracts negative charges. These attractions form hydrogen bonds. In ice, water molecules form an organized lattice of hydrogen-bonded oxygens and hydrogens, as shown above. But water isn’t the only polar molecule. Remember all those hydrophilic amino acids? They’re polar, too, and their partially charged atoms form hydrogen bonds with water. That’s what makes them hydrophilic.

What about the hydrophobic amino acids, then? These amino acids are nonpolar, which means that their atoms share their electrons equally. If we think back to atom kids, the kids in a nonpolar molecule are equally matched. Thus, they each possess the electron toys for equal amounts of time, and they all remain neutrally charged. These neutral charges don’t attract the partial charges of polar molecules like water, so nonpolar molecules end up avoiding water and interacting with each other.

Fat prevents proteins from reaching water.

So what does this mean for a protein in the kitchen? Remember, a protein’s native shape is stable in a watery environment, where there are plenty of water molecules for hydrophilic amino acids to anchor themselves. The water also stabilizes the hydrophilic amino acids if the protein begins to denature. In the kitchen, proteins are often submerged in a world of water molecules, yes, but also of nonpolar fat molecules. If fat molecules reach proteins before water, they prevent the hydrophilic amino acids from reaching their anchors, and the proteins cannot denature or interact with other molecules. Thus, fats are used to prevent gluten formation. They also prevent egg white proteins from denaturing in meringues, which is why the equipment for beating egg whites must be squeaky clean.

Air reorganizes protein structure.

In the mixing bowl, we also introduce proteins to air bubbles, which force proteins to reorient. Egg white meringue is a great example of this. We start with wads of egg white proteins folded in water. When we beat the whites, we introduce air bubbles and start to denature the proteins. The hydrophobic amino acids, now exposed to water, would rather interact with air, so they move to surround the air bubbles. As shown in the illustration below, the hydrophobic amino acids line the air bubbles as the hydrophilic ones continue to interact with water. As we beat more and more air into the egg whites, the proteins form an intricate network of air, protein, and water. In addition to preventing the proteins from denaturing in the first place, nonpolar fat molecules also interfere with this network because they compete with the hydrophobic amino acids to avoid water and line the air bubbles. However, fats are not as strong as proteins, so as more air enters the meringue, a bubble coated in fat swells quickly, breaks its lining, and escapes, leaving the meringue with less volume.

Meringues are a network of air, coagulated protein, and water. Proteins fold their hydrophilic amino acids to the surface and the hydrophobic ones to the interior. Mixing denatures the proteins and exposes hydrophobic amino acids. The hydrophobic amino acids prefer to interact with air, so they line air bubbles while hydrophilic amino acids continue to bond with water.

Expanding air bubbles in proofing bread also press against protein strands and reorganize them. This is actually the mechanism behind no-knead bread: as the bread rises and the air bubbles expand, the gluten strands around each air bubble realign to accommodate it. But if egg whites are whipped too long or bread is over proofed, the proteins aggregate too much and form large, rigid clumps. Because the proteins are no longer flexible, air escapes and the meringue or loaf loses volume.

Mechanical motion denatures proteins.

Mixing and kneading also encourage proteins to denature and aggregate. It’s how the egg white proteins denature in the first place⁠—we physically pull them apart. However, if we mix or knead too much, we bring bigger and bigger protein clumps into contact until they form rigid aggregates that cannot hold air.

Acids and bases mediate bond strengths.

Many molecular interactions, such as the polar bonds we discussed, result from electric charges. Acids and bases affect these interactions globally by changing the number of electrons available to the atoms. If we think back to the kids, acids are like the parents who stop the fighting by taking away toys, and bases are the ones who get more toys. Acids and bases also neutralize each other: if we take away one toy (add acid) and then give them one (add base), it’s as if we hadn’t done anything at all. Note that acids are commonly referred to as proton/hydrogen/H+ donors. This is the same idea, just said the opposite way: acids add a kid to the group. Either way, there are more kids than toys. Ultimately, by changing the magnitudes of the electric charges, acids and bases mediate the strengths of molecular interactions. Strong bonds weaken, and weak bonds strengthen. An environment that is too acidic or too basic denatures proteins, so in living organisms, pH (a measure of acidity and basicity) is strictly regulated in part to maintain the structural integrity of proteins.

In baking, acidity is important for the coagulation of structural proteins. We often add lemon juice, vinegar, or cream of tartar to egg whites before whipping them into meringue. The acidic environment encourages the proteins to denature more quickly, thus stabilizing the meringue. Acidity is also important in setting baked goods. Because acid encourages coagulation, there’s less work for heat to do in the oven and batters set at lower temperatures. In fact, batters that are not acidic enough will not set.

Salts mediate bond strengths.

Like acids and bases, salts also influence the electrical attractions and repulsions between amino acids, but they target a specific type of bond: ionic bonds. Some molecules are so polar that the stronger atom kids steal the toy from the weaker ones and the weaker kids never get it back. This creates an atom with a full negative charge and leaves the other atom with a full positive charge. Molecules with full positive or negative charges are considered ionic, which really just means that they are extremely polar. Since opposite charges attract, a positive and a negative ion form an ionic bond. There are five ionic amino acids. In the environment of the human body, three are positively charged and two are negatively charged.

As with polar molecules, however, the magnitude of the charges and the strength of their attraction (or repulsion) is dependent on the environment. Living organisms need to maintain a specific concentration of ions to perform basic cellular functions, so proteins are designed to maintain their shape at those concentrations. In the kitchen, however, we can change ion concentrations (and thus protein shape) with salts.

To a scientist, “salt” is a general term for any solid that creates ions when it’s dissolved in water. Table salt is a salt that dissolves into sodium and chloride ions. Hard water contains calcium and magnesium ions. Baking soda is also a salt. Once a salt is dissolved in water, its positive and negative ions can interact with the ionic amino acids in proteins. As we discussed, with gluten, this means shielding like charges on the proteins to allow gluten strands to draw closer and tighter. In eggs, salt can loosen the ionic bonds holding the proteins together to create thinner egg washes.

Heat denatures proteins.

In most recipes, heat is the step that ultimately coagulates structural proteins and inactivates enzymes, but it affects every molecule that enters the oven. Heat is a form of energy. Just as every atom kid in our protein is constantly fighting, every atom in existence constantly moves, whether it just wiggles in place or zooms around. Adding heat to atoms is like feeding the atom kids sugar. They will move faster and faster until they’re bouncing off the walls.

Imagine that we now have a room full of these atom kids fighting for toys. If we give the kids sugar, they would start running all around the room, fighting anyone to get as many toys as they can. Proteins (and all atoms) are similar. If we heat them up and give them enough energy, amino acids become disorganized, bonds break, and the protein denatures. At levels of energy we can’t create in the kitchen, amino acid beads could entirely separate from each other and break the protein string. The hotter the environment, the more energy the atoms have, the faster they move, and the more bonds break.

The opposite is also true. If the kids in our room have been playing for hours and need naps, they will only fight for the toys near them. With proteins, the colder it gets, the less energy the amino acids have, the slower they move, and the more likely they are to stay bonded.

Heat coagulates structural proteins.

Thermal energy is the reason room-temperature egg whites are easier to whip than egg whites from the fridge. The warmer egg white proteins have more energy. Their amino acid bonds are more readily broken, so the proteins denature sooner to hold air. Ultimately, this makes the meringue more stable. Heat from the oven is also crucial to set our baked goods. Without heat, the structural proteins from eggs and flour would never have the energy they need to denature and coagulate. This is the reason temperature is a useful metric of “doneness,” not only for baked goods, but also for meat. If the inside of a loaf of bread is still too cold, for example, its proteins have not yet acquired enough heat to denature and coagulate, so the structure of the bread has not set.

Heat inactivates enzymes.

As we mentioned in the introduction, enzymes are proteins that facilitate chemical reactions that are crucial to life. Reacting molecules are like keys that fit into an enzyme lock, and when all the keys are inserted, the enzyme reacts them together. Although the aforementioned factors affect enzyme efficiency, heat is most often used to denature and inactivate enzymes. A specific enzyme’s resistance to heat depends on the amino acids that make it up and the strength of the bonds that hold them together. Thus, different enzymes denature at different temperatures.

Enzymes facilitate chemical reactions of specific molecules that fit into them.

At temperatures slightly warmer than what the enzyme is designed for, everything moves faster, the locks are more likely to find the enzyme key, and enzyme efficiency increases. But as temperatures rise still higher, the enzyme denatures, the keys no longer fit, and the enzyme is inactivated. This is why microorganisms, like the yeast in our bread or the bacteria that cause disease, die when we cook food. The high temperatures inactivate the enzymes that perform life-sustaining functions and the organisms die.

Recipes know how proteins behave.

Proteins are complicated molecules; there’s no question about it. The good news is that recipes are formulated to stabilize the desired protein shape (even if the developer wasn’t consciously thinking about proteins), so most of the time, we don’t have to worry about them at a molecular level. But to successfully modify recipes to our own preferences and tastes, it can be helpful to understand the importance of factors like fats, acidity, and temperature.


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

Derrickson, B. H. Human Physiology, 2nd ed.; John Wiley & Sons, Inc.: Hoboken, 2019.

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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