This summer I volunteered at a dairy farm in Belgium. Although it was a medium-sized farm, having around 40 cows, I got to experience the whole dairy farming experience from milking the cows to processing the milk and turning it into cheese, butter and all things in between — like mascarpone or creme fraiche. I was given many instructions and taught a lot about the process… And thus I wanted to know more, not about how to make cheese and butter, but what happens to the literal chemical structure of milk when it is processed and how this allows for an incredible variety as seen in e.g. different cheese types. Why is cottage cheese soft and liquid but mascarpone thick and stiff? Why is blue cheese blue? And so here I go, having done my best to research the versatile substance, let’s start by diving into the chemical structure of milk, in particular that of cow’s milk.

‘Anatomy’ of milk

Milk is a suspension, meaning it is a heterogeneous mixture consisting of solid and liquid particles dispersed in a fluid. It is mostly made up of water, some fat, the sugar lactose and proteins such as casein.¹

Milk is an energy rich drink. A 244g glass of whole milk contains about 146 calories, so it won’t come as a surprise that a good part of that glass is made up of sugars.
The most prevalent of which is lactose, which is also called ‘milk sugar’, and makes up up to 5% of milk. In our bodies, lactose is broken down by the enzyme lactase into monosaccharides (simple sugars) like glucose and galactose. This makes it important for energy storage.

Lactose

When thinking about lactose, a certain deficiency thereof immediately springs to mind. As a matter of fact, in the U.S. as much as 36% of the population is believed to be lactose intolerant. In Asia, these percentages are even higher: 85% in China and 61% in India, respectively². This intolerance comes from a deficiency of the lactase enzyme and is therefore also closely linked to genes. It is believed that, originally, everyone was lactose intolerant, but as dairy became part of our daily diets, a mutation in our DNA, which allows us to digest lactose, became more prevalent due to natural selection. As a result, in Europe fewer people are lactose intolerant, presumably due to dairy products’ strong roots in our culture. For example, cheese originated in Europe around 7’000 years ago.³

A good part of milk is also made up of fatty acids. Most of these lipids are found in the form of saturated triglycerides. The remaining 2% of milk fatty acids are made up of branched-chain fatty acids (BCFAs). Triglycerides are stores in fat cells in the human body and make up an important energy source that is found in meat, oils and butter alike. In the milk triglycerides are stored inside fat globule membranes (MFGMs). These surround the triglycerides with a triple-layer of phospholipids and allow for stability and uniformity. They prevent the fat globules from being digested too quickly and keep them well-distributed throughout the milk. MFGMs’ health benefits, such as immunoregulation and enhancement of intellectual development have made it especially interesting in past years. MFGMs are currently also used as emulsifiers. These are substances which help mix two substances that usually don’t mix. In the case of milk, MFGMs help the fatty parts of the milk mix with water molecules. MFGMs thus have substantial potential on the market.⁴

Lastly, about 200 different types of proteins are found in milk. The most abundant of which is casein, a group of related proteins which make up about 80% of proteins in cow’s milk. Casein also works as an emulsifier, just like fat globule membranes, and are used in industry in products such as lotions and creams.⁵ Most of the remaining proteins in milk are classified as whey proteins. The name unsurprisingly comes from ‘whey’, the liquid that is created as a byproduct during the production of cheese. ⁶When opening a cup of yogurt, you might see some water at the top of it. Rest assured, this water is nothing but whey. You’ll also see gym-goers regularly try to promote this stuff, as it is commonly marketed as a protein supplement that might or might not give you gigantic muscles!

Processing of milk into cheese – Acidification

Surprisingly, most cheeses are made with the same basic process. The variety in flavor and textures mostly comes from the aging time and the bacteria cultures used when fermenting the milk. However, it is important to note that cheese making practices vary immensely from region to region, as do natural raw materials, cultures and production methods.

As such, the first step to making cheese is acidification, where bacteria cultures are added to milk and heated to an adequate temperature that allows bacteria to thrive. These bacteria turns lactose into lactic acid by fermentation.

Lactic acid

In his book ‘Vanity, Vitality, and Virility’, John Emsley, a popular science and chemistry book writer, reports of the following features of lactic acid:
“Lactic acid is present in the human body in large amounts as a perfectly natural by-product of the metabolism of carbohydrates. (In fact, we emit a little lactic acid on our breath and this is what mosquitoes use to locate us.) […] It is added to skin preparations in the belief that it will compensate if it is naturally lacking. Lactic acid helps sun-damaged skin to heal, and reduces fine lines, wrinkles, and liver spots […] Lactic acid is sometimes added to shaving creams, and is used to bleach freckles.”

The bacteria used in this step varies from cheese type and production method. Bacteria that is used in acidification can be homofermentative, meaning it produces only lactic acid during fermentation, such as lactococcus lactis which is commonly used in cheddar. On the other hand, also heterofermentative bacteria, which produces byproducts alongside the lactic acid, is used. When making Emmental, heterofermentative lactic acid bacteria is used. For example, Leuconostoc mesenteroides emits CO2 gas during fermentation, which creates the characteristic holes found in emmental cheese.⁷

The bacterial colonies, also called lactic acid bacteria (LAB), produce enzymes that introduce the lactose sugars into their cells. Once inside, lactose is broken down into its most basic components, glucose and galactose. LAB use this glucose and galactose to make pyruvate in a step that you might recognize as glycolysis. Subsequently, pyruvate is transformed into lactic acid by an enzyme.⁸

Glycolysis

Glycolysis is a pretty long metabolic pathway which converts glucose into pyruvate using many different enzymes. (It is also known as the Emden-Meyerhof-Parnas pathway) It is found in many organisms, including in us. Without glycolysis, you would miss out on a fundamental part of cellular respiration as pyruvate is an important reactant that drives many metabolic processes. On top of that, you would produce less ATP (energy source). Glycolysis.

NADH, NAD+?

These processes produce by-products such as NADH which are later reused to make lactic acid. As they are produced and used up, they don’t have a big effect on the reaction that is of interest: namely the one which produces lactic acid. Feel free to ‘ignore’ the NADH — but be conscious that it is an important product of glycolsis which acts as an electron carrier.

At this point you might recall that heterofermentative bacteria produce by-products such as CO₂. As a matter of fact, the above is only really true for cheeses with homofermentative bacteria, the ones that convert lactose only into lactic acid.

[^7]On the whole, the production of lactic acid lowers the pH of milk. A lower pH affects proteins in the milk and therewith has potential to change its structure. Acidification is the building block for coagulation — where milk finally starts to change its state of matter.

Step 2 – Coagulation

In the second step, rennet is usually added to the milk. Rennet refers to enzymes (such as chymosin) that turn liquid milk into two parts: the curd and the whey. To understand the effect of this enzyme on milk’s consistency, it’s best to take a look at its proteins.

Milk’s most abundant protein, casein, has a micelle-like structure.⁹ Figure 5 illustrates this.

In this casein micelle we find the subunits alpha-caseins and beta-caseins in the interior and k-caseins generally on the exterior. K-caseins form a hydrophilic layer on the exterior (water-loving), which allows the protein to dissolve in water. Hence, casein proteins are suspended in the milk.

Rennet cleaves k-casein, in such a way that the hydrophilic layer that encompasses the protein is removed. The casein micelle adopts a hydrophobic nature. Seen as it is surrounded by a substance that is composed of at least 80% water, this newly attained hydrophobic “shell” encourages casein micelles to conglomerate. This binding together of casein micelles due to instability caused by a hydrophobic shell is called aggregation. As this happens all throughout the milk, casein micelles start to bind together, forming a matrix that traps other molecules such as fat and water inside it. A cheesemaker will call this the curd and as you can see in figure () it has a very seperate identity from the whey. The whey — the liquid part — is mostly made up of water and whey proteins. Whey proteins do not aggregate because the rennet enzyme does not cleave them and they do not naturally aggregate unless under high temperatures.¹⁰.

Milk can still become thick and be processed into dairy products without any help from enzymes. For example during the production of yogurt, casein proteins aggregate because of low pH values. The proteins lose solubility and aggregate into a gel-like texture. This is enough for some cheese types such as ricotta, which don’t have to be inherently firm.

The following steps

Assuming we want to make a more firm cheese, then the following steps are focused on expelling as much whey as possible. Less whey will typically mean less moisture, which is typically desirable with cheeses such as parmesan or cheddar. On top of that, whey contains some lactose sugars which might turn into lactic acid if left with the curds, affecting the cheese’s texture. At the farm I volunteered at, they fed the whey leftover from cheese production to their pigs.

The curds are cut into small pieces for those dairy farms who are particularly unhappy with whey. Bigger curds are made for those cheesemakers who specialize in more moist cheeses, such as brie or camenbert. The cheese is then salted. Some dairy farms even dye their cheeses in this step. It is subsequently molded and pressed into a desired form and typically brought into a cellar where temperatures and humidity are closely monitored. The aging process hereby begins.

When a cheese ages, the bacteria and acids that are inside of it change its flavor and texture. For example, pH can still drop once the cheese is left to mature, as some lactose is still present. In this case, glycolysis drives the reaction of lactose into lactic acid. In cheeses with heterofermentative bacteria, such emmental, microbes further convert lactic acid into other substances like CO2 or water.

However perhaps most importantly is proteolysis, the breakdown of proteins during the aging process. Chymosin (rennet) has already cleaved k-caseins at this step and a tight network of casein submicelles and fat have already formed. During aging, plasmin, a naturally occuring enzyme in milk, reacts with beta-casein, whereby beta-casein is broken down. This releases free amino acids and peptides. These impart the flavor of the cheese. Some peptides might pull an umami taste out of the cheese, whilst other contribute to bitterness.¹¹

Many other things happen as cheese ages as well. I’m sure far more than many cheese makers are even aware of. Making cheese is like controlling an ecosystem of microbes and bacteria. It is safe to say quite a challenge to get right if one isn’t a professional. But chemistry can help us understand processes that go on behind the scenes. And with more understanding, comes proficiency and in this case, a happy stomach.

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2. Lactose Intolerance by Country 2025. (n.d.). worldpopulationreview.com. ↩︎
3. Wikipedia contributors. (2025e, June 28). Lactase persistence. Wikipedia. Link ↩︎
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5. Wikipedia contributors. (2025c, June 17). Casein. Wikipedia. Link ↩︎
6. Wikipedia contributors. (2025d, June 28). Whey protein. Wikipedia. Link ↩︎
7. Wikipedia contributors. (2025c, June 13). Cheesemaking. Wikipedia. Link ↩︎
8. Bintsis, T. (2018). Lactic acid bacteria as starter cultures: An update in their metabolism and genetics. AIMS Microbiology, 4(4), 665–684. Link ↩︎
9. Li, Q. L., & Zhao, Z. Z. (2019). Acid and rennet-induced coagulation behavior of casein micelles with modified structure. Food Chemistry, 291, 231–238. Link ↩︎
10. Chen, C., Chen, L., Li, W., Chang, K., Kuo, M., Chen, C., & Hsieh, J. (2021). Influence of chymosin on physicochemical and hydrolysis characteristics of casein micelles and individual caseins. Nanomaterials, 11(10), 2594. Link ↩︎
11. Tunick, M. H., & Park, Y. W. (2023). Introduction to cheese chemistry. In The Royal Society of Chemistry eBooks (pp. 1–7). Link ↩︎