Food chemistry basics - Atoms and molecules, fats, carbohydrates, proteins

Atoms & Molecules – Introducing proteins, carbohydrates & fats in food

When you zoom in on your food, what will you see? First thing you’ll notice is the detail in all the complex structures of food. Zooming in closer you’ll probably run into some cells. When you ‘look’ even closer though you will see that these cells again are build up of a lot of different molecules. And these molecules again are made up of atoms.

These molecules & atoms form our food, they determine the structure of your food, the nutritional value and what type of reactions can occur during cooking or processing. Understanding these atoms and molecules to a certain extent will surely help you understand your food and the more in-depth posts on our blog where we tend to assume certain knowledge sometimes.

If the words, molecules & atoms make you scared continue reading, we’ll be explaining what they are and how they work and will introduce three very important groups of molecules: carbohydrates, proteins & fats. At the end of this post, chemistry shouldn’t sound as scary anymore :-).

Interested in learning more of these fundamental concepts of food science? Have a look at our ‘Food chemistry basics‘ course, we’ve placed all the basics together, with quizzes and slideshows to help you understand the basics even better!

Introducing: Atoms in food

Food chemistry often starts with atoms, atoms form molecules and it’s these molecules that we study in food chemistry. So, we’ll start this food chemistry foundation series with atoms.

Atoms are the building blocks of molecules, each and everything in this world is build up of atoms. Atoms can’t be see in a light microscope, they are very very small, typically 1 billionth of a meter!

There are different atom types (we’ll come back to that later) but each atom type is build in a similar way. The basic building blocks of all atoms are three basic ‘pieces’: protons, neutrons & electrons. Different atom types will have different numbers of these building blocks, but they will contain the same type of building blocks.

Protons,  neutrons & electrons

An important concept of these three building blocks is that they each have an electric charge. Protons have a positive charge, electrons are negatively charged and neutrons don’t have a charge, as their name says, they’re neutral.

The protons and neutron of an atom form the center (nucleus) of an atom, the negatively charger electrons float around this center at a slightly further distance. Electrons are small compared to protons and neutrons. Since they float away from the nucleus these can tend to be exchanged between atoms more easily. They play an important role in chemical reactions, and when making molecules.

Role of protons: determine element

The number of protons in an atom determines which type of atom we’re looking at. These types of atoms are also called ‘elements’. There is a limited number of the elements (or atom types) in the world, only 118. These are all grouped in the so-called period table of elements, of which you might have heard in chemistry lessons. The simplest element has only one proton, every subsequent element has one additional proton, up to that 118.

Whereas electrons can be exchanged quite easily, that is not the case for the protons and neutrons. There are reactions in which these get exchanged, but in most food chemistry that won’t happen (think: nuclear chemistry).

We’ll be looking at the elements most common in food (luckily that’s not all 118) furtheron in this post, but as an introduction it’s good to get an idea of which elements exist at all. What better way to do so than through a song?

Neutrons determine isotope

So the electrons ‘swirl’ around the nucleus of protons and neutrons and role an important role in chemical reactions. The number of protons defines the element, so what do neutrons do? The number of neutrons determines the isotope of an element. For food this isn’t very relevant, but for nuclear chemistry this is a very important concept. For that reason, we won’t discuss it any further here.

Most common elements (atom types) in food

Since there are 118 elements, chemists had to find a convenient way to name them. Using their full names all the time, would be confusing, especially when we start describing molecules, which are again build up of atoms. Therefore, each element has it’s own abbreviation of one, two or three letters (as you could see in the periodic system movie).

Within food there is a relatively small number of common atoms. Four of them are especially common, carbon, oxygen, nitrogen and hydrogen. Let’s discuss the most important ones:

  • Carbon (C): this is the building block of most of the molecules we’ll come across in food. It’s important for fats, carbohydrates and proteins. Without carbon most molecules in food cannot be formed.
  • Oxygen (O): oxygen is particularly good in participating in all sorts of chemical reactions. Oxygen has quite a lot of electrons available which are often used to attach two molecules to one another or split molecules in pieces.
  • Nitrogen (N): this atom is essential for making proteins. Without nitrogen proteins couldn’t be formed. The nitrogen group is also a common place for reactions to take place.
  • Hydrogen (H): is probably the most prevalent atom, however, not that interesting in most systems. Hydrogen often ‘fills up’ empty spaces in molecules. You will see that once we discuss acids and bases this is indeed a very important atom!

After the 4 ‘big’ atoms there are a few others worthy to discuss:

  • Phosphorus (P) & Sulfur (S): often play an interesting role in protein chemistry.
  • Sodium (Na) & Chloride (Cl): you’ve heard about salt which essentially is a combination of these two, thus sodium and chloride!
  • Calcium (Ca): an important mineral for your bones.


Molecules are larger structures of atoms which have reacted with one another to form a stable component. Most atoms are not stable by themselves, you will not find a pure oxygen atom in the air, instead, two oxygen atoms will have reacted to form one oxygen molecule (O2). The same goes for hydrogen (H2).

We use the abbreviations of atoms we just learned to indicate which of these atoms are all present in a molecule. Each molecule will be a different combination of these atoms.The atoms will be attached to each other in different ways and orders.

Molecules are represented by showing the letters of the atoms they are built from and using a small subscript number to indicate how many of this atom are present in the molecule (as I did for the oxygen and hydrogen molecules). For chemists these molecular formulae are essential to describe the processes they’re studying.

In a separate post we discuss these formulas in more detail.

Structure of molecules

It’s very helpful to know which atoms are present in a molecule. However, that doesn’t tell chemists the complete story. Instead, you also need to know how these atoms are attached to one another. The way the atoms are attached to each other greatly influences the way they will react.

There are molecules which may have the same chemical formula (so are made up of the same type and number of atoms) but have a totally different structure and thus structural formula! These can actually react and behave pretty differently, even though they might look similar at first.

An example from food are glucose and fructose. The are both made up of the same atoms: C6H12O6. However, their chemical structures and behaviour are quite different (read more about sweeteners here).

For now we won’t dive into how these molecules are build, drawn and shown. Instead, let’s start applying what we learned so far by looking at the most common groups of molecules in food: carbohydrates, proteins and fats. These molecules are also called ‘macronutrients’ and are essential for us from a nutritional point of view. The three groups of molecules have very distinct characteristics that will influence how your food will turn out. They play a major role in browning reactions for example as well as flavour development and taste.


Carbohydrates are built from carbon (C), oxygen (O) and hydrogen (H) atoms. Most carbohydrates can be described by the following chemical formula: CxH2yOy. In other words, the number of hydrogen atoms is twice that of oxygen. The number of carbon atoms does not have to be related to the number of oxygen and hydrogen atoms. (Note, there are a few exceptions to this rule!)

Carbohydrates can also be called saccharides. When talking about saccharides, a common split is made into four groups: monosaccharides, disaccharides, oligosaccharides and polysaccharides. The split is done based on the size of molecules.

Monosaccharides are the smallest carbohydrates, they cannot split to form even smaller saccharides. Glucose and fructose are probably the most well known monosaccharides. Both have the same chemical formula: C6H12O6. Nevertheless, they are built in a slightly different way which makes them react completely different in your body.

Glucose molecule, see the ring of black carbon atoms with one red oxygen atom.

Disaccharides are the next smallest saccharides. They are always built from 2 monosaccarchides. For instance, lactose is made from glucose and galactose. Sucrose (regular table sugar) is made from fructose and glucose.

sucrose molecule
A sucrose molecule (source: Wikipedia). Note, the left side is glucose and the right side is a fructose molecule. This is a disaccharide.

The next step are the oligosaccharides, they are made from more than 2 monosaccharides, generally 3 to 10. These molecules can often be found in plants, giving them structure. Oligosaccharides often form the fibrous part of a plant.

Last but not least come the polysaccharides. These are huge molecules made up of more than 10 monosaccharides. They can form complex structures, the monosaccharide don’t necessarily form one long chain, instead they can form complex networks. Even though polysaccharides are all made of monosaccharides, they can behave pretty different. A common example of a polysaccharide in food is starch (again consisting of two different polysaccharides: amylose & amylopectin).


Proteins are another main nutrient for us humans with a distinct molecular structure. Proteins are essentially very long chains of molecules, with some side chains that fold up in very complicated was. Proteins are a lot larger than carbohydrates. Of most proteins you won’t be able to write down the molecular formula, they are way to complex, with way too many different atoms.

That said, that long chain does have a continuously repeating pattern. It’s a long chain of so-called amino acids that have reacted to form this long chain. There are currently 23 known different amino acids (each with a different R-group in the drawing below) which, when combined, can create all proteins. Amino acids form proteins by forming one long strand. The OH-group will react with the NH2 group (releasing a water molecule) to form a bond between the two amino acids.

Amino acid
The basic structure of an amino acid. The R depends on the type of amino acid.

Unlike carbohydrates, there isn’t a distinction based on the size of the proteins. There are loads of different proteins and they all tend to be huge and highly complex. Since it is such a long chain of amino acids, a lot of interactions can occur within the chain. Different side groups (the R- in the drawing above) can interact. They won’t ‘bind’ like the molecules in the chains do, but they can repel or attract one another. There are a lot of different interactions that can occur. These interactions can cause the long strands to fold up, or twirl around into all sorts of 3-dimensional structures and these again will organize themselves in a specific way.

illustration of sulphur and hydrogen bonds in proteins

The overall shape of protein molecules is very important for its activity. That shape is determined by how this long strand of amino acids folds and turns itself. Once the 3D structure is destroyed the proteins will behave very differently, we see this when cooking eggs, heating enzymes (which are a specific type of proteins), cooking meat or making cheese!


Last but not least: fats. Even though low-fat products can be seen all around, you cannot go without consuming any fats. Fats are just as important for us humans as proteins and carbohydrates are.

Fats belong to a larger group of molecules which are called lipids, fats are a specific subgroup of lipids. All lipids are hydrophobic molecules (they don’t like water). An example of a lipid that is not a fat is cholesterol.

The chemically correct description for fats is: triglycerides. When fats are liquid at room temperature they are commonly called oils. The name triglyceride describes the basic structure of fats: one glycerol molecule, with three fatty acids attached to it (see below).

Triglyceride with glycerol and fatty acid

As was the case with proteins and carbohydrates, there are a lot of different fats. There are a lot of different fatty acids and those again can be combined in a lot of different ways to form different triglycerides!

In the structural drawing of a fatty acid above you can see an A. This A stands for the fact that there can be a lot of different chains starting at this point. The A will always consist of a long chain of carbon atoms. The number of carbon atoms in this chain can vary from only 4 to over 20 carbon atoms.

Another very important characteristic is whether there are so called double-bonds between carbon atoms. As you can see in the image below these double bonds can cause molecules to change direction instead of forming a straight line. Fatty acids without a double bond are called saturated, those with a double bond are unsaturated.

Fatty acids
Note, the kink in palmitoleic acid should all go down instead of bending horizontal again, for clarity purposes it was made horizontal agani.

The types of fatty acids present in a triglyceride will determine the properties of the actual fat or oil. One of them is the melting point.

The longer the chain of the fatty acids, the higher the melting point of the fat will be. Smaller molecules can move around more easily so they need a lower temperature to become liquid. The same goes for molecules which have double bonds, if the double bond is of the type that causes the fatty acid to have a kink in is structure it will lower the melting point. Reason being that these kinks make it harder for the fats to structure themselves next to one another.

Applying our knowledge

This has all been quite theoretical, unfortunately, if you’re new to the topic, that’s what you’ll need to understand the phenomena you see in your food. But now it’s time to see some knowledge come to life!

Enjoyed what you learned and want to learn more food science basics? Consider signing up for our food chemistry basics course where we dive a little deeper and we give you the chance to test your knowledge in our quizzes!

Learn more about the basics of food chemistry

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  1. Your online journal furnished us with profitable data to work with. Each and every tips of your post are great. Much obliged for sharing. Continue blogging

  2. Thank you so much ! , i was struggling to understand a lot of things which needed the knowledge of some of these terms, the post made it really easy as a beginner to understand it.

  3. Atoms are the basic building blocks of matter, and all the substances we encounter, including food, are composed of various combinations of atoms. The most common atoms found in food include carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. These atoms combine to form molecules such as carbohydrates, proteins, fats, vitamins, and minerals, which are essential components of our diet. Here’s a brief overview of how some of these atoms contribute to the composition of food:

    Carbon (C):

    Found in all organic compounds, including carbohydrates, proteins, fats, and vitamins. Carbon forms the backbone of these molecules.
    Hydrogen (H):

    Present in carbohydrates, proteins, and fats. It is particularly abundant in fats, where it combines with carbon to form hydrocarbons.
    Oxygen (O):

    Essential in carbohydrates, proteins, and fats. It is also a component of water (H₂O), which is present in many foods.
    Nitrogen (N):

    A key component of proteins and nucleic acids (such as DNA and RNA), which are found in various foods, especially in meat, fish, eggs, and legumes.
    Phosphorus (P):

    Found in nucleic acids, ATP (adenosine triphosphate, an energy carrier in cells), and in the structure of phospholipids, which are important components of cell membranes. Foods rich in phosphorus include meat, dairy products, and nuts.
    Sulfur (S):

    Present in certain amino acids, which are the building blocks of proteins. Sulfur-containing amino acids contribute to the structure and function of proteins. Foods high in sulfur include garlic, onions, and cruciferous vegetables.
    Trace Minerals:

    In addition to the major elements mentioned above, various trace minerals are essential for health and are present in small amounts in food. These include elements like iron, zinc, copper, selenium, and others.
    Understanding the atomic composition of food is crucial for grasping the chemical basis of nutrition. The way atoms are arranged and bonded in molecules determines the nutritional value and biological function of different compounds in our diet. This knowledge is fundamental to fields such as biochemistry and nutrition, as it helps scientists and researchers understand how different nutrients are absorbed, metabolized, and utilized by the body

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