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Last post was a less science oriented part of the book I'm working on. This post dives into the science the way I like it :). It's a basic rundown of how the body deals with carbohydrates and proteins. I don't take particularly much effort to dumb it down, but most people should be able to understand this as is.

Digestion & metabolism

Digestion is the act of processing foor for absorbtion. Absorbtion brings food into the body. Metabolism is the process of processing this absorbed food in the body.

It can be viewed as crossing 4 important digestive organs:

  1. Mouth
  2. Stomach
  3. Small intestine
  4. Large intestine
Place Digestion Absorbtion
Mouth Starch by Amylase N/A
Stomach Proteins by Pepsin Minor amounts fat soluable substances (e.g. alcohol/drugs)
Small intestine All food types All food types
Large intestine Bacteria do digestion Water and products of bacterial digestion


The mouth is used to mechanically crush food, making it easier for the intestines to absorb foods. Were we not to chew the enzymes and acids in digestion would not for example be able to break down for example a whole carrot.

In addition the mouth contains enzymes that superficially break down starches. It contains the enzyme amylase, which breaks down starches into more simple carbohydrate structures like sugars.


The stomach is not the place where most foods are absorbed. It's main function is to use acidity and the enzyme pepsin to break proteins down into their constituent amino acids.

The stomach does absorb some fat soluable substances like alcohol and some drug types. This is usually however in small amounts.

Small intestine

This is where most of the magic happens. Here a cascade of enzymes and bile break down and solve macronutrients and micronutrients for absorbtion.

Large intestine

Most digestion here is done by bacteria. They are responsible for producing vital vitamins like vitamin K and some forms of vitamin B. Also the last water and electrolytes (like NaCl salt) are absorbed here.


After passing the intestines the processed substances pass the liver. This happens before the substances reach the overall blood circulation.

The liver is a filter that processes absorbed foor before it reaches the blood.

After having passed the liver the absorbed substances circulate the blood where they await absorbtion and processing my whatever body part uses them.

Understand carbohydrates

Carbohydrates are a macronutrient class that most people associate with bread, potato, rice and sweet things. They are however present in most foods.

Chemical profile

Carbohydrates (carbs) are substances consisting of:

  • Carbon (C atoms)
  • Hydrogen (H atoms)
  • Oxygen (O atoms)

The name carbohydrate stems fron the ratio of H to O usually being 2:1. That means that for example glucose (C6 with H12 and O6) can be seen as C6 and 6(H2O), H2O being water.

Classifying carbs

Most carbohydrates that humans eat consist out of ring structures. For example glucose & fructose are rings of 6 carbons (Note that most circular monosacharides can also exist as straight unringed forms).

Glucose ring structure

Carbohydrates are classified based on their length, e.g. how many rings are linked together.

Rings in the chain Name of type Example
1 or 2 Sugar Glucose
3 to 9 Oligosaccharides Maltodextrins
9+ Polysaccharides Starch

Amylose is an example of a starch, it is a long chain of glucose rings.

Amylose starch structure, the chain length varies

While the most commonly know sugar is glucose, there are many more substances classifying as sugars:

Sugar Type
Glucose Single ring monosacharide
Fructose Single ring monosacharide
Galactose Single ring monosacharide
Sucrose Ring of fructose + ring of glucose attached
Maltose Two glucose rings attached
Lactose Ring of galactose + ring of glucose attached

Sucrose is also knows as table sugar.

Carbohydrate digestion

Longer carb chains like starches and oligosacharides are not absorbed into the body as such. They are first broken down to their constituent sugars. The majority of carbohydrates is broken down to and absorbed in the form of:

  1. Galactose
  2. Glucose
  3. Fructose

All of the above are single rings or monosacharides. Their metabolism happens in the following order:

  1. Amylase enzyme in the mouth breaking long starches into shorter ones
  2. Amylase in the small intestine to break them down forther
  3. Brush border enzymes (dextrinase, glucoamylase, lactase, maltase, sucrase) in the small intestines to break them down to basic sugars
  4. Absorbtion of basic sugars (cotransport with sodium ions)
Location Digestive activity Digested by
Mouth Long starches to shorter ones Salivary amylase
Small intestine Long starches to shorter ones Pancreatic amylase
Small intestine Short starches to simple sugars Dextrinase, glucoamylase, lactase, maltase, sucrase
Small intestine Absorbtion Cotransport with sodium ions

Sugar metabolism

The body does not use sugars as energy directly. It first uses them to create ATP (adenosine tri phosphate) which is the energy currency of human cells.

Glucose and fructose are metabolised in different areas. As a rule fructose can only be converted into ATP by the liver. Glucose on the other hand can be metabolised throughout the entire body.

Glucose metabolism

When glucose hits the bloodstream the body produces insulin to stimulate it's absorbtion by cells all over the body.

Glucose itself is not good at entering cells

Glucose when it goes up triggers the release of insulin.

Insulin is a signalling molecule that tells cells all over the body to open their doors for glucose. If these doors would always be open blood sugar could get dangerously low, and if they are do not open, well, you have diabetes.

This glucose door is a class of transport proteins called the GLUT transporters, of which GLUT-4 is the most relevant with insulin. Basically what happens is:

  1. Glucose levels in the blood are high
  2. The pancreas senses this and produces insulin
  3. Insulin triggers the connection of GLUT-4 to the cell membrane
  4. GLUT-4 transports glucose to the inside of the cell

Insulin and GLUT-4 system

Once inside the cell glucose is metabolised and broken down:

  1. Through glycolysis glucose is converted to pyruvate
  2. Piruvate is processed to AcetylCoA
  3. The (krebs) citric acid cycle in mitochondria use acetylCoA to procude energy
  4. Oxydative phosporilation from the citric acid cycle used to produce more energy

| Stage | Location | Net energy output | | ------|--------------------| | Glycolysis | Cytosol | 2ATP | Pyruvate to Acetyl-CoA | Mitochondrial matrix | 0 ATP | Citric Acid Cycle | Mitochondrial matrix | 2 ATP | Oxidative phosphorilation | Mitrochondrial matrix/inner membrane | 38 ATP

The overall efficiency of the above aerobic system is about 66%. In anaerobic conditions (not enough oxygen) the body relies on other systems that are far less efficient.

Full resporatory cycle of a cell for glycose

Understand Proteins

The protein macronutrient class is usually associated with meats, cheese, fish and other calorie dense foods.

Chemical profile

Proteins are chains of amino acids linked together. An amino acid has:

  • An amine group (-NH2)
  • A carbolic acid group (-COOH)
  • A side chain (R) differing per amino acid

Amino acid structure with amine (left), carbolic acid (right) and side chain (bottom) groups

When two amino acids link we call the result a peptide. There are 22 amino acids that make up protein/peptide chains. 20 of those are coded in our DNA code, the remaining two are not used directly by our DNA code.

Amino acids linking into a chain

Chain length Name Example
1 Amino acid Glutamine
2 Dipeptide (di = two) Aspartame
3 Tripeptide (tri = three) Glutathione
4 Tetrapeptide (tetra = four) Endomorphins
Any multiple Polypeptide (poly = many) All of the above

Classifying proteins

So when does a polypeptide become a protein? Technically all proteins are polypeptides. There is no clear boundary, but as a rule of thumb polypeptides that fold into a set structure are often called proteins.

The chain of amino acids will give rise to a specific structure. While the details can get quite complex the basic essence is that amino acids have electromagnetic charges that make parts of a protein chain attract and repell each other.

It's kind of like taking a shoe string and rolling it between your hands to create a ball. Depending on the length and consistency of the shoestring you'll get a tangled ball of a certain type.

A number of proteins represented in 3D. From left to right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), adenylate kinase (an enzyme), and glutamine synthetase (an enzyme)

Protein digestion

The digestion of a protein breaks it down into the amino acids it consists out of. Remember, a protein is a chain. Each of the links is an amino acid.

The basic digestion steps are:

  1. Proteins are cut into smaller peptides (this is called cleaving) by pepsin in the stomach
  2. Trypsin and chymotrypsin continue the cleaving of proteins into smaller peptides in the small intestine
  3. Peptides of a length of 4 and smaller are absorbed in the small intestine
  4. Inside the cells of the intestine most peptides are broken down into their base amino acids
Location Digestive activity Digested by
Stomach Protein chains into smaller peptides Pepsin
Small intestine Protein chains & peptides into smaller peptides & amino acids Trypsin & chemotrypsin
Small intestine Absorbtion of 4 and shorter peptides Intestinal cells (enterocytes)
Intestinal cells Peptides into amin oacids Peptidases

Amino acid metabolism

Amino acids are the building blocks of many functional structures in the human body. They are used to construct proteins that have functions in the body, but can also be used to create evergy like carbohydrates do (though through a different mechanism).

Examples of proteins built by the body are:

  • Muscle fibers
  • Immune system receptors
  • Bone

Pretty much all organs in the body use proteins to some extent.

Essential amino acids are amino acids the body can not produce itself and thus needs to extract from food. There are 9 essential and thus 13 non-essential amino acids.

Essential amino acids are not more important than the non-essential.