The last article about how our gastric acids kill pervasive clostridium botulinum bacteria in our environment raised an interesting question: How come such strong gastric acids do not cause the stomach to digest itself?

A chemical dance

And the answer is a sophisticated dance of chemicals, involving hydrochloric acid and a vigorous enzyme called pepsin. The way this chemical tango works involves precise timing and ingenious co-ordination involving the secretion of other compounds – any tiny misstep would be severely injurious to our digestive system.

Hydrochloric acid

The main gastric acid is hydrochloric acid, an acid potent enough to pickle steel, and powerful enough to destroy most of the strains of bacteria and fungi that we are constantly inadvertently ingesting in our food, including clostridium botulinum.

The initial pH of hydrochloric acid emitted into the stomach can be 10 times the acidity of pure lemon juice. Photo: Rob Bertholf/Flickr

Depending on concentration, the initial pH of hydrochloric acid (HCl) discharged into the stomach cavity (or lumen) can be less than pH 1, more than 10 times the acidity of pure lemon juice. However, this pH is usually diluted by the presence of food and other ingested fluids.

The parietal cells in the inner layer of the stomach (the mucosa) are responsible for secreting HCl into the lumen. How this works is ingenious. One function of the parietal cell involves a “proton pump” mechanism where potassium ions (K+), are recycled by hydrogen ions (H+) directly in the lumen – this involves the cell combining carbon dioxide with water to form carbonic acid which is then catalysed by an enzyme called carbonic anhydrase into H+ and bicarbonate (HCO3-) – the H+ then swaps out the K+ ions originally output from the parietal cell.

This function is complemented by another chloride ion “exchanger” in the parietal cell which picks up chloride ions (Cl-) from blood by exchanging them with bicarbonate ions from the previous function. The resulting free H+ and Cl- ions then combine as HCl outside of the parietal cells, in the lumen. This avoids damage to the parietal cells themselves.

During the secretion of HCl, an additional protective layer of mucus is also secreted by goblet cells in the mucosa to further shield other parts of the inner stomach from HCl.

Resistant bacteria

Despite the extreme acidity of gastric HCl, there is a famous species of bacteria that can survive and breed in the harsh environment in our stomachs. The bacteria is called Helicobacter pylori, and is believed to be the cause of chronic gastritis and gastric ulcers.

Curiously, over 80% of humans are infected with Helicobacter pylori and do not display any symptoms, so a theory suggests that this bacteria may form part of the stomach’s bacterial fauna and becomes problematic only under certain (currently unknown) circumstances.

Large molecules

The dance with HCl continues with a large molecule called pepsinogen which is secreted by gastric chief cells in the mucosa. By itself, pepsinogen is inert because it is a zymogen, which is a precursor to a potent enzyme called pepsin.

Production of pepsinogen is stimulated by a hormone called gastrin which is produced as a response to signals from the stomach, such as distension or the detection of proteins in the lumen. Gastric chief cells also produce pepsinogen due to other signals received from the vagus nerve, usually as a result of emotional or other types of stress.

On contact with HCl, pepsinogen unwraps itself, losing 44 amino acids in the process from the molecule, which results in a new pepsin enzyme molecule. Pepsin molecules then initiate a chain reaction as they also act as catalysts to cleave away the same 44 amino acids from other pepsinogen molecules without the need for further HCl, resulting in more pepsin.


Pepsin is a one of the earliest known enzymes to be isolated from stomach tissue. This was done in 1836 by a German physician called Theodor Schwann, who found that pepsin can break down proteins in egg albumin into shorter peptides chains. Basically, Schwann discovered that pepsin is a digestive enzyme which targets proteins. Such protein digestive enzymes are now known as proteases.

Pepsin is a potent protease, and particular good at cleaving away many types of peptide bonds holding together peptides (chains of amino acids) that make up proteins. It works efficiently in strongly acidic environments where the acid also helps to unfurl proteins by denaturing them.

There are two other proteases in the human stomach, chymotrypsin and trypsin and between these three proteases, the stomach is able to pre-process all the types of digestible proteins in our diets, ensuring that they are ready for absorption later by the intestines. Pepin is most efficient at cleaving peptide bonds between hydrophobic (water-resistant) amino acids as well as amino acid chains containing phenylalanine, tryptophan, and tyrosine molecules.

Pepsin & acid reflux

From understanding how proteases work, you should now be wondering how come pepsin does not attack and digest the inner lining of the stomach, which is made of protein-based muscle tissues. The answer is two-fold. The mucus layer secreted by the goblet cells in the mucosa also helps to prevent pepsin reaching the inner stomach lining. Additionally, pepsin is only released when pepsinogen is unbundled by HCl, and this happens inside the lumen, away from the stomach wall.

However, when there is some malfunction in the stomach, then pepsin can digest away the stomach lining, resulting in potentially dangerous stomach ulcers.

An example of how potent pepsin and HCL are is the raw, burning feeling in the throat whenever one vomits or there is any reflux from the stomach going back up the oesophagus. That tingly, painful, extremely sour/acidic sensation in the throat is actually due to HCl and pepsin denaturing and pre-digesting the oesophagus.

Tough bacteria

Most bacteria are unlikely to survive the harsh conditions in the human stomach. In most cases, the extreme acidity would denature the cell walls of bacteria, causing holes in the cell membranes into which HCl can flow in and destroy the bacteria.

Food has to be cooked properly before consumption. Hillary V/Flickr

But we can get ill because of toxins already produced by bacteria in food before we eat such contaminated food. Toxins are chemicals which are not affected by digestive systems, so never ingest food that has been left out for too long.

However, there are other bacteria other than Helicobacter pylori which can also survive the conditions in human stomachs. They include strains of salmonella, Escherichia coli (commonly known as E. coli) and shigella.

Their methods of evading the effects of our digestive tracts vary. Salmonella can hide and shield itself behind peptides that have been cleaved by pepsin, and then flow into the calmer intestinal tract where they can breed and cause severe illnesses. E. coli and shigella have evolved resistance to strong acids and can breed once in the intestinal tract.

Other types of bacteria disperse via spores which are unaffected by gastric acid. Two such examples of bacterial spores are Clostridium perfringens and Clostridium difficile which will activate only once they are in the intestinal tract.

Temperature, kinetic energy & tasteHeat can also kill bacteria. The latest UK food safety guidelines state that the danger zone for bacterial growth is between 8°C and 63°C, and recommend that food be cooked to reach an internal temperature of 75°C before serving. However, using temperature alone as a guideline to cooking usually means some meats would be overdone as temperature alone does not take into account the use of kinetic energy for cooking.

By this, I mean that one can cook and kill all bacteria if food is cooked to reach an internal temperature of 60°C (or more) and then left at that temperature for a longer cooking time – kinetic energy can also kill bacteria, not just temperature. This technique is used in sous vide cookers and can preserve taste better. More on this can be found in my previous article, The temperature of heat.

Note: This article was originally published in Star2.

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