How Digestion Works: From First Bite to the Colon

Food doesn’t just dissolve when you swallow it. It goes through a 25-foot system of mechanical grinding, acid treatment, enzymatic breakdown, and selective absorption before what remains arrives at the colon.

Each segment has a distinct job. Understanding what those jobs are explains why so many digestive symptoms trace back to specific failures in specific segments.

The Mouth: Where Chemistry Starts

Digestion begins before you swallow. Saliva contains salivary amylase, an enzyme that cleaves alpha-1,4 glycosidic bonds in starch, beginning the process of breaking it into smaller carbohydrate chains. Saliva also contains lingual lipase, which starts a minor degree of fat digestion.

But the most important function of chewing is mechanical: it increases the surface area of food. Surface area determines how much enzyme can contact the substrate simultaneously. A well-chewed bite of food exposes dramatically more surface to amylase than a poorly chewed one, speeding downstream digestion.

Saliva also coats food in mucin, a lubricating glycoprotein that makes swallowing possible and begins protecting the esophageal and gastric lining from the abrasive food bolus.

The Stomach: The Acid Chamber

The stomach is a muscular bag that does two main things: churns food into a semi-liquid called chyme, and creates a highly acidic environment (pH 1.5-3.5) using hydrochloric acid secreted by parietal cells.

That acid serves several purposes. It activates pepsinogen (secreted by chief cells) into pepsin, the primary protein-digesting enzyme. Pepsin begins unraveling protein structure by cleaving specific peptide bonds. Stomach acid also kills most swallowed bacteria, reducing pathogen load before food reaches the intestine.

Gastric lipase handles a modest amount of fat digestion. The stomach also secretes intrinsic factor from parietal cells, which is required for vitamin B12 absorption later in the small intestine.

The churning action of the stomach’s muscular walls grinds food into particles typically under 1-2mm before the pyloric sphincter allows them to pass into the small intestine. Fat slows gastric emptying significantly. High-fat meals stay in the stomach longer, which is partly why fatty foods feel more filling.

The Small Intestine: Where Most Absorption Happens

The small intestine is the primary absorption site for essentially all nutrients. It’s roughly 20 feet long and lined with a structure optimized for surface area.

The mucosal surface has circular folds (plicae circulares). Those folds are covered in finger-like projections called villi. Each villus is covered in even smaller projections called microvilli, which together form the brush border. This three-level structure gives the small intestine an absorptive surface area of roughly 250 square meters in an adult. The same area as a tennis court.

The first section, the duodenum, receives two important secretions:

Bile, made in the liver and stored in the gallbladder, is released into the duodenum when fat is detected. Bile is an emulsifier: it coats fat droplets, breaking large globules into smaller ones that pancreatic lipase can access. Without emulsification, fat digestion is severely impaired.

Pancreatic juice contains a mixture of digestive enzymes: pancreatic amylase (completing starch breakdown), pancreatic lipase (the main fat-digesting enzyme), and protease enzymes including trypsin, chymotrypsin, and elastase (breaking proteins into smaller peptides and amino acids). Pancreatic juice also contains bicarbonate, which neutralizes stomach acid as chyme enters the duodenum.

The middle section, the jejunum, is where most carbohydrate, protein, and fat absorption occurs. Brush border enzymes in the microvilli complete the final breakdown of disaccharides to monosaccharides and short peptides to amino acids.

Glucose and amino acids are absorbed by active transport into intestinal cells and then into the portal bloodstream. Fats are reassembled into triglycerides inside intestinal cells, packaged into lipoprotein particles called chylomicrons, and released into the lymphatic system rather than directly into the blood.

The final section, the ileum, absorbs bile acids (recycling them back to the liver via enterohepatic circulation), vitamin B12 (via the intrinsic factor receptor system), and some remaining nutrients.

The Large Intestine: Water, Electrolytes, and Fermentation

About 1.5 liters of liquid material enters the colon daily. The large intestine recovers most of it: about 1.3-1.4 liters of water are absorbed, leaving roughly 100-200ml in stool.

The colon also houses the gut microbiome: approximately 100 trillion bacteria that ferment the dietary fiber that the small intestine couldn’t digest. This fermentation produces short-chain fatty acids (butyrate, propionate, acetate), which feed colonocytes and have various systemic effects covered in the short-chain fatty acids guide.

Colonic motility (the coordinated contractions that move stool toward the rectum) is driven by the enteric nervous system and modulated by diet. Fiber increases stool bulk and speeds transit. Dehydration slows transit and increases water reabsorption, leading to harder, drier stools. Most constipation is a motility and hydration problem, not a structural one.

Gut Motility: The Invisible Machinery

Movement through the GI tract is controlled by peristalsis, the coordinated contraction and relaxation of circular and longitudinal muscle layers in the gut wall. This is orchestrated by the enteric nervous system.

Between meals, the migrating motor complex sweeps through the small intestine every 90-120 minutes, pushing undigested residue toward the colon. Eating interrupts this cycle.

The time food spends in the stomach, small intestine, and large intestine varies substantially by meal composition. High-fiber meals move faster. High-fat meals move slower. Individual variation in motility is large and is one reason healthy people have very different normal bowel habits.

This article is for educational purposes only. It’s not medical advice. Talk to your doctor or a registered dietitian before making significant changes to your diet.