11.7 Chemical Digestion and Absorption
The process of mechanical digestion is relatively simple. It involves the physical breakdown of food but does not alter its chemical makeup. Chemical digestion, on the other hand, is a complex process that reduces food into its chemical building blocks, which are then absorbed to nourish the cells of the body.
Chemical Digestion
Large food molecules (for example, proteins, lipids, nucleic acids, and starches) must be broken down into subunits that are small enough to be absorbed by the lining of the gastrointestinal tract. This is accomplished by enzymes through hydrolysis.
Carbohydrate Digestion
Carbohydrates are classified according to the number of monomers they contain of simple sugars (monosaccharides and disaccharides) and/or complex sugars (polysaccharides).
Glucose, galactose, and fructose are the three monosaccharides that are commonly consumed and are readily absorbed. While indigestible polysaccharides do not provide any nutritional value, they do provide dietary fibre, which helps propel food through the gastrointestinal tract.
In the small intestine, pancreatic amylase does the ‘heavy lifting’ for starch and carbohydrate digestion (Figure 11.27). After amylases break down starch into smaller fragments, the brush border enzyme α-dextrinase starts working on α-dextrin, breaking off one glucose unit at a time. Three brush border enzymes hydrolyse sucrose, lactose, and maltose into monosaccharides. Sucrase splits sucrose into one molecule of fructose and one molecule of glucose; maltase breaks down maltose and maltotriose into two and three glucose molecules, respectively; and lactase breaks down lactose into one molecule of glucose and one molecule of galactose. Insufficient lactase can lead to lactose intolerance.

Case study

Protein Digestion
Proteins are polymers composed of amino acids linked by peptide bonds to form long chains. Digestion reduces them to their constituent amino acids.
Protein-digesting enzymes
Protein-digesting enzymes are either endopeptidase or exopeptidase. Endopeptidases break peptide bonds within the primary structure into smaller fragments. Exopeptidases cleave amino acids off the terminal end of the protein molecule. Carboxypeptidases remove an amino acid from the end with a free carboxyl group, and aminopeptidase act on the terminal amino acid with a free amino group.
Types of protein-digesting enzymes
- Endopeptidase
- Exopeptidase
- Carboxypeptidase
- Aminopeptidase
Protein digestion
Protein digestion begins in the stomach.
Gastrin, a hormone, initiates the breakdown of proteins in the stomach. The presence of food in the stomach leads to the secretion of pepsinogen by the chief cells of the gastric mucosa. Pepsinogen is activated to form pepsin (active form) through HCl produced by parietal cells of the gastric mucosa. Pepsin is an endopeptidase. In young animals, milk-coagulating rennin is secreted into the stomach for clot formation, which aids in transport into the small intestine.
Protein-digesting enzymes, site of production, and active forms
- Pepsin (Stomach)
- Enterokinase (Duodenum)
- Trypsinogen (Pancreas, inactive) to trypsin (small intestine)
- Chymotrypsinogen (Pancreas, inactive) to chymotrypsin (small intestine) by trypsin
- Procarboxypeptidase (Pancreas, inactive) to carboxypeptidase (chymotrypsin, small intestine) by trypsin
The next portion of digestion occurs in the small intestine, which plays a major role in protein digestion. The hormone secretin, in the duodenum, stimulates enzymatic secretions from the pancreas, which includes three inactive forms: trypsinogen, chymotrypsinogen, and procarboxypeptidase. Enterokinase, also secreted at the duodenum, converts trypsinogen into trypsin, which then converts chymotrypsinogen and procarboxypeptidase to their active forms—chymotrypsin and carboxypeptidase.
Trypsin plays a very crucial role in protein digestion in the small intestine.
Digestion is finished off by other enzymes including aminopeptidases and dipeptidases from mucosal membranes. The goal of this process is to bring polypeptides down to single free amino acids.
Just like carbohydrates and fats, absorption is facilitated by the villi within the small intestine into the bloodstream. Normal free proteins are transported via active transport, energy requiring, and use sodium as a kind of cotransported molecule. Whole proteins use a direct transport method that does not require energy. Free amino acids are the major form for absorption into the circulatory system. However, some di-, tri-, and oligopeptides are also absorbed. Specific carrier proteins based on the nature of the amino acid (for example, neutral, basic, acid, large, small) are involved in amino acid transport. The naturally occurring L-forms of amino acids are absorbed preferentially to D-forms. Some amino acids may compete with others for carrier proteins and transport. For example, arginine inhibits lysine transport and high concentrations of leucine increase the need for isoleucine. Some neutral amino acids inhibit basic amino acid transport.
The fate of amino acids
Absorbed amino acids could be used for tissue protein, enzyme, and hormone synthesis and deamination or transamination, and the carbon skeleton can be used for energy. Undigested proteins in the hindgut are subjected to microbial fermentation leading to the production of ammonia and other polyamines.
Protein digestion in ruminants
Protein digestion in the ruminant animals can be divided into two phases: (i) digestion (degradation) in the reticulorumen and (ii) digestion in the abomasum and small intestine. Therefore, in ruminant animals, dietary proteins are classified as rumen degradable and rumen undegradable proteins.
In ruminants, dietary proteins can be classified as degradable or undegradable proteins.
Like monogastric animals, the main goal for protein supplementation is to provide amino acids to the animal. However, in ruminants, proteins serve as a source of nitrogen for rumen microbes so they can make their own microbial protein from scratch. Microbes do not care where the nitrogen sources come from and can use nonprotein nitrogenous substances such as urea for microbial protein synthesis. Urea is 100% degradable in the rumen by microbial urease (can be toxic at higher levels).
Protein entering the rumen may be degraded by both bacteria and protozoa, which produce proteolytic enzymes. The rumen microbes provide proteases and peptidases to cleave peptide bonds in polypeptides to release the free amino acids from proteins. Several factors such as solubility and the physical structure of protein can affect rumen degradation. These rumen-degraded amino acids release NH3 and the C skeleton by a process called deamination. Along with volatile fatty acids (from carbohydrates), rumen microbes synthesize their own microbial protein, which serves as a primary source of protein to the host ruminant animals.
Microbial protein is enough for maintenance and survival but not for high-producing animals. Ammonia absorbed from rumen is converted to urea and secreted into the blood as blood urea nitrogen (BUN). Urea can be filtered and recycled to the rumen via saliva or through the rumen wall. The concentration of BUN in ruminants reflects the efficiency of protein utilisation.
Not all proteins are degraded in the rumen.
Proteins that are not degraded by rumen microbes are called escaped, bypassed, or undegradable (rumen undegradable protein, RUP), and have a low rumen degradation rates (for example, proteins in corn).
RUP enters the abomasum and small intestine of the ruminant animal for digestion and absorption. Proteins reaching the small intestine could be RUP or those from microbial sources. The amino acid needs of the host animal are met by RUP and microbial proteins. Both ruminants and monogastrics require the essential amino acids in their diet, and amino acids cannot be stored within the body, so a constant dietary supply is necessary. Some of the similarities and differences in monogastric and ruminant animals in protein digestion or degradation are shown in table 5.1 below.
Table 5.1. Comparison of protein digestion in monogastric and ruminant animals
Monogastrics | Differences (Ruminants) |
Amino acid profile at small intestine reflects the diet | Amino acid profile at the small intestine is different from diet |
No upgrading of low quality dietary protein | Up-grade low quality dietary protein |
Protein quality not downgraded | Down-grade high quality dietary protein |
Cannot use non protein nitrogen | Able to use non protein nitrogen (for example, urea) |
Constant supply of amino acids are required | Constant supply of amino acids are required |
Case study
Optimising Protein Intake in Livestock
Livestock fed with corn-based diets showed signs of protein deficiency, such as poor growth rates, reduced milk production, and overall poor health. Testing revealed low levels of essential amino acids, particularly lysine and methionine.
Research
Among the cereal grains, corn has the highest bypass potential. However, it should be noted that corn is deficient in essential amino acids such as lysine and methionine. Different feed formulations are tested in feed trials, including corn-based diets supplemented with animal protein sources like fish meal and meat meal. Animal protein sources such as fish meal and meat meal have high bypass potential. Forages are dried and subjected to heat treatment to increase bypass potential. Feed processing methods, such as pelleting, steam rolling or flaking, tend to denature the feed protein due to the generation of heat, thereby ‘protecting’ the protein from lysis in the rumen. Rumen protected protein sources (through formaldehyde treatment) that remain intact in the rumen and dissolve in the abomasum are commercially available.
Outcome
Supplementing with animal protein sources and using heat-treated forages improves protein intake and overall livestock health. Feed processing methods and rumen-protected proteins effectively protect feed protein from lysis in the rumen, ensuring better protein absorption in the abomasum and addressing the deficiencies observed with corn-based diets.
All proteins in the body are in a state of constant flux, the size of the amino acid pool depends on a balance between synthesis and degradation. Amino acid metabolism involves protein and nonessential amino acid synthesis and disposal of toxic ammonia.
The fate of absorbed proteins
Absorbed proteins are used for anabolic purposes such as synthesis of nonessential amino acids, tissue protein synthesis, enzyme or hormone synthesis, deamination, or transamination.
Amino acid synthesis and degradation are brought about by two reactions called transamination and deamination that occur in the liver.

Lipid Digestion
The most common dietary lipids are triglycerides, which are made up of a glycerol molecule bound to three fatty acid chains. Small amounts of dietary cholesterol and phospholipids are also consumed.
The three lipases responsible for lipid digestion are lingual lipase, gastric lipase, and pancreatic lipase. However, because the pancreas is the only consequential source of lipase, virtually all lipid digestion occurs in the small intestine. Pancreatic lipase breaks down each triglyceride into two free fatty acids and a monoglyceride. The fatty acids include both short-chain (less than 10 to 12 carbons) and long-chain fatty acids.
Monogastric animals
The digestion process involves the breakdown of lipid molecules into smaller ones that are eventually absorbed into the blood. Lipids are not soluble in water, which is the aqueous medium of the digestive tract (lipids are hydrophobic). Therefore, the initial step in lipid digestion is to make them dissolve in water. How? Through a process called emulsification, or the dispersion of lipids in small droplets.
Emulsification is the dispersion of lipids in small droplets.
Dietary lipids (mostly triglycerides), upon their entry into the small intestine, are emulsified by bile salt (also called bile acid) released from the gall bladder. Bile salt functions as a detergent (due to their OH and COOH groups), and large lipid molecules form smaller lipid droplets surrounded by a layer of bile. Emulsified lipids are acted upon by enzyme pancreatic lipase and converted into fatty acids, monoglycerides and glycerol.
The lipid digestion products are assembled into micelles. These are temporary combinations of bile salt, fatty acids, monoglycerides, and other fat-soluble substances such as vitamins and cholesterol. The micelles are water soluble and enable the lipid digestion products to be transported to the small intestinal surface for absorption. At the site of absorption, the micelle breaks down and the bile salt returns to the intestine for continuing emulsification processes (bile salt recycling). The components are absorbed into the small intestine by passive diffusion. In a nutshell, the ability to form micelles and the presence of bile salt are very important for lipid digestion, and the lack of it can affect digestibility. For example, saturated fatty acids are less efficient than unsaturated fatty acids in forming micelles. So a blend of saturated and unsaturated fatty acids is used in animal rations.
Micelles and chylomicrons are temporary compounds formed during lipid absorption.
Once inside the intestinal cell (or enterocyte), the monoglycerides and fatty acids are reesterified, and together with free and esterified cholesterol, lipoproteins and phospholipids are assembled into chylomicrons. The chylomicrons are secreted into the lymphatic system.
Ruminant animals
In ruminant animals, the lipid content of the diet is low (under 5%) and comes from different sources such as grass, leaves, oil seeds, or cereal grains. Leaf or grass lipids are mainly galactolipids, phospholipids, waxes, pigments, and essential oils, and oil seed or grain lipids are mainly triglycerides.
In the rumen, there is no emulsifying agent or pancreatic lipase enzyme. Instead, there are rumen microbes producing microbial lipases. When dietary lipids enter the rumen, the initial step is the hydrolysis of the ester linkages in triglycerides, phospholipids, and glycolipids. Hydrolysis of dietary lipids is done by microbial lipases, which releases glycerol and fatty acids (free fatty acids) from the lipid backbone. Glycerol is readily metabolised by the rumen bacteria to form propionic acid. Feeding of supplemental fat increases the proportion of propionic acid (one of the volatile fatty acids, or VFAs) and the propionate:acetate ratio in ruminants. Hydrolysis is a prerequisite for the next step.
Lipids undergo hydrolysis, biohydrogenation, and conjugated fatty acid formation in the rumen.
Biohydrogenation of unsaturated fatty acids is the second major transformation that dietary lipids can undergo in the rumen. Fatty acids with double bonds are altered by microbes to form more stable fatty acids. Fatty acids such as linoleic acid are converted “conjugated” fatty acids (e.g., conjugated linoleic acid, or CLA) in which the double bonds are not separated by methylene (CH2) groups. The position of double bonds is altered, and the fatty acids are converted to more stable “trans” fats. Some odd-numbered (e.g., C19:0) and branched-chain fatty acids are also created during this process. For example, linoleic acid (C18:2 n-6), where the double bonds are in the cis position (cis9-cis12), is converted to several isomers of CLAs during this conversion step.
Reflective question
Why biohydrogenation?
Too much unsaturated fatty acids can be toxic to rumen microbes.
Lipid digestion in the ruminant small intestine is very similar to lipid digestion in monogastric animals. The two key secretions enabling this process are bile and pancreatic juices. These secretions enable the lipids to form micelles for absorption. Bile supplies bile salts and pancreatic juice and enzymes. These compounds desorb the fatty acids from feed particles and bacteria, allowing the formation of micelles. Once micelles are formed, they facilitate the transfer of water-insoluble lipids across the intestinal epithelial cells of the jejunum, where the fatty acids are absorbed. Within the intestinal epithelial cells, the fatty acids are reesterified into triglycerides and then packaged into chylomicrons for transport in lymph to the blood.
Nucleic Acid Digestion
Two types of pancreatic nuclease are responsible for their digestion: deoxyribonuclease, which digests DNA, and ribonuclease, which digests RNA. The nucleotides produced by this digestion are further broken down by two intestinal brush border enzymes (nucleosidase and phosphatase) into pentoses, phosphates, and nitrogenous bases, which can be absorbed through the gastrointestinal tract wall. The large food molecules that must be broken down into subunits are summarised Table 11.7.
Table 11.7 Absorbable food substances
Source | Substance |
Carbohydrates | Monosaccharides: glucose, galactose and fructose |
Proteins | Single amino acids, dipeptides and tripeptides |
Triglycerides | Monoacylglycerides, glycerol and free fatty acids |
Nucleic acids | Pentose sugars, phosphates and nitrogenous bases |
Absorption
The mechanical and digestive processes have one goal: to convert food into molecules small enough to be absorbed by the epithelial cells of the intestinal villi. The absorptive capacity of the gastrointestinal tract is almost endless. Although the entire small intestine is involved in the absorption of water and lipids, most absorption of carbohydrates and proteins occurs in the jejunum. Notably, bile salts and vitamin B12 are absorbed in the terminal ileum. By the time chyme passes from the ileum into the large intestine, it is essentially indigestible food residue (mainly plant fibres like cellulose), some water and millions of bacteria and other microorganisms.
Absorption can occur through five mechanisms: (1) active transport, (2) passive diffusion, (3) facilitated diffusion, (4) co-transport (or secondary active transport), and (5) endocytosis.
The routes of absorption for each food category are summarised in Table 11.8.
Table 11.8 Absorption in the gastrointestinal tract
Food | Breakdown products | Absorption mechanisms | Entry to bloodstream | Destination |
Carbohydrates | Glucose | Co-transport with sodium ions | Capillary blood in villi | Liver via hepatic portal vein |
Galactose | Co-transports with sodium ions | Capillary blood via villi | Liver via hepatic portal vein | |
Fructose | Facilitated diffusion | Capillary blood in villi | Liver via hepatic portal vein
|
|
Protein | Amino acids | Co-transported with sodium ions | Capillary blood in villi | Liver in hepatic portal vein
|
Lipids | Long-chain fatty acids | Diffusion into intestinal cells where they are combined with proteins to create chylomicrons
|
Lacteals of villi | Systemic circulation via lymph entering thoracic duct |
Monoacylglycerides | Diffusion into intestinal cells, where they are combined with proteins to create chylomicrons
|
Lacteals of villi | Systemic circulation via lymph entering the thoracic duct | |
Short-chain fatty acids | Simple diffusion | Capillary blood in villi | Liver via hepatic portal vein | |
Glycerol | Simple diffusion | Capillary blood in villi | Liver via hepatic portal vein
|
|
Nucleic acid digestion products | Active transport via membrane carriers | Capillary blood in villi | Liver via hepatic portal vein |
Carbohydrate Absorption
All carbohydrates are absorbed in the form of monosaccharides. All normally digested dietary carbohydrates are absorbed; indigestible fibres are eliminated in the faeces. The monosaccharides glucose and galactose are transported into the epithelial cells by common protein carriers via secondary active transport (that is, co-transport with sodium ions). The monosaccharides leave these cells via facilitated diffusion and enter the capillaries through intercellular clefts. The monosaccharide fructose (which is in fruit) is absorbed and transported by facilitated diffusion alone. The monosaccharides combine with the transport proteins immediately after the disaccharides are broken down.
Protein Absorption
Active transport mechanisms, primarily in the duodenum and jejunum, absorb most proteins as their breakdown products, amino acids. Almost all (95 to 98 percent) protein is digested and absorbed in the small intestine. The type of carrier that transports an amino acid varies. Most carriers are linked to the active transport of sodium. Short chains of two amino acids (dipeptides) or three amino acids (tripeptides) are also transported actively. However, after they enter the absorptive epithelial cells, they are broken down into their amino acids before leaving the cell and entering the capillary blood via diffusion.
Lipid Absorption
About 95 percent of lipids are absorbed in the small intestine. Bile salts not only speed up lipid digestion, they are also essential for the absorption of the end products of lipid digestion. Short-chain fatty acids are water soluble and can enter the absorptive cells (enterocytes) directly. Despite being hydrophobic, the small size of short-chain fatty acids enables them to be absorbed by enterocytes via simple diffusion, and then take the same path as monosaccharides and amino acids into the blood capillary of a villus.
The products of nucleic acid digestion—pentose sugars, nitrogenous bases, and phosphate ions—are transported by carriers across the villus epithelium via active transport. These products then enter the bloodstream.
Mineral Absorption
The electrolytes absorbed by the small intestine are from both GI secretions and ingested foods. Since electrolytes dissociate into ions in water, most are absorbed via active transport throughout the entire small intestine. During absorption, co-transport mechanisms result in the accumulation of sodium ions inside the cells, whereas anti-port mechanisms reduce the potassium ion concentration inside the cells. To restore the sodium-potassium gradient across the cell membrane, a sodium-potassium pump requiring ATP pumps sodium out and potassium in.
In general, all minerals that enter the intestine are absorbed, whether you need them or not. Iron and calcium are exceptions; they are absorbed in the duodenum in amounts that meet the body’s current requirements, as follows:
Iron—The ionic iron needed for the production of haemoglobin is absorbed into mucosal cells via active transport. Once inside mucosal cells, ionic iron binds to the protein ferritin, creating iron-ferritin complexes that store iron until needed. When the body has enough iron, most of the stored iron is lost when worn-out epithelial cells slough off. When the body needs iron because, for example, it is lost during acute or chronic bleeding, there is increased uptake of iron from the intestine and accelerated release of iron into the bloodstream. Since women experience significant iron loss during menstruation, they have around four times as many iron transport proteins in their intestinal epithelial cells as do men.
Calcium—Blood levels of ionic calcium determine the absorption of dietary calcium. When blood levels of ionic calcium drop, parathyroid hormone (PTH) secreted by the parathyroid glands stimulates the release of calcium ions from bone matrices and increases the reabsorption of calcium by the kidneys. PTH also upregulates the activation of vitamin D in the kidney, which then facilitates intestinal calcium ion absorption.
Vitamin Absorption
The small intestine absorbs the vitamins that occur naturally in food and supplements. Fat-soluble vitamins (A, D, E, and K) are absorbed along with dietary lipids in micelles via simple diffusion. This is why you are advised to eat some fatty foods when you take fat-soluble vitamin supplements. Most water-soluble vitamins (including most B vitamins and vitamin C) also are absorbed by simple diffusion. An exception is vitamin B12, which is a very large molecule. Intrinsic factor secreted in the stomach binds to vitamin B12, preventing its digestion and creating a complex that binds to mucosal receptors in the terminal ileum, where it is taken up by endocytosis.
Case study
A 2-year-old Beagle, Muffin, presented with acute vomiting and mild abdominal discomfort. Beagles are known for their strong food drive and are predisposed to dietary indiscretion, often ingesting inappropriate or spoiled food items. Clinical signs and history suggested mild gastritis. Diagnostic imaging ruled out obstruction or foreign body ingestion. Muffin responded well to treatment, with vomiting resolving within 48 hours and appetite returning to normal. This case highlights the importance of owner awareness and dietary supervision in breeds prone to indiscriminate eating.
Beagle by Daniel Flathagen is CC BY SA
Water Absorption
Each day, about nine litres of fluid enter the small intestine. About 2.3 litres are ingested in foods and beverages, and the rest is from GI secretions. About 90 percent of this water is absorbed in the small intestine. Water absorption is driven by the concentration gradient of the water: The concentration of water is higher in chyme than it is in epithelial cells. Thus, water moves down its concentration gradient from the chyme into cells. As noted earlier, much of the remaining water is then absorbed in the colon.
Section Review
The small intestine is the site of most chemical digestion and almost all absorption. Chemical digestion breaks large food molecules down into their chemical building blocks, which can then be absorbed through the intestinal wall and into the general circulation. Intestinal brush border enzymes and pancreatic enzymes are responsible for most of the chemical digestion. The breakdown of fat also requires bile.
Most nutrients are absorbed by transport mechanisms at the apical surface of enterocytes. Exceptions include lipids, fat-soluble vitamins, and most water-soluble vitamins. With the help of bile salts and lecithin, the dietary fats are emulsified to form micelles, which can carry the fat particles to the surface of the enterocytes. There, the micelles release their fats to diffuse across the cell membrane. The fats are then reassembled into triglycerides and mixed with other lipids and proteins into chylomicrons that can pass into lacteals. Other absorbed monomers travel from blood capillaries in the villus to the hepatic portal vein and then to the liver.
Review Questions
Critical Thinking Questions
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