Proteins are essential nutrients for the human body. They are one of the building blocks of body tissue, and can also serve as a fuel source. As fuel, proteins contain 4 kcal per gram, just like carbohydrates and unlike lipids, which contain 9 kcal per gram.

Proteins are polymer chains made of amino acids linked together by peptide bonds. In nutrition, proteins are broken down in the stomach during digestion by enzymes known as proteases into smaller polypeptides to provide amino acids for the body, including the essential amino acids that cannot be biosynthesized by the body itself.

Amino acids can be divided into three categories: essential amino acids, non-essential amino acids and conditional amino acids. Essential amino acids cannot be made by the body, and must be supplied by food. Non-essential amino acids are made by the body from essential amino acids or in the normal breakdown of proteins. Conditional amino acids are usually not essential, except in times of illness, stress or for someone challenged with a lifelong medical condition.

Essential amino acids are leucine, isoleucine, valine, lysine, threonine, tryptophan, methionine, phenylalanine and histidine. Non-essential amino acids include alanine, asparagine, aspartic acid and glutamic acid. Conditional amino acids include arginine, cysteine, glutamine, glycine, proline, serine, and tyrosine.

Amino acids are found in animal sources such as meats, milk, fish and eggs, as well as in plant sources such as whole grains, pulses, legumes, soy, fruits, nuts and seeds. Vegetarians and vegans can get enough essential amino acids by eating a variety of plant proteins.

Protein functions in body

Protein is a nutrient needed by the human body for growth and maintenance. Aside from water, proteins are the most abundant kind of molecules in the body. Protein can be found in all cells of the body and is the major structural component of all cells in the body, especially muscle. This also includes body organs, hair and skin. Proteins also are utilized in membranes, such as glycoproteins. When broken down into amino acids, they are used as precursors to nucleic acid, co-enzymes, hormones, immune response, cellular repair and molecules essential for life. Finally, protein is needed to form blood cells.

Proteins are very important molecules in our cells. They are involved in virtually all cell functions. Each protein within the body has a specific function. Some proteins are involved in structural support, while others are involved in bodily movement, or in defense against germs. Proteins vary in structure as well as function. They are constructed from a set of 20 amino acids and have distinct three-dimensional shapes. Below is a list of several types of proteins and their functions.

Protein Functions

Antibodies - are specialized proteins involved in defending the body from antigens (foreign invaders). They can travel through the blood stream and are utilized by the immune system to identify and defend against bacteria, viruses, and other foreign intruders. One way antibodies counteract antigens is by immobilizing them so that they can be destroyed by white blood cells.

Contractile Proteins - are responsible for movement. Examples include actin and myosin. These proteins are involved in muscle contraction and movement.

Enzymes - are proteins that facilitate biochemical reactions. They are often referred to as catalysts because they speed up chemical reactions. Examples include the enzymes lactase and pepsin. Lactase breaks down the sugar lactose found in milk. Pepsin is a digestive enzyme that works in the stomach to break down proteins in food.

Hormonal Proteins - are messenger proteins which help to coordinate certain bodily activities. Examples include insulin, oxytocin, and somatotropin. Insulin regulates glucose metabolism by controlling the blood-sugar concentration. Oxytocin stimulates contractions in females during childbirth. Somatotropin is a growth hormone that stimulates protein production in muscle cells.

Structural Proteins - are fibrous and stringy and provide support. Examples include keratin, collagen, and elastin. Keratins strengthen protective coverings such as hair, quills, feathers, horns, and beaks. Collagens and elastin provide support for connective tissues such as tendons and ligaments.

Storage Proteins - store amino acids. Examples include ovalbumin and casein. Ovalbumin is found in egg whites and casein is a milk-based protein.

Transport Proteins - are carrier proteins which move molecules from one place to another around the body. Examples include hemoglobin and cytochromes. Hemoglobin transports oxygen through the blood. Cytochromes operate in the electron transport chain as electron carrier proteins.


Newborns of mammals are exceptional in protein digestion and assimilation in that they can absorb intact proteins at the small intestine. This enables passive immunity from milk.



Digestion of proteins starts in the stomach and accomplishes in the small intestine. Several hormones take part in protein digestion. They include trypsin, chymotrypsin, pepsin, etc. To learn more, keep reading.

There is a process by which the body converts the ingested foods into its simpler constituents that can be easily absorbed and assimilated. This above mentioned process gives us an idea of what is digestion. Proteins are defined as the group of complex organic macromolecules containing carbon, oxygen, hydrogen, nitrogen and sulfur and are composed of one or more amino acid chains. Proteins are components of enzymes, hormones and antibodies, and therefore are very important for an organism's survival. The present article focuses its discussion on how protein is digested inside a human's body. The digestion of proteins takes place in two organs, stomach and small intestine. Let's learn what happens in each of them during protein digestion.


Digestion of Protein in Stomach

Protein digestion does not start with chewing of food in the mouth. It begins in the stomach. The stomach is especially designed for the purpose of digestion of foods. Its walls are composed of strong muscles. These muscles mix and churn the ingested food. They do it with the help of rhythmic contractions, occurring at the average rate of 3 per min. The lining of the stomach contains glands. Their function is to secrete gastric juice. It is a colorless and strong acidic liquid at a pH of 1-3. The main components of gastric juice are digestive enzymes, hydrochloric acid and mucus.

Hydrochloric acid produced in the stomach is a very strong acid. It is produced by the type of epithelial cells called parietal cells present in the lining of the stomach. HCl is so strong that it can easily digest the stomach itself. But such a destructive process is prevented from occurring by another secretion of the stomach called mucus. It protects the delicate cell lining of the stomach as well as moistens the food present there. However, the cells in the stomach lining keep getting destroyed by hydrochloric acid. It gets replaced by newer cells. According to studies, the lining of the stomach gets completely replaced every third day. Protein digestion in the stomach occurs mainly by the action of hydrochloric acid (HCl) and enzyme called pepsin. The enzyme pepsin forms in the stomach when its precursor pepsinogen reacts with HCl. Pepsin and HCl breaks the protein bonds. The foods containing proteins are separated from each other. The proteins get separated out, which is necessary for the action of enzymes. The enzymes needed for digesting proteins are proteinases and proteases. These enzymes break down the molecules of proteins into its constituents, amino acids by a depolymerisation process called hydrolysis. It is described as a chemical reaction wherein a water molecule breaks down into hydrogen cations and hydroxide anions. The rate of action of these protein digestive enzymes is influenced by a number of factors. Some of them are concentration and amount of the enzyme, amount of protein food needed to be digested, temperature of the food, acidity of the food, acidity of the stomach and presence of antacids or other inhibitors of digestion. The task of enzymes is to breakdown of protein molecules into simpler structures called peptones and proteose. They leave the stomach and enter the small intestine with the help of peristalsis movement of the body. It is called chyme. The entire process of protein digestion in the stomach takes about 4 hours.

Digestion of Protein in Small Intestine

The chyme first enters duodenum, which is a part of small intestine. It is a C-shaped structure about 25 centimeters long. The chyme is very acidic but here it mixes with an alkaline secretion and becomes neutral. Pancreas secrete digestive enzyme, trypsin and chymotrypsin, which reach the duodenum through bloodstream and aid in the breakdown of proteins. They break the complex protein molecules into its constituents, amino acids. They accomplish this task of breaking down by hydrolysis, described above. The walls of the small intestine are covered with numerous finger like projections, known as villi. They increase the surface area of the small intestine by about 600 times. Each villus contains a network of blood capillaries and lymph vessels. The amino acids pass through the capillary walls, and get carried away by the blood flowing through the network. In this manner, the amino acids thus produced get absorbed, reach different body parts and finally get converted to human proteins. The human body uses proteins for building and maintaining its structures, sometimes for energy generation as well.

Trypsin is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. Trypsin is produced in the pancreas as the inactive proenzyme trypsinogen. Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, except when either is followed by proline. It is used for numerous biotechnological processes. The process is commonly referred to as trypsin proteolysis or trypsinisation, and proteins that have been digested/treated with trypsin are said to have been trypsinized.


In the duodenum, trypsin catalyzes the hydrolysis of peptide bonds, breaking down proteins into smaller peptides. The peptide products are then further hydrolyzed into amino acids via other proteases, rendering them available for absorption into the blood stream. Tryptic digestion is a necessary step in protein absorption as proteins are generally too large to be absorbed through the lining of the small intestine.

Trypsin is produced in the pancreas, in the form of the inactive zymogen trypsinogen. When the pancreas is stimulated by cholecystokinin, it is then secreted into the first part of the small intestine (the duodenum) via the pancreatic duct. Once in the small intestine, the enzyme enteropeptidase activates it into trypsin by proteolytic cleavage. Auto catalysis does not happen with trypsin since trypsinogen is a poor substrate for trypsin. This activation mechanism is common for most serine proteases, and serves to prevent autodegradation of the pancreas.


The enzymatic mechanism is similar to that of other serine proteases. These enzymes contain a catalytic triad consisting of histidine-57, aspartate-102, and serine-195. These three residues form a charge relay that serves to make the active site serine nucleophilic. This is achieved by modifying the electrostatic environment of the serine. The enzymatic reaction that trypsins catalyze is thermodynamically favorable but requires significant activation energy (it is "kinetically unfavorable"). In addition, trypsin contains an "oxyanion hole" formed by the backbone amide hydrogen atoms of Gly-193 and Ser-195, which serves to stabilize the developing negative charge on the carbonyl oxygen atom of the cleaved amides.

The aspartate residue (Asp 189) located in the catalytic pocket (S1) of trypsins is responsible for attracting and stabilizing positively charged lysine and/or arginine, and is, thus, responsible for the specificity of the enzyme. This means that trypsin predominantly cleaves proteins at the carboxyl side (or "C-terminal side") of the amino acids lysine and arginine except when either is bound to a C-terminal proline., although large-scale mass spectrometry data suggest cleavage occurs even with proline. Trypsins are considered endopeptidases, i.e., the cleavage occurs within the polypeptide chain rather than at the terminal amino acids located at the ends of polypeptides.


Trypsins has an optimal operating pH of about 7.5-8.5 and optimal operating temperature of about 37C.

The activity of trypsins is not affected by the inhibitor tosyl phenylalanyl chloromethyl ketone, TPCK, which deactivates chymotrypsin. This is important because, in some applications, like mass spectrometry, the specificity of cleavage is important.

Trypsins should be stored at very cold temperatures (between −20C and −80C) to prevent autolysis, which may also be impeded by storage of trypsins at pH 3 or by using trypsin modified by reductive methylation. When the pH is adjusted back to pH 8, activity returns.

Clinical significance

Activation of trypsin from proteolytic cleavage of trypsinogen in the pancreas can lead to a series of events that cause pancreatic self-digestion, resulting in pancreatitis. One consequence of the autosomal recessive disease cystic fibrosis is a deficiency in transport of trypsin and other digestive enzymes from the pancreas. This leads to the disorder termed meconium ileus. This disorder involves intestinal obstruction (ileus) due to overly thick meconium, which is normally broken down by trypsins and other proteases, then passed in faeces.

Trypsin is available in high quantity in pancreases, and can be purified rather easily. Hence it has been used widely in various biotechnological processes.

In a tissue culture lab, trypsins are used to re-suspend cells adherent to the cell culture dish wall during the process of harvesting cells. Some cell types have a tendency to "stick" - or adhere - to the sides and bottom of a dish when cultivated in vitro. Trypsin is used to cleave proteins bonding the cultured cells to the dish, so that the cells can be suspended in fresh solution and transferred to fresh dishes.

Trypsin can also be used to dissociate dissected cells (for example, prior to cell fixing and sorting).

Trypsins can be used to break down casein in breast milk. If trypsin is added to a solution of milk powder, the breakdown of casein will cause the milk to become translucent. The rate of reaction can be measured by using the amount of time it takes for the milk to turn translucent.

Trypsin is commonly used in biological research during proteomics experiments to digest proteins into peptides for mass spectrometry analysis, e.g. in-gel digestion. Trypsin is particularly suited for this, since it has a very well defined specificity, as it hydrolyzes only the peptide bonds in which the carbonyl group is contributed either by an Arg or Lys residue.

Trypsin can also be used to dissolve blood clots in its microbial form and treat inflammation in its pancreatic form.


Gastric acid is a digestive fluid, formed in the stomach. It has a pH of 1.5 to 3.5 and is composed of hydrochloric acid (HCl) (around 0.5%, or 5000 parts per million) as high as 0.1 N, and large quantities of potassium chloride (KCl) and sodium chloride (NaCl). The acid plays a key role in digestion of proteins, by activating digestive enzymes, and making ingested proteins unravel so that digestive enzymes break down the long chains of amino acids.

Gastric acid is produced by cells lining the stomach, which are coupled to systems to increase acid production when needed. Other cells in the stomach produce bicarbonate, a base, to buffer the fluid, ensuring that it does not become too acidic. These cells also produce mucus, which forms a viscous physical barrier to prevent gastric acid from damaging the stomach. Cells in the beginning of the small intestine, or duodenum, further produce large amounts of bicarbonate to completely neutralize any gastric acid that passes further down into the digestive tract.

Gastric acid is produced by parietal cells (also called oxyntic cells) in the stomach. Its secretion is a complex and relatively energetically expensive process. Parietal cells contain an extensive secretory network (called canaliculi) from which the gastric acid is secreted into the lumen of the stomach. These cells are part of epithelial fundic glands in the gastric mucosa. The pH of gastric acid is 1.35 to 3.5 [2] in the human stomach lumen, the acidity being maintained by the proton pump H+/K+ ATPase. The parietal cell releases bicarbonate into the blood stream in the process, which causes a temporary rise of pH in the blood, known as alkaline tide.

The resulting highly acidic environment in the stomach lumen causes proteins from food to lose their characteristic folded structure (or denature). This exposes the protein's peptide bonds. The chief cells of the stomach secrete enzymes for protein breakdown (inactive pepsinogen and rennin). Hydrochloric acid activates pepsinogen into the enzyme pepsin, which then helps digestion by breaking the bonds linking amino acids, a process known as proteolysis. In addition, many microorganisms have their growth inhibited by such an acidic environment, which is helpful to prevent infection.

Role in disease

In hypochlorhydria and achlorhydria, there is low or no gastric acid in the stomach, potentially leading to problems as the disinfectant properties of the gastric lumen are decreased. In such conditions, there is greater risk of infections of the digestive tract (such as infection with Vibrio or Helicobacter bacteria).

In ZollingerEllison syndrome and hypercalcemia, there are increased gastrin levels, leading to excess gastric acid production, which can cause gastric ulcers.

In diseases featuring excess vomiting, patients develop hypochloremic metabolic alkalosis (decreased blood acidity by H+ and chlorine depletion).

Absorption of Amino Acids and Peptides

Dietary proteins are, with very few exceptions, not absorbed. Rather, they must be digested into amino acids or di- and tripeptides first. In previous sections, we've seen two sources secrete proteolytic enzymes into the lumen of the digestive tube:

                    the stomach secretes pepsinogen, which is converted to the active protease pepsin by the action of acid.

                    the pancreas secretes a group of potent proteases, chief among them trypsin, chymotrypsin and carboxypeptidases.

Through the action of these gastric and pancreatic proteases, dietary proteins are hydrolyzed within the lumen of the small intestine predominantly into medium and small peptides (oligopeptides).

The brush border of the small intestine is equipped with a family of peptidases. Like lactase and maltase, these peptidases are integral membrane proteins rather than soluble enzymes. They function to further the hydrolysis of lumenal peptides, converting them to free amino acids and very small peptides. These endproducts of digestion, formed on the surface of the enterocyte, are ready for absorption.

Absorption of Amino Acids

The mechanism by which amino acids are absorbed is conceptually identical to that of monosaccharides. The lumenal plasma membrane of the absorptive cell bears at least four sodium-dependent amino acid transporters - one each for acidic, basic, neutral and amino acids. These transporters bind amino acids only after binding sodium. The fully loaded transporter then undergoes a conformational change that dumps sodium and the amino acid into the cytoplasm, followed by its reorientation back to the original form.

Thus, absorption of amino acids is also absolutely dependent on the electrochemical gradient of sodium across the epithelium. Further, absorption of amino acids, like that of monosaccharides, contributes to generating the osmotic gradient that drives water absorption.

The basolateral membrane of the enterocyte contains additional transporters which export amino acids from the cell into blood. These are not dependent on sodium gradients.

General pathways of amino acids transformation

Deamination of amino acids, it kinds. The role of vitamins in deamination of amino acids.

Removal of an amino group from a molecule.

the elimination of an amino group (NH2) from organic compounds. Deamination is accompanied by the substitution of some other group, such as H, OH, OR, or Hal, for the amino group or by the formation of a double bond. In particular, deamination is brought about by the action of nitrous acid on primary amines. In this reaction, acyclic amines yield alcohols (I) and olefins (II), for example:


The deamination of alicyclic amines is accompanied by ring expansion or contraction. In the presence of strong inorganic acids, aromatic amines and nitrous acid yield diazonium salts. Such reactions as hydrolysis, hydrogenolysis, decomposition of quaternary ammonium salts, and pyrolytic reactions also result in deamination.

Deamination plays an important part in the life processes of animals, plants, and microorganisms. Oxidative deamination, with the formation of ammonia and α-keto acids, is characteristic of d-amino acids. Amines also undergo oxidative deamination. Except for glutamate dehydrogenase, which deaminates L-glutamic acid, oxidases of natural amino acids are not very active in animal tissues. Therefore, most L-amino acids undergo indirect deamination by means of prior transamination, with the formation of glutamic acid, which then undergoes oxidative deamination or other transformations. Other types of deamination are reductive, hydrolytic (deamination of amino derivatives of purines, pyrimidines, and sugars), and intramolecular (histidine deamination), which occur mainly in microorganisms.

Oxidative Deamination Reaction


Deamination is also an oxidative reaction that occurs under aerobic conditions in all tissues but especially the liver. During oxidative deamination, an amino acid is converted into the corresponding keto acid by the removal of the amine functional group as ammonia and the amine functional group is replaced by the ketone group. The ammonia eventually goes into the urea cycle.

Oxidative deamination occurs primarily on glutamic acid because glutamic acid was the end product of many transamination reactions.

The glutamate dehydrogenase is allosterically controlled by ATP and ADP. ATP acts as an inhibitor whereas ADP is an activator.

 Central Role for Glutamic Acid:

Apparently most amino acids may be deaminated but this is a significant reaction only for glutamic acid. If this is true, then how are the other amino acids deaminated? The answer is that a combination of transamination and deamination of glutamic acid occurs which is a recycling type of reaction for glutamic acid. The original amino acid loses its amine group in the process. The general reaction sequence is shown on the left.


Deamination of adenine results in the formation of hypoxanthine. Hypoxanthine, in a manner analogous to the imine tautomer of adenine, selectively base pairs with cytosine instead of thymine. This results in a post-replicative transition mutation, where the original A-T base pair transforms into a G-C base pair.

Transamination of amino acids, mechanism, role of enzymes and coenzymes.

In the degradation of most standard amino acids, an early step in degradation consists in transamination, which is the transfer of the α-amino group from the amino acid to an α-keto acid. There are several different aminotransferases, each of which is specific for an individual amino acid or for a group of chemically similar ones, such as the branched amino acids leucine, isoleucine, and valine. The α-keto acid that accepts the amino group is always α-ketoglutarate (Figure). Transamination is freely reversible; therefore, both glutamate and α-ketoglutarate are substrates of every single transaminase. If amino groups are to be transferred between two amino acids other than glutamate, this will still occur by transient formation of glutamate (Figure).

Transamination reactions. a: Glutamate pyruvate transaminase (also called alanine amino transferase) transfers the α-amino group from alanine to α-ketoglutarate, which yields glutamate and pyruvate. b: All transaminases have α-ketoglutarate as one of their substrates. Transfer of amino groups between arbitrary amino and α-keto acids (here: alanine and oxaloacetate) occurs by transient transfer to α-ketoglutarate.



The mechanism of transamination is depicted in Figure for alanine, yet is the same with all transaminases. The reaction occurs in two stages:

1.     Transfer of the amino group from alanine to the enzyme, which releases pyruvate, and

2.     Transfer of the amino group from the enzyme to α-ketoglutarate, which releases glutamate.

In Figure, only the first half-reaction is shown, since the second half-reaction is the exact reversal of the first one; this also implies that the entire reaction is reversible. Overall, the mechanism consists in the first substrate arriving and leaving before the second substrate enters and leaves; this is dubbed a Ping Pong Bi Bi reaction (Figure).1 While two different substrates must be used for the the reaction to have a net effect, it is of course possible for amino acid 1 and amino acid 2 to be identicalthe reaction will work just fine but achieve no net turnover.

The reaction mechanism revolves around the coenzyme pyridoxal phosphate (PLP):

1.     At the outset of the reaction, PLP is bound as a Schiff base to the ε-amino group of a lysine residue in the active site (Figure).

2.     The bond between PLP and the enzyme is separated, and PLP forms a Schiff base with the amino acid substrate instead (Figure, steps 1 and 2).

3.     The liberated lysine residue abstracts the α hydrogen as a proton (step 3), and the electron left behind travels all the way down the PLP ring. PLP is often said to act as an 'electron sink'. This has the effect of turning the bond between the α carbon and the α nitrogen into a Schiff base.

4.     The Schiff base is hydrolyzed to yield the α-keto acid and the amino derivative of the PLP (called pyridoxamine phosphate; steps 4 and 5).

The PLP in its various forms stays within the the active site throughout, even when not bound to the enzyme covalently. As stated above, the second half reaction is the exact reversal of the first, and you might want to draw the individual steps for yourself.

Decarboxylisation of amino acids, role of enzymes and co-enzymes.



Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is the first chemical step in photosynthesis, is called carboxylation, the addition of CO2 to a compound. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases.

The term "decarboxylation" literally means removal of the COOH (carboxyl group) and its replacement with a proton. The term simply relates the state of the reactant and product. Decarboxylation is one of the oldest organic reactions, since it often entails simple pyrolysis, and volatile products distill from the reactor. Heating is required because the reaction is less favorable at low temperatures. Yields are highly sensitive to conditions. In retrosynthesis, decarboxylation reactions can be considered the opposite of homologation reactions, in that the chain length becomes one carbon shorter. Metals, especially copper compounds, are usually required. Such reactions proceed via the intermediacy of metal carboxylate complexes.

Decarboxylation of aryl carboxylates can generate the equivalent of the corresponding aryl anion, which in turn can undergo cross coupling reactions.

Alkylcarboxylic acids and their salts do not always undergo decarboxylation readily. Exceptions are the decarboxylation of beta-keto acids, α,β-unsaturated acids, and α-phenyl, α-nitro, and α-cyanoacids. Such reactions are accelerated due to the formation of a zwitterionic tautomer in which the carbonyl is protonated and the carboxyl group is deprotonated. Typically fatty acids do not decarboxylate readily. Reactivity of an acid towards decarboxylation depends upon stability of carbanion intermediate formed in above mechanism. Many reactions have been named after early workers in organic chemistry. The Barton decarboxylation, Kolbe electrolysis, Kochi reaction and Hunsdiecker reaction are radical reactions. The Krapcho decarboxylation is a related decarboxylation of an ester. In ketonic decarboxylation a carboxylic acid is converted to a ketone.


Amino acid Amine Function

serine ethanolamine Conversion of phosphatidyl serine to phosphatidyl ethanolamine in bacteria

lysine →cadaverine

arginine/ornithine putrescine→ leads to spermine and spermidine

S-adenosylmethionine aminopropane donor→decarboxylase contains pyruvate in place of PLP; leads to spermine and spermidine

histidine→histamine→vasodilator, inflammatory agent, stimulates acid secretion in stomach; formed and stored for secretion in granulocytes, e.g. mast cells

glutamate →gamma-aminobutyrate, GABA →important neurotransmitter in brain

3,4-dihydroxyphenylalanine (Dopa) →dopamine, hydroxytyramine→ inhibitory neurotransmitter in brain, precursor of catecholamines, melanin

5-hydroxytryptophan →serotonin →precursor of melatonin

phenylalanine→phenylethylamine → antidepressant, mild amphetamine-like stimulant, present in chocolate