Protein

Proteins are compounds composed of carbon, hydrogen, oxygen , and nitrogen , which are arranged as strands of amino acids . They play an essential role in the cellular maintenance, growth, and functioning of the human body. Serving as the basic structural molecule of all the tissues in the body, protein makes up nearly 17 percent of the total body weight. To understand protein's role and function in the human body, it is important to understand its basic structure and composition.

Amino Acids

Amino acids are the fundamental building blocks of protein. Long chains of amino acids, called polypeptides, make up the multicomponent, large complexes of protein. The arrangement of amino acids along the chain determines the structure and chemical properties of the protein. Amino acids consist of the following elements: carbon, hydrogen, oxygen, nitrogen, and, sometimes, sulfur. The general structure of amino acids consists of a carbon center and its four substituents, which consists of an amino group (NH₂), an organic acid (carboxyl) group (COOH), a hydrogen atom (H), and a fourth group, referred to as the R-group, that determines the structural identity and chemical properties of the amino acid. The first three groups are common to all amino acids. The basic amino acid structure is R-CH(NH2)-COOH.

There are twenty different forms of amino acids that the human body utilizes. These forms are distinguished by the fourth variable substituent, the R-group, which can be a chain of different lengths or a carbon-ring structure. For example, if hydrogen represents the R-group, the amino acid is known as glycine, a polar but uncharged amino acid, while methyl (CH₃) group is known as alanine, a nonpolar amino acid. Thus, the chemical components of the R-group essentially determine the identity, structure, and function of the amino acid.

The structural and chemical relatedness of the R-groups allows classification of the twenty amino acids into chemical groups. Amino acids can be classified according to optical activity (the ability to polarize light), acidity and basicity, polarity and nonpolarity, or hydrophilicity (water-loving) and hydrophobicity (water-fearing). These categories offer clues to the function and reactivity of the amino acids in proteins. The biochemical properties of amino acids determine the role and function of protein in the human body.

Of the twenty amino acids, eleven are considered nonessential (or dispensable ), meaning that the body is able to adequately synthesize them, and nine are essential (or indispensable ), meaning that the body is unable to adequately synthesize them to meet the needs of the cell. They must therefore be supplied through the diet . Foods that have protein contain both nonessential and essential amino acids, the latter of which the body can use to synthesize some of the nonessential amino acids. A healthful diet, therefore, should

consist of a sufficient and balanced supply of both essential and nonessential amino acids in order to ensure high levels of protein production.

Protein Quality: Nutritive Value

The quality of protein depends on the level at which it provides the nutritional amounts of essential amino acids needed for overall body health, maintenance, and growth. Animal proteins, such as eggs, cheese, milk, meat, and fish, are considered high-quality, or complete, proteins because they provide sufficient amounts of the essential amino acids. Plant proteins, such as grain, corn, nuts, vegetables and fruits, are lower-quality, or incomplete, proteins because many plant proteins lack one or more of the essential amino acids, or because they lack a proper balance of amino acids. Incomplete proteins can, however, be combined to provide all the essential amino acids, though combinations of incomplete proteins must be consumed at the same time, or within a short period of time (within four hours), to obtain the maximum nutritive value from the amino acids. Such combination diets generally yield a high-quality protein meal, providing sufficient amounts and proper balance of the essential amino acids needed by the body to function.

Protein Processing: Digestion, Absorption, and Metabolism

Protein digestion begins when the food reaches the stomach and stimulates the release of hydrochloric acid (HCl) by the parietal cells located in the gastric mucosa of the GI (gastrointestinal ) tract. Hydrochloric acid provides for a very acidic environment , which helps the protein digestion process in two ways: (1) through an acid-catalyzed hydrolysis reaction of breaking peptide bonds (the chemical process of breaking peptide bonds is referred to as a hydrolysis reaction because water is used to break the bonds); and (2) through conversion of the gastric enzyme pepsinogen (an inactive precursor) to pepsin (the active form). Pepsinogen is stored and secreted by the "chief cells" that line the stomach wall. Once converted into the active form, pepsin attacks the peptide bonds that link amino acids together, breaking the long polypeptide chain into shorter segments of amino acids known as dipeptides and tripeptides. These protein fragments are then further broken down in the duodenum of the small intestines . The brush border enzymes, which work on the surface of epithelial cells of the small intestines, hydrolyze the protein fragments into amino acids.

The cells of the small intestine actively absorb the amino acids through a process that requires energy . The amino acids travel through the hepatic portal vein to the liver, where the nutrients are processed into glucose or fat (or released into the bloodstream). The tissues in the body take up the amino acids rapidly for glucose production, growth and maintenance, and other vital cellular functioning. For the most part, the body does not store protein, as the metabolism of amino acids occurs within a few hours.

Amino acids are metabolized in the liver into useful forms that are used as building blocks of protein in tissues. The body may utilize the amino acids for either anabolic or catabolic reactions. Anabolism refers to the chemical process through which digested and absorbed products are used to effectively build or repair bodily tissues, or to restore vital substances broken down through metabolism. Catabolism , on the other hand, is the process that results in the release of energy through the breakdown of nutrients, stored materials, and cellular substances. Anabolic and catabolic reactions work hand-in-hand, and the energy produced in catabolic processes is used to fuel essential anabolic processes. The vital biochemical reaction of glycolysis (in which glucose is oxidized to produce carbon dioxide, water, and cellular energy) in the form of adenosine triphosphate, or ATP, is a prime example of a catabolic reaction. The energy released, as ATP, from such a reaction is used to fuel important anabolic processes, such as protein synthesis.

The metabolism of amino acids can be understood from the dynamic catabolic and anabolic processes. In the process referred to as deamination , the nitrogen-containing amino group (NH₂) is cleaved from the amino acid unit. In this reaction, which requires vitamin B6 as a cofactor, the amino group is transferred to an acceptor keto-acid , which can form a new amino acid. Through this process, the body is able to make the nonessential amino acids not provided by one's diet. The keto-acid intermediate can also be used to synthesize glucose to ultimately yield energy for the body, and the cleaved nitrogen-containing group is transformed into urea, a waste product, and excreted as urine.

Vital Protein Functions

Proteins are vital to basic cellular and body functions, including cellular regeneration and repair, tissue maintenance and regulation, hormone and enzyme production, fluid balance, and the provision of energy.

Cellular and tissue provisioning.

Protein is an essential component for every type of cell in the body, including muscles, bones, organs, tendons, and ligaments. Protein is also needed in the formation of enzymes, antibodies , hormones, blood-clotting factors, and blood-transport proteins. The body is constantly undergoing renewal and repair of tissues. The amount of protein needed to build new tissue or maintain structure and function depends on the rate of renewal or the stage of growth and development . For example, the intestinal tract is renewed every couple of days, whereas blood cells have a life span of 60 to 120 days. Furthermore, an infant will utilize as much as one-third of the dietary protein for the purpose of building new connective and muscle tissues.

Hormone and enzyme production.

Amino acids are the basic components of hormones, which are essential chemical signaling messengers of the body. Hormones are secreted into the bloodstream by endocrine glands, such as the thyroid gland, adrenal glands, pancreas, and other ductless glands, and regulate bodily functions and processes. For example, the hormone insulin , secreted by the pancreas, works to lower the blood glucose level after meals. Insulin is made up of forty-eight amino acids.

Enzymes, which play an essential kinetic role in biological reactions, are composed of large protein molecules . Enzymes facilitate the rate of reactions by acting as catalysts and lowering the activation energy barrier between the reactants and the products of the reactions. All chemical reactions that occur during the digestion of food and the metabolic processes in tissues require enzymes. Therefore, enzymes are vital to the overall function of the body, and thereby indicate the fundamental and significant role of proteins.

Fluid balance.

The presence of blood protein molecules, such as albumins and globulins, are critical factors in maintaining the proper fluid balance between cells and extracellular space. Proteins are present in the capillary beds, which are one-cell-thick vessels that connect the arterial and venous beds, and they cannot flow outside the capillary beds into the tissue because of their large size. Blood fluid is pulled into the capillary beds from the tissue through the mechanics of oncotic pressure, in which the pressure exerted by the protein molecules counteracts the blood pressure . Therefore, blood proteins are essential in maintaining and regulating fluid balance between the blood and tissue. The lack of blood proteins results in clinical edema , or tissue swelling, because there is insufficient pressure to pull fluid back into the blood from the tissues. The condition of edema is serious and can lead to many medical problems.

Energy provision.

Protein is not a significant source of energy for the body when there are sufficient amounts of carbohydrates and fats available, nor is protein a storable energy, as in the case of fats and carbohydrates. However, if insufficient amounts of carbohydrates and fats are ingested, protein is used for energy needs of the body. The use of protein for energy is

not necessarily economical for the body, because tissue maintenance, growth, and repair are compromised to meet energy needs. If taken in excess, protein can be converted into body fat. Protein yields as much usable energy as carbohydrates, which is 4 kcal/gm (kilocalories per gram). Although not the main source of usable energy, protein provides the essential amino acids that are needed for adenine, the nitrogenous base of ATP, as well as other nitrogenous substances, such as creatine phosphate (nitrogen is an essential element for important compounds in the body).

Protein Requirement and Nutrition

The recommended protein intake for an average adult is generally based on body size: 0.8 grams per kilogram of body weight is the generally recommended daily intake. The recommended daily allowances of protein do not vary in times of strenuous activities or exercise, or with progressing age. However, there is a wide range of protein intake which people can consume according to their period of development. For example, the recommended allowance for an infant up to six months of age, who is undergoing a period of rapid tissue growth, is 2.2 grams per kilogram. For children ages seven through ten, the recommended daily allowance is around 36 total grams, depending on body weight. Pregnant women need to consume an additional 30 grams of protein above the average adult intake for the nourishment of the developing fetus.

Sources of protein.

Good sources of protein include high-quality protein foods, such as meat, poultry, fish, milk, egg, and cheese, as well as prevalent low-quality protein foods, such as legumes (e.g., navy beans, pinto beans, chick peas, soybeans, split peas), which are high in protein.

Protein–Calorie Malnutrition

The nitrogen balance index (NBI) is used to evaluate the amount of protein used by the body in comparison with the amount of protein supplied from daily food intake. The body is in the state of nitrogen (or protein) equilibrium when the intake and usage of protein is equal. The body has a positive nitrogen balance when the intake of protein is greater than that expended by the body. In this case, the body can build and develop new tissue. Since the body does not store protein, the overconsumption of protein can result in the excess amount to be converted into fat and stored as adipose tissue . The body has a negative nitrogen balance when the intake of protein is less than that expended by the body. In this case, protein intake is less than required, and the body cannot maintain or build new tissues.

A negative nitrogen balance represents a state of protein deficiency, in which the body is breaking down tissues faster than they are being replaced. The ingestion of insufficient amounts of protein, or food with poor protein quality, can result in serious medical conditions in which an individual's overall health is compromised. The immune system is severely affected; the amount of blood plasma decreases, leading to medical conditions such as anemia or edema; and the body becomes vulnerable to infectious diseases and other serious conditions. Protein malnutrition in infants is called kwashiorkor , and it poses a major health problem in developing countries, such as Africa, Central and South America, and certain parts of Asia. An infant with kwashiorkor suffers from poor muscle and tissue development, loss of appetite, mottled skin, patchy hair, diarrhea, edema, and, eventually, death (similar symptoms are present in adults with protein deficiency). Treatment or prevention of this condition lies in adequate consumption of protein-rich foods.

see also Amino Acids.

Jeffrey Radecki
Susan Kim

Bibliography

Berdanier, Carolyn D. (1998). CRC Desk Reference for Nutrition. Boca Raton, FL: CRC Press.

Briggs, George M., and Calloway, Doris Howes (1979). Bogert's Nutrition and Physical Fitness, 10th edition. Philadelphia, PA: W. B. Saunders.

Johnston, T. K. (1999). "Nutritional Implications of Vegetarian Diets." In Modern Nutrition in Health and Disease, 9th edition. M. E. Shills, et al, eds. Baltimore, MD: Williams & Wilkins.

Robinson, Corrinne H. (1975). Basic Nutrition and Diet Therapy. New York: Macmillan.

U.S. Department of Agriculture (1986). Composition of Foods. (USDA Handbooks 8–15.) Washington, DC: U.S. Government Printing Office.

Wardlaw, Gordon M., and Kesse, Margaret (2002). Perspectives in Nutrition, 5th edition. Boston: McGraw-Hill.

Internet Resources

Institute for Chemistry. "Amino Acids." Available from <http://www.chemie.fuberlin.de>

Protein

Amino Acids

Protein Quality: Nutritive Value

Protein Processing: Digestion, Absorption, and Metabolism

Vital Protein Functions

Protein Requirement and Nutrition

Protein–Calorie Malnutrition

Resources

Protein are compounds composed of carbon, hydrogen, oxygen, and nitrogen, which are arranged as strands of amino acid. They play an essential role in the cellular maintenance, growth, and functioning of the human body. Serving as the basic structural molecule of all the tissues in the body, protein makes up nearly 17% of the total body weight. To understand

Protein

AI = Adequate Intake

g = gram

(Illustration by GGS Information Services/Thomson Gale.)

protein's role and function in the human body, it is important to understand its basic structure and composition.

Amino Acids

Amino acids are the fundamental building blocks of protein. Long chains of amino acids, called poly-peptides , make up the multicomponent, large complexes of protein. The arrangement of amino acids along the chain determines the structure and chemical properties of the protein. Amino acids consist of the following elements: carbon, hydrogen, oxygen, nitrogen, and, sometimes, sulfur. The general structure of amino acids consists of a carbon center and its four substituents, which consists of an amino group (NH₂), an organic acid (carboxyl) group (COOH), ahydrogen

KEY TERMS

adipose tissue— Tissue containing fat deposits.

amino acid— Building block of proteins, necessary dietary nutrient.

anabolic— Promoting building up.

catabolism— Breakdown of complex molecules.

epithelial cell— Sheet of cells lining organs throughout the body.

glycolysis— Cellular reaction that begins the breakdown of sugars.

hydrolyze— To break apart through reaction with water.

kwashiorkor— Severe malnutrition characterized by swollen belly, hair loss, and loss of skin pigment.

nonpolar— Without a separation if charge within the molecule; likely to be hydrophobic.

polar— Containing regions of positive and negative charge; likely to be soluble in water.

atom (H ), and a fourth group, referred to as the R-group, that determines the structural identity and chemical properties of the amino acid. The first three groups are common to all amino acids. The basic amino acid structure is R-CH(NH₂)-COOH.

There are twenty different forms of amino acids that the human body utilizes. These forms are distinguished by the fourth variable substituent, the R-group, which can be a chain of different lengths or a carbon-ring structure. For example, if hydrogen represents the R-group, the amino acid is known as gly-cine, a polar but uncharged amino acid, while methyl (CH₃) group is known as alanine, a nonpolar amino acid. Thus, the chemical components of the R-group essentially determine the identity, structure, and function of the amino acid.

The structural and chemical relatedness of the R-groups allows classification of the twenty amino acids into chemical groups. Amino acids can be classified according to optical activity (the ability to polarize light), acidity and basicity, polarity and nonpolarity, or hydrophilicity (water-loving) and hydrophobicity (water-fearing). These categories offer clues to the function and reactivity of the amino acids in proteins. The biochemical properties of amino acids determine the role and function of protein in the human body.

Of the twenty amino acids, eleven are considered nonessential (or dispensable ), meaning that the body is able to adequately synthesize them, and nine are essential (or indispensable), meaning that the body is unable to adequately synthesize them to meet the needs of the cell. They must therefore be supplied through the diet. Foods that have protein contain both nonessential and essential amino acids, the latter of which the body can use to synthesize some of the nonessential amino acids. A healthful diet, therefore, should consist of a sufficient and balanced supply of both essential and nonessential amino acids in order to ensure high levels of protein production.

Protein Quality: Nutritive Value

The quality of protein depends on the level at which it provides the nutritional amounts of essential amino acids needed for overall body health, maintenance, and growth. Animal proteins, such as eggs, cheese, milk, meat, and fish, are considered high-quality, or complete, proteins because they provide sufficient amounts of the essential amino acids. Plant proteins, such as grain, corn, nuts, vegetables and fruits, are lower-quality , or incomplete, proteins because many plant proteins lack one or more of the essential amino acids, or because they lack a proper balance of amino acids. Incomplete proteins can, however, be combined to provide all the essential amino acids, though combinations of incomplete proteins must be consumed at the same time, or within a short period of time (within four hours), to obtain the maximum nutritive value from the amino acids. Such combination diets generally yield a high-quality protein meal, providing sufficient amounts and proper balance of the essential amino acids needed by the body to function.

Protein Processing: Digestion, Absorption, and Metabolism

P rotein digestion begins when the food reaches the stomach and stimulates the release of hydrochloric acid (HCl ) by the parietal cells located in the gastric mucosa of the GI (gastrointestinal) tract. H ydrochloric acid provides for a very acidic environment, which helps the protein digestion process in two ways: (1) through an acid-catalyzed hydrolysis reaction of breaking peptide bonds (the chemical process of breaking peptide bonds is referred to as a hydrolysis reaction because water is used to break the bonds); and (2) through conversion of the gastric enzyme pep-sinogen (an inactive precursor) to pepsin (the active form). Pepsinogen is stored and secreted by the “chief cells” that line the stomach wall. Once converted into the active form, pepsin attacks the peptide bonds that link amino acids together, breaking the long polypep-tide chain into shorter segments of amino acids known as dipeptides and tripeptides. These protein fragments are then further broken down in the duodenum of the small intestines. The brush border enzymes, which work on the surface of epithelial cell of the small intestines, hydrolyze the protein fragments into amino acids.

The cells of the small intestine actively absorb the amino acids through a process that requires energy. The amino acids travel through the hepatic portal vein to the liver, where the nutrient are processed into glucose or fat (or released into the bloodstream). The tissues in the body take up the amino acids rapidly for glucose production, growth and maintenance, and other vital cellular functioning. For the most part, the body does not store protein, as the metabolism of amino acids occurs within a few hours.

Amino acids are metabolized in the liver into useful forms that are used as building blocks of protein in tissues. The body may utilize the amino acids for either anabolic or catabolic reactions . Anabolism refers to the chemical process through which digested and absorbed products are used to effectively build or repair bodily tissues, or to restore vital substances broken down through metabolism. Catabolism, on the other hand, is the process that results in the release of energy through the breakdown of nutrients, stored materials, and cellular substances. Anabolic and catabolic reactions work hand-in-hand, and the energy produced in catabolic processes is used to fuel essential anabolic processes. The vital biochemical reaction of glycolysis (in which glucose is oxidized to produce carbon dioxide, water, and cellular energy) in the form of adenosine triphosphate, or ATP, is a prime example of a catabolic reaction. The energy released, as ATP, from such a reaction is used to fuel important anabolic processes, such as protein synthesis.

The metabolism of amino acids can be understood from the dynamic catabolic and anabolic processes. In the process referred to as deamination, the nitrogen-containing amino group (NH₂) is cleaved from the amino acid unit. In this reaction, which requires vitamin B₆ as a cofactor, the amino group is transferred to an acceptor keto-acid, which can form a new amino acid. Through this process, the body is able to make the nonessential amino acids not provided by one's diet. The keto-acid intermediate can also be used to synthesize glucose to ultimately yield energy for the body, and the cleaved nitrogen-containing group is transformed into urea, a waste product, and excreted as urine.

Vital Protein Functions

Proteins are vital to basic cellular and body functions, including cellular regeneration and repair, tissue maintenance and regulation, hormone and enzyme production, fluid balance, and the provision of energy.

Cellular and tissue provisioning. Protein is an essential component for every type of cell in the body, including muscles, bones, organs, tendons, and ligaments. Protein is also needed in the formation of enzymes, antibody, hormones, blood-clotting factors, and blood-transport proteins. The body is constantly undergoing renewal and repair of tissues. The amount of protein needed to build new tissue or maintain structure and function depends on the rate of renewal or the stage of growth and development. For example, the intestinal tract is renewed every couple of days, whereas blood cells have a life span of 60 to 120 days. Furthermore, an infant will utilize as much as one-third of the dietary protein for the purpose of building new connective and muscle tissues.

Hormone and enzyme production. Amino acids are the basic components of hormones, which are essential chemical signaling messengers of the body. Hormones are secreted into the bloodstream by endocrine glands, such as the thyroid gland, adrenal glands, pancreas, and other ductless glands, and regulate bodily functions and processes. For example, the hormone insulin, secreted by the pancreas, works to lower the blood glucose level after meals. Insulin is made up of forty-eight amino acids.

Enzymes, which play an essential kinetic role in biological reactions, are composed of large protein molecule. Enzymes facilitate the rate of reactions by acting as catalysts and lowering the activation energy barrier between the reactants and the products of the reactions. All chemical reactions that occur during the digestion of food and the metabolic processes in tissues require enzymes. Therefore, enzymes are vital to the overall function of the body, and thereby indicate the fundamental and significant role of proteins.

Fluid balance. The presence of blood protein molecules, such as albumins and globulins, are critical factors in maintaining the proper fluid balance between cells and extracellular space. Proteins are present in the capillary beds, which are one-cell-thick vessels that connect the arterial and venous beds, and they cannot flow outside the capillary beds into the tissue because of their large size. Blood fluid is pulled into the capillary beds from the tissue through the mechanics of oncotic pressure, in which the pressure exerted by the protein molecules counteracts the blood pressure. Therefore, blood proteins are essential in maintaining and regulating fluid balance between the blood and tissue. The lack of blood proteins results in clinical edema, or tissue swelling, because there is insufficient pressure to pull fluid back into the blood from the tissues. The condition of edema is serious and can lead to many medical problems.

Energy provision. Protein is not a significant source of energy for the body when there are sufficient amounts of carbohydrate and fats available, nor is protein a storable energy, as in the case of fats and carbohydrates . However, if insufficient amounts of carbohydrates and fats are ingested, protein is used for energy needs of the body. The use of protein for energy is not necessarily economical for the body, because tissue maintenance, growth, and repair are compromised to meet energy needs. If taken in excess, protein can be converted into body fat. Protein yields as much usable energy as carbohydrates, which is 4 kcal/gm (kilocalories per gram). Although not the main source of usable energy, protein provides the essential amino acids that are needed for adenine, the nitrogenous base of ATP, as well as other nitrogenous substances, such as creatine phosphate (nitrogen is an essential element for important compounds in the body).

Protein Requirement and Nutrition

The recommended protein intake for an average adult is generally based on body size: 0.8 grams per kilogram of body weight is the generally recommended daily intake. The recommended daily allowances of protein do not vary in times of strenuous activities or exercise, or with progressing age. However, there is a wide range of protein intake which people can consume according to their period of development. For example, the recommended allowance for an infant up to six months of age, who is undergoing a period of rapid tissue growth, is 2.2 grams per kilogram. For children ages seven through ten, the recommended daily allowance is around 36 total grams, depending on body weight. Pregnant women need to consume an additional 30 grams of protein above the average adult intake for the nourishment of the developing fetus.

Sources of protein. Good sources of protein include high-quality protein foods, such as meat, poultry, fish, milk, egg, and cheese, as well as prevalent low-quality protein foods, such as legumes (e.g., navy beans, pinto beans, chick peas, soybeans, split peas), which are high in protein.

Protein–Calorie Malnutrition

The nitrogen balance index (NBI) is used to evaluate the amount of protein used by the body in comparison with the amount of protein supplied from daily food intake. The body is in the state of nitrogen (or protein) equilibrium when the intake and usage of protein is equal. The body has a positive nitrogen balance when the intake of protein is greater than that expended by the body. In this case, the body can build and develop new tissue. Since the body does not store protein, the overconsumption of protein can result in the excess amount to be converted into fat and stored as adipose tissue. The body has a negative nitrogen balance when the intake of protein is less than that expended by the body. In this case, protein intake is less than required, and the body cannot maintain or build new tissues.

A negative nitrogen balance represents a state of protein deficiency, in which the body is breaking down tissues faster than they are being replaced. The ingestion of insufficient amounts of protein, or food with poor protein quality, can result in serious medical conditions in which an individual's overall health is compromised. The immune system is severely affected; the amount of blood plasma decreases, leading to medical conditions such as anemia or edema; and the body becomes vulnerable to infectious diseases and other serious conditions. Protein malnutrition in infants is called kwashiorkor, and it poses a major health problem in developing countries, such as Africa, Central and South America, and certain parts of Asia. An infant with kwashiorkor suffers from poor muscle and tissue development, loss of appetite, mottled skin, patchy hair, diarrhea, edema, and, eventually, death (similar symptoms are present in adults with protein deficiency). Treatment or prevention of this condition lies in adequate consumption of protein-rich foods.

Resources

BOOKS

Berdanier, Carolyn D. (1998). CRC Desk Reference for Nutrition. Boca Raton, FL: CRC Press.

Briggs, George M., and Calloway, Doris Howes (1979). Bogert's Nutrition and Physical Fitness, 10th edition. Philadelphia, PA: W. B. Saunders.

Johnston, T. K. (1999). “Nutritional Implications of Vegetarian Diets.” In Modern Nutrition in Health andDisease, 9th edition. M. E. Shills, et al, eds. Baltimore, MD: Williams & Wilkins.

Robinson, Corrinne H. (1975). Basic Nutrition and Diet Therapy. New York: Macmillan.

U.S. Department of Agriculture (1986). Composition of Foods. (USDA Handbooks 8–15.) Washington, DC: U.S. Government Printing Office.

Wardlaw, Gordon M., and Kesse, Margaret (2002). Perspectives in Nutrition, 5th edition. Boston: McGraw-Hill.

OTHER

Institute for Chemistry. “Amino Acids.” Available from <http://www.chemie.fuberlin.de>

Jeffrey Radecki

Susan Kim

Pyridoxine seeVitamin B₆

PROTEINS

CONCEPT

Most of us recognize the term protein in a nutritional context as referring to a class of foods that includes meats, dairy products, eggs, and other items. Certainly, proteins are an important part of nutrition, and obtaining complete proteins in one's diet is essential to the proper functioning of the body. But the significance of proteins extends far beyond the dining table. Vast molecules built from enormous chains of amino acids, proteins are essential building blocks for living systems—hence their name, drawn from the Greek proteios, or "holding first place." Proteins are integral to the formation of DNA, a molecule that contains genetic codes for inheritance, and of hormones. Most of the dry weight of the human body and the bodies of other animals is made of protein, as is a vast range of things with which we come into contact on a daily basis. In addition, a special type of protein called an enzyme has still more applications.

HOW IT WORKS

The Complexities of Biochemistry

Protein is a foundational material in the structure of most living things, and as such it is rather like concrete or steel. Just as concrete is a mixture of other ingredients and steel is an alloy of iron and carbon, proteins, too, are made of something more basic: amino acids. These are organic compounds made of carbon, hydrogen, oxygen, nitrogen, and (in some cases) sulfur bonded in characteristic formations.

Amino acids are discussed in more depth within the essay devoted to that topic, though, as noted in that essay, it is impossible to treat such a subject thoroughly without going into an extraordinarily lengthy and technical discussion. Such is the case with many topics in biochemistry, the area of the biological sciences concerned with the chemical substances and processes in organisms: the deeper within the structure of things one goes, and the smaller the items under investigation, the more complex are the properties and interactions.

The Basics

Amino acids react with each other to form a bond, called a peptide linkage, between the carboxyl group of one amino acid (symbolized as-COOH) and the amino group (-NH₂) of a second amino acid. In this way they can make large, chainlike molecules called polymers, which may contain as few as two or as many as 3,000 amino-acid units. If there are more than 10 units in a chain, the chain is called a polypeptide, while a chain with 50 or more amino-acid units is known as a protein.

All the millions of different proteins in living things are formed by the bonding of only 20 amino acids into long polymer chains. Because each amino acid can be used many times along the chain, and because there are no restrictions on the length of the chain, the number of possible combinations for the creation of proteins is truly enormous: about two quadrillion, or 2,000,000,000,000,000. Just as not all sequences of letters make sense, however, not all sequences of amino acids produce functioning proteins. In fact, the number of proteins that have significance in the functioning of nature is closer to about 100,000. This number is considerably smaller than two quadrillion—about 1/2,000,000,000th of that larger number, in fact—but it is still a very large number.

COMPONENTS OTHER THAN AMINO ACIDS.

The specific properties of each kind of protein are largely dependent on the kind and sequence of the amino acids in it, yet many proteins include components other than amino acids. For example, some may have sugar molecules (sugars are discussed in the essay on Carbohydrates) chemically attached. Exactly which types of sugars are attached and where on the protein chain attachment occurs vary with the specific protein. Other proteins may have lipid, or fat, molecules chemically bonded to them. Sugar and lipid molecules always are added when synthesis of the protein's amino-acid chain is complete. Many other types of substance, including metals, also may be associated with proteins; for instance, hemoglobin, a pigment in red blood cells that is responsible for transporting oxygen to the tissues and removing carbon dioxide from them, is a protein that contains an iron atom.

STRUCTURES AND SYNTHESIS.

Protein structures generally are described at four levels: primary, secondary, tertiary, and quaternary. Primary structure is simply the two-dimensional linear sequence of amino acids in the peptide chain. Secondary and tertiary structures both refer to the three-dimensional shape into which a protein chain folds. The distinction between the two is partly historical: secondary structures are those that were first discerned by scientists of the 1950s, using the techniques and knowledge available then, whereas an awareness of tertiary structure emerged only later. Finally, quaternary structure indicates the way in which many protein chains associate with one another. For example, hemoglobin consists of four protein chains (spirals, actually) of two slightly different types, all attached to an iron atom.

Protein synthesis is the process whereby proteins are produced, or synthesized, in living things according to "directions" given by DNA (deoxyribonucleic acid) and carried out by RNA (ribonucleic acid) and other proteins. As suggested earlier, this is an extraordinarily complex process that we do not attempt to discuss here. Following synthesis, proteins fold up into an essentially compact three-dimensional shape, which is their tertiary structure.

The steps involved in folding and the shape that finally results are determined by such chemical properties as hydrogen bonds, electrical attraction between positively and negatively charged side chains, and the interaction between polar and nonpolar molecules. Non Polar molecules are called hydrophobic, or "water-fearing," because they do not mix with water but instead mix with oils and other substances in which the electric charges are more or less evenly distributed on the molecule. Polar molecules, on the other hand, are termed hydrophilic, or "water-loving," and mix with water and water-based substances in which the opposing electric charges occupy separate sides, or ends, of the molecule. Typically, hydrophobic amino-acid side chains tend to be on the interior of a protein, while hydrophilic ones appear on the exterior.

REAL-LIFE APPLICATIONS

Proteins Are Everywhere

Although it is very difficult to discuss the functions of proteins in simple terms, and it is similarly challenging to explain exactly how they function in everyday life, it is not hard at all to name quite a few areas in which these highly important compounds are applied. As we noted earlier, much of our bodies' dry weight—that is, the weight other than water, which accounts for a large percentage of the total—is protein. Our bones, for instance, are about one-fourth protein, and protein makes up a very high percentage of the material in our organs (including the skin), glands, and bodily fluids.

Humans are certainly not the only organisms composed largely of protein: the entire animal world, including the animals we eat and the microbes that enter our bodies (see Digestion and Parasites and Parasitology) likewise is constituted largely of protein. In addition, a whole host of animal products, including leather and wool, are nearly pure protein. So, too, are other, less widely used animal products, such as hormones for the treatment of certain conditions—for example, insulin, which keeps people with diabetes alive and which usually is harvested from the bodies of mammals.

Proteins allow cells to detect and react to hormones and toxins in their surroundings, and as the chief ingredient in antibodies, which help us resist infection, they play a part in protecting our bodies against foreign invaders. The lack of specific proteins in the brain may be linked to such mysterious, terrifying conditions as Alzheimer and Creutzfeldt-Jakob diseases (discussed in Disease). Found in every cell and tissue and composing the bulk of our bodies' structure, proteins are everywhere, promoting growth and repairing bone, muscles, tissues, blood, and organs.

ENZYMES.

One particularly important type of protein is an enzyme, discussed in the essay on that topic. Enzymes make possible a host of bodily processes, in part by serving as catalysts, or substances that speed up a chemical reaction without actually participating in, or being consumed by, that reaction. Enzymes enable complex, life-sustaining reactions in the human body—reactions that would be too slow at ordinary body temperatures—and they manage to do so without forcing the body to undergo harmful increases in temperature. They also are involved in fermentation, a process with applications in areas ranging from baking bread to reducing the toxic content of wastewater. (For much more on these subjects, see Enzymes.)

Inside the body, enzymes and other proteins have roles in digesting foods and turning the nutrients in them—including proteins—into energy. They also move molecules around within our cells to serve an array of needs and allow healthful substances, such as oxygen, to pass through cell membranes while keeping harmful ones out. Proteins in the chemical known as chlorophyll facilitate an exceptionally important natural process, photosynthesis, discussed briefly in Carbohydrates.

PROTEINS, BLOOD, AND CRIME.

The four blood types (A, B, AB, and O) are differentiated on the basis of the proteins present in each. This is only one of many key roles that proteins play where blood is concerned. If certain proteins are missing, or if the wrong proteins are present, blood will fail to clot properly, and cuts will refuse to heal. For sufferers of the condition known as hemophilia, caused by a lack of the proteins needed for clotting, a simple cut can be fatal.

Similarly, proteins play a critical role in forensic science, or the application of medical and biological knowledge to criminal investigations. Fingerprints are an expression of our DNA, which is linked closely with the operation of proteins in our bodies. The presence of DNA in bodily fluids, such as blood, semen, sweat, and saliva, makes it possible to determine the identity of the individual who perpetrated a crime or of others who were present at the scene. In addition, a chemical known as luminol assists police in the investigation of possible crime scenes. If blood has ever been shed in a particular area, such as on a carpet, no matter how carefully the perpetrators try to conceal or eradicate the stain, it can be detected. The key is luminol, which reacts to hemoglobin in the blood, making it visible to investigators. This chemical, developed during the 1980s, has been used to put many a killer behind bars.

DESIGNER PROTEINS.

These are just a very few of the many applications of proteins, including a very familiar one, discussed in more depth at the conclusion of this essay: nutrition. Given the importance and complexity of proteins, it might be hard to imagine that they can be produced artificially, but, in fact, such production is taking place at the cutting edge of biochemistry today, in the field of "designer proteins."

Many such designs involve making small changes in already existing proteins: for example, by changing three amino acids in an enzyme often used to improve detergents' cleaning power, commercial biochemists have doubled the enzyme's stability in wash water. Medical applications of designer proteins seem especially promising. For instance, we might one day cure cancer by combining portions of one protein that recognizes cancer with part of another protein that attacks it. One of the challenges facing such a development, however, is the problem of designing a protein that attacks only cancer cells and not healthy ones.

In the long term, scientists hope to design proteins from scratch. This is extremely difficult today and will remain so until researchers better understand the rules that govern tertiary structure. Nevertheless, scientists already have designed a few small proteins whose stability or instability has enhanced our understanding of those rules. Building on these successes, scientists hope that one day they may be able to design proteins to meet a host of medical and industrial needs.

Proteins in the Diet

Proteins are one of the basic nutrients, along with carbohydrates, lipids, vitamins, and minerals (see Nutrients and Nutrition). They can be broken down and used as a source of emergency energy if carbohydrates or fats cannot meet immediate needs. The body does not use protein from food directly: after ingestion, enzymes in the digestive system break protein into smaller peptide chains and eventually into separate amino acids. These smaller constituents then go into the bloodstream, from whence they are transported to the cells. The cells incorporate the amino acids and begin building proteins from them.

ANIMAL AND VEGETABLE PROTEINS.

The protein content in plants is very small, since plants are made largely of cellulose, a type of carbohydrate (see Carbohydrates for more on this subject); this is one reason why herbivorous animals must eat enormous quantities of plants to meet their dietary requirements. Humans, on the other hand, are omnivores (unless they choose to be vegetarians) and are able to assimilate proteins in abundant quantities by eating the bodies of plant-eating animals, such as cows. In contrast to plants, animal bodies (as previously noted) are composed largely of proteins. When people think of protein in the diet, some of the foods that first come to mind are those derived from animals: either meat or such animal products as milk, cheese, butter, and eggs. A secondary group of foods that might appear on the average person's list of proteins include peas, beans, lentils, nuts, and cereal grains.

There is a reason why the "protein team" has a clearly defined "first string" and "second string." The human body is capable of manufacturing 12 of the 20 amino acids it needs, but it must obtain the other eight—known as essential amino acids —from the diet. Most forms of animal protein, except for gelatin (made from animal bones), contain the essential amino acids, but plant proteins do not. Thus, the nonmeat varieties of protein are incomplete, and a vegetarian who does not supplement his or her diet might be in danger of not obtaining all the necessary amino acids.

For a person who eats meat, it would be extremely difficult not to get enough protein. According to the U.S. Food and Drug Administration (FDA), protein should account for 10% of total calories in the diet, and since protein contains 4 calories per 0.035 oz. (1 g), that would be about 1.76 oz. (50 g) in a diet consisting of 2,000 calories a day. A pound (0.454 kg) of steak or pork supplies about twice this much, and though very few people sit down to a meal and eat a pound of meat, it is easy to see how a meat eater would consume enough protein in a day.

For a vegetarian, meeting the protein needs may be a bit more tricky, but it can be done. By combining legumes or beans and grains, it is possible to obtain a complete protein: hence, the longstanding popularity, with meat eaters as well as vegetarians, of such combinations as beans and rice or peas and cornbread. Other excellent vegetarian combos include black beans and corn, for a Latin American touch, or the eastern Asian combination of rice and tofu, protein derived from soybeans.

WHERE TO LEARN MORE

"DNA and Protein Synthesis." John Jay College of Criminal Justice, City University of New York (Web site). <http://web.jjay.cuny.edu/~acarpi/NSC/12-dna.htm>.

Inglis, Jane. Proteins. Minneapolis, MN: Carolrhoda Books, 1993.

Kiple, Kenneth F., and Kriemhild Coneé Ornelas. The Cambridge World History of Food. New York: Cambridge University Press, 2000.

"Proteins and Protein Foods." Food Resource, Oregon State University (Web site). <http://www.orst.edu/food-resource/protein/>.

Silverstein, Alvin, Virginia B. Silverstein, and Robert A. Silverstein. Proteins. Brookfield, CT: Millbrook Press, 1992.

Structural Classification of Proteins (Web site). <http://scop.mrc-lmb.cam.ac.uk/scop/>.

THINK: Teenage Health Interactive Network (Web site). <http://library.thinkquest.org/29500/nutrition/nutrition.fap.shtml>.

KEY TERMS

AMINO ACIDS:

Organic compounds made of carbon, hydrogen, oxygen, nitrogen and (in some cases) sulfur bonded in characteristic formations. Strings of amino acids make up proteins.

AMINO GROUP:

The chemical forma tion-NH₂, which is part of all amino acids.

BIOCHEMISTRY:

The area of the biological sciences concerned with the chemical substances and processes in organisms.

CARBOXYL GROUP:

The formation-COOH, which is common to all amino acids.

DNA:

Deoxyribonucleic acid, a molecule in all cells, and many viruses, containing genetic codes for inheritance.

ENZYME:

A protein material that speeds up chemical reactions in the bodies of plants and animals.

ESSENTIAL AMINO ACIDS:

Amino acids that cannot be manufactured by the body and therefore must be obtained from the diet. Proteins that contain essential amino acids are known as complete proteins.

HEMOGLOBIN:

An iron-containing protein in red blood cells that is responsible for transporting oxygen to the tissues and removing carbon dioxide from them. Hemoglobin is known for its deep red color.

HERBIVORE:

A plant-eating organism.

HORMONE:

Molecules produced by living cells, which send signals to spots remote from their point of origin and induce specific effects on the activities of other cells.

OMNIVORE:

An organism that eats both plants and other animals.

ORGANIC:

At one time chemists used the term organic only in reference to living things. Now the word is applied to compounds containing carbon and hydrogen.

PEPTIDE LINKAGE:

A bond between the carboxyl group of one amino acid and the amino group of a second amino acid.

POLYMERS:

Large, chainlike molecules composed of numerous subunits known as monomers.

POLYPEPTIDE:

A group of between 10 and 50 amino acids.

PROTEINS:

Large molecules built from long chains of 50 or more amino acids. Proteins serve the functions of promoting normal growth, repairing damaged tissue, contributing to the body's immune system, and making enzymes.

RNA:

Ribonucleic acid, the molecule translated from DNA in the cell nucleus, the control center of the cell, that directs protein synthesis in the cytoplasm, or the space between cells.

Proteins

Proteins are polymers of amino acids that provide structure and control reactions in all cells. When humans think of expressing the meaning of life, they often resort to words. From poems to sonnets to short stories to novels, words tell the stories of life. But in biological terms, the words of life are proteins. While DNA holds the code of life, proteins are the language in which that code is expressed.

To observe the mosaic of proteins in life is to observe nature in its finest array. The feathers of a bird and the silk of a spider's web are both almost pure protein. The most numerous proteins in an animal are the collagen proteins joining animal body parts. Other proteins include the positively charged histone proteins that condense the cell's negatively charged DNA and the transcription factor proteins that control which genes are expressed (made into proteins) and which remain silent. A plant traps CO₂ to make sugar with Earth's most abundant protein, the enzyme ribulose 1,5-biphosphate carboxylase. The protein hemoglobin transports gases through the bloodstream necessary for the metabolism of life. Other proteins store minerals (ferritin) or fats (ovalbumin), contract muscles (myosin), protect against infection (anti-bodies), or act as toxins (botulinum) or hormones (insulin).

Properties of Amino Acids

The English language consists of thousands of words, created from any of twenty-six letters arranged in a precise order. In an analogous fashion, proteins are made up of twenty common amino acids in a precise order dictating the protein's structure and function. Every amino acid has a common structure, in which a central carbon is covalently bonded to a carboxyl group (COOH), an amino group (NH₂), a hydrogen, and a variable "R" group.

The chemical properties of the R group are what give an amino acid its character. The R group can be hydrophilic (attracted to water and other polar molecules) or hydrophobic (attracted to nonpolar molecules and repelled by water or other polar molecules). Hydrophilic R groups can have basic charges, as in the amino acid valine, or acidic , as in glutamic acid, or they may even be an uncharged polar group such as-OH (alcohol) or-NH₂ (amino), as in serine. A nonpolar or hydrophobic R group can be a hydro-carbon chain, as in leucine. There are also three special amino acids: cysteine, glycine, and proline. Cysteine has a reactive sulfhydryl R group that forms disulfide bridges (S-S) between regions of the protein chain. These bridges increase toughness and resistance to unfolding of the protein structure. Glycine is the smallest amino acid, with hydrogen as its R group, and it fits into tight places within a protein's structure. Proline has a cyclic ring involving the central carbon, and it causes kinks to occur in a protein chain. Both proline and glycine are common at the corner of turns in the protein foldings.

Primary Structure

The unique sequence of amino acids in a protein is termed the primary structure. When amino acids form a protein chain, a unique bond, termed the peptide bond, exists between two amino acids. The sequence of a protein begins with the amino of the first amino acid and continues to the carboxyl end of the last amino acid.

The unique sequence of amino acids results from the translation of codons present in messenger RNA (mRNA). The mRNA, in turn, is a complementary copy of the gene that codes for that protein. Protein structure and function can change when "misspellings" occur in the order of amino acids during their transcription and translation. Sickle-cell hemoglobin, for example, is "misspelled" in only one amino acid; the sixth amino acid in the beta chain, where a valine is substituted for a glutamic acid. This occurs because the codon for valine, GUG, has replaced the codon for glutamic acid, GAG. This change from acidic to basic amino acid causes the hemoglobin molecules to stick to one another, forming long chains and blocking oxygen binding. These chains of hemoglobin precipitate in the cell, causing the red blood cells to assume a sickle shape. All of these structural and functional changes occur because of the mutation in the hemoglobin gene and a "misspelling" in the hemoglobin's amino acid sequence.

Secondary Structure and Motifs

The secondary structure of proteins is due to foldings that occur within their structure. These foldings are either in a helical shape, called the "alpha-helix" (which was first proposed by Linus Pauling), or a beta-pleated sheet shaped similar to the zig-zag foldings of an accordion. The turns of the alpha-helix are stabilized by hydrogen bonding between every fourth amino acid in the chain. The alpha-helix can cover specific regions of the protein or it may involve the entire protein, as in the alpha-keratin found in claws and horns. The two sides of the alpha-helix may differ in polarity, with hydrophilic R groups projecting to the lining of the channel, while hydrophobic R groups project to the outside of the channel, where they embed in the hydrophobic membrane. This structure is exemplified in membrane channel proteins, proteins that channel ions across from one surface to another. The beta-pleated sheet is formed by folding successive planes. Each plane is five to eight amino acids long. The folds are stabilized by hydrogen bonding. The strength observed in silk fibers is due to their stacks of beta-pleated sheets.

Combinations of secondary structure form "motifs." A coiled-coil motif is common among proteins that associate with the DNA helix. The helix-loop-helix motif is a knobby structure, and the zinc finger projects outward like its name. These last two motifs allow associations between RNA and proteins that form the basis of their interactions.

Tertiary Structure and Protein Domains

Domains are large functional regions of the protein, such as an enzyme's active site, which binds the substrate to the enzyme. Myoglobin, the muscle protein that stores and releases oxygen, contains several alpha-helices wound around a central crevice. It is in this central crevice that the O₂ molecule binds. Just as words take on their meanings when completed, the functional domains unite to form the overall purpose of a protein. For example, a membrane protein stabilizes itself by anchoring itself with a hydrophilic cytoplasmic domain, then weaves its alpha-helices throughout the membrane domain and projects its carbohydrate hydrophilic side chains into the extracellular surface domain. Such membrane proteins often act as receptors, important for receiving signals such as hormones, or work in the immune system to recognize infected cells.

The local foldings, evident in secondary structure, then combine into a single polypeptide chain. This chain is called the tertiary structure, or conformation . For example, the pancreatic enzyme ribonuclease, which aids in digestion of RNA in the diet, consists mainly of beta sheet folds, with three small alpha-helical regions. Tertiary structure is often stabilized by disulfide bonds between adjacent cysteine in different regions of the protein. For example, the tertiary structure of ribonuclease contains four disulfide bonds, located at specific sites. The stability of the tertiary structure of proteins is destroyed by toxic heavy metals such as mercury. Concentrations of mercury in the environment, for example, result in the displacement of hydrogen on the sulfur atom (SH), thereby blocking functional disulfide bonds.

Several other weak, noncovalent interactions also help stabilize tertiary structure. These noncovalent interactions can be disrupted by heating a protein or exposing it to extremes in pH (acidity or alkalinity), which alters the charge of polar groups on the amino acids. Such disruptions cause the protein to unfold, often exposing hydrophobic groups and leading to precipitation (clumping together) of the protein. If these disruptive factors are removed, some proteins can refold to their original conformation. This ability to refold confirms that protein folding is a self-assembly process that is dependent upon the sequence of amino acids.

Quaternary Structure

Some proteins need to functionally associate with others as subunits in a multimeric structure. This is called the quaternary structure of the protein. This can also be stabilized by disulfide bonds and by noncovalent interactions with reacting substrates or cofactors. For example an antibody consists of two "light" polypeptide chains covalently linked to two longer "heavy" chains, forming a Y-shaped molecule with each branch able to bond to an identical antigen . The protein subunits of the single-stranded binding protein of Escherichia coli bind to DNA only as a tetramer (a multimeric form), acting to stabilize the separated DNA strands during replication.

Another excellent example of quaternary structure is that of hemoglobin. Adult hemoglobin consists of two alpha subunits and two beta subunits, held together by noncovalent interactions. Each of the four subunits contains a heme group that binds an oxygen molecule, O₂. This binding of oxygen is a cooperative process whereby the binding of one oxygen molecule occurs slowly, but once achieved then speeds the binding of the remaining three oxygen molecules. The fourth oxygen molecule binds 300 times faster than the first oxygen molecule. This cooperativity assures that maximum oxygen is captured and retained as it enters into the capillaries within the lungs.

The unloading of oxygen is also facilitated by cooperativity, such that after one oxygen molecule is released, the other three soon follow. This assures that the tissues will receive maximum oxygen once it is delivered. Alpha-hemoglobin by itself, or tetramers of all beta subunits, also bind oxygen, but not with the same cooperativity. Such evidence indicates that there is some form of molecular interaction between the subunits of the tetramer of adult hemoglobin.

Signal Sequences in Protein Synthesis

Protein must be delivered to the proper destination in the cell to function properly. Signal sequences within the protein itself act like "zip codes" to ensure correct delivery. The synthesis of secreted proteins like insulin and of proteins that will be integral to the plasma membrane occurs at a ribo-some tethered to the endoplasmic reticulum , which is a system of membranes that transport materials within cells. The peptides formed there are then translocated into the lumen , or channel, of the endoplasmic reticulum, where they will be formed into a polypeptide chain. This translocation occurs because of a specific signal sequence that is formed by the first twenty or so amino acids in the protein. The core of this sequence consists of ten to fifteen amino acids that have hydrophobic side chains such as alanine, leucine, valine, isoleucine, and phenylalanine, which are usually cleaved from the protein later on. The nascent polypeptide chain is guided along this path by a signal receptor protein.

Proteins targeted for internal cellular functions are synthesized on ribosomal assemblages that float free in the cytoplasm. Such proteins also have their signal sequences. Proteins destined for the cell's nucleus have a specific nuclear signal sequence consisting of a small series of basic amino acids such as arginine and lysine bounded by proline. This nuclear signaling sequence can be located anywhere in the protein's sequence as long as it projects outward from the three-dimensional tertiary structure. Signal sequences for proteins targeted to be part of organelles such as the mitochondria and chloroplasts are anywhere from twenty to seventy amino acids long and are mostly hydrophilic. This charged nature allows easy travel through the hydrophilic cytoplasm to the organelle.

Molecular Chaperones

Although the folding of the protein into its tertiary structure is determined by the primary order of amino acids, the process of folding occurs with the assistance of molecular chaperone proteins. These molecular chaperones often have pockets or tunnels that envelop the nascent polypeptide. This enveloping allows the folding of the protein to occur unhindered by unwanted interaction with other cellular components.

Chemical Modification and Processing of Proteins

Most proteins are structurally altered after synthesis through chemical modification or processing. These alterations help the cell determine a protein's fate, such as whether that protein is active or inactive, how long the protein will function, and to some degree the location where that protein will function. Chemical modifications, which are additions of chemical groups to the R groups in the amino acids, are made after translation. Such modifications may include the attachment of a phosphate group (phosphorylation) to the alcohol group on the amino acids of serine, threonine, or tyrosine. The amino acid proline in proteins such as collagen is often hydroxylated, which means that an alcohol group is attached. Other amino acids with amino groups in their R region, such as lysine or arginine, may be chemically modified through methylation, which is the addition of a methyl group (-CH₃), or through acetylation, in which an acetyl group (-CH₃CO) is added. Larger modifications, such as the addition of a carbohydrate group, occur to create glycoproteins in specialized organelles termed Golgi apparati.

Modifications change the charge of the protein, and often cause a change in the protein's activity level. For many DNA-associated proteins their regional acetylations cause them to "loosen" their grip on the DNA helix, thereby enabling transcription factors to enter, signaling gene activation. A cascade of internal protein phosphorylation (successive additions of a phosphate group) is a common mechanism for carrying a hormone's message from the membrane, where it docks into the cell and induces a metabolic change inside the target cell.

Processing results in cutting off specific parts of the protein (cleavage). Many digestive proteins such as pepsin and hormones such as insulin are processed. Pepsin, which is a digestive protein secreted into the lumen of the stomach, remains in an inactive form until stomach acid is also secreted. The timing of the acid secretion, pepsin activation, and entry of food coincide so that pepsin's activity will be directed toward the food and not the wall of the stomach.

Conformational Changes in Protein Structure

As noted above, a protein's activity can be regulated when it undergoes a change in its conformation. A dramatic and extensively studied model of protein conformational change is that of the Na⁺/K⁺ ATPase pump. This is an integral membrane protein with one side facing the exterior of the cell and the other facing the cytosol. It is used for the specific transport of sodium or potassium across the membrane, and one of its most important functions is the repolarization of a nerve fiber after it "fires."

The first step in the transport process is the binding of three Na⁺ (sodium) ions to the inside face of the protein. This is followed by protein phosphorylation using ATP , which causes the protein to change its conformation. This moves the sodium ions from the cytosol to the exterior. This conformational change also opens up exterior binding sites, which tightly bind two potassium ions outside the cell. Following the potassium binding, the protein is dephosphorylated, losing its recently added phosphate group. This dephosphorylation then changes the protein back to the original conformation, causing the protein to loosen its binding of potassium and deliver those two ions to the cytosol. This process demonstrates that protein structure can be reversibly changed. The net result is that the inside of the cell develops a slight negative charge compared to the outside. The disruption of this "polarized" state constitutes nerve cell firings, which allow the cells of the nervous system to communicate with one another.

Proteomics

Proteomics is a new field of study that seeks to describe which proteins are expressed in a cell, when they are expressed, what consequences result from their expression, and how they fit into biochemical pathways. The first step in the study of proteomics is to define the language of protein structure. The field of proteomics promises to bring a complex understanding to the role of proteins in living cells.

see also Cell, Eukaryotic; Chaperones; Genetic Code; Hemoglobinopathies; Immune System Genetics; Mutation; Nucleases; Proteomics.

Paul K. Small

Bibliography

Fairbanks, Daniel, J., and W. Ralph Anderson. Genetics: The Continuity of Life. PacificGrove, CA: Brooks/Cole, 1999.

Lodish, Harvey, et al. Molecular Cell Biology, 4th ed. New York: W. H. Freeman, 2000.

Sadava, David E. Cell Biology: Organelle Structure and Function. Boston: Jones and Bartlett, 1993.

Stryer, Lubert. Biochemistry, 3rd ed. New York: W. H. Freeman, 1988.

Proteins

Excluding the water present in the human body, about one half of the remaining mass is composed of a class of molecules called proteins. It should therefore be of no surprise that proteins carry out many important biological processes.

Amino Acids

Proteins are essentially natural polymers composed of long chains of subunits. These smaller units are called amino acids. One "end" of an amino acid has acidic character because it has a carboxyl (COOH) functional group . The other end has basic character because it has an amino (NH₂) functional group. When two amino acids react, they form what is called a peptide bond. The resulting molecule, called a dipeptide, still has one end that is acidic and another that is basic (Figure 1). With this fundamental reactive pattern, it is possible to string together many amino acids to form a polypeptide . For such a chain, the end that has the carboxyl group is referred to as the C-terminus; the amino end is referred to as the N-terminus.

Some proteins, including a number of hormones, have only a relatively small number of amino acid units, while others have literally thousands. Once an amino acid is incorporated into the polypeptide, it is referred to as a residue. When biochemists identify a particular portion of a protein, they usually refer to the residue with its name and a number, referring to how far from the N-terminus that residue is located.

In the human body, there are twenty different amino acids that are found in proteins^✶. The body is capable of synthesizing most of the amino acids it needs, but there are eight molecules that cannot be made. These are called

^✶See table of amino acids in the Amino Acids article.

the essential amino acids, and they must be present in the diet or a person will develop malnutrition. Many people gain the amino acids they need by eating a diet that contains complete proteins. Most meats (such as beef, poultry, or fish) have complete proteins. The body metabolizes (breaks down) these ingested proteins and in so doing provides the raw materials needed for making the proteins.

People who do not eat meat must be careful to eat a diet that includes the essential amino acids. This can be accomplished by eating complementary proteins. For example, corn has many essential amino acids but is low in tryptophan. Beans, however, have ample tryptophan; cultures that use cornmeal often complement this food source with beans. Similarly, cultures in Asia often eat rice with soy sauce; this combination provides complementary proteins in the diet.

Protein Structure

The order of the amino acids in a protein dictates the primary structure of the protein. While other levels of structure are important, they all follow from the order of the residues. The primary structure is dictated by genetic information found in a cell; deoxyribonucleic acid (DNA ) contains the code that directs which amino acids are linked together. The processes by which the genetic code is read and proteins are synthesized are called transcription and translation.

The next level of protein structure is called the secondary structure. The side chains of the residues have various functional groups that can have different types of forces: some are hydrophobic and others are hydrophilic ; some participate in hydrogen bonding interactions while others do not. These forces lead to conformations (geometric arrangements of the residues) that result in lower energies. Two specific arrangements that are found regularly are shown in Figure 2: a helix (which looks like a corkscrew) and a pleated sheet (which looks like a paper that has been folded and opened).

The secondary structure of the protein is the result of interactions of side chains that are located within a few residues of each other. Proteins are sufficiently long that they can eventually fold back on themselves, allowing residues that are farther apart in the primary structure to interact with each other. These interactions give rise to the tertiary structure of the protein

(Figure 2). Some proteins can form structures with multiple units (dimers, trimers, or tetramers). These collections of units provide yet another level of structure called the quaternary structure.

Solubility is one property that can be used to classify the proteins that result from the various levels of structure. For example, fibrous proteins are not soluble in water. Many familiar components of tissues are composed of fibrous proteins, including keratin (the protein present in hair), collagen (a structural protein found in tendons and cartilage), myosin (a protein found in most muscle tissue), and fibrin (the protein that allows blood to clot and form scabs). Conversely, globular proteins are soluble in water. For example, albumins are water-soluble proteins that provide a familiar example of what happens when a protein loses its secondary and tertiary structure, a process called denaturation. When an egg is cooked, the egg white changes from translucent to white; this color change is indicative of the change in structure that has taken place in the albumin proteins.

In many cases, the structure of a protein defines a key location called the active site, the region that is associated with the primary activity of a protein, even though it is often made up of only a small number of residues.

Biological Functions

The variety of structures associated with proteins suggests the large number of biological tasks that they carry out. It is possible to classify proteins based on their biological functions.

Enzymes are proteins that catalyze chemical reactions that take place in living systems. A catalyst is a molecule that speeds up a reaction but is not consumed by that reaction. Enzymes are particularly interesting because they often are quite specific, capable of catalyzing only one type of biochemical reaction. Learning about the structure of the active site is often a crucial component of studies that look at the catalytic properties of an enzyme.

Many hormones are proteins, often containing only a relatively small number of residues. Insulin is perhaps the most well known peptide hormone; because of its role in the metabolism of carbohydrates, it plays an important role in the control of diabetes. Growth hormone is another example of a protein.

Some neurotransmitters are closely related to proteins, differing from them only because they have relatively few residues. There are many known neurotransmitters; endorphins and enkephalins are examples of peptides that carry out this role.

Many antibodies and other components of the immune response system are proteins. One important component of a body's defenses is the ability to form clots to stop bleeding from cuts. A protein called fibrinogen plays a key role in this.

Proteins comprise a majority of muscle tissue. Two classes of protein, actin (which makes moving filaments) and myosin (which remains stationary), are primary components of the muscles in the body.

Proteins are often involved in the storage of nutrients in the body. For example, iron is stored (mostly in the spleen) in a protein called ferritin. In plants, nutrients needed for the growth of a new plant are a major component of seeds, and storage proteins carry out this task.

In addition to storing nutrients, proteins can transport them. Perhaps the most critical transport protein is hemoglobin, which transports oxygen and carbon dioxide in the bloodstream. In the lungs the percentage of oxygen is high, so it binds to the protein in an equilibrium process. When hemoglobin reaches tissue that has produced carbon dioxide, the oxygen is released and used by cells in metabolism. The hemoglobin can then bind carbon dioxide and carry it to the lungs to be released.

There are several ways that proteins contribute to the structure of living things. Glycoproteins play a major role in the structures of cell membranes. While lipids are more numerous in the membrane, many of the key functions that occur at the membrane level, such as transport of materials, are carried out by transmembrane proteins. Receptors , including those in nerve cells, are proteins that help cells interact with their external environment. Some tissues like cartilage have proteins that help provide structure on a larger scale.

Proteins can also be dangerous or unhealthy. For many who suffer from allergies to agents like pollen, it is proteins on the surface of the pollen that cause an immune response that triggers the allergic reaction. More seriously, many natural toxins are proteins. Snake venom is one example of a naturally occurring protein-based toxin.

CARBON MONOXIDE POISONING

Carbon monoxide, CO, poisons the body by combining with hemoglobin some 250 times more tightly than O₂, thus hindering the transport of O₂ to the body's tissues. In an environment of 0.1 percent CO (within the lung), more than half the binding sites of hemoglobin become occupied with CO, and the victim dies within an hour.

—N. M. Senozan

see also Active Site; Amino Acid; Denaturation; Enzymes; Fibrous Proteins; Globular Proteins; Neurotransmitters; Peptide Bond; Protein Solubility; Protein Synthesis; Protein Translation; Rna Synthesis; Secondary Structure; Tertiary Structure; Transmembrane Proteins; Venom.

Thomas A. Holme

Bibliography

Branden, C., and Tooze, J. (1999). Introduction to Protein Structure, 2nd edition. New York: Garland Publishing.

Creighton, T. E. (1993). Proteins, 2nd edition. New York: Freeman.

Davies, J. S., ed. (1985). Amino Acids and Peptides. New York: Chapman & Hall.

Lesk, A. M. (2000). Introduction to Protein Architecture: The Structural Biology of Proteins. Oxford: Oxford University Press.

Voet, D., and Voet, J. G. (1995). Biochemistry, 2nd edition. New York: Wiley.