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.