Proteins

The word protein is derived from the Greek word proteios, meaning "of first importance." Proteins are the most versatile molecules in the body, and many discussions in this book will draw on your understanding of protein structure and behavior.

Amino Acids and Peptides

A protein is a polymer of amino acids. An amino acid has a central carbon atom with an amino (—NH2) and a car-boxyl (—COOH) group bound to it (fig. 2.23a). The 20 amino acids used to make proteins are identical except for a third functional group called the radical (R group) attached to the central carbon. In the simplest amino acid, glycine, R is merely a hydrogen atom, while in the largest amino acids it includes rings of carbon. Some R groups are hydrophilic and some are hydrophobic. Being composed of many amino acids, proteins as a whole are therefore often amphiphilic. The 20 amino acids involved in proteins are listed in table 2.8 along with their abbreviations.

A peptide is any molecule composed of two or more amino acids joined by peptide bonds. A peptide bond, formed by dehydration synthesis, joins the amino group of one amino acid to the carboxyl group of the next (fig. 2.23b). Peptides are named for the number of amino acids they have—for example, dipeptides have two and tripeptides have three. Chains of fewer than 10 or 15 amino acids are

Chapter 2 The Chemistry of Life 79

called oligopeptides,23 and chains larger than that are called polypeptides. An example of an oligopeptide is the childbirth-inducing hormone oxytocin, composed of 9 amino acids. A representative polypeptide is adrenocorti-cotropic hormone (ACTH), which is 39 amino acids long. A protein is a polypeptide of 50 amino acids or more. A typ-

ical amino acid has a

molecular weight of about 80

amu,

23 oligo = a few

Table 2.8

The 20 Amino Acids and

Their Abbreviations

Alanine

Ala

Leucine

Leu

Arginine

Arg

Lysine

Lys

Asparagine

Asn

Methionine

Met

Aspartic acid

Asp

Phenylalanine

Phe

Cysteine

Cys

Proline

Pro

Glutamine

Gln

Serine

Ser

Glutamic acid

Glu

Threonine

Thr

Glycine

Gly

Tryptophan

Trp

Histidine

His

Tyrosine

Tyr

Isoleucine

Ile

Valine

Val

Some nonpolar amino acids

Some polar amino acids

Peptide Hormone DiagramPeptide Hormone Diagram

Amino acid 1

Amino acid 2

C OH

Peptide bond

A dipeptide

Figure 2.23 Amino Acids and Peptides. (a) Four representative amino acids. Note that they differ only in the R group, shaded in pink. (b) The joining of two amino acids by a peptide bond, forming a dipeptide. Side groups R1 and R2 could be the groups indicated in pink in figure a, among other possibilities.

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Physiology: The Unity of Companies, 2003 Form and Function, Third Edition

80 Part One Organization of the Body and the molecular weights of the smallest proteins are around 4,000 to 8,000 amu. The average protein weighs in at about 30,000 amu, and some of them have molecular weights in the hundreds of thousands.

Protein Structure

Proteins have complex coiled and folded structures that are critically important to the roles they play. Even slight changes in their conformation (three-dimensional shape) can destroy protein function. Protein molecules have three to four levels of complexity, from primary through quaternary structure (fig. 2.24).

Primary structure is the protein's sequence of amino acids. Their order is encoded in the genes (see chapter 4).

Secondary structure is a coiled or folded shape held together by hydrogen bonds between the slightly negative C—O group of one peptide bond and the slightly positive N—H group of another peptide bond some distance away. The most common secondary structures are a springlike shape called the a helix and a pleated, ribbonlike shape, the p sheet (or p-pleated sheet). Many proteins have multiple a-helical and p-pleated regions joined by short segments with a less orderly geometry. A single protein molecule may fold back on itself and have two or more p-pleated regions linked to each other by hydrogen bonds. Separate, parallel protein molecules also may be hydrogen-bonded to each other through their p-pleated regions.

Tertiary24 (TUR-she-air-ee) structure is formed by the further bending and folding of proteins into various globular and fibrous shapes. It results from hydrophobic R groups associating with each other and avoiding water, while the hydrophilic R groups are attracted to the surrounding water. Globular proteins, somewhat resembling a wadded ball of yarn, have a compact tertiary structure well suited for proteins embedded in cell membranes and proteins that must move around freely in the body fluids, such as enzymes and antibodies. Fibrous proteins such as myosin, keratin, and collagen are slender filaments better suited for such roles as muscle contraction and providing strength to skin, hair, and tendons.

The amino acid cysteine (Cys), whose R group is —CH2—SH (see fig. 2.23), often stabilizes a protein's tertiary structure by forming covalent disulfide bridges. When two cysteines align with each other, each can release a hydrogen atom, leaving the sulfur atoms to form a disul-fide (—S—S—) bridge. Disulfide bridges hold separate polypeptide chains together in such molecules as antibodies and insulin (fig. 2.25).

Quaternary25 (QUA-tur-nare-ee) structure is the association of two or more polypeptide chains by noncovalent forces such as ionic bonds and hydrophilic-hydrophobic interactions. It occurs in only some proteins. Hemoglobin, for example, consists of four polypeptides—two identical a chains and two identical, slightly longer p chains (see fig. 2.24).

One of the most important properties of proteins is their ability to change conformation, especially tertiary structure. This can be triggered by such influences as voltage changes on a cell membrane during the action of nerve cells, the binding of a hormone to a protein, or the dissociation of a molecule from a protein. Subtle, reversible changes in conformation are important to processes such as enzyme function, muscle contraction, and the opening and closing of pores in cell membranes. Denaturation is a more drastic conformational change in response to conditions such as extreme heat or pH. It is seen, for example, when you cook an egg and the egg white protein (albumen) turns from clear to opaque. Denaturation is sometimes reversible, but often it permanently destroys protein function.

Conjugated proteins have a non-amino-acid moiety called a prosthetic26 group covalently bound to them. Hemoglobin, for example, not only has the four polypeptide chains described earlier, but each chain also has a complex iron-containing ring called a heme moiety attached to it (see fig. 2.24). Hemoglobin cannot transport oxygen unless this group is present. In glycoproteins, as described earlier, the carbohydrate moiety is a prosthetic group.

Protein Functions

Proteins have more diverse functions than other macro-molecules. These include:

• Structure. Keratin, a tough structural protein, gives strength to the nails, hair, and skin surface. Deeper layers of the skin, as well as bones, cartilage, and teeth, contain an abundance of the durable protein collagen.

• Communication. Some hormones and other cell-to-cell signals are proteins, as are the receptors to which the signal molecules bind in the receiving cell. A hormone or other molecule that reversibly binds to a protein is called a ligand27 (LIG-and).

• Membrane transport. Some proteins form channels in cell membranes that govern what passes through the membranes and when. Other proteins act as carriers that briefly bind to solute particles and transport them to the other side of the membrane. Among their other roles, such proteins turn nerve and muscle activity on and off.

• Catalysis. Most metabolic pathways of the body are controlled by enzymes, which are globular proteins that function as catalysts.

• Recognition and protection. The role of glycoproteins in immune recognition was mentioned earlier.

24tert = third 2iquater = fourth

26prosthe = appendage, addition 27lig = to bind

Saladin: Anatomy & Physiology: The Unity of Form and Function, Third Edition

2. The Chemistry of Life

Text

-»Amino acids

sheet

-»Amino acids

sheet

Primary Nursing Structure

Primary structure

Peptide bonds Sequence of amino acids joined by peptide bonds

Heme groups a chain a chain

Figure 2.24 Four Levels of Protein Structure. The molecule shown for quaternary structure is hemoglobin, which is composed of four polypeptide chains. The heme groups are iron-containing nonprotein moieties.

Primary structure

Peptide bonds Sequence of amino acids joined by peptide bonds

Heme groups a chain

Secondary structure a helix or p sheet formed by hydrogen bonding

Tertiary structure

Folding and coiling due to interactions among R groups and between R groups and surrounding water a chain

Quaternary structure

Association of two or more polypeptide chains with each other

Figure 2.24 Four Levels of Protein Structure. The molecule shown for quaternary structure is hemoglobin, which is composed of four polypeptide chains. The heme groups are iron-containing nonprotein moieties.

Saladin: Anatomy & I 2. The Chemistry of Life I Text I I © The McGraw-Hill

Physiology: The Unity of Companies, 2003 Form and Function, Third Edition

82 Part One Organization of the Body

82 Part One Organization of the Body

Primary Structure Insulin
Figure 2.25 Primary Structure of Insulin. Insulin is composed of two polypeptide chains joined by disulfide bridges.

and trypsin. The modern system of naming enzymes, however, is more uniform and informative. It identifies the substance the enzyme acts upon, called its substrate; sometimes refers to the enzyme's action; and adds the suffix -ase. Thus, amylase digests starch (amyl- = starch) and carbonic anhydrase removes water (anhydr-) from carbonic acid. Enzyme names may be further modified to distinguish different forms of the same enzyme found in different tissues (see insight 2.4).

Insight 2.4 Clinical Application

The Diagnostic Use of Isoenzymes

A given enzyme may exist in slightly different forms, called isoenzymes, in different cells. Isoenzymes catalyze the same chemical reactions but have enough structural differences that they can be distinguished by standard laboratory techniques. This is useful in the diagnosis of disease. When organs are diseased, some of their cells break down and release specific isoenzymes that can be detected in the blood. Normally, these isoenzymes would not be present in the blood or would have very low concentrations. If their blood levels are elevated, it can help pinpoint what cells in the body have been damaged.

For example, creatine kinase (CK) occurs in different forms in different cells. An elevated serum level of CK-1 indicates a breakdown of skeletal muscle and is one of the signs of muscular dystrophy. An elevated CK-2 level indicates heart disease, because this isoenzyme comes only from cardiac muscle. There are five isoenzymes of lactate dehydrogenase (LDH). High serum levels of LDH-1 may indicate a tumor of the ovaries or testes, while LDH-5 may indicate liver disease or muscular dystrophy. Different isoenzymes of phosphatase in the blood may indicate bone or prostate disease.

Antibodies and other proteins attack and neutralize organisms that invade the body. Clotting proteins protect the body against blood loss.

• Movement. Movement is fundamental to all life, from the intracellular transport of molecules to the galloping of a racehorse. Proteins, with their special ability to change shape repeatedly, are the basis for all such movement. Some proteins are called molecular motors for this reason.

• Cell adhesion. Proteins bind cells to each other, which enables sperm to fertilize eggs, enables immune cells to bind to enemy cancer cells, and keeps tissues from falling apart.

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