Macromolecules: Giant Polymers

The four kinds of large molecules are made the same way and they are present in roughly the same proportions in all living organisms. A protein that has a certain role in an apple tree probably has a similar role in a human being because their basic chemistry is the same. One important advantage of this biochemical unity is that organisms acquire needed biochemicals by eating other organisms. When you eat an apple, the molecules you take in include carbohydrates, lipids and proteins that can be refashioned into the special varieties of those molecules used by humans.

Macromoleculesare giant polymers(poly-, “many”; -mer, “unit”) constructed by the covalent linking of smaller molecules called monomers.These monomers may or may not be identical, but they always have similar chemical structures. Molecules with molecular weights exceeding 1,000 are usually considered macromolecules, and the proteins, polysaccharides (large carbohydrates) and nucleic acids of living systems certainly fall into this category. Each type of macromolecule performs some combination of functions: energy storage, structural support, protection, catalysis, transport, defence, regulation, movement and information storage. These roles are not necessarily exclusive. For example, both carbohydrates and proteins can play structural roles, supporting and protecting tissues and organisms. However, only nucleic acids specialize in information storage and function as hereditary material carrying both species and individual traits from generation to generation. The functions of macromolecules are directly related to their shapes and to the sequences and chemical properties of their monomers. Some macromolecules fold into compact spherical forms with surface features that make them water-soluble and capable of intimate interaction with other molecules. Other proteins and carbohydrates form long, fibrous systems that provide strength and rigidity to cells and organisms. Still other long, thin assemblies of proteins can contract and cause movement. Because macromolecules are so large, they contain many different functional groups. For example, a large protein may contain hydrophobic, polar and charged functional groups that give specific properties to local sites on the macromolecule. As we will see, this diversity of properties determines the shapes of macromolecules and their interactions with both other macromolecules and smaller molecules.

Condensation and Hydrolysis Reactions

Polymers are constructed from monomers by a series of reactions called condensation reactionsor dehydration reactions (both terms refer to the loss of water). Condensation reactions result in covalently bonded monomers and release a molecule of water for each bond formed. The condensation reactions that produce the different kinds of polymers differ in detail, but in all cases, polymers form only if energy is added to the system. In living systems, specific energy-rich molecules supply this energy. The reverse of a condensation reaction is a hydrolysis reaction (hydro-, “water”; -lysis, “break”). Hydrolysis reactions digest polymers and produce monomers. Water reacts with the bonds that link the polymer together and the products are free monomers. The elements (H and O) of H₂O become part of the products. These two types of reactions are universal in living things and as we have seen, were an important step in the origin of life in an aqueous environment. We begin our study of biological macromolecules with a very diverse group of polymers, the proteins.

Proteins: Polymers of Amino Acids

The functions of proteinsinclude structural support, protection, transport, catalysis, defence, regulation and movement.

Among the functions of macromolecules listed earlier, only energy storage and information storage are not usually performed by proteins. Proteins range in size from small ones such as the RNA digesting enzyme ribonuclease A, which has a molecular weight of 5,733 and 51 amino acid residues, to huge molecules such as the cholesterol transport protein a polipoprotein B which has a molecular weight of 513,000 and 4,636 amino acid residues. (The word residue refers to a monomer when it is part of a polymer.) Each of these proteins consists of a single unbranched polymer of amino acids (a polypeptide chain), which is folded into a specific three-dimensional shape. Many proteins require more than one polypeptide chain to make up the functional unit. For example, the oxygen-carrying protein haemoglobin has four chains that are folded separately and associate together to make the functional protein. As we will see later in this book, numerous functional proteins can associate, forming “multi-protein machines” to carry out complex roles such as DNA synthesis.

The composition of a protein refers to the relative amounts of the different amino acids it contains. Not every protein contains all kinds of amino acids, nor an equal number of different ones. The diversity in amino acid content and sequence is the source of the diversity in protein structures and functions. The next several chapters will describe the many functions of proteins. To understand them, it is necessary first to explore a protein structure. The properties of amino acids will be examined and how they link together to form proteins. Then will sbe ystematically examined a protein structure and how a linear chain of amino acids is consistently folded into a compact three-dimensional shape. Finally, will be seen how this three-dimensional structure provides a specific physical and chemical environment that influences the interaction of other molecules with the protein.

Proteins are composed of amino acids

The structure of amino acids: identified four different groups attached to a central carbon atom – a hydrogen atom, an amino group (NH₃ +), a carboxyl group (COO–), - and a unique side chain or R group. The R groups of amino acids are important in determining the three-dimensional structure and function of the protein macromolecule. Amino acids are grouped and distinguished by their side chains.

The five amino acids that have electrically charged side chains attract water (are hydrophilic) and oppositely charged ions of all sorts.

The five amino acids that have polar side chains tend to form weak hydrogen bonds with water and with other polar or charged substances. These amino acids are hydrophilic.

Seven amino acids have side chains that are nonpolar hydrocarbons or very slightly modified hydrocarbons. In the watery environment of the cell, these hydrophobic side chains may cluster together in the interior of the protein. These amino acids are hydrophobic.

Three amino acids — cysteine, glycine and praline — are special cases, although their R groups are generally hydrophobic.

The cysteine side chain which has a terminal —SH group, can react with another cysteine side chain to form a covalent bond called a disulfide bridge(—S—S—). Disulfide bridges help determine how a polypeptide chain folds. When cysteine is not part of a disulfide bridge, its side chain is hydrophobic. The glycine side chain consists of a single hydrogen atom and is small enough to fit into tight corners in the interior of a protein molecule where a larger side chain could not fit. Proline differs from other amino acids because it possesses a modified amino group lacking a hydrogen on its nitrogen which limits its hydrogen-bonding ability. Also, the ring system system of proline limits rotation about its carbon, thus, proline isoften found at bends or loops in a protein.

Peptide linkages covalently bond amino acids together

When amino acids polymerize, the carboxyl and amino groups attached to the carbon are the reactive groups. The carboxyl group of one amino acid reacts with the amino group of another, undergoing a condensation reaction that forms a peptide linkage. (In living systems, other molecules must activate the amino acids in order for this reaction to proceed and there are intermediate steps in the process. Just as a sentence begins with a capital letter and ends with a period, polypeptide chains have a linear order. The chemical “capital letter” marking the beginning of a polypeptide is the amino group of the first amino acid in the chain and is known as the N terminus. The “punctuation mark” for the end of the chain is the carboxyl group of the last amino acid—the C terminus. All the other amino and carboxyl groups in the chain (except those in side chains) are involved in peptide bond formation, so they do not exist in the chain as “free,” intact groups (the “N →C” or “amino-to-carboxyl” orientation of polypeptides).

The peptide linkage has two characteristics that are important in the three-dimensional structure of proteins: unlike many single covalent bonds, in which the groups on either side of the bond are free to rotate in space, the C—N peptide linkage is relatively inflexible. The adjacent atoms (the alpha-carbons of the two adjacent amino acids) are not free to rotate because of the partial double bond character of the peptide bond. This characteristic limits the folding of the polypeptide chain. The oxygen bound to the carbon (C−O) in the carboxyl group carries a slight negative charge, whereas the hydrogen bound to the nitrogen (N—H) in the amino group is slightly positive. This asymmetry of charge favors hydrogen bonding within the protein molecule itself and with other molecules contributing to both the structure and the function of many proteins. Before exploring the significance of such hydrogen bonds, it is necessary to examine the importance of the order of amino acids.

The primary structure of a protein is its amino acid sequence.

There are four levels of protein structure called primary, secondary, tertiary and quaternary. The precise sequence of amino acids in a polypeptide constitutes the primary structure of a protein. The peptide backbone of this primary structure consists of a repeating sequence of three atoms (—N—C—C—): the N from the amino group, the alpha-carbon, and the C from the carboxyl group of each amino acid. Scientists have deduced the primary structure of many proteins. The single-letter abbreviations for amino acids are used to record the amino acid sequence of a protein. Here, for example, are the first 20 amino acids (out of a total of 124) in the protein ribonuclease from a cow: KETAAAKFERQHMDSSTSAA

The theoretical number of different proteins is enormous. Since there are 20 different amino acids, there could be 20 x 20 = 400 distinct dipeptides (two linked amino acids) and 20 x 20 x 20 = 8,000 different tripeptides (three linked amino acids). Imagine this process of multiplying by 20 extended to a protein made up of 100 amino acids (which is considered a small protein). There could be 20100 such small proteins, each with its own distinctive primary structure. How large is the number 20100? There aren’t that many electrons in the entire universe. At the higher levels of protein structure, local coiling and folding give the molecule its final functional shape but all of these levels derive from the primary structure—that is, the precise location of specific amino acids in the polypeptide chain. The properties associated with a precise sequence of amino acids determine how the protein can twist and fold, thus adopting a specific stable structure that distinguishes it from every other protein. Primary structure is determined by covalent bonds. But the next level of protein structure is determined by weaker hydrogen bonds.

The secondary structure of a protein requires hydrogen bonding

A protein’s secondary structureconsists of regular, repeated patterns in different regions of a polypeptide chain. There are two basic types of secondary structure, both of them determined by hydrogen bonding between the amino acid residues that make up the primary structure: a-helix and b-pleated sheet.

The a helix

The a (alpha) helixis a right-handed coil that is “threaded” in the same direction as a standard wood screw. The R groups extend outward from the peptide backbone of the helix. When this pattern of hydrogen bonding is established repeatedly over a segment of the protein, it stabilizes the coil resulting in a helix. The presence of amino acids with large R groups that distort the coil or otherwise prevent the formation of the necessary hydrogen bonds will keep a helix from forming. The helical secondary structure is common in the fibrous structural proteins called keratins, which make up hair, hooves and feathers. Hair can be stretched because stretching requires that only the hydrogen bonds of the helix, not the covalent bonds, be broken; when the tension on the hair is released, both the hydrogen bonds and the helix re-form.

The b (beta) pleated sheet.

A b (beta) pleated sheetis formed from two or more polypeptide chains that are almost completely extended and lying next to one another. The sheet is stabilized by hydrogen bonds between the N—H groups on one chain and the C−−O groups on the other (Figure). A pleated sheet may form between separate polypeptide chains, as in spider silk, or between different regions of the same polypeptide chain that is bent back on itself.

The tertiary structure of a protein is formed by bending and folding

In many proteins, the polypeptide chain is bent at specific sites and then folded back and forth, resulting in the tertiary structureof the protein. Although the helices and pleated sheets contribute to the tertiary structure, only parts of the macromolecule usually have these secondary structures and large regions consist of structures unique to a particular protein. While hydrogen bonding between the N—H and C−−O groups within and between chains is responsible for secondary structure, the interactions between R groups—the amino acid side chains—determine tertiary structure. Many of these interactions are involved in determining tertiary structure.

Covalent disulfide bridges can form between specific cysteine residues, holding a folded polypeptide in place. Hydrophobic side chains can aggregate together in the interior of the protein, away from water, folding the polypeptide in the process. Van der Waals forces can stabilize the close interactions between the hydrophobic residues. Ionic bonds can form between positively and negatively charged side chains buried deep within a protein, away from water forming a salt bridge. A complete description of a protein’s tertiary structure specifies the location of every atom in the molecule in three-dimensional space in relation to all the other atoms. The first tertiary structures to be determined took years to figure out but today, dozens of new structures are published every week. The major advances making this possible have been the ability to produce large quantities of specific proteins by biotechnology and the use of computers to analyze the atomic data. Bear in mind that both tertiary structure and secondary structure derive from a protein’s primary structure. If lysozyme is heated slowly, the heat energy will disrupt only the weak interactions and cause only the tertiary structure to break down. But the protein will return to its normal tertiary structure when it cools, demonstrating that all the information needed to specify the unique shape of a protein is contained in its primary structure.

The quaternary structure of a protein consists of subunits

As mentioned earlier, many functional proteins contain two or more polypeptide chains called subunits, each of them folded into its own unique tertiary structure. The protein’s quaternary structure results from the ways in which these subunits bind together and interact. Quaternary structure is illustrated by haemoglobin. Hydrophobic interactions, van der Waals forces, hydrogen bonds and ionic bonds all help hold the four subunits together to form the haemoglobin molecule. The function of hemoglobin is to carry oxygen in red blood cells. As hemoglobin binds one O2 molecule, four subunits shift their relative positions slightly, changing the quaternary structure. Ionic bonds are broken, exposing buried side chains that enhance the binding of additional O2 molecules. The structure changes again when hemoglobin releases its O2 molecules to the cells of the body.

The surfaces of proteins have specific shapes

Small molecules in a solution are in constant motion. They vibrate, rotate and move from place to place like corn in a popper. If two of them collide in the right circumstances, a chemical reaction can occur. The specific shapes of proteins allow them to bind noncovalently to other molecules that, in turn, allows other important biological events to occur.

Here are just a few examples:

Two adjacent cells can stick together because proteins protruding from each of the cells interact with each other.

A substance can enter a cell by binding to a carrier protein in the cell surface membrane.

A chemical reaction can be speeded up when an enzyme protein binds to one of the reactants. A “multi-protein machine,” DNA polymerase, can bind to and copy DNA. Another “multi-protein machine,” RNA polymerase, can synthesize RNA.

Chemical signals such as hormones can bind to proteins on a cell’s outer surface. Defensive proteins, called antibodies, can recognize the shape of a virus coat and bind to it. The biological specificity of protein function depends on two general properties of the protein: its shape and the chemistry of its exposed surface groups. When a molecule collides with and binds to a much larger protein, it is like a baseball being caught by a catcher’s mitt: the mitt has a shape that binds to the ball and fits around it. A hockey puck or a ping-pong ball would not fit a baseball catcher’s mitt. The binding of a molecule to a protein involves a general “fit” between two three-dimensional objects that becomes even more specific after initial binding.

Chemistry of proteins

The surface of a protein has certain chemical groups that it presents to a substance attempting to bind to it. These groups are the R groups of the exposed amino acids, and are therefore a property of the protein’s primary structure. Charged R groups can bind to oppositely charged groups on the ligand. Polar R groups containing a hydroxyl (—OH) group can form a hydrogen bond with the ligand. These three types of interactions—hydrophobic, ionic and hydrogen bonding—are weak by themselves but strong when all of them act together. Thus, the exposure of appropriate amino acid R groups on the protein surface allows the binding of a specific ligand to occur. Knowing the exact shape of a protein and what can bind to it is important not only in understanding basic biology but also in applied fields such as medicine. For example, the three-dimensional structure of a protease, a protein essential for the replication of HIV—the virus that causes AIDS—was first determined, then specific proteins were designed to bind to it and block its action. These protease inhibitors have prolonged the lives of countless people living with HIV.

Protein shapes are sensitive to the environment

Because it is determined by weak forces, protein shape is sensitive to environmental conditions that would not break covalent bonds, but do upset the weaker noncovalent interactions that determine secondary and tertiary structure. Increases in temperature cause more rapid molecular movements and thus can break hydrogen bonds and hydrophobic interactions. High concentrations of polar substances such as urea can disrupt the hydrogen bonding that is crucial to protein structure. Nonpolar solvents may also disrupt normal protein structure.

The loss of a protein’s normal three-dimensional structure is called denaturation and it is always accompanied by a loss of the normal biological function of the protein. Denaturation is often irreversible because amino acids that were buried may now be exposed at the surface and vice versa, causing a new structure to form or different molecules to bind to the protein. Boiling an egg denatures its proteins and is, as you know, not reversible. However, as we saw earlier in the case of lysozyme, denaturation may be reversible in the laboratory. If the protein is allowed to cool or the denaturing chemicals are removed, the protein may return to its “native” shape and normal function.

Chaperonins help shape proteins

There are two occasions when a polypeptide chain is in danger of binding the wrong ligand. First, following denaturation, hydrophobic R groups, previously on the inside of the protein away from water, become exposed on the surface. Since these groups can interact with similar groups on other molecules, the denatured proteins may aggregate and become insoluble, losing their function. Second, when a protein has just been made and has not yet folded completely, it can present a surface that binds the wrong molecule. In the cell, a protein can sometimes fold incorrectly as it is made. This can have serious consequences: In Alzheimer’s disease, misfolded proteins accumulate in the brain and bind to one another, forming fibers in the areas of the brain that control memory, mood and spatial awareness. Living systems limit inappropriate protein interactions by making a class of proteins called,appropriately, chaperonins (recall the chaperones—usually teachers—at school dances who try to prevent “inappropriate interactions” among the students). Chaperonins were first identified in fruit flies as “heat shock” proteins which prevented denaturing proteins from clumping together when the flies’ temperatures were raised. Some chaperonins work by trapping proteins in danger of inappropriate binding inside a molecular “cage”. This cage is composed of several identical subunits and is itself a good example of quaternary protein structure. Inside the cage, the targeted protein folds into the right shape, and then is released at the appropriate time and place.

Carbohydrates: Sugars and Sugar Polymers

The second class of biological molecules, the carbohydrates, is a diverse group of compounds. Carbohydrates contain primarily carbon atoms flanked by hydrogen atoms and hydroxyl groups (H—C—OH). They have two major biochemical roles:

They act as a source of energy that can be released in a form usable by body tissues.

They serve as carbon skeletons that can be rearranged to form other molecules that are essential for biological structures and functions.

Some carbohydrates are relatively small, with molecular weights of less than 100. Others are true macromolecules, with molecular weights in the hundreds of thousands. There are four categories of biologically important carbohydrates:

Monosaccharides (mono-, “one”; saccharide, “sugar”), such as glucose, ribose, and fructose, are simple sugars. They are the monomers out of which the larger carbohydrates are constructed.

Disaccharides (di-, “two”) consist of two monosaccharides linked together by covalent bonds.

Oligosaccharides (oligo-, “several”) are made up of several (3 to 20) monosaccharides.

Polysaccharides (poly-, “many”), such as starch, glycogen, and cellulose, are large polymers composed of hundreds or thousands of monosaccharides.

The general formula for carbohydrates, CH₂O, gives the relative proportions of carbon, hydrogen, and oxygen in a monosaccharide (i.e., the proportions of these atoms are 1:2:1). In disaccharides, oligosaccharides and polysaccharides, these proportions differ slightly from the general formula because two hydrogens and an oxygen are lost duringeach of the condensation reactions that form them.

Monosaccharides are simple sugars

Green plants produce monosaccharides through photosynthesis, and animals acquire them directly or indirectly from plants. All living cells contain the monosaccharide glucose. Cells use glucose as an energy source, breaking it down through a series of reactions that release stored energy and produce water and carbon dioxide. Glucose exists in two forms, the straight chain and the ring. The ring form predominates in more than 99 percent of circumstances because it is more stable under cellular conditions. Different monosaccharides contain different numbers of carbons. Most of the monosaccharides found in living systems belong to the D series of optical isomers. But some monosaccharides are structural isomers, which have the same kinds and numbers of atoms, but arranged differently. For example, the hexoses (hex-, “six”), a group of structural isomers, all have the formula C₆H₁₂O₆. Included among the hexoses are glucose, fructose (so named because it was first found in fruits), mannose and galactose. Pentoses (pent-, “five”) are five-carbon sugars. Some pentoses are found primarily in the cell walls of plants. Two pentoses are of particular biological importance: Ribose and deoxyribose form part of the backbones of the nucleic acids RNA and DNA, respectively. These two pentoses are not isomers; rather, one oxygen atom is missing from carbon 2 in deoxyribose (de-, “absent”). The absence of this oxygen atom has important consequences for the functional distinction of RNA and DNA.

Glycosidic linkages bond monosaccharides together

The disaccharides and polysaccharides described above are all constructed from monosaccharides that are covalently bonded together by condensation reactions that form glycosidic linkages. One such linkage between two monosaccharides forms a disaccharide. For example, a molecule of su-crose (table sugar) is formed from a glucose molecule and a fructose molecule, while lactose (milk sugar) contains glucose and galactose. The disaccharide maltose contains two glucose molecules but it is not the only disaccharide that can be made from two glucoses. Maltose and cellobiose are disaccharide isomers, both having the formula C₁₂H₂₂O₁₁. However, they are different compounds with different properties. They undergo different chemical reactions and are recognized by different enzymes. For example, maltose can be hydrolyzed to its monosaccharides in the human body, whereas cellobiose cannot. Certain microorganisms have the chemistry needed to break down cellobiose. Oligosaccharides contain several monosaccharides bound by glycosidic linkages at various sites. Many oligosaccharides have additional functional groups, which give them special properties. Oligosaccharides are often covalently bonded to proteins and lipids on the outer cell surface, where they serve as cell recognition signals. The human blood groups (such as ABO) get their specificity from oligosaccharide chains.

Polysaccharides serve as energy stores or structural materials

Polysaccharides are giant polymers of monosaccharides connected by glycosidic linkages. Starchis a polysaccharide of glucose. Glycogenis a highly branched polysaccharide of glucose. Starch actually comprises a large family of giant molecules of broadly similar structure. Some plant starches are unbranched, as in plant amylose; others are moderately branched, as in plant amylopectin. Starch readily binds water and when that water is removed, unbranched starch tends to form hydrogen bonds between the polysaccharide chains, which then aggregate. This is what causes bread to become hard and stale. Adding water and gentle heat separates the chains and the bread becomes softer. The polysaccharide glycogen stores glucose in animal livers and muscles. Starch and glycogen serve as energy storage compounds for plants and animals, respectively. These polysaccharides are readily hydrolyzed to glucose monomers, which in turn can be further degraded to liberate their stored energy and convert it to forms that can be used for cellular activities. If it is glucose that is actually needed for fuel, why must it be stored as a polymer? The reason is that 1,000 glucose molecules would exert 1,000 times the osmotic pressure of a single glycogen molecule. If it were not for polysaccharides, many organisms would expend a lot of time and energy expelling excess water. Cellulose is the predominant component of plant cell walls and is by far the most abundant organic(carbon-containing) compound on Earth. Starch can be easily degraded by the actions of chemicals or enzymes. Thus starch is a good storage medium that can be easily broken down to supply glucose for energy-producing reactions, while cellulose is an excellent structural material that can withstand harsh environmental conditions without changing.

Chemically modified carbohydrates contain other groups

Some carbohydrates are chemically modified by the addition of functional groups, such as phosphate and amino groups. For example, carbon 6 in glucose may be oxidized from —CH₂OH to a carboxyl group (—COOH), producing glucuronic acid. Or a phosphate group may be added to one or more of the —OH sites. Some of the resulting sugar phosphates, such as fructose 1,6-bisphosphate, are important intermediates in cellular energy reactions. When an amino group is substituted for an —OH group, amino sugars, such as glucosamine and galactosamine, are produced. These compounds are important in the extracellular matrix, where they form parts of proteins involved in keeping tissues together. Galactosamine is a major component of cartilage, the material that forms caps on the ends of bones and stiffens the protruding parts of the ears and nose. A derivative of glucosamine produces the polymer chitin, which is the principal structural polysaccharide in the skeletons of insects, crabs and lobsters, as well as in the cell walls of fungi. Fungi and insects (and their relatives) constitute more than 80 percent of the species ever described, and so chitin is one of the most abundant substances on Earth.