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a-pdf split demo purchase from www.a-pdf.com to remove the watermark the structu e and functio 0 large biologlca molecules key concepts figure 5.1 why do scientists study the structures of macromolecules 5.1 5.2 5.3 5.4 5.5 macromolecules are polymers built from monomers carbohydrates serve as fuel and building material lipids are a diverse group of hydrophobic molecules proteins have many structures resulting in a wide range of functions nucleic acids store and transmit hereditary r 7r o u esare polymers built from monomers the macromolecules in three of the four classes of life s organic compounds-carbohydrates proteins and nucleic acids-are chain-like molecules called polymers from the greekpolys many and meris part a polymer is a long mol· ecule consisting of many similar or identical building blocks linked by covalent bonds much as a train consists of a chain of cars the repeating units that serve as the building blocks of a polymer are smaller molecules called monomers some of the molecules that serve as monomers also have other functions of their own information iven the rich complexity of life on earth we might expect organisms to have an enormous diversity of molecules remarkably however the critically important large molecules ofall living things-from bacteria to elephantsfall into just four main classes carbohydrates lipids proteins and nucleic acids on the mole

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ho .h short polymer dehydration remo~es a water molecule forming a new bond unlinked monomer ho longer polymer h a dehydration read ion in the synthesis of a polymer ho h hydrolysis adds a water molecule breaking a bond als are more extensive and those between species greater still the diversity of macromolecules in the living world is vast and the possible variety is effectively limitless what is the basis for such diversity in life s polymers these molecules are constructed from only 40 to 50 common monomers and some others that occur rarely building a huge variety of polymers from such a limited number of monomers is analogous to constructing hundreds of thousands of words from only 26 letters of the alphabet the key is arrangement-the particular linear sequence that the units follow however this analogy falls far short of describing the great diversity of macromolecules because most biological polymers have many more monomers than the number of letters in the longest word proteins for example are built from 20 kinds of amino acids arranged in chains that are typically hundreds of amino acids long the molecular logic of life is simple but elegant small molecules common to all organisms are ordered into unique macromolecules despite this immense diversity molecular structure and function can still be grouped roughly by class let s look at each of the four major classes of large biological molecules for each class the large molecules have emergent properties not found in their individual building blocks concept check 5.1 b hydrolysis of a polymer figure 5.2 the synthesis and breakdown of polymers reaction figure 5.2b hydrolysis means to break using water from the greek hydro water and lysis break bonds between the monomers are broken by the addition of water molecules with a hydrogen from the water attaching to one monomer and a hydroxyl group attaching to the adjacent monomer an example of hydrolysis working within our bodies is the process of digestion the bulk of the organic material in our food is in the form of polymers that are much too large to enter our cells within the digestive tract various enzymes attack the polymers speeding up hydrolysis the released monomers are then absorbed into the bloodstream for distribution to all body cells those cells can then use dehydration reactions to assemble the monomers into new different polymers that can perform specific functions required by the cell 1 what are the four main classes of large biological molecules 2 how many molecules of water are needed to completely hydrolyze a polymer that is ten monomers long 3 milra suppose you eat a serving of green beans what reactions must occur for the amino acid monomers in the protein of the beans to be converted to proteins in your body for suggested answers see append,x a d es serve as fuel and building material carbohydrates include both sugars and polymers of sugars the simplest carbohydrates are the monosaccharides also known as simple sugars disaccharides are double sugars consisting oftwo monosaccharides joined by a covalent bond carbohydrates also include macromolecules called polysac· charides polymers composed of many sugar building blocks the diversity of polymers each cell has thousands ofdifferent kinds ofmacromolecules the collection varies from one type of cell to another even in the same organism the inherent differences between human siblings reflect variations in polymers particularly dna and proteins molecular differences between unrelated individu sugars monosaccharides from the greek monos single and sacchar sugar generally have molecular formulas that are the structure and function of large biological molecules 69 c~apte five

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some multiple of the unit ch 2 0 figure 5.3 glucose c 6 h i2 0 6 the most common monosaccharide is of central importance in the chemistry of life in the structure of glucose we can see the trademarks of a sugar the molecule has a carbonyl group c=o and multiple hydroxyl groups oh depending on the location of the carbonyl group a sugar is either an aldose aldehyde sugar or a ketose ketone sugar glucose for example is an aldose fructose a structural isomer of glucose is a ketose most names for sugars end in -ose another criterion for classifying sugars is the size of the carbon skeleton which ranges from three to seven carbons long glucose fructose and other sugars that have six carbons are called hexoses trioses three-carbon sugars and pentoses five-carbon sugars are also common still another source of diversity for simple sugars is in the spatial arrangement of their parts around asymmetric carbons recall that an asymmetric carbon is a carbon attached to four different atoms or groups ofatoms glucose and galactose for example differ only in the placement of parts around one asymmetric carbon see the purple boxes in figure 5.3 fhat seems like a small difference is significant enough to give the m o sugars distinctive shapes and behaviors although it is convenient to draw glucose with a linear carbon skeleton this representation is not completely accurate figure 5.3 tne structure and classification of some monosaccharides sugars may be aldoses aldehyde sugars top row or ketoses ketone sugars bottom row depending on the location of the carbonyl group dark orange sugars are also classified according to the length of their carbon skeletons athird point of variation is the spatial arrangement around asymmetric carbons compare for example the purple portions of glucose and galactose in aqueous solutions glucose molecules as well as most other sugars form rings figure 5.4 monosaccharides particularly glucose are major nutrients for cells in the process known as cellular respiration cells extract energy in a series of reactions starting with glucose molecules not only are simple-sugar molecules a major fuel for cellular work their carbon skeletons also serve as raw material for the synthesis of other types of small organic molecules such as amino acids and fatty acids sugar molecules that are not immediately used in these ways are generally incorporated as monomers into disaccharides or polysaccharides adisaccharide consists oftwo monosaccharides joined by a glycosidic linkage a covalent bond formed between two monosaccharides by a dehydration reaction for example maltose is a disaccharide formed by the linking of two molecules of glucose figure 5.5a also known as malt sugar maltose is an ingredient used in brewing beer the most prevalent disaccharide is sucrose which is table sugar its m o monomers are glucose and fructose figure 5.5b plants generally transport carbohydrates from leaves to roots and other nonphotosynthetic organs in the form of sucrose lactose the sugar present in milk is another disaccharide in this case a glucose molecule joined to a galactose molecule trioses c 3 h60 3 h pentoses c sh10 os h ~o h h-c-oh ho-c-h h h-c-oh ho-c-h o-c~h h-c-oh · · · 0 i h-c-oh i h h-c-oh glyceraldehyde an initial breakdown product of glucose i h-c-oh i h-c-oh i h-c-oh ihiih-c-oh h-c-oh h ribose acomponent of rna i i glucose an energy source for organisms h galactose an energy source for organisms h h h-c-oh i h-c-oh i h-c-oh i b · · · 0 h-c~oh h-c-oh h ho -c-h · i oihydroxyacetone an initial breakdown product of glucose i h-c-oh i h~c~oh i h ribulose an intermediate in photosynthesis i i h~c~oh i h-c-oh i h-c-oh h fructose an energy source for organisms 70 unit one thechemistryoflife

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h c 0 h-c-oh ho-c-h h-c-oh h-c-oh h-c-oh 1 1 31 ,i h oh ,1 ,i h a linear and ring forms chemical equilibrium between the linear and ring strudures greatly fa~ors the formation of rings the carbons of the sugar are numbered 1 to 6 as shown to form the glucose ring carbon 1 bonds to the oxygen attached to carbon s b abbreviated ring structure each corner represents a carbon the ring s thicker edge indicates that you are looking at the ring edge-on the components attached to the ring lie above or below the plane of the ring figure 5.4 linear and ring forms of glucose ·· f·w 1 start with the linear form of fructose see figure 5.3 and draw the formation of the fructose ring in two steps number the carbons attach carbon 5 via oxygen to carbon 2 compare the number of carbons in the fructose and glucose rings a dehydration reaction in the synthesis of maltose the bonding of two glucose units forms maltose the glycosidic linkage joins the number 1carbon of one glucose to the number 4 carbon of the second glucose joining the glucose monomers in a different way would result in a different disaccharide h oh glucose · · ~h ~oo h oh h ch10h h oh oh ho 0 h oh h oh glucose maltose b dehydration reaction in the synthesis of sucrose sucrose is a disaccharide formed from glucose and fructose notice that fructose though a hexose like glucose forms a five-sided ring ~h 00 h ho hph oh h ch10h 1-2 glycosidic 1 linkage ch 20h oh h ho h oh 0 h oh glucose fructose sucrose figure 5.s examples of disaccharide synthesis polysaccharides polysaccharides are macromolecules polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages some polysaccharides serve as storage material hydrolyzed as needed to provide sugar for cells other polysaccharides serve as building material for structures that protect the cell or the whole organism the architecture and function of a polysaccharide are determined by its sugar monomers and by the positions of its glycosidic linkages storage polysaccharides both plants and animals store sugars for later use in the form of storage polysaccharides plants store starch a polymer of c~apte glucose monomers as granules within cellular structures known as plastids which include chloroplasts synthesizing starch enables the plant to stockpile surplus glucose because glucose is a major cellular fuel starch represents stored energy the sugar can later be withdrawn from this carbohydrate bank by hydrolysis which breaks the bonds between the glucose monomers most animals including humans also have enzymes that can hydrolyze plant starch making glucose available as a nutrient for cells potato tubers and grains-the fruits of wheat maize corn rice and other grasses-are the major sources of starch in the human diet most ofthe glucose monomers in starch are joined by 1-4 linkages number 1 carbon to number 4 carbon like the glucose units in maltose see figure 5.5a the angle of these five the structure and function of large biological molecules 71

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chloroplast starch mitochondria glycogen granules amylose amylopectin a starch a plant polysaccharide two forms of starch are amylose unbranched and amylopedln branched the light ovals in the micrograph are granules of starch within a chloroplast of a plant cell b glycogen an animal polysaccharide glycogen is more branched than amylopectin animal cells stockpile glycogen as dense clusters of granules within liver and mu>cle cells the micrograph shqla pan of a liver cell mitochondria are organelles that help break down sugars figure 5.6 storage polysaccharides of plants and animals these examples starch and glycogen are composed entirely of glucose monomers represented here by hexagons because of their molecular strudure the polymer chains tend to form helices bonds makes the polymer helical the simplest form of starch amylose is unbranched figure s.6a amylopectin a more complex starch is a branched polymer with 1-6 linkages at the branch points animals store a polysaccharide called glycogen a polymer of glucose that is like amylopectin but more extensively branched figure 5.6b humans and other vertebrates store glycogen mainly in liver and muscle cells hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases this stored fuel cannot sustain an animal for long however in humans for example glycogen stores are depleted in about a day unless they are replen· ished by consumption offood this is an issue of concern in low·carbohydrate diets cellulose per year it is the most abundant organic compound on earth like starch cellulose is a polymer of glucose but the glycosidic linkages in these two polymers differ the difference is based on the fact that there are actually two slightly different ring structures for glucose figure s.7a when glucose forms a ring the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring these two ring forms for glucose are called alpha 0 and beta 13 respectively in starch all the glucose monomers are in the ex configuration figure 5.7b the arrangement we sawin figures 5.4 and 5.5 in contrast the glucose monomers of cellulose are all in the 13 configuration making every other glucose monomer upside down with respect to its neighbors figure 5.7c the differing glycosidic linkages in starch and cellulase give the two molecules distinct three-dimensional shapes whereas a starch molecule is mostly helical a cellulose molecule is straight cellulose is never branched and some hydroxyl groups on itsglu· case monomers are free to hydrogen-bond with the hydroxyis of other cellulose molecules lying parallel to it in plant cell walls parallel cellulose molecules held together in this way are grouped into units called microfibrils figure 5.8 these cable-like structural polysaccharides organisms build strong materials from structural polysaccharides for example the polysaccharide called ceuulose is a major component of the tough walls that enclose plant cells on a global scale plants produce almost 10 14 kg 100 billion tons of 72 unit one thechemistryoflife

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h ;0 a a and glucose ring structures these two mterconvertible forms of glucose differ in the placement of the hydroxyi group {highlighted in blue attached to the number 1 carbon c i h-c-oh ho-c-h i i · h-c-oh h oh a glucose i i h-c-oh i h-c-oh h h oh glucose oh h2&o o~o~h oh chph oh 0h ch 2 b starch 1-4 linkage of a glucose monomers all monomers are in the same orientation compare the positions of the -oh groups highlighted m yellow with those in cellulose cl figure 5.7 starch and cellulose structures c cellulose 1-4 linkage of glucose monomers in cellulose every other pglucose monomer is upside down with respect to its neighbors cellulose microfibrils in a plant cell wall t f i 10 j1m about 80 cellulose molecules associate to form a microfibril the main architectural unit of the plant cell wall 0.51!m a cellulose molecule is an unbranched p glucose polymer pglucose monomer figure 5.8 the arrangement of cellulose in plant cell walls c~apte five the structure and function of large biological molecules 73

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figure 5.9 cellulose-digesting prokaryotes are found in grazing animals such as this cow microfibrils are a strong building material for plants and an im· portant substance for humans because cellulose is the major constituent of paper and the only component of cotton enzymes that digest starch by hydrolyzing its a linkages are unable to hydrolyze the f3 linkages of cellulose because of the distinctly different shapes of these two molecules in fact few organisms possess enzymes that can digest cellulose humans do not the cellulose in our food passes through the digestive tract and is eliminated with the feces along the way the cellulose abrades the wall ofthe digestive tract and stimulates the lining to secrete mucus which aids in the smooth passage of food through the tract thus although cellulose is not a nutri· ent for humans it is an important part ofa healthful diet most fresh fruits vegetables and whole grains are rich in cellulose on food packages uinsoluble fiber refers mainly to cellulose some prokaryotes can digest cellulose breaking it down into glucose monomers a cow harbors cellulose·digesting prokaryotes in its rumen the first compartment in its stomach figure 5.9 the prokaryotes hydrolyze the cellulose of hay and grass and convert the glucose to other nutrients that nourish the cow similarly a termite which is unable to digest cellulose by itself has prokaryotes living in its gut that can make a meal of wood some fungi can also digest cellulose thereby helping re

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lipids are varied in form and function they include waxes and certain pigments but we will focus on the most biologically important types of lipids fats phospholipids and steroids fats although fats are not polymers they are large molecules assembled from a few smaller molecules by dehydration reactions a fat is constructed from two kinds ofsmaller molecules glycerol and fatty acids figure 5.11a glycerol is an alcohol with three carbons each bearing a hydroxyl group a fatty acid has a long carbon skeleton usually 16 or 18 carbon atoms in length the carbon at one end of the fatty add is part of a carboxyl group the functional group that gives these molecules the name fatty acid attached to the carboxyl group is a long hydrocarbon chain the relatively nonpolar c-h bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic fats separate from water because the water molecules hydrogenbond to one another and exclude the fats this is the reason that vegetable oil a liquid fat separates from the aqueous vinegar solution in a bottle of salad dressing in making a fat three fatty acid molecules each join to glycerol by an ester linkage a bond between a hydroxyl group and a carboxyl group the resulting fat also called a triacylglycerol thus consists ofthree fatty acids linked to one glycerol molecule still another name for a fat is triglyceride a word often found in the list ofingredients on packaged foods the fatty adds in a fat can be the same as in figure 5.11b or they can be of two or three different kinds fatty adds vary in length and in the number and locationsof double bonds the terms saturated fats and unsaturated fats are commonly used in the context of nutrition figure 5.12 i h o-c structural formula of a saturated fat molecule h-c-o-c h-c-o-c iiii stearic acid a saturated fatty acid i a saturated fat at room temperature the molecules of a saturated fat such as this butter are packed closely together forming a solid glycerol a dehydration reaction in the synthesis of a fat structural formula of an unsaturated fat molecule oleic acid an unsaturated fatty acid cis double bond causes bending h b fat molecule triacylglyceroll figure 5.11 the synthesis and structure of a fat or triacylglycerol the molecular building blocks of a fat are one molecule of glycerol and three molecules of fatty acids a one water molewle is removed for each fatty acid joined to the glycerol b a fat molecule with three identical falty acid units the carbons of the laity acids are arranged zig-zag to suggest the actual orientations 01 the four single bonds extending from each carbon see figure 4.3a b unsaturated fat at room temperature the molecules of an unsaturated fat such as this olive oil cannot pack together closely enough to solidify because of the kinks in some of their fatty acid hydrocarbon chains figure 5.12 examples of saturated and unsaturated fats and fatty acids the structural formula for each fat follows a common chemical convention of omitting the carbons and attached hydrogens of the hydrocarbon regions in the space-filling models of the fatty acids black carbon gray hydrogen and red oxygen the structure and function of large biological molecules 75 chapte five

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these terms refer to the structure ofthe hydrocarbon chains of the fatty acids if there are no double bonds between carbon atoms composing the chain then as many hydrogen atoms as possible are bonded to the carbon skeleton such a structure is described as being saturated with hydrogen so the resulting fatty acid is called a saturated fatty acid figure 5.12a an unsaturated fatty acid has one or more double bonds formed by the removal of hydrogen atoms from the carbon skeleton the fatty acid will have a kink in its hydrocarbon chain wherever a cis double bond occurs figure 5.12b a fat made from sarurated fatty acids is called a saturated fat most animal fats are saturated the hydrocarbon chains of their fatty acids-the tails of the fat molecules-lack double bonds and their flexibility allows the fat molecules to pack together tightly saturated animal fats-such as lard and but ter-are solid at room temperature in contrast the fats of plants and fishes are generally unsaturated meaning that they are built of one or more types of unsaturated fatty acids usually liquid at room temperature plant and fish fats are referred to as oils-olive oil and cod liver oil are examples the kinks where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temperature the phrase hydrogenated vegetable oils on food labels means that unsaturated fats have been synthetically converted to saturated fats by adding hydrogen peanut butter margarine and many other products are hydrogenated to prevent lipids from separating out in liquid oil form adiet rich in saturated fats is one ofseveral factors that may contribute to the cardiovascular disease known as atheroscle rosis in this condition deposits called plaques develop within the walls of blood vessels causing inward bulges that impede blood flow and reduce the resilience ofthe vessels recent studies have shown that the process of hydrogenating vegetable oils produces not only saturated fats but also unsaturated fats with trans double bonds these trans fats may contribute more than sarurated fats to atherosclerosis see chapter42 and other problems because trans fats are especially common in baked goods and processed foods the usda requires trans fatcontent information on nutritional labels fat has come to have such a negative connotation in our culture that you might wonder what useful purpose fats serve the major function of fats is energy storage the hydrocarbon chains of fats are similar to gasoline molecules and just as rich in energy agram offat stores more than twice as much energy as a gram ofa polysaccharide such as starch because plants are relatively immobile they can function with bulky energy storage in the form of starch vegetable oils are generally obtained from seeds where more compact storage is an asset to the plant animals however must carry their energy stores with them so there is an advantage to having a more compact reservoir of fuel-fat humans and other mammals stock their longterm food reserves in adipose cells see figure 4.6a which swell and shrink as fat is deposited and withdrawn from storage.ln addition to storing energy adipose tissue also cushions such vital organs as the kidneys and a layer of fat beneath the skin insulates the body this subcutaneous layer is especially thick in whales seals and most other marine mammals protecting them from cold ocean water phospholipids cells could not exist without another type of lipidphospholipids figure 5.13 phospholipids are essential 1 ch1-ikhll ~h choline 6-· · ·· ·i o o phosphate · ··· ·· · 2 tl 0 1 h t 0 i ch h 1 0 i 1 glycerol 1 i ···················· 0 0 figure 5.13 the structure of a phospholipid a phospholipid has a hydrophilic polar head and two hydrophobic nonpolar tails phospholipid diversity is based on differences in the two fatty acids and in the groups attached to the phosphate group of the head this particular phospholipid called a phosphatldylcholine has an attached choline group the kink in one of its tails is due to a cis double bond shown here are a the structural formula b the space-filling model yellow phosphorus blue nitrogen and e the symbol for a phospholipid that will appear throughout this book fatty acids hydrophilic head ii-t7 hydrophobic tails a structural formula b space-filling model c phospholipid symbol 76 unit one thechemistryoflife

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hydrophilic head water ho hydrophobic tail water figure 5.15 cholesterol a steroid cholesterol is the molecule from which other steroids including the sex hormones are synthesized steroids ~ary in the chemical groups altached to their four interconnected rings shown in gold figure 5.14 bilayer structure formed by self.assembly of phospholipids in an aqueous environment the phospholipid bilayer shown here is the main fabric of biological membranes note that the hydrophilic heads of the phospholipids are in contad with water in this structure whereas the hydrophobic tails are in contact with each other and remote from water for cells because they make up cell membranes their structure provides a classic example of how form fits function at the molecular level as shown in figure 5.13 a phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three the third hydroxyl group of glycerol is joined to a phosphate group which has a negative electrical charge additional small molecules which are usually charged or polar can be linked to the phosphate group to form a variety of phospholipids the rn o ends of phospholipids show different behavior toward water the hydrocarbon tails are hydrophobic and are excluded from water however the phosphate group and its attachments form a hydrophilic head that has an affinity for water vhen phospholipids are added to water they selfassemble into double-layered aggregates-bilayers-that shield their hydrophobic portions from water figure 5.14 at the surface ofa cell phospholipids are arranged in a similar bilayer the hydrophilic heads of the molecules are on the outside of the bilayer in contact with the aqueous solutions inside and outside of the cell the hydrophobic tails point toward the interior of the bilayer away from the water the phospholipid bilayer forms a boundary bern een the cell and its external environment in fact cells could not exist without phospholipids vertebrates cholesterol is synthesized in the liver many hormones including vertebrate sex hormones are steroids produced from cholesterol see figure 4.9 thus cholesterol is a crucial molecule in animals although a high level of it in the blood may contribute to atherosclerosis both saturated fats and trans fats exert their negative impact on health by affecting cholesterol levels concept check 5.3 i compare the structure of a fat triglyceride with that of a phospholipid 2 why are human sex hormones considered lipids 3 muia suppose a membrane surrounded an oil droplet as it does in the cells of plant seeds describe and explain the form it might take for suggested answers see appendix a r many structures resulting in a wide range of functions nearly every dynamic function of a living being depends on proteins in fact the importance of proteins is underscored by their name which comes from the greek word proteios meaning first place proteins account for more than 50 of the dry mass ofmost cells and they are instrumental in almost everything organisms do some proteins speed up chemical reactions while others play a role in structural support the structure and function of large biological molecules 77 steroids many hormones as well as cholesterol are steroids which are lipids characterized by a carbon skeleton consisting offour fused rings figure 5.15 different steroids vary in the chemical groups attached to this ensemble of rings cholesterol is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized in c~apte five

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an overview of protein functions type of protein enzymatic proteins structural proteins function selective acceleration of chemical reactions support examples digestive enzymes catalyze the hydrolysis of the polymers in food insects and spiders use silk fibers to make their cocoons and webs respectively collagen and elastin provide a fibrous framework in animal connective tissues keratin is the protein of hair horns feathers and other skin appendages ovalbumin is the protein of egg white used as an amino acid source for the developing embryo casein the protein of milk is the major source of amino acids for baby mammals plants have storage proteins in their seeds hemoglobin the iron-containing protein of vertebrate blood transports oxygen from the lungs to other parts of the body other proteins transport molecules across cell membranes insulin a hormone secreted by the pancreas helps regulate the concentration of sugar in the blood of vertebrates receptors built into the membrane of a nerve cell detect chemical signals released by other nerve cells actin and myosin are responsible for the contmction of muscles other proteins are responsible for the undulations of the organelles called cilia and flagella storage proteins storage of amino acids transport proteins transport of other substances coordination of an organism s activities response of cell to chemical stimuli movement hormonal proteins receptor proteins contractile and motor proteins defensive proteins protection against disease antibodies combat bacteria and viruses because an enzyme can perform its function over and over again these molecules can be thought of as workhorses that keep cells running by carrying out the processes oflife a human has tens of thousands of different proteins each with a specific structure and function proteins in fact are the most structurally sophisticated molecules known consistent with their diverse functions they vary extensively in structure each type of protein having a unique three-dimensional shape storage transport cellular communication movement and defense against foreign substances table 5.1 life would not be possible without enzymes most of which are proteins enzymatic proteins regulate metabolism by acting as catalysts chemical agents that selectivelyspeed up chemical reactions without being consumed by the reaction figure 5.16 active site is available for a molecule of substrate the reactant on which the enzyme acts o 8 substrate binds to enzyme s polypeptides diverse as proteins are they are all polymers constructed from the same set of 20 amino acids polymers of amino adds are called polypeptides a protein consists of one or more polypeptides each folded and coiled into a spedfic three-dimensional structure amino acid monomers q ~sucrose o products are released f substrate is converted to products figure 5.16 the catalytic cycle of an enzyme the enzyme sucrase accelerates hydrolysis of sucrose into glucose and fructose acting as a catalyst the sucrase protein is not consumed during the cycle but remains available for further catalysis 78 unit one all amino acids share a common structure amino acids are organic molecules possessing both cl carbon carboxyl and amino groups see r chapter 4 the illustration at the h n yp right shows the general formula for hi i oh an amino acid at the center of the h amino acid is an asymmetric carbon amino carboryl atom called the alpha a carbon its group group four different partners are an amino group a carboxyl group a hydrogen atom and a variable group symbolized by r the r group also called the side chain differs with each amino acid figure 5.17 shows the 20 amino acids that cells use to build their thousands of proteins here the amino and carboxyl thechemistryoflife

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ch 3 ch 3 ch j h i ch h ch h h w-c-c i ;0 ch 3 h w-c-c i h 0 i i h 0 0 h ;0 ch 2 h w-c-c 3 h w-c-c 3 i h 0 h i i 0 0 h3c-i h i a 0 h w-c-c h i glycine glyor g nonpolar ch s alanine ala or a valine valor v leucine leu or l isoleucine lie or l iithh2 w c h ch 2 a h 3 i 0 w c h 9 ch 2 p nh 0 i 0 i h w i 0h ch 2 0 h2c /ch ch 2 0 i i hw-c-c i h 0 methionine met or m phenylalanine phe or f tryptophan trp or w proline pro or p oh polar h /ch sh w-t-c i h th 0 ch h w-c-c i 0 3 i ch 2 h w-c-c i h a ¢ h oh n o nh2 0 c i 0 h 3 ch 0 h i 0 i a w c h ch 2 i 0 w-i-c ]w-t-c i i h h ch 2 0 h 2 h i i 0 0 0 serine ser or s threonine thr or n cysteine cys or c tyrosine tyr or y asparagine asn or n glutamine gin or 0 bask addic nh · ~h2 electrically charged 000 c c ° 0 i i i c-nh 2 nh ch ch ih ch i h w c i h ch 2 0 h 2 h w-c-c iiiii ch i h i p nh 0 i h h 0 w-i-c i h ch 2 0 ch 2 0 i ;h n c-c ch 2 h 0 0 h i 0 w-c-c i h i 0 aspartic acid asp or d figure 5.17 the 20 amino acids of proteins the amino acids are grouped here according to the properties of their side chains r groups highlighted in white the amino glutamic acid glu or e lysine lys or k arginine arg or r histidine his or h acids are shown in their prevailing ionic forms at ph 7.2 the ph within a cell the three-letter and more commonly used one-letter abbreviations for the amino acids are in parentheses all the amino acids used in proteins are the same enantiomer called the l form as shown here see figure 4.7 chapte five the structure and function of large biological molecules 79

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groups are all depicted in ionized form the way they usually exist at the ph in a cell tile r group may be as simple as a hydrogen atom as in the amino acid glycine the one amino acid lacking an asymmetric carbon since two of its a carbon s partners are hydrogen atoms or it may be a carbon skeleton with various functional groups attached as in glutamine organisms do have other amino acids some of which are occasionally found in proteins because these are relatively rare they are not shown in figure 5.17 the physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid thus affecting its functional role in a polypeptide in figure 5.17 the amino acids are grouped according to the properties of their side chains one group consists of amino acids with nonpolar side chains which are hydrophobic another group consists of amino acids with polar side chains which are hydrophilic acidic amino acids are those with side chains that are generally negative in charge owing to the presence of a carboxyl group which is usually dissociated ionized at cellular ph basic amino acids have amino groups in their side chains that are generally positive in charge notice that all amino acids have carboxyl groups and amino groups the terms acidic and basic in this context refer only to groups on the side chains because they are charged acidic and basic side chains are also hydrophilic oh bol d i chz oh peptlde¢ i chz sh i ch2 h-ll iii hq ll l c-oh iii hq oh oh ¢ i peptide sh i bond i h-ll-ll1ll-oh}eackbone ch2 ch2 chl · ihiqs;d h i i i t b amino end n-terminus t carboxyl end c-terminus amino acid polymers now that we have examined amino acids let s see how they are linked to form polymers figure 5.18 when two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other they can become joined by a dehydration reaction with the removal of a water molecule the resulting covalent bond is called a peptide bond repeated over and over this process yields a polypeptide a polymer of many amino acids linked by peptide bonds at one end of the polypeptide chain is a free amino group at the opposite end is a free carboxyl group thus the chain has an amino end n-terminus and a carboxyl end c-terminus the repeating sequence of atoms highlighted in purple in figure 5.18b is called the polypeptide backbone extending from this backbone are different kinds ofappendages the side chains of the amino acids polypeptides range in length from a few monomers to a thousand or more each specific polypeptide has a unique linear sequence of amino acids the immense variety of polypeptides in nature illustrates an important concept introduced earlier-that cells can make many different polymers by linking a limited set of monomers into diverse sequences figure 5.18 making a polypeptide chain a peptide bonds formed by dehydration reactions link the carboxylgfoup of one amino acid to the amino group of the next b the peptide bonds are formed one at a time starting with the amino acid at the amino end n·terminus the polypeptide has a repetitive backbone purple to which the amino acid side chains are attached ··ijl.w 1 in a circle and label the carboxyl and amino groups that will form the peptide bond shown in b protein structure and function the specific activities of proteins result from their intricate three-dimensional architecture the simplest level of which is 80 the sequence of their amino acids the pioneer in determining the amino acid sequence of proteins was frederick sanger who with his colleagues at cambridge university in england worked on the hormone insulin in the late 1940s and early 1950s he used agents that break polypeptides at specific places followed by chemical methods to determine the amino acid sequence in these small fragments sanger and his co-workers were able after years of effort to reconstruct the complete amino acid sequence of insulin since then most of the steps involved in sequencing a polypeptide have been automated once we have learned the amino acid sequence of a polypeptide what can it tell us about the three-dimensional structure commonly referred to simply as the structure of the protein and its function the term polypeptide is not synonymous with the term protein even for a protein consisting of a single polypeptide the relationship is somewhat analogous to that behveen a long strand of yarn and a sweater of particular size and shape that can be knit from the yarn a functional protein is not just a polypeptide chain but one or more polypeptides precisely twisted folded and coiled into a molecule of unique shape figure 5.19 and it unit one thechemistryoflife

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a a ribbon model shows how the single polypeptide chain folds and coils to form the fundional protein the yellow lines represent crosslinking bonds between cysteines that stabilize the protein s shape b a space-filling model shows more clearly the globular shape seen in many proteins as well as the specific three-dimensional structure unique to lysozyme figure 5.19 structure of a protein the enzyme lysozyme present in our sweat tears and sali~a lysozyme is an enzyme that helps pre~ent infedion by binding to and destroying specific molecules on the surface of many kinds of bacteria the groo~e is the part of the protein that recognizes and binds to the target molecules on bacterial walls is the amino acid sequence of each polypeptide that determines what three-dimensional structure the protein will have vilen a cell synthesizes a polypeptide the chain generally folds spontaneously assuming the functional structure for that protein this folding is driven and reinforced by the formation ofa variety of bonds between parts ofthe chain which in turn depends on the sequence of amino acids many proteins are roughly spherical globular proteins while others are shaped like long fibers fibrous proteins even within these broad categories countless variations exist a protein s specific structure determines how it works in almost every case the function of a protein depends on its ability to recognize and bind to some other molecule in an especially striking example ofthe marriage ofform and function figure 5.20 shows the exact match of shape between an antibody a protein in the body and the particular foreign substance on a flu virus that the antibody binds to and marks for destruction a second example is an enzyme which must recognize and bind closely to its substrate the substance the enzymeworkson see figure 5.16 also you learned in chapter 2 that natural signaling molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans producing euphoria and relieving pain morphine heroin and other opiate drugs are able to mimic endorphins because they all share a similar shape with endorphins and can thus fit into and bind to endorphin receptors in the brain this fit is very specific something like a lock and key see figure 2.18 thus the function ofa protein-for instance the ability ofa receptor protein to bind to a particular pain-relieving signaling moleculeis an emergent property resulting from exquisite molecular order four leyels of protein structure vith the goal ofunderstanding the function ofa protein learningabout its structure is often productive in spite oftheir great diversity all proteins share three superimposed levels of structure known as primary secondary and tertiary structure a fourth level quaternary structure arises when a protein consists of two or more polypeptide chains figure 5.21 on the following two pages describes these four levels of protein structure be sure to study this figure thoroughly before going on to the next section antibody protein protein from flu virus figure 5.20 an antibody binding to a protein from a flu virus a technique called x-ray crystallography was used to generate a computer model of an antibody protein blue and orange left bound to a flu virus protein green and yellow right computer software was then used to back the imag away from each other revealing the exad complementarity of shape between the two protein surfaces c~apte five the structure and function of large biological molecules 81

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· fii ft 5.21 ·· · levels of protein structure primary structure secondary structure pleated sheet ii helix the primary structure of a protein is its unique sequence of amino adds as an example let s consider transthyretin a globular protein found in the blood that transports vitamin a and one of the thyroid hormones throughout the body each ofthe four identical polypeptide chains that together make up tr,msthyretin is composed of 127 amino adds shown here is one ofthese chains unraveled for a closer look at its primary structure each of the 127 positions along the chain is occupied by one of the 20 amino acids indicated here by its three-letter abbreviation the primary structure is like the order of letters in avery long word if left to chance there would be 20 127 different ways of making a polypeptide chain 127 amino acids long however the precise primary structure of a protein is determined not by the random linking ofamino acids but by inherited genetic infonnation most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein s overall shape these coils and folds collectively referred to as secondary structure are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone not the amino acid side chains both the oxygen and the nitrogen atoms of the backbone are electronegative with partial negative charges see figure 2.16 the weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond individually these hydrogen bonds are we3k but because they are repeated many times over a relatively long region of the polypeptide chain they can support a particular shape for that part ofthe protein one such secondary structure is the a helix a delicate coil held together by hydrogen bonding between every fourth amino acid shown above although transthyretin has only one a helix region see tertiary structure other globular proteins have multiple stretches of a helix separated by nonhelical regions some fibrous proteins such as a-keratin the structural protein ofhair have the a helix formation over most of their length the other main type ofsecond3ry structure is the ii pleated sheet as shown above in this structure two or more regions ofthe polypeptide chain lying side by side are connected by hydrogen bonds between parts ofthe two parallel polypeptide backbones pleated sheets make up the core of many globular proteins as is the case for transthyretin and dominate some fibrous proteins including the silk protein ofaspider s web the teamwork ofso many hydrogen bonds makes each spider silk fiber stronger than a steel strand of the same weight abdominal glands of the spider secrete silk fibers made of a structural protein containing pleated sheets the radiating strands made of dry silk fibers maintain the shape of the web /0 c om carboxyl end the spiral strands capture strands are elastic stretching in response to wind rain and the touch of insects 82 unit one thechemistryoflife

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