Unit 2 – Biochemistry of Life Name ______

Home , Dehydration reaction, Stanley Miller

Chapter 4: Carbon and the Molecular Diversity of Life

Overview: Carbon

4.1 Organic chemistry is the study of carbon compounds  Organic chemistry focuses on organic compounds containing carbon. o Organic compounds can range from simple molecules, such as CH4, to complex molecules such as proteins, with thousands of atoms. o Most organic compounds contain hydrogen atoms as well as carbon.  The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one organism to another.  Because of carbon’s versatility, these few elements can be combined to build an inexhaustible variety of organic molecules.  The science of organic chemistry began with attempts to purify and improve the yield of products obtained from organisms. o Initially, chemists learned to synthesize simple compounds in the laboratory but had no success with more complex compounds.  Early organic chemists proposed vitalism, the belief that physical and chemical laws do not apply to living things. o In the early 1800s, the German chemist Friedrich Wöhler and his students synthesized urea. A few years later, Hermann Kolbe, a student of Wöhler’s, made the organic compound acetic acid from inorganic substances prepared directly from pure elements.  In 1953, Stanley Miller at the University of Chicago set up a laboratory simulation of possible chemical conditions on the primitive Earth and demonstrated the spontaneous synthesis of organic compounds. o The mixture of gases Miller created probably did not accurately represent the atmosphere of the primitive Earth. o Spontaneous abiotic synthesis of organic compounds, possibly near volcanoes, may have been an early stage in the origin of life on Earth.  Organic chemists finally embraced mechanism, the belief that the same physical and chemical laws govern all natural phenomena, including the processes of life.  Organic chemistry was redefined as the study of carbon compounds, regardless of their origin.

Stanley Miller experiment

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms  Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons to complete its valence shell.  Carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds, which may include single and double bonds.

 The ability of carbon to form four covalent bonds makes large, complex molecules possible. o When a carbon atom forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles of 109.5°. o In molecules with multiple carbon atoms, every carbon atom bonded to four other atoms has a tetrahedral shape. o When two carbon atoms are joined by a double bond, all bonds around those carbons are in the same plane as the carbons. Shape of simple organic molecules

 In carbon dioxide (CO2), one carbon atom forms two double bonds with two O=C=O oxygen atoms. o In the structural formula, , each line represents a pair of shared electrons.

 Although CO2 can be classified as either organic or inorganic, its importance to the living world is clear: CO2 is the source of carbon for all organic molecules found in organisms.

 Urea, CO(NH2)2, is another simple organic molecule in which each atom forms covalent bonds to complete its valence shell.

Molecular diversity arises from variations in the carbon skeleton.  Carbon chains form the skeletons of most organic molecules. o Carbon skeletons vary in length and may be straight, branched, or arranged in closed rings. o Carbon skeletons may include double bonds. o Atoms of other elements can be bonded to the atoms of the carbon skeleton. Ways that carbon skeletons can vary

 Hydrocarbons are organic molecules that consist of only A fat molecule carbon and hydrogen atoms.  Hydrocarbons are the major component of petroleum, a fossil fuel that consists of the partially decomposed remains of organisms that lived millions of years ago.  Fats are biological molecules that have long hydrocarbon tails attached to a nonhydrocarbon component.  Petroleum and fat are hydrophobic compounds that cannot dissolve in water because of their many nonpolar carbon- hydrogen bonds.  Hydrocarbons can undergo reactions that release a relatively large amount of energy.

 Isomers are compounds that have the same molecular formula but different structures and, therefore, different chemical properties.  Structural isomers have the same molecular formula but differ in the covalent arrangement of atoms. o Structural isomers may also differ in the location of the double bonds.  Cis-trans isomers have the same covalent partnerships but differ in the spatial arrangement of atoms around a carbon-carbon double bond. o The double bond does not allow the atoms to rotate freely around the bond axis. o Consider a simple molecule with two double-bonded carbons, each of which has an H and an X attached to it. The arrangement with both Xs on the same side of the double bond is called a cis isomer; the arrangement with the Xs on opposite sides is called a trans isomer.  Enantiomers are molecules that are mirror images of each other.  Enantiomers are possible when four different atoms or groups of atoms are bonded to an asymmetric carbon. o The four groups can be arranged in space in 2 different ways that are mirror images of each other; They are like left-handed and right-handed versions of the molecule. o Usually one is biologically active, while the other is inactive.  Even subtle structural differences in two enantiomers may have important functional significance because of emergent properties from specific arrangements of atoms.

Three types of isomers

4.3 A few chemical groups are key to molecular function  The distinctive properties of an organic molecule depend not only on the arrangement of its carbon skeleton but also on the chemical groups attached to that skeleton.  If we start with hydrocarbons as the simplest organic molecules, characteristic chemical groups can replace one or more of the hydrogen atoms bonded to the carbon skeleton of a hydrocarbon.

 These chemical groups may be involved in chemical reactions or may contribute to the shape and function of the organic molecule in a characteristic way, giving it unique properties. o As an example, the basic structure of testosterone (a male sex hormone) and estradiol (a female sex hormone) is the same. o Both are steroids with four fused carbon rings, but the hormones differ in the chemical groups attached to the rings.

o As a result, testosterone and estradiol have different shapes, causing them to interact differently with many targets throughout the body.  In other cases, chemical groups known as functional groups affect molecular function through their direct involvement in chemical reactions.  Seven chemical groups are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups.  The first six chemical groups are functional groups. They are hydrophilic and increase the solubility of organic compounds in water.

 Methyl groups are not reactive but may serve as important markers on organic molecules.

 In a hydroxyl group (—OH), a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton. o Because of these polar covalent bonds, hydroxyl groups increase the solubility of organic molecules. o Organic compounds with hydroxyl groups are alcohols, and their names typically end in -ol.

 A carbonyl group (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond. o If the carbonyl group is on the end of the skeleton, the compound is an aldehyde. o If the carbonyl group is within the carbon skeleton, the compound is a ketone. o Isomers with aldehydes and those with ketones have different properties.

 A carboxyl group (—COOH) consists of a carbon atom with a double bond to an oxygen atom and a single bond to the oxygen atom of a hydroxyl group. o Compounds with carboxyl groups are carboxylic acids. o A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the chance of dissociation of hydrogen as an ion (H+).

 An amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton. o Organic compounds with amino groups are amines. o The amino group acts as a base because it can pick up a hydrogen ion (H+) from the solution. o Amino acids, the building blocks of proteins, have amino and carboxyl groups.

 A sulfhydryl group (—SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. o This group resembles a hydroxyl group in shape. o Organic molecules with sulfhydryl groups are thiols. o Two sulfhydryl groups can interact to help stabilize the structure of proteins.

2−  A phosphate group (—OPO3 ) consists of a phosphorus atom bound to four oxygen atoms (three with single bonds and one with a double bond). o A phosphate group connects to the carbon backbone via one of its oxygen atoms. o Phosphate groups are anions with two negative charges because 2 protons dissociate from the oxygen atoms. o One function of phosphate groups is to transfer energy between organic molecules.

ATP is an important source of energy for cellular processes.  Adenosine triphosphate, or ATP, is the primary energy transfer molecule in living cells.  ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups.

 When one inorganic phosphate ion is split off as a result of a reaction with water, ATP becomes adenosine diphosphate, or ADP.

 In a sense, ATP ―stores‖ the potential to react with water, releasing energy that can be used by the cell.

Chapter 5: The Structure and Function of Large Biological Molecules

Overview: The Molecules of Life

Concept 5.1 Macromolecules are polymers, built from monomers  All living things are made up of four main classes of macromolecules: carbohydrates, lipids, proteins, and nucleic acids.  Biochemists have determined the detailed structures of many macromolecules, which exhibit unique emergent properties arising from the orderly arrangement of their atoms.  Three of the four classes of macromolecules—carbohydrates, proteins, and nucleic acids—form chain-like molecules called polymers. ○ A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds. ○ The repeated units are small molecules called monomers. ○ Some of the molecules that serve as monomers have other functions of their own.  The chemical mechanisms which cells use to make and break polymers are similar for all classes of macromolecules. ○ These processes are facilitated by enzymes, specialized macromolecules that speed up chemical reactions in cells.  Monomers are connected by covalent bonds that form through the loss of a water molecule. This reaction is called a dehydration reaction. ○ When a bond forms between two monomers, each monomer contributes part of the water molecule that is lost. One monomer provides a hydroxyl group (—OH), while the other provides a hydrogen atom (—H). ○ Cells invest energy to carry out dehydration reactions.

 The covalent bonds that connect monomers in a polymer are disassembled by hydrolysis, a reaction that is effectively the reverse of dehydration. ○ In hydrolysis, bonds are broken by the addition of water molecules. A hydrogen atom attaches to one monomer, and a hydroxyl group attaches to the adjacent monomer. ○ The process of digestion is an example of hydrolysis within the human body. ○ The cells of our body then use dehydration reactions to assemble the monomers into new and different polymers that carry out functions specific to the particular cell type.

An immense variety of polymers can be built from a small number of monomers.  Each cell has thousands of different kinds of macromolecules.  Macromolecules vary among cells of the same individual. They vary more among unrelated individuals of a species, and even more between species.  This diversity comes from various combinations of the 40–50 common monomers and some others that occur rarely.  The molecular logic of life is simple but elegant: Small molecules common to all organisms are ordered into unique macromolecules.  Despite the great diversity in organic macromolecules, members of each of the four major classes of macromolecules are similar in structure and function.

5.2 Carbohydrates serve as fuel and building material  Carbohydrates include sugars and their polymers. ○ The simplest carbohydrates are monosaccharides, or simple sugars. ○ Disaccharides, or double sugars, consist of two monosaccharides joined by a covalent bond. ○ Polysaccharides are polymers of many monosaccharides.

Sugars, the smallest carbohydrates, serve as fuel and a source of carbon.  Monosaccharides generally have molecular formulas that are some multiple of the unit CH2O. ○ For example, glucose has the formula C6H12O6.  Monosaccharides have a carbonyl group (>C=O) and multiple hydroxyl groups (—OH). ○ Depending on the location of the carbonyl group, the sugar is an aldose (aldehyde sugar) or a ketose (ketone sugar). ○ Most names for sugars end in -ose.  Monosaccharides are also classified by the size of the carbon skeleton. ○ The carbon skeleton of a sugar ranges from three to seven carbons long. ○ Glucose and other six-carbon sugars are hexoses. ○ Five-carbon sugars are pentoses; three-carbon sugars are trioses.  Another source of diversity for simple sugars is the spatial arrangement of their parts around asymmetric carbon atoms. ○ For example, glucose and galactose, both six-carbon aldoses, differ only in the spatial arrangement of their parts around asymmetric carbons.

Structure and classification of some monosaccharides

Glyceraldehyde- breakdown product of glucose

Dihydroxyacetone- breakdown product of glucose

Ribose-component of RNA

Ribulose- intermediate in photosynthesis

Glucose & Galactose & Fructose – all energy sources for organisms

 Although glucose is often drawn with a linear carbon skeleton, most sugars (including glucose) form rings in aqueous solution.  Monosaccharides, particularly glucose, are major nutrients for cellular work. ○ Cells extract energy from glucose molecules in the process of cellular respiration.  Simple sugars also function as the raw material for the synthesis of other monomers, such as amino acids and fatty acids. Linear & ring forms of glucose

 Two monosaccharides can join with a glycosidic linkage to form a disaccharide via dehydration. ○ Maltose, malt sugar, is formed by joining two glucose molecules. ○ Sucrose, table sugar, is formed by joining glucose and fructose. Sucrose is the major transport form of sugars in plants. ○ Lactose, milk sugar, is formed by joining glucose and galactose. Disaccharide synthesis

Polysaccharides, the polymers of sugars, have storage and structural roles.  Polysaccharides are polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages. ○ Some polysaccharides serve for storage and are hydrolyzed as sugars are needed. ○ Other polysaccharides serve as building materials for 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.  Starch is a storage polysaccharide composed entirely of glucose monomers.  Plants store surplus glucose as starch granules within plastids, including chloroplasts, and withdraw it as needed for energy or carbon. ○ Animals that feed on plants, especially parts rich in starch, have digestive enzymes that can hydrolyze starch to glucose, making the glucose available as a nutrient for cells. ○ Grains and potato tubers are the main sources of starch in the human diet.  Most of the glucose monomers in starch are joined by 1–4 linkages (number 1 carbon to number 4 carbon). ○ The simplest form of starch, amylose, is unbranched. ○ Branched forms such as amylopectin are more complex.  Animals store glucose in a polysaccharide called glycogen. ○ Glycogen is similar to amylopectin , but more highly branched. ○ Humans and other vertebrates store a day’s supply of glycogen in the liver and muscles, hydrolyzing it to release glucose to meet the body’s demand for sugar.  Cellulose is a major component of the tough walls of plant cells.

Structures of polysaccharides Starch and cellulose structures

 Like starch, cellulose is a polymer of glucose. However, the glycosidic linkages in these two polymers differ. ○ The linkages are different because glucose has two slightly different ring structures. ○ These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above ( glucose) or below ( glucose) the plane of the ring.  Starch is a polysaccharide of alpha () glucose monomers.  Cellulose is a polysaccharide of beta () glucose monomers, making every other glucose monomer upside down with respect to its neighbors.  The differing glycosidic linkages in starch and cellulose give the two molecules distinct three- dimensional shapes.  Enzymes that digest starch by hydrolyzing its  linkages cannot hydrolyze the  linkages in cellulose. ○ Cellulose in human food passes through the digestive tract and is eliminated in feces as ―insoluble fiber.‖  Some microbes can digest cellulose to its glucose monomers through the use of cellulase enzymes.  Many eukaryotic herbivores, from cows to termites, have symbiotic relationships with cellulose- digesting prokaryotes and protists, providing the microbes and the host animal access to a rich source of energy.  Another important structural polysaccharide is chitin, found in the exoskeletons of arthropods (including insects, spiders, and crustaceans). ○ Chitin is similar to cellulose, except that it has a nitrogen-containing appendage on each glucose monomer. ○ Chitin also provides structural support for the cell walls of many fungi.

5.3 Lipids are a diverse group of hydrophobic molecules  Unlike other macromolecules, lipids do not form polymers.  The unifying feature of lipids is that they have little or no affinity for water because they consist of mostly hydrocarbons, which form nonpolar covalent bonds.

Fats store large amounts of energy.  Although fats are not strictly polymers, they are large molecules assembled from smaller molecules via dehydration reactions.  A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids. ○ Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon. ○ A fatty acid consists of a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long. ○ The many nonpolar C—H bonds in the long hydrocarbon skeleton make fats hydrophobic. ○ Fats separate from water because the water molecules hydrogen-bond to one another and exclude the fats.  In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride. o The three fatty acids in a fat can be the same or different.

Glycerol & fatty acid Fat molecule – triglyceride (triacylglycerol )

 Fatty acids vary in length (number of carbons) and in the number and locations of double bonds. ○ If the fatty acid has no carbon-carbon double bonds, then the molecule is a saturated fatty acid, saturated with hydrogens at every possible position. ○ If the fatty acid has one or more carbon-carbon double bonds formed by the removal of hydrogen atoms from the carbon skeleton, then the molecule is an unsaturated fatty acid.  A saturated fatty acid is a straight chain, but an unsaturated fatty acid has a kink wherever there is a cis double bond. ○ The kinks caused by the cis double bonds prevent the molecules from packing tightly enough to solidify at room temperature.  Fats made from saturated fatty acids are saturated fats. Fats made from unsaturated fatty acids are unsaturated fats. ○ Most animal fats are saturated and are solid at room temperature. ○ Plant and fish fats are liquid at room temperature and are known as oils.

Saturated triglyceride Monounsaturated triglyceride

 The phrase ―hydrogenated vegetable oils‖ on food labels means that unsaturated fats have been synthetically converted to saturated fats by the addition of hydrogen. ○ Peanut butter and margarine are hydrogenated to prevent lipids from separating out as oil.  A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits.  Some unsaturated fatty acids cannot be synthesized by humans and must be supplied by diet. ○ Omega-3 fatty acids are essential fatty acids.  The major function of fats is energy storage. ○ A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch. ○ Because plants are immobile, they can function with bulky energy storage in the form of starch. Plants use oils when dispersal and compact storage are important, as in seeds. ○ Animals must carry their energy stores with them, so they benefit from having a more compact fuel reservoir of fat.  Humans and other mammals store fats as long-term energy reserves in adipose cells that swell and shrink as fat is deposited and withdrawn from storage.  A layer of fat can function as insulation.

Phospholipids are major components of cell membranes.  Phospholipids have two fatty acids attached to glycerol and a phosphate group at the third position. ○ The phosphate group carries a negative charge. ○ Additional smaller groups (usually charged or polar) may be attached to the phosphate group to form a variety of phospholipids.  The interaction of phospholipids with water is complex. ○ The fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head.  Phospholipids are arranged as a bilayer at the surface of a cell. ○ The hydrophilic heads are on the outside of the bilayer, in contact with the aqueous solution, and the hydrophobic tails point toward the interior of the bilayer. ○ The phospholipid bilayer forms a barrier between the cell and the external environment. ○ Phospholipids are the major component of all cell membranes.

Structural formula of a phospholipid Phospholipid bilayer

Phospholipid symbol

Steroids include cholesterol and certain hormones.  Steroids are lipids with a carbon skeleton consisting of four fused rings.  Different steroids are created by varying the functional groups attached to the rings.  Cholesterol, an important steroid, is a component in animal cell membranes.

 Cholesterol is the precursor from which all other steroids are synthesized. ○ Many of these other steroids are hormones, including the vertebrate sex hormones.  Although cholesterol is an essential molecule in animals, high levels of cholesterol in the blood may contribute to cardiovascular disease.

5.4 Proteins include a diversity of structures, resulting in a wide range of functions  Proteins account for more than 50% of the dry mass of most cells. They are instrumental in almost everything an organism does. ○ Protein functions include structural support, storage, transport, cellular communication, movement, and defense against foreign substances. ○ Most important, protein enzymes function as catalysts in cells, regulating metabolism by selectively accelerating certain chemical reactions without being consumed.  Humans have tens of thousands of different proteins, each with a specific structure and function.  Proteins are the most structurally complex molecules known.

○ Each type of protein has a complex three-dimensional shape.  All proteins are unbranched polymers constructed from the same 20 amino acid monomers.  Polymers of amino acids are called polypeptides.  A protein is a biologically functional molecule that consists of one or more polypeptides folded and coiled into a specific conformation. Overview of protein functions

Amino acids are the monomers from which proteins are constructed.  Amino acids are organic molecules with both carboxyl and amino groups.  At the center of an amino acid is an asymmetric carbon atom called the alpha () carbon.

Amino acid monomer

 Four components are attached to the α carbon: a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain). ○ Different R groups characterize the 20 different amino acids. ○ An R group may be as simple as a hydrogen atom (as in the amino acid glycine), or it may be a carbon skeleton with various functional groups attached (as in glutamine).  The physical and chemical properties of the R group determine the unique characteristics of a particular amino acid. ○ One group of amino acids has nonpolar R groups, which are hydrophobic. ○ Another group of amino acids has polar R groups, which are hydrophilic. ○ A third group of amino acids has functional groups that are charged (ionized) at cellular pH. o Some acidic R groups have negative charge due to the presence of a carboxyl group. o Basic R groups have amino groups with positive charge. o All amino acids have carboxyl and amino groups. The terms acidic and basic in this context refer only to these groups in the R groups. Examples of amino acid types

Nonpolar; hydrophobic Polar; hydrophilic Acidic (negative charge) Basic (positive charge)

 Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen atom from the amino group of another. ○ The resulting covalent bond is called a peptide bond.  Repeating the process over and over creates a polypeptide chain. ○ At one end is an amino acid with a free amino group (the N-terminus), and at the other end is an amino acid with a free carboxyl group (the C-terminus).  Polypeptides range in size from a few monomers to thousands.  Each polypeptide has a unique linear sequence of amino acids.

Making a polypeptide chain

Scientists have determined the amino acid sequences of polypeptides.  Frederick Sanger and his colleagues at Cambridge University determined the amino acid sequence of insulin in the early 1950s.

Protein conformation determines protein function.  A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape.  It is the order of amino acids that determines the three-dimensional structure of the protein under normal cellular conditions.  A protein’s specific structure determines its function.  When a cell synthesizes a polypeptide, the chain generally folds spontaneously to assume the functional structure for that protein.  The folding is reinforced by a variety of bonds between parts of the chain, which in turn depend on the sequence of amino acids.  Many proteins are globular (round & functional) , while others are fibrous (long/narrow & structural) in shape.  In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule. ○ For example, an antibody binds to a particular foreign substance. ○ Natural signal molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans, producing euphoria and relieving pain.  The function of a protein is an emergent property resulting from its specific molecular order.  Three levels of structure—primary, secondary, and tertiary structures—organize the folding within a single polypeptide. ○ Quaternary structure arises when two or more polypeptides join to form a protein.  The primary structure of a protein is its unique sequence of amino acids.  Transthyretin is a globular protein found in the blood that transports vitamin A and a particular thyroid hormone throughout the body. ○ Each of the four identical polypeptide chains that, together, make up transthyretin is composed of 127 amino acids.  Most proteins have segments of their polypeptide chains repeatedly coiled or folded.  These coils and folds are referred to as secondary structure and result from hydrogen bonds between the repeating constituents of the polypeptide backbone.

○ The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond. ○ Each hydrogen bond is weak, but the sum of many hydrogen bonds stabilizes the structure of part of the protein.  One secondary structure is the  helix, a delicate coil held together by hydrogen bonding between every fourth amino acid ○ Some fibrous proteins, such as -keratin, the structural protein of hair, have the  helix formation over most of their length.  The other main type of secondary structure is the  pleated sheet. ○ In this structure, two or more regions of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of the two parallel polypeptide backbones. ○ Pleated sheets are found in many globular proteins, such the silk protein of a spider’s web. ○ The presence of so many hydrogen bonds makes each silk fiber stronger than a steel strand of the same weight.

Primary structure – linear chain of amino Secondary structure- stabilized by hydrogen bonds acids between atoms of the polypeptide backbone

 Tertiary structure is determined by interactions among various R groups. ○ These interactions include hydrogen bonds between polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups. ○ Although these three interactions are relatively weak, their cumulative effect helps give the protein a unique shape. ○ Strong covalent bonds called disulfide bridges that form between the sulfhydryl groups (SH) of two cysteine monomers act to rivet parts of the protein together.

Tertiary Structure- three dimensional shape Interactions that shape a tertiary structure stabilized by interactions between side chains

 Quaternary structure results from the aggregation of two or more polypeptide subunits. ○ For example, globular transthyretin protein is made up of four polypeptides. ○ Collagen is a fibrous protein made up of three polypeptides that are supercoiled into a larger triple helix. ○ Hemoglobin is a globular protein with quaternary structure. . Hemoglobin consists of four polypeptide subunits: two  and two  chains. . Both types of subunits consist of primarily -helical secondary structure. . Each subunit has a nonpeptide heme component with an iron atom that binds oxygen.

Quarternary structure- association of two or more polypeptides (some proteins only)

 A polypeptide chain with a given amino acid sequence can spontaneously arrange itself into a three- dimensional shape determined and maintained by the interactions responsible for secondary and tertiary structure. ○ The folding occurs as the protein is synthesized within the cell.  Protein structure also depends on the physical and chemical conditions of the protein’s environment. ○ Alterations in pH, salt concentration, temperature, or other factors can unravel or denature a protein. 21

○ These forces disrupt the weak chemical bonds and interactions within a protein that maintain its shape. ○ Because it is misshapen, a denatured protein is biologically inactive.  Most proteins become denatured if they are transferred from an aqueous environment to a nonpolar solvent. ○ The polypeptide chain refolds so that its hydrophobic regions face outward, toward the solvent.  Other denaturation agents include chemicals that disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain a protein’s shape.  Denaturation can also be caused by heat, which disrupts the weak interactions that stabilize conformation. ○ This explains why extremely high fevers can be fatal. Proteins in the blood become denatured by the high body temperatures.  Some, but not all, proteins can return to their functional shape after denaturation. ○ This suggests that the information for building a specific shape is intrinsic to the protein’s primary structure.

 Most proteins appear to undergo several intermediate stages before reaching their ―mature‖ structure.  Even a slight change in the primary structure can affect a protein’s conformation and ability to function. ○ The substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin, the protein that carries oxygen in red blood cells, can cause sickle-cell disease, an inherited blood disorder.

Sickle cell disease from a single amino acid substitution

 The folding of many proteins is assisted by chaperonins, or chaperone proteins. ○ Chaperonins do not specify the final structure of a polypeptide but rather work to segregate and protect the polypeptide while it folds spontaneously. Chaperonins

o Molecular systems in the cell interact with chaperonins, marking incorrectly folded proteins for refolding or for destruction.  Accumulation of incorrectly folded polypeptides is associated with many diseases, including Alzeimer’s, Parkinson’s, and mad cow disease.  In 2006, Roger Kornberg received the Nobel Prize in Chemistry for elucidating the structure of RNA polymerase, which plays a crucial role in the expression of genes. ○ Kornberg and his colleagues used X-ray crystallography to determine the three-dimensional structure of this protein. ○ Nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization, can also be used to determine protein structure.  Bioinformatics uses computer programs to predict the three-dimensional structures of polypeptides from their amino acid sequences.  X-ray crystallography, NMR spectroscopy, and bioinformatics are complementary approaches, contributing a great deal to our understanding of protein structure and function.

5.5 Nucleic acids store, transmit, and help express hereditary information  The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene. o A gene consists of DNA, a polymer known as a nucleic acid. o Nucleic acids are made of monomers called nucleotides.

There are two types of nucleic acids: RNA and DNA.  The two types of nucleic acids are ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).  RNA and DNA are the molecules that enable living organisms to reproduce their complex components from generation to generation. o DNA provides directions for its own replication. o DNA also directs RNA synthesis and, through RNA, controls protein synthesis; this entire process is called gene expression.  Organisms inherit DNA from their parents. ○ Each DNA molecule is very long, carrying several hundred or more genes. ○ Before a cell reproduces itself by dividing, its DNA is copied. The copies are then passed to the next generation of cells. 23

 Although DNA encodes the information that programs all the cell’s activities, it is not directly involved in the day-to-day operations of the cell.  Each gene along a DNA molecule directs the synthesis of a specific type of RNA called messenger RNA (mRNA). ○ The mRNA molecule interacts with the cell’s protein-synthesizing machinery to direct the ordering of amino acids in a polypeptide.  The flow of genetic information is DNA  mRNA  protein.

 Protein synthesis occurs on cellular structures called ribosomes.  In eukaryotes, DNA is located in the nucleus, but most ribosomes are in the cytoplasm. ○ mRNA functions as an intermediary, moving genetic instructions for building proteins from the nucleus to the cytoplasm.  Prokaryotes lack nuclei but still use mRNA as an intermediary to carry a message from DNA to the ribosomes.

A nucleic acid strand is a polymer of nucleotides.  Nucleic acids are polymers made of nucleotide monomers organized as polynucleotides.  Each nucleotide consists of three parts: a nitrogenous base, a pentose sugar, and one or more phosphate groups.  The nitrogenous bases are rings of carbon and nitrogen that come in two types: purines and pyrimidines. ○ Pyrimidines have a single six-membered ring of carbon and nitrogen atoms. . There are three different pyrimidines: cytosine (C), thymine (T), and uracil (U). . Thymine is found only in DNA and uracil is found only in RNA. ○ Purines have a six-membered ring joined to a five-membered ring. . The two purines are adenine (A) and guanine (G).  The pentose joined to the nitrogenous base is ribose in nucleotides of RNA and deoxyribose in DNA. ○ The only difference between the sugars is the lack of an oxygen atom on carbon 2 in deoxyribose. ○ Because the atoms in both the nitrogenous base and the sugar are numbered, the sugar atoms are distinguished by a prime () after the number. ○ Thus, the second carbon in the sugar ring is the 2 (2 prime) carbon, and the carbon that sticks up from the ring is the 5 carbon. ○ The combination of a pentose and a nitrogenous base is a nucleoside.  The addition of a phosphate group creates a nucleoside monophosphate or nucleotide.

 Polynucleotides are synthesized when adjacent nucleotides are joined by covalent bonds called phosphodiester linkages that form between the —OH group on the 3 of one nucleotide and the phosphate on the 5 carbon of the next. ○ This process creates a repeating backbone of sugar-phosphate units, with appendages consisting of the nitrogenous bases.  The two free ends of the polymer are distinct. ○ One end has a phosphate attached to a 5 carbon; this is the 5 end. ○ The other end has a hydroxyl group on a 3 carbon; this is the 3 end DNA

 The sequence of bases along a DNA or mRNA polymer is unique for each gene. ○ Because genes are normally hundreds to thousands of nucleotides long, the number of possible base combinations is virtually limitless.  The linear order of bases in a gene specifies the order of amino acids—the primary structure—of a protein, which in turn determines three-dimensional structure and function. Messenger RNA

Components of nucleic acids

Inheritance is based on replication of the DNA double helix.  An RNA molecule is usually a single polynucleotide chain.  DNA molecules have two polynucleotide strands that spiral around an imaginary axis to form a double helix.  The sugar-phosphate backbones of the two polynucleotides are on the outside of the helix. ○ The two backbones run in opposite 5  3 directions from each other, an arrangement referred to as antiparallel.  The two polynucleotides or strands are held together by hydrogen bonds between the paired bases.  Most DNA molecules have thousands to millions of base pairs.  Because of their shapes, only some bases are compatible with each other. ○ Adenine (A) always pairs with thymine (T) and guanine (G) with cytosine (C). ○ With these base-pairing rules, if we know the sequence of bases on one strand, we know the sequence on the opposite strand. ○ The two strands are complementary.  Prior to cell division, each of the strands serves as a template to order nucleotides in a new complementary strand. 26

○ This results in two identical copies of the original double-stranded DNA molecule, which are then distributed to the daughter cells. o This mechanism ensures that a full set of genetic information is transmitted whenever a cell reproduces. Structure of DNA and tRNA

 Complementary base pairing can also occur between parts of two RNA molecules or even between two stretches of nucleotides in the same RNA molecule. ○ For example, transfer RNA or tRNA brings amino acids to the ribosome during polypeptide synthesis. ○ The functional shape of tRNA results from base pairing between nucleotides where complementary stretches of the molecule run antiparallel to each other.  In RNA, adenine pairs with uracil; thymine is not present in RNA.  Another difference between RNA and DNA is that DNA almost always exists as a double helix, whereas RNA molecules are more variable in shape.

5.6 Genomics and proteomics have transformed biological inquiry and applications  The structure of the DNA molecule was described in 1952, and the linear sequence of nucleotide bases was understood to specific the amino acid sequence of proteins.  The first chemical techniques for DNA sequencing were developed in the 1970s.  Between 1990 and the early 2000s, the entire sequence of the full complement of the human genome was sequenced, the human genome project.  Rapid development of faster and less expense sequencing methods have led to the sequencing of numerous genomes, other than humans. o A new disciple, bioinformatics, using computer software and computational tools, was formed to handle and analyze the large reams of data generated from these endeavors. o Genomics is an approach of addressing problems by analyzing large sets of genes or comparing whole genomes of different species. o Similar to genomics, proteomic is the approach that analyzes large sets of protein sequences.

DNA and proteins are used as a tape measures of evolution.  Genes (DNA) and their products (proteins) document the hereditary background of an organism.  Because DNA molecules are passed from parents to offspring, siblings have greater similarity in their DNA and protein than do unrelated individuals of the same species.  This argument can be extended to develop a ―molecular genealogy‖ to relationships between species.  Two species that appear to be closely related based on fossil and molecular evidence should also be more similar in DNA and protein sequences than are more distantly related species. ○ Scientists can compare the sequence of 146 amino acids in the polypeptide chain of human hemoglobin to the sequences in five other vertebrates. ○ Humans and gorillas differ in just 1 amino acid, while humans and frogs differ in 67 amino acids. ○ Despite these differences, all the species have functional hemoglobin.

Chapter 8: An Introduction to Metabolism

Overview:

Concept 8.1 An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics.  The sum total of an organism’s chemical reactions is called metabolism.  Metabolism is an emergent property of life that arises from interactions between molecules within the orderly environment of the cell.

The chemistry of life is organized into metabolic pathways.  A metabolic pathway begins with a specific molecule, which is then altered in a series of defined steps to form a specific product.  A specific enzyme catalyzes each step of the pathway.

 Catabolic pathways release energy by breaking down complex molecules to simpler compounds.  A major pathway of catabolism is cellular respiration, in which the sugar glucose is broken down in the presence of oxygen to carbon dioxide and water.  The energy released by catabolic pathways becomes available to do the work of the cell, such as ciliary beating or membrane transport.  Anabolic pathways, also called biosynthetic pathways, consume energy to build complicated molecules from simpler compounds.  The synthesis of amino acids from simpler molecules and the synthesis of a protein from amino acids are both examples of anabolism.  Energy released from the ―downhill‖ reactions of catabolic pathways can be stored and then used to drive the ―uphill‖ reactions of anabolic pathways.  Energy is fundamental to all metabolic processes, and therefore an understanding of energy is key to understanding how the living cell works.  Bioenergetics is the study of how energy flows through living organisms. Organisms transform energy.  Energy is the capacity to cause change. 29

 In everyday life, some forms of energy can be used to do work—that is, to move matter against opposing forces, such as gravity and friction.  Energy exists in various forms, and cells transform energy from one type to another.  Kinetic energy is the energy associated with the relative motion of objects.  Objects in motion can perform work by imparting motion to other matter.  Thermal energy is kinetic energy associated with the random movement of atoms or molecules.  Heat is the transfer of thermal energy from one body of matter to another.  The energy of light can be harnessed to power photosynthesis in green plants.  Potential energy is the energy that matter possesses because of its location or structure.  Water behind a dam possesses energy because of its altitude above sea level.  Molecules possess energy because of the arrangement of electrons in the bonds between their atoms.  Chemical energy is a term used by biologists to refer to the potential energy available for release in a chemical reaction.  During a catabolic reaction, some bonds are broken and others are formed, releasing energy and producing lower-energy breakdown products.  Energy can be converted from one form to another.

The energy transformations of life are subject to two laws of thermodynamics.  Thermodynamics is the study of energy transformations that occur in a collection of matter.  In this field, the term system refers to the matter under study, and the surroundings include the rest of the universe—everything outside the system.  An isolated system, approximated by liquid in a thermos, is unable to exchange either energy or matter with its surroundings.  In an open system, energy and matter can be transferred between the system and its surroundings.  Organisms are open systems: They absorb energy—light or chemical energy in the form of organic molecules—and release heat and metabolic waste products, such as urea or CO2, to their surroundings.  Two laws of thermodynamics govern energy transformations in organisms and all other collections of matter.  The first law of thermodynamics states that the energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed. ○ The first law is also known as the principle of conservation of energy.  Plants do not produce energy; they transform light energy to chemical energy.  During every transfer or transformation of energy, some energy is converted to heat, which is the energy associated with the random movement of atoms and molecules.  A system can use heat to do work only when there is a temperature difference that results in heat flowing from a warmer location to a cooler one.  If temperature is uniform, as in a living cell, heat can be used only to warm the organism.  Energy transfers and transformations make the universe more disordered due to the loss of usable energy. Examples of the laws of thermodynamics

 Entropy is a measure of disorder or randomness: The more random a collection of matter, the greater its entropy.  The second law of thermodynamics states: Every energy transfer or transformation increases the entropy of the universe.  Although order can increase locally, there is an unstoppable trend toward randomization of the universe.  Much of the increased entropy of the universe takes the form of increasing heat, which is the energy of random molecular motion.  In most energy transformations, ordered forms of energy are converted at least partly to heat.  Automobiles convert only 25% of the energy in gasoline to motion; the rest is lost as heat.  Living cells unavoidably convert organized forms of energy to heat.  For a process to occur on its own, without outside help in the form of energy input, it must increase the entropy of the universe.  Spontaneous processes can occur without an input of energy, although they need not occur quickly.  Some spontaneous processes, such as an explosion, are instantaneous. Some, such as the rusting of an old car, are very slow.  A spontaneous process is one that is energetically favorable. A process that cannot occur on its own is said to be nonspontaneous: it will happen only if energy is added to the system.  Water flows downhill spontaneously but moves uphill only with an input of energy, such as when a machine pumps the water against gravity.  Here is another way to state the second law of thermodynamics: For a process to occur spontaneously, it must increase the entropy of the universe.  Living systems increase the entropy of their surroundings, even though they create ordered structures from less ordered starting materials.  For example, amino acids are ordered into polypeptide chains.  The structure of a multicellular body is organized and complex.  However, an organism also takes in organized forms of matter and energy from its surroundings and replaces them with less ordered forms.  For example, an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide and water.

8.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously.  How can we determine which reactions occur spontaneously and which ones require an input of energy?  The concept of free energy (symbolized by the letter G) is useful for measuring the spontaneity of a system.  Free energy is the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell.  The change in free energy, ∆G, can be calculated for any specific chemical reaction by applying the following equation: ∆G = ∆H – T∆S  In this equation, ∆H symbolizes the change in the system’s enthalpy (in biological systems, equivalent to total energy); ∆S is the change in the system’s entropy; and T is the absolute temperature in Kelvin (K) units (K = °C + 273).  For a process to occur spontaneously, the system must give up enthalpy (H must decrease), give up order (T∆S must increase), or both.  ∆G must have a negative value (∆G < 0) in order for a process to be spontaneous.  In other words, every spontaneous process decreases the system’s free energy, and processes that have positive or zero ∆G are never spontaneous. 31

 Knowing the value of G gives biologists the power to predict which kinds of change can happen without help.  Such spontaneous changes can be harnessed to perform work.  This information is important in the study of metabolism, where a major goal is to determine which reactions can supply energy to do work in the living cell.  In any spontaneous process, the free energy of a system decreases (∆G is negative).  We can represent the change in free energy from the start to the finish of a process by G = Gfinal state − Gstarting state  ∆G can be negative only when the process involves a loss of free energy during the change from initial state to final state.  Because it has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously.  A system at equilibrium is at maximum stability.  Unstable systems (higher G) tend to change in such a way that they become more stable (lower G).  Another term for a state of maximum stability is equilibrium.  In a chemical reaction at equilibrium, the rates of forward and backward reactions are equal, and there is no change in the relative concentrations of products or reactants.  At equilibrium, G = 0, and the system can do no work.  A process is spontaneous and can perform work only when it is moving toward equilibrium.  Movements away from equilibrium are nonspontaneous and will have a positive G.

The relationship of free energy (G) to stability, work capacity, and spontaneous change

Chemical reactions can be classified as either exergonic or endergonic.  An exergonic reaction proceeds with a net release of free energy; G is negative.  The magnitude of G for an exergonic reaction is the maximum amount of work the reaction can perform.  The greater the decrease in free energy, the greater the amount of work that can be done.

 For the overall reaction of cellular respiration, C6H12O6 + 6O2  6CO2 + 6H2O, G = 686 kcal/mol.  For each mole (180 g) of glucose broken down by respiration under standard conditions (1 M of each reactant and product, 25°C, pH 7), 686 kcal of energy are made available to do work in the cell.  The products have 686 kcal less free energy per mole than the reactants.

Free energy changes (G) in exergonic and endergonic reactions

 An endergonic reaction is one that absorbs free energy from its surroundings.  Endergonic reactions store energy in molecules; G is positive.  Endergonic reactions are nonspontaneous, and the magnitude of G is the quantity of energy required to drive the reaction.  If cellular respiration releases 686 kcal/mol, then photosynthesis, the reverse reaction, must require an equivalent investment of energy.  For the conversion of carbon dioxide and water to sugar, G = +686 kcal/mol.  Photosynthesis is strongly endergonic, powered by the absorption of light energy.  Reactions in an isolated system eventually reach equilibrium and can do no work.  A cell that has reached metabolic equilibrium has a G = 0 and is dead!  Metabolic disequilibrium is one of the defining features of life.  Cells maintain disequilibrium because they are open systems. The constant flow of materials into and out of the cell keeps metabolic pathways from ever reaching equilibrium.  A cell continues to do work throughout its life.  A catabolic process in a cell releases free energy in a series of reactions, not in a single step. Work in an open system

 Some reversible reactions of respiration are constantly ―pulled‖ in one direction, as the product of one reaction does not accumulate but becomes the reactant in the next step.  The overall sequence of reactions is kept going by the huge free-energy difference between glucose and oxygen at the top of the energy ―hill‖ and carbon dioxide and water at the ―downhill‖ end.  As long as cells have a steady supply of glucose or other fuels and oxygen and can expel waste products to the surroundings, their metabolic pathways never reach equilibrium and can continue to do the work of life.  Sunlight provides a daily source of free energy for photosynthetic organisms.  Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.

8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions.  A cell does three main kinds of work: 1. Chemical work, pushing endergonic reactions such as the synthesis of polymers from monomers; 2. Transport work, pumping substances across membranes against the direction of spontaneous movement; 3. Mechanical work, such as the beating of cilia, contraction of muscle cells, and movement of chromosomes during cellular reproduction;  Cells manage their energy resources to do this work by energy coupling, using an exergonic process to drive an endergonic one.  ATP is responsible for mediating most energy coupling in cells

ATP mediates most energy coupling in cells.  ATP (adenosine triphosphate) is a nucleotide triphosphate consisting of the sugar ribose, the nitrogenous base adenine, and a chain of three phosphate groups.

Structure of ATP Hydrolysis of ATP

 In most cases, ATP acts as the immediate source of energy that powers cellular work.  The bonds between the phosphate groups on ATP can be broken by hydrolysis. 2-  When the terminal phosphate bond is broken, a molecule of inorganic phosphate (HOPO3 , abbreviated Pi here) leaves ATP, which then becomes adenosine diphosphate, or ADP: ATP + H2O  ADP + Pi G = 7.3 kcal/mol (30.5 kJ/mol).  In the cell, G for the hydrolysis of ATP is about −13 kcal/mol because reactant and product concentrations differ from 1 M.  Although the phosphate bonds of ATP are sometimes referred to as high-energy phosphate bonds, these are actually fairly weak covalent bonds.

 The reactants (ATP and water) themselves have high energy relative to the energy of the products (ADP and Pi).  The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.  Why does the hydrolysis of ATP yield so much energy? o Each of the three phosphate groups has a negative charge. o These three like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule. o The triphosphate tail of ATP is the chemical equivalent of a compressed spring.  In the cell, the energy from the hydrolysis of ATP is directly coupled to endergonic processes by the transfer of the phosphate group to another molecule.  This recipient molecule with a phosphate group covalently bonded to it is called a phosphorylated intermediate. It is more reactive (less stable) than the original unphosphorylated molecule.  Mechanical, transport, and chemical work in the cell are nearly always powered by the hydrolysis of ATP.  In each case, ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind another molecule.  This change may occur via a phosphorylated intermediate. ATP drives chemical work – energy coupling and ATP hydrolysis

 In most examples of mechanical work involving motor proteins ―walking‖ on cytoskeletal elements, a cycle occurs in which ATP is bound noncovalently to the motor protein and hydrolyzed, then ADP and Pi are released, followed by binding of another ATP molecule.  In each state, the motor protein exhibits a different shape and ability to bind the cytoskeleton, resulting in movement of the protein along the cytoskeletal track.

How ATP drives transport and mechanical work

ATP is a renewable resource.  Although organisms use ATP continuously, ATP is a renewable resource that can be regenerated by the addition of a phosphate group to ADP.  The free energy to phosphorylate ADP comes from exergonic (catabolic) reactions in the cell.  The ATP cycle, the shuttling of inorganic phosphate and energy, couples the cell’s energy-yielding (exergonic) processes to the energy-consuming (endergonic) ones. The ATP cycle

 A working muscle cell recycles its entire pool of ATP once each minute.  More than 10 million ATP molecules are consumed and regenerated per second per cell.  Regeneration of ATP is an endergonic process, requiring an investment of energy: ADP + Pi  ATP + H2O G = +7.3 kcal/mol  Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic regeneration of ATP.  Plants also use light energy to produce ATP.  The chemical potential energy temporarily stored in ATP drives most cellular work.

Concept 8.4 Enzymes speed up metabolic reactions by lowering energy barriers.  Spontaneous chemical reactions may occur so slowly as to be imperceptible.  The hydrolysis of table sugar (sucrose) to glucose and fructose is exergonic, with G = −7 kcal/mol.  Despite this, a solution of sucrose dissolved in sterile water may sit for years at room temperature with no appreciable hydrolysis.  If a small amount of the enzyme sucrase is added to a solution of sugar, all the sucrose is hydrolyzed within seconds.  An enzyme is a macromolecule that acts as a catalyst, a chemical agent that speeds up the rate of a reaction without being consumed by the reaction.  Every chemical reaction involves bond breaking and bond forming.

 To hydrolyze sucrose, the bond between glucose and fructose must be broken and new bonds must form with hydrogen and hydroxyl ions from water.

 To reach a state at which bonds can break and reform, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat as the molecules assume stable shapes with lower energy.  The initial investment of energy for starting a reaction is the free energy of activation, or activation energy (EA).  Activation energy is the amount of energy necessary to push the reactants over an energy barrier so that the ―downhill‖ part of the reaction can begin.  Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from the surroundings.  The absorption of thermal energy accelerates the reactant molecules, which then collide more often with more force.  It also agitates the atoms within the molecules, making the breakage of bonds more likely.  When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition called the transition state.  Consider a hypothetical exergonic reaction that swaps portions of two reactant molecules: AB + CD  AC + BD Energy profile of an exergonic reaction

 The energizing, or activation, of the reactants is represented by the uphill portion of the graph, with the free-energy content of the reactant molecules increasing.

 At the summit, when the energy equivalent to EA has been absorbed, the reactants are in the transition state. They are activated and their bonds can be broken.  The bond-forming phase of the reaction corresponds to the downhill part of the curve, which shows the loss of free energy by the molecules.  As the molecules settle into new, stable bonding arrangements, energy is released to the surroundings.

 The overall decrease in free energy means that EA is repaid with interest.  For some processes, EA is not high, and the thermal energy provided by room temperature is sufficient for many reactants to reach the transition state. 37

 In most cases, EA is high enough that the transition state is rarely reached and the reaction hardly proceeds at all. In these cases, the reaction will occur at a noticeable rate only if the reactants are heated.  A spark plug provides the activation energy to energize a gasoline-oxygen mixture and cause combustion.  Without a spark, the hydrocarbons of gasoline are too stable to react with oxygen.  Proteins, DNA, and other complex organic molecules are rich in free energy. Their hydrolysis is spontaneous, with the release of large amounts of energy.  However, there is not enough energy at the temperatures typical of the cell for the vast majority of organic molecules to make it over the hump of activation energy.  How are the barriers for selected reactions surmounted to allow cells to carry out the processes of life?  Heat would speed up all reactions, not just those that are needed.  Heat also denatures proteins and kills cells.

 Enzymes speed reactions by lowering EA. The transition state can then be reached even at moderate temperatures.  Enzymes do not change G; they hasten reactions that would occur eventually.  Because enzymes are so selective, they determine which chemical processes will occur at any time. The effect of an enzyme on activation energy Exergonic

Endergonic

Enzymes are substrate specific.  The reactant that an enzyme acts on is the substrate.  The enzyme binds to a substrate, or substrates, forming an enzyme-substrate complex.  While the enzyme and substrate are bound, the catalytic action of the enzyme converts the substrate to the product or products.

 The reaction catalyzed by each enzyme is very specific.  What accounts for this molecular recognition? The specificity of an enzyme results from its three- dimensional shape, which is a consequence of its amino acid sequence.  Only a restricted region of the enzyme binds to the substrate.  The active site of an enzyme is typically a pocket or groove on the surface of the protein where catalysis occurs.  The active site is usually formed by only a few amino acids. The rest of the protein molecule provides a framework that determines the configuration of the active site.  The specificity of an enzyme is due to the fit between the active site and the substrate.  As the substrate enters the active site, interactions between the chemical groups on the substrate and those on the side chains of the amino acids that form the active site cause the enzyme to change shape slightly.  This change leads to an induced fit that brings the chemical groups of the active site into position to catalyze the reaction.

The active site is an enzyme’s catalytic center  Enzymes use a variety of mechanisms to lower the activation energy and speed up a reaction.  In reactions involving more than one reactant, the active site brings substrates together in the correct orientation for the reaction to proceed.  As the active site binds the substrate, the enzyme may stretch the substrate molecules toward their transition-state form, stressing and bending critical chemical bonds that must be broken during the reaction.  The R groups at the active site may create a microenvironment that is conducive to a specific reaction. For example, an active site may be a pocket of low pH, facilitating H+ transfer to the substrate as a key step in catalyzing the reaction.  Enzymes may briefly bind covalently to substrates. Subsequent steps of the reaction restore the side chains of amino acids within the active site to their original state.

The active site and catalytic cycle of an enzyme

 The rate at which a specific number of enzymes convert substrates to products depends in part on substrate concentrations.  At low substrate concentrations, an increase in substrate concentration speeds binding to available active sites.  There is a limit to how fast a reaction can occur, however.  At high substrate concentrations, the active sites on all enzymes are engaged.  The enzyme is saturated, and the rate of the reaction is determined by the speed at which the active site can convert substrate to product. ○ The only way to increase productivity at this point is to add more enzyme molecules.

A cell’s physical and chemical environment affects enzyme activity.  The activity of an enzyme is affected by general environmental conditions, such as temperature and pH.  Each enzyme works best at certain optimal conditions, which favor the most active conformation for the enzyme molecule.  Temperature has a major impact on reaction rate.  As temperature increases, collisions between substrates and active sites occur more frequently as molecules move more rapidly.  As temperature increases further, thermal agitation begins to disrupt the weak bonds that stabilize the protein’s active conformation, and the protein denatures.  Each enzyme has an optimal temperature that allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules. o Most human enzymes have optimal temperatures of about 35–40°C.  Each enzyme also has an optimal pH.  Maintenance of the active conformation of the enzyme requires a particular pH.  This optimal pH falls between 6–8 for most enzymes.  However, digestive enzymes in the stomach are designed to work best at pH 2, whereas those in the intestine have an optimal pH of 8. 40

Environmental factors affecting enzyme activity

 Many enzymes require nonprotein helpers, called cofactors, for catalytic activity.  Cofactors bind permanently or reversibly to the enzyme.  Some inorganic cofactors are zinc, iron, and copper in ionic form.  Organic cofactors are called coenzymes.  Most vitamins are coenzymes or the raw materials from which coenzymes are made.

Binding by inhibitors prevents enzymes from catalyzing reactions.  Certain chemicals selectively inhibit the action of specific enzymes.  If inhibitors attach to the enzyme by covalent bonds, inhibition may be irreversible.  If inhibitors bind by weak bonds, inhibition may be reversible. Types of enzyme inhibition

 Some reversible inhibitors resemble the substrate and compete for binding to the active site. These molecules are called competitive inhibitors.  Competitive inhibition can be overcome by increasing the concentration of the substrate.  Noncompetitive inhibitors impede enzymatic reactions by binding to another part of the molecule.  Binding by the inhibitor causes the enzyme to change shape, rendering the active site less effective at catalyzing the reaction.  Toxins and poisons are often irreversible enzyme inhibitors. o DDT acts as a pesticide by inhibiting key enzymes in the nervous system of insects.  Many antibiotics are inhibitors of specific enzymes in bacteria.  Penicillin blocks the active site of an enzyme that many bacteria use to make their cell walls.  Not all enzyme inhibitors are metabolic poisons.  Molecules naturally present in the cell often regulate enzyme activity by acting as inhibitors.  Such regulation—selective inhibition—is essential to the control of cellular metabolism.

How did the great diversity of enzymes arise?  So far, biochemists have discovered and named more than 4,000 different enzymes in various species; there are certainly many more.  How did this diversity arise? Most enzymes are proteins, and proteins are encoded by genes. 41

 A permanent change in a gene, known as a mutation, can result in a protein with one or more changed amino acids.  In an enzyme, if the changed amino acids are in the active site or some other crucial region, the altered enzyme might have a novel activity or it might bind to a different substrate.  Under environmental conditions where the new function benefits the organism, natural selection would tend to favor the mutated form of the gene, causing it to persist in the population.  Researchers have used a lab procedure that mimics evolution in natural populations.  Using molecular techniques, the researchers introduced random mutations into E. coli genes and then tested the bacteria for their ability to break down a slightly different disaccharide.  The researchers found that six amino acids had changed in the enzyme altered in this experiment.  Two of these changed amino acids were in the active site, two were nearby, and two were on the surface of the protein.

8.5 Regulation of enzyme activity helps control metabolism. Metabolic control often depends on allosteric regulation.  Many molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors.  In allosteric regulation, a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site.  This regulation may result in either inhibition or stimulation of an enzyme’s activity.  Most allosterically regulated enzymes are constructed of two or more polypeptide chains.  The complex oscillates between two shapes, one catalytically active and the other inactive.  In the simplest case of allosteric regulation, an activating or inhibiting regulatory molecule binds to a regulatory site (sometimes called an allosteric site), often located where subunits join.  The binding of an activator stabilizes the conformation that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme.  The subunits of an allosteric enzyme fit together in such a way that a shape change in one subunit is transmitted to all others.  Through this interaction of subunits, a single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits. Allosteric activators and inhibitors

 As the chemical conditions in the cell shift, the pattern of allosteric regulation may shift as well.  By binding to key enzymes, the reactants and products of ATP hydrolysis may play a major role in balancing the flow of traffic between anabolic and catabolic pathways.

 For example, ATP binds to several catabolic enzymes allosterically, inhibiting their activity by lowering their affinity for substrate.  ADP functions as an activator of the same enzymes.  ATP and ADP also affect key enzymes in anabolic pathways.  In this way, allosteric enzymes control the rates of key reactions in metabolic pathways.  In enzymes with multiple catalytic subunits, binding by a substrate molecule to one active site in a multisubunit enzyme triggers a shape change in all the subunits.  This mechanism, called cooperativity, amplifies the response of enzymes to substrates, priming the enzyme to accept additional substrates.  Cooperativity is considered to be ―allosteric‖ regulation because binding of the substrate to one active site affects catalysis in a different active site. Cooperativity – another type of allosteric activation

 The vertebrate oxygen-transport protein hemoglobin is a classic example of cooperativity.  Hemoglobin is made up of four subunits, each with an oxygen-binding site.  The binding of an oxygen molecule to each binding site increases the affinity for oxygen of the remaining binding sites.  Under conditions of low oxygen, as in oxygen-deprived tissues, hemoglobin is less likely to bind oxygen and releases it where it is needed.  When oxygen is at higher levels, as in the lungs or gills, the protein has a greater affinity for oxygen as more binding sites are filled.  Although allosteric regulation is probably widespread, relatively few of the many known metabolic enzymes are known to be regulated in this way.  Allosteric regulatory molecules tend to bind the enzyme at low affinity and are thus hard to isolate.  Pharmaceutical companies are turning their attention to allosteric regulators, which exhibit higher specificity for particular enzymes than do inhibitors that bind to the active site.  A common method of metabolic control is feedback inhibition.  An early step in a metabolic pathway is switched off by inhibitory binding of the pathway’s final product to an enzyme acting early in the pathway.  Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.

Feedback inhibition in isoleucine synthesis

The localization of enzymes within a cell helps order metabolism.  The cell is compartmentalized: The organization of cellular structures helps bring order to metabolic pathways.  A team of enzymes for several steps of a metabolic pathway may be assembled as a multienzyme complex.  The product from the first reaction becomes the substrate for an adjacent enzyme in the complex until the final product is released.  Some enzymes and enzyme complexes have fixed locations within the cells as structural components of particular membranes.  Others are confined within membrane-enclosed eukaryotic organelles.  Metabolism, the intersecting set of chemical pathways characteristic of life, is a choreographed interplay of thousands of different kinds of cellular molecules.