Chapter One: The Chemistry of Life
Living organisms display amazing diversity, ranging from the simplest bacteria to blue whales, but all living organisms share basic unifying principles starting with the chemistry of life. For example, water is essential to all forms of life, no matter how simple or complex. A second principle is that all living organisms, and the molecules and reactions they are composed of, must obey the same physical laws of chemistry and energy that rule the rest of the universe.
All life shares common biological molecules including carbohydrates, lipids, proteins, and nucleic acids. Organisms from fungi to man even share many reactions and metabolic pathways. These basic features of all life will play a role in the more complex life activities of cells, organs, organisms, and ecosystems presented later.
At a molecular level the human cell shares a great deal in common with the single-cell yeasts that make bread, a fact that may not be immediately evident to the baker. Simple organisms like yeasts, worms, and fruit flies have proven invaluable to biologists in discerning the complexities of human biology since there are so many features that they share despite their differences. These common traits contribute to the interdependence of all living organisms on earth, another important trait common to all life, including man.
1.1 The Properties of Water
Water is essential to all life on Earth. Water covers a majority of the surface of the earth and is the site of some of the key ecosystems of the earth. Each cell contains water that bathes the reactions of life and is indispensable to all life. The presence of liquid water on Earth is one of the features of the planet that probably allowed life to originate and persist. It is the physical properties of water that allow it to play this key role for life. The properties of water that make it ideally suited to play this unique role are:
1. Water molecules are polar.
2. Water expands when it freezes.
3. Water absorbs a great deal of heat when it evaporates.
4. Water absorbs a large amount of heat when it is heated.
5. Water is cohesive and has a high surface tension.
6. Water is an excellent solvent for a large variety of molecules.
7. Water dissociates to form protons and hydroxyls in solution.
Water molecules are polar.
Water molecules have one atom of oxygen with two atoms of hydrogen at an angle from each other. Each water molecule as a whole lacks a net charge, but within each molecule the oxygen atom pulls electrons toward itself more than the hydrogens, causing the oxygen to have a partial negative charge and the hydrogens to have a partial positive charge (see figure). This unequal distribution of charges is what makes water a polar substance.
The polarity of water allows water molecules to readily form hydrogen bonds with each other. A hydrogen bond is formed when a hydrogen atom with a partial positive charge interacts with a negatively charged atom such as oxygen in another molecule. The polarity of a water molecule allows it to form hydrogen bonds with other polar molecules as well, such as sugars or proteins, allowing water to dissolve these substances. The polar nature of water molecules is involved in most of the exceptional properties of water.
Water expands when it freezes.
One of the consequences of the polarity of water is that water molecules interact with each other in a network of hydrogen bonds. In liquid water, these bonds form and break very rapidly as the individual water molecules move. When water freezes, the individual water molecules stop moving and the hydrogen bonds between molecules are frozen in place in a rigid crystalline structure. The positions of the water molecules are further apart in frozen water than in liquid water, leading to one of the unusual properties of water. In most substances, the solid occupies less space than the liquid as molecules fall into the crystalline lattice. Since solid water occupies more space than liquid water, water expands as it freezes and ice is less dense than liquid water. This property of water affects life on earth. When the temperature of the environment falls below the freezing point for water, a lake or ocean will freeze on the surface, with ice floating on top of the denser liquid water beneath. The ice on top insulates the water beneath it, and slows further freezing, allowing life to continue beneath the surface ice. If, like most substances, water became denser as it froze, then a lake or ocean would freeze from the bottom up and would freeze solid, fish, plankton and all. Freezing of lakes and oceans would be far more extensive and destructive to life in this scenario and it is possible that if ice were denser than liquid water, a past period of glaciation would have frozen the oceans solid, perhaps forever.
Water absorbs a great deal of heat when it evaporates.
Water molecules in liquid water interact with each other through a large number of hydrogen bonds. When water molecules are converted into a gas in the process called evaporation, the water molecules are separated from each other in space and no longer have these hydrogen bonds. When water is heated on a stove, the molecules have more kinetic energy and are able to break the hydrogen bonds more readily. Breaking the hydrogen bonds to cause evaporation takes a large amount of energy called the molar heat of evaporation.
The heat of evaporation is used by terrestrial organisms as a cooling mechanism. Since heat energy is required for evaporation, evaporating water will absorb heat (see figure). Water on the skin when it evaporates on a hot day will draw heat from the skin. The sweating or panting of mammals on a hot day uses the absorption of heat by evaporating water to draw heat out of the body and make it possible to maintain a cooler interior temperature than the external environment. In the absence of this, the body temperature would equilibrate with the exterior temperature on a hot day, causing harm or even death.
Water absorbs a large amount of heat when it is heated.
The temperature of a liquid is a measure of the kinetic energy of its molecules. The quicker molecules move, the greater the temperature. When heat energy is added to water, a great deal of the heat goes to breaking hydrogen bonds between molecules and not directly to making the molecules move faster. As a result, water can absorb a large amount of heat energy while its temperature changes little. If this were not the case, it would be much more difficult for the body to maintain a constant internal temperature. It also means that the temperature of aquatic environments does not fluctuate dramatically or rapidly. Fish do not need to adapt to sudden temperature changes the same way that a terrestrial mammal does. In fact, the oceans of the earth have a strong moderating influence on the climate of the planet, absorbing and redistributing heat around the globe and moderating the larger changes in temperature found on land. The role of the oceans in absorbing heat is likely to play an important role in the effects of global warming on the world's weather.
Water is cohesive and has a high surface tension.
In solution, water molecules have many hydrogen bonds with each other, and therefore stick readily to each other. The hydrogen bonds make water molecules near the surface stick to each other, pulling inward causing a force called surface tension. Surface tension causes water to pull together into round droplets on wax paper rather than spreading out flat and allows insects like water striders to float on the surface of water instead of sinking. Surface tension plays a role at any interface between air and liquid, such as in the lungs. Detergents tend to break up surface tension. Detergents play an essential role in the human lungs where they are secreted, and a harmful role in the environment when dumped as pollutants in the environment. The cohesiveness between water molecules is also what draws water up from roots into trees in an unbroken column.
Water is an excellent solvent for a large variety of molecules.
The polar nature of water makes it an excellent solvent for a wide variety of polar and charged substances, including salts, sugars, amino acids, and other molecules essential to life. Water hydrogen bonds with these substances in the same manner it does to itself, drawing these substances into the water, surrounded by a shell of interacting water molecules. Polar substances that water interacts with are called hydrophilic (water loving). The ability of water to dissolve substances is essential to life.
Water does not dissolve nonpolar molecules well. Hydrocarbons such as benzene or long-chain alkyl groups do not have any polar groups that water can hydrogen bond with and so are repelled from water and will not mix with it. These molecules are called hydrophobic (water hating). The repulsion of hydrophobic groups from water causes hydrophobic groups to draw together to present the smallest possible surface to water. An example of this occurs when oil is stirred with water in salad dressing -- the hydrophobic oil separates, unable to dissolve or mix with the water. This repulsion is what causes membranes to form spontaneously from lipids mixed with water, allowing one region of the cell to be separated from another by the lipid bilayer membrane. Hydrophobic interactions also cause proteins to fold with hydrophobic regions on the inside of the protein, hidden from water.
Water dissociates to form protons and hydroxyls in solution.
The aqueous portion of a cell contains a large variety of solutes, including salt ions, sugars and macromolecules such as nucleic acids. Some of the most important solutes in water are acids and bases. At a small but predictable frequency, water molecules in solution will break down into a hydrogen ion (H+) and a hydroxide (OH-). The hydrogen ion is not really a free proton in solution, as it is often referred to, but complexes with another water molecule to make a hydronium ion: H3O+. For the sake of simplicity though it will be referred to as the H+ ion. The concentration of H+ ions is the acidity of a solution and is given by a term called pH, the negative log of the concentration of H+ ions.
pH = -log[H+]
A concentration of 107M H+ ions translates into a pH of 7, for example. At a pH of 7, the concentration of H+ ions is equal to the concentration of hydroxide ions and the pH is said to be neutral, neither acidic or basic. Pure water has a pH of seven, with equal concentrations of H+ ions and hydroxide ions. The inside of the body and the cytoplasm of the cell have a pH of 7.4, close to neutral pH. At acidic pHs, in which the pH is lower than 7, the concentration of H+ ions is greater than 107M, and the concentration of hydroxide ions is lower.
If a substance donates H+ ions in water, it is called an acid, and if it accepts H+ ions in water, it is called a base. A base will decrease the H+ ion concentration in water, increase the hydroxide ion concentration and increase the pH. Depending on how strongly a molecule donates or accepts H+ ions, it will be called a weak acid or a strong acid. HCl ions completely dissociate in water for example, making HCl a strong acid. If one mole of HCl is placed in water, at equilibrium virtually all of it will dissociate to create one mole of H+ ions, as well as one mole of Cl- ions. A weak acid has more affinity for the H+ ions and dissociates more weakly in water, leaving less than a mole of H+ ions for every mole of acid added to water.
A measure of how strong an acid binds protons (H+ ions) is the pKa of an acid. The pKa is the negative log of the equilibrium constant for the dissociation of an acid. For example, for acetic acid, the dissociation of the acid is given by the equation:
HA <-> H+ + A-
For this equation, the equilibrium constant is Ka, where
Ka = [H+][A-]/[HA]
The smaller the value of pKa, the stronger the acid.
Some materials called buffers have properties that allow them to act as either an acid or a base, minimizing changes in pH. Biological molecules and reactions can be quite sensitive to changes in pH, making buffers important for life. A change in the pH of blood from 7.4 to 7 can be enough of a change to cause a coma in humans. In the absence of a buffer, the addition of a very small amount of acid, 1 X 10-6 micrometer acid, will cause a large change in pH, a whole pH unit, while with sufficient buffer present, the hydrogen ions will be neutralized and the change in pH will be negligible.
A common laboratory procedure is to add acid (or base) to a solution, note the volume of acid added, and measure the change in pH that occurs. The resulting plot from this experiment is termed a titration curve (see figure). When a buffer is present in the solution being titrated, the pH changes very rapidly until the pH nears the pKa of the buffering material. For example, in the figure shown, a base is added to the solution, so that the pH is basic. As acid is added to the base, the pH changes rapidly at first, with most + hydrogen ions remaining in solution. When the concentration of hydrogen ions in solution nears the pKa for the buffer, the hydrogen ions start to bind to the buffer, driving it into the acid form. As the buffer binds the hydrogen ions, the pH changes little. When the buffer is fully protonated, additional acid causes a large change in pH. When the pH equals the pKa for the buffer, half of the buffer is protonated and the other half is not.
There are many different buffers in the body, but the most important buffer in blood in humans is carbonic acid. Carbon dioxide dissolved in water can react with water to form carbonic acid. Carbonic acid can dissociate to release H+ ions and form bicarbonate ions in a reversible reaction. If hydrogen ions are added to blood, some of them will combine with the bicarbonate ion to reform carbonic acid. The body actively controls the pH of the blood to ensure the maintenance of the pH in the range fit for life. One means to control pH is by changing the rate of breathing to alter the rate of carbon dioxide removal from the body.
1.2 Organic Molecules of Life
All living organisms use the same basic molecules to form the structures and perform the activities of life. The primary types of biological molecules are carbohydrates, lipids, proteins, and nucleic acids. All of these molecules are organic, meaning that they are based on carbon skeletons.
Carbon is extremely flexible in its chemistry, with four valence electrons that can form covalent bonds with many other molecules. The simplest organic molecules are hydrocarbons, containing chains or rings of carbons with hydrogens attached. Carbon molecules are reactive enough to be useful, since inert molecules are of little use to perform reactions that will support life, but carbon-based biochemistries are also stable enough that biological molecules do not rapidly degrade. Methane, ethane and butane are examples of hydrocarbons with 1, 2 or 3 carbon atoms. Hydrocarbons are very nonpolar, and hydrophobic as a result, repelling water.
While all biological molecules are organic and based on carbon backbones, functional groups containing other atoms are often responsible for the unique form and function of each type of biological molecule. Functional groups are attached to carbon skeletons and give compounds their functionality. These groups are commonly involved in chemical reactions. Examples of important functional groups found in biological molecules include the following:
Hydroxyl (OH). Hydroxyl groups are contained in polar compounds, such as ethanol or glucose, making them more soluble in water. Hydroxyl groups are commonly involved in hydrogen bonds.
Carbonyl (C=O). Carbonyl groups are polar groups with a double-bond between C and O. Carbonyl groups are contained in aldehydes and ketones, including formaldehyde and chain-form monosaccharides.
Carboxyl (COOH). Carboxylic groups are polar groups contained in carboxylic acids. They donate their H+ ions in solution to dissociate as acids such as acetic acid (vinegar), producing a negative charge (COO-). Fatty acids and amino acids have carboxylic acid groups.
Amino (NH2). Amines have a polar nature and depending on the pH and the pKa of the amine may be charged. Primary amines such as those in amino acids can often act as bases to accept protons to have a positive charge (NH3+) at a physiological pH. Secondary amines are also found in many biological molecules.
Sulfhydryl (SH). Sulfhydryl groups play a specific role in proteins. The amino acid cysteine has a sulfhydryl functional group that can form a disulfide bond with another cysteine to stabilize protein structure. Sulfhydryl-containing compounds such as b-mercaptoethanol are also sometimes used as reducing agents.
Phosphates (PO42-). Found in organic phosphates like glycerol phosphate, these groups store energy that can be passed from one molecule to another by the transfer of a phosphate group. Nucleic acids and ATP contain phosphate.
Biological Macromolecules
There are four main types of biological macromolecules: carbohydrates, lipids, nucleic acids, and proteins. Carbohydrates, lipids, and proteins will be discussed in this section, but the structure of nucleic acids will primarily be presented in a later chapter. Carbohydrates, proteins and nucleic acids are all polymers, composed of subunits that are covalently joined together into long chains. Polymers allow the subunits to be joined in specific sequences along the chain in proteins and nucleic acids. Different sequences of subunits allows proteins to assume a multitude of forms and functions and allow nucleic acids to contain and transmit information.
Carbohydrates (Simple Sugars and Polysaccharides).
Monosaccharides are simple sugars that contain carbon, hydrogen, and oxygen, and have the general formula (CH2O)n where n indicates the number of carbons. The most ubiquitous monosaccharide is the sugar glucose (see figure), found in all living cells as an energy source. Glucose has six carbons, making it a hexose with the molecular formula C6H12O6. In water, the hydroxyl on the last carbon reacts with the aldehyde in glucose to make a cyclic molecule. At equilibrium in water, most glucose is found in ring form. Since the hydroxyl can attack the aldehyde from either the top or the bottom, there are two different ring forms of glucose, a-glucose and b-glucose. The different ring forms of a sugar are called anomers.
There are other common monosaccharides in addition to glucose. Fructose is also a hexose, with six carbons, and has the same molecular formula as glucose, C6H12O6>, but has a different structure, making it a structural isomer of glucose (see figure). Fructose is commonly found in fruit. Since fructose has a ketone group rather than an aldehyde, ring formation results in a five-membered ring instead of a ring with six members. Three carbon sugars such as glyceraldhyde are key metabolic intermediates when glucose is burned for energy, and the five-carbon sugars ribose and deoxyribose are key components of nucleic acids.
Monosaccharides are all chiral molecules, with complex stereochemistry. In the straight chain drawings of the sugars above, the last carbon (drawn at the bottom, farthest from the carbonyl-carbon) describes the stereochemistry of a sugar. In the drawings of straight chain version of these sugars, if the hydroxyl on the last carbon is to the right, the sugar is the D-stereoisomer. Almost all natural sugars are the D-form, and only D-forms are usually metabolized. Glucose is normally found as D-glucose stereoisomer and the enzymes that catalyze reactions involving glucose will recognize only the D-form, providing an important example of the specificity of enzymes in catalyzing reactions.
Disaccharides contain two monosaccharides joined by a glycosidic bond. Common disaccharides include sucrose, table sugar, and lactose, from milk. Sucrose (see figure) is composed of a glucose unit joined to a fructose unit, with the removal of a water molecule during the synthesis. The orientation of the glycosidic linkage can be either alpha or beta, changing the orientation of the two monosaccharides to each other.
Polysaccharides such as starch, cellulose, and glycogen are chains of repeating monosaccharides of a particular type, usually glucose, joined one to another by glycosidic bonds. Glucose is a commonly used source of energy for both plants and animals, and it is highly soluble, but takes up a lot of space, making it inefficient for storage of energy. Plants such as potatoes store glucose as starch, a polysaccharide containing large numbers of glucose monomers joined together. Glycogen is the storage form of glucose found in animals, mostly the liver and skeletal muscle in humans, and also consists of polymerized glucose as a branched polymer, rather than simply a straight chain linear structure (see figure).
Specific enzymes are responsible for the storage of glucose in these forms and the release of glucose from these forms when energy is needed. For example, when glucose is needed, liver enzymes will break down glycogen and release the glucose into the blood. After a meal, however, a different set of liver enzymes will respond to hormonal control by synthesizing glycogen for storage until the energy is needed later on, between meals or during exercise.
Another function of polysaccharides is as a structural component. An abundant biopolymer is the structural polysaccharide cellulose, found in the cell walls of plants. Cellulose fibers are very strong, providing strength to trees and other plants. Cellulose is also composed of glucose, like starch and glycogen, but with beta-1,4 glycosidic bonds unlike the alpha-1,4 linkages in glycogen. This difference not only makes cellulose strong, but also makes it indigestible to humans since humans do not make an enzyme that can digest the beta-1,4 glycosidic bonds in cellulose. Chitin, found in the exoskeletons of arthropods and crustaceans, is another structural polysaccharide that is very similar to cellulose.
Lipids (Fats and Oils)
The next major class of biological molecules is the lipids. Like sugars, lipids are also composed of carbon, hydrogen, and oxygen, but their hydrogen-to-oxygen ratio is much greater than carbohydrates. There are several different types of lipids that are very different structurally, but they are all very hydrophobic and do not dissolve well in water. The high degree of hydrophobicity of lipids is caused by the large number of nonpolar bonds they contain, primarily C-H and C-C bonds. The hydrophobic portion of lipids tend to group together to stay away from water, such as when oil is mixed with water.
One of the roles of lipids is as an energy source. Fat tissue in animals (known as adipose tissue) is composed largely of lipids called tryglycerides. Triglycerides are a much more efficient form of energy storage than polysaccharides. Triglycerides have more energy that can be burned for metabolism per gram of weight since they have more high-energy (reduced) C-C and C-H bonds than sugars, and they exclude water so they take up less space than glycogen to store. Most animals store only a temporary small amount of energy as glucose or glycogen, and most of their energy as fats. Storage of energy in triglycerides occurs in animals while plants use starch.
The structure of triglycerides includes two components: a glycerol chain and three fatty acid molecules joined to the glycerol. Fatty acids are a component in many lipids, including triglycerides (see figure). Fatty acids each have a long carbon chain, with a carboxylic acid group at one end. In triglycerides, fatty acids form ester linkages with the glycerol and are no longer charged. Since triglycerides have no charge they are sometimes called neutral fats. Fatty acids differ in their length, how many carbons long the carbon chain is, and in the number of double bonds contained in the carbon/chain. Fatty acids that lack double bonds are saturated and fatty acids with one or more double bonds are called unsaturated. The charged carboxylate in fatty acids is hydrophilic while the carbon tail is very hydrophobic. This dual nature of fatty acids tends to make the tails cluster together, with the heads sticking out when they are mixed with water. When mixed with a hydrophobic greasy substance, fatty acids will surround it with their tails and bring it into solution with their hydrophilic heads oriented outward. In this way, fatty acids can act as detergents. Soap was commonly derived in the past from animal fat, by hydrolyzing triglycerides to release fatty acids that could be used as soap.
Lipids also play an important role in membranes. The predominant class of lipid in membranes is phospholipids, with a glycerol and two fatty acids, similar to triglycerides, but with a phosphate group and an additional polar group joined to the glycerol (see figure). The phosphate and the additional polar group make the glycerol end of phospholipids very polar, referred to sometimes as the polar head compared to the nonpolar fatty acid tails. The fatty acid chains in phospholipids are very hydrophobic while the phosphate-alcohol end is very hydrophilic. As a result, phospholipids are like detergents and when mixed with water will spontaneously form structures with the fatty acids gathered together to keep out water and the phosphate group pointing out toward water. This is the basic structure of the lipid bilayer formed by phospholipids in cell membranes.
Waxes are esters of fatty acids and alcohols. Waxes form protective coatings to repel water on skin, fur, leaves of higher plants, and the exoskeleton of many insects. Bees use waxes to form their hive. Waxes are solid but malleable, making them useful to humans.
Steroids have three fused cyclohexane rings and one fused cyclopentane ring. Examples of this lipid derivative include cholesterol (see figure), the sex hormones estrogen and testosterone, and corticosteroids. Cholesterol is present in the membranes of eukaryotes, and modifies the fluidity of membranes.
Proteins
Proteins make up 50 percent of the dry weight of a cell and are vital to almost everything a cell does. Proteins are formed from building blocks called amino acids, of which there are 20 common types. Amino acids each contain an amino group and a carboxyl group, and each amino acid has a unique R group that is distinct in each of the 20 amino acids (see figure). There are several classes of amino acids, including some that are very hydrophobic (phenylalanine, isoleucine, leucine, alanine, tryptophan), some that are polar with a hydroxyl group (serine, threonine, tyrosine), some that have polar amide side chains (glutamine, asparagine), some charged basic amines (lysine, arginine), and some charged carboxylic acids (glutamate, aspartate). Proline is a unique amino acid since it is cyclic, and affects the structure of proteins containing it. The sulfhydryl of cysteine also plays an important role in protein structure. The chemical nature of the amino acid side groups in a protein determines the structure and function of the protein.
The ® could be a hydrogen atom, a carbon, or a chain of carbons or other groups.
Proteins are formed by the covalent linking of amino acids. When two amino acids are joined, they form a peptide bond (see figure) between the carboxyl group of one amino acid and the amino group of the next. A peptide bond is formed with the input of energy and the loss of water; this process is called dehydration synthesis. Amino acids are joined together by peptide bonds during translation (see chapter 5, Molecular Genetics). The biosynthesis of two amino acids together forms a dipeptide, in which each amino acid is called a residue. Many amino acids joined together form a polypeptide. With twenty different possible amino acids at each position in a polypeptide, there is an enormous number of possible proteins that could be made, far more than are formed in nature. Even for a relatively small polypeptide with only four amino acid residues, there are 20 X 20 X 20 X 20 = 160,000 possible proteins that could be formed.
The primary structure of a protein is the linear sequence of amino acids.
The sequence of amino acids and their R groups in a protein determine how the protein folds its polymer chain into a 3D shape and what the protein does. If a protein is made with the wrong amino acids or folds incorrectly, it cannot do its job properly. Globular proteins are typically functional proteins, such as carriers or enzymes. Long fibrous proteins are structural proteins; one example is collagen.
Functions
Various types of proteins and their functions are listed in the table below.
Type of Protein: Function: Examples
Hormonal: Chemical messengers: Insulin, glucagon
Transport: Transport of other: Hemoglobin, carrier substances, proteins
Structural: Physical support: Collagen
Contractile: Movement: Actin, myosin
Antibodies: Immune defense: Immunoglobulins, interferons
Enzymes: Biological catalysts: Amylase, lipase, ATPase
Levels of Protein Structure
To do their job, proteins must have a specific shape or structure. An enzyme that has the wrong shape will not catalyze its reaction, for example. If an enzyme is heated, subjected to changes in pH or other environmental changes, it may lose its structure as well as its function. Such a protein is denatured. The denaturation process is reversible in some cases, but not always. An example of protein denaturation can be observed when lemon juice is mixed with milk. The acid in the lemon juice will cause the milk proteins to unfold and denature, exposing hydrophobic amino acids from their interior that are normally hidden from water. When exposed, the hydrophobic regions of one denatured protein can interact with hydrophobic regions from other denatured proteins, causing a visible mass of tangled denatured proteins; the milk looks curdled.
Protein structure has four levels: primary, secondary, tertiary, and quaternary.
Primary structure is the sequence of amino acids joined by peptide bonds in the linear polypeptide chain. When proteins are synthesized, the first amino acid is left with the amino end free, not in a peptide bond. The last amino acid in a protein has a free carboxyl group. When the amino acid sequence of a protein is written on paper it is written from the free amino terminus on the left to the carboxyl terminus on the right.
The secondary level of protein structure involves coils or folds of the local polypeptide chain in patterns that contribute to the overall conformation of the protein. Secondary structure is caused by hydrogen bonds at regular intervals along the local region of the polypeptide backbone; alpha-helices and beta-pleated sheets are the most common types of secondary structure. The structure of proline does not allow it to fit within the normal alpha-helix structure, making it a helix-breaker. The small size of glycine, with only a hydrogen side chain, makes it fit well within tight turns in secondary structure, such as between stretches of beta-sheet.
The tertiary level of structure can be characterized as folding due to bonding between side chains of the various amino acids. Tertiary structure can be reinforced by strong covalent bonds, called disulfide briþGes, between cysteines in different parts of the primary structure of the protein. A protein with disulfide briþGes in its structure will be more resistant to denaturation. Tertiary structure can also be modular, with two or more globular regions called domains that fold independently which are connected by relatively flexible regions of the polypeptide chain. Secondary structure involves bonds between nearby amino acids in the linear sequence. Tertiary structure can bring amino acids that are far apart in the linear polymer very near each other in the 3D protein structure. Amino acids with hydrophobic side chains tend to fold in the interior of proteins, away from water, while charged or polar amino acids fold near the surface.
The final quaternary level of protein structure of the protein results from the relationship between different polypeptides, called subunits. For example, some proteins, especially cell surface receptors, are made up of two proteins that interact to produce large protein complexes. Such interactions between subunits can be involved in the regulation of the process in which the protein is involved.
Proteins fold spontaneously as they are synthesized to form the lowest energy folded structure. Sometimes proteins called chaperonins are required for a protein to fold correctly. When heated, a protein will often lose activity, then refold as it is cooled and regain activity. The process of protein folding probably proceeds from one level of organization to the next, starting with the linear primary protein sequence, followed by interactions between nearby amino acids to form secondary structure, then folding of the alpha-helices and beta-sheets to form tertiary structure. Finally, subunits come together to form tertiary structure and the complete protein.
Scientists often wish to study the function of individual proteins, a difficult task when proteins are present in a dense mixture of other proteins in the cell. To study the function of proteins, biochemists in the laboratory will purify proteins from the cell, isolating a given protein for study. Different proteins have different physical properties, including size, shape, and charge, that the biochemist can use to separate proteins. If the protein of interest is an enzyme, the location of the enzyme during purification can be determined by following the activity of the enzyme in various fractions of proteins produced during the purification.
A means of examining the proteins in a mixture iting with the linear primary protein sequence, followed by interactions between nearby amino acids to form secondary structure, then folding of the alpha-helices and beta-sheets to form tertiary structure. Finally, subunits come together to form tertiary structure and the complete protein.
Scientists often wish to study the function of individual proteins, a difficult task when proteins are present in a dense mixture of other proteins in the cell. To study the function of proteins, biochemists in the laboratory will purify proteins from the cell, isolating a given protein for study. Different proteins have different physical properties, including size, shape, and charge, that the biochemist can use to separate proteins. If the protein of interest is an enzyme, the location of the enzyme during purification can be determined by following the activity of the enzyme in various fractions of proteins produced during the purification.
A means of examining the proteins in a mixture is SDS-polyacrylamide gel electrophoresis. When placed in an electric field, a charged molecule will move according to its charge. SDS is a charged detergent that denatures proteins, giving them all the same denatured globular shape, and binds to them, giving them a charge in addition to other charges. Gel electrophoresis involves the migration of the proteins treated with SDS in an electric field through a matrix of cross-linked acrylamide polymers. If the proteins are placed in the gel with SDS and a charge is then applied to the gel, the proteins will separate in the gel according to their molecular weight. Small proteins move through the gel more quickly since they can fit more easily through the holes in the porous gel, while large proteins move more slowly. After the proteins have moved through the gel, their position can be visualized by staining the gel with a dye that binds to proteins and not to the gel (see figure). The molecular weight of proteins in the sample analyzed can be determined by comparison to standard proteins in the same gel that have a known molecular weight.
SDS combines with proteins, giving them a net negative charge. The negatively charged SDS-protein complexes travel through the gel toward the positive anode.
Nucleic Acids
Nucleic acids are the information molecules of the cell. DNA is a polymer that carries genetic information from one generation to another and encodes the information for producing proteins. RNA is the nucleic acid that helps to take the protein-coding information in DNA and produce the proteins of the cell. DNA and RNA are both polymers composed of nucleotide building blocks. Each nucleotide consists of a nitrogenous base, a five-carbon sugar (either ribose or deoxyribose) and phosphate groups. There are four types of nitrogenous bases in both DNA and RNA. The nitrogenous bases in DNA are adenine, thymine, cytosine and guanine. RNA differs in having uracil instead of thymine. The bases of RNA and DNA possess the information content of the nucleic acids, since it is these that vary from one subunit in the polymer to the next. The backbone of DNA and RNA is composed of the alternating pentose sugar and phosphate groups. The structure and function of DNA and RNA will be discussed in detail in chapter 5, Molecular Genetics.
Some nucleotides play roles other than as building blocks for nucleic acids. ATP, for example, is a nucleotide that also acts as a key energy currency in all cells (see figure). Other nucleotides, such as NADH, NADPH and FADH2, are coenzymes, playing a key role in enzymatic reactions and energy transfer.
1.3 Free Energy Changes
Energy is continually flowing in the universe in many different forms, including heat, vibrational energy, chemical energy, kinetic energy, potential energy, and light. The reactions of life involve the flow of energy within organisms and the environment, using the energy to drive the activities of life. Whether the energy is used to drive formation of proteins or to move a muscle, it must still follow rules of thermodynamics that govern all energy in the universe. Thermodynamics is the study of the relationship between different forms of energy.
The laws of thermodynamics can be used to predict if a reaction such as a metabolic pathway in a cell will occur or not. If the products have less free energy (þG) than the reactants, then the reaction has a negative þG and will occur spontaneously, without putting additional energy into the reaction. The energy in a reaction is like water flowing down a river -- water will only flow downhill on its own, with a release of energy (see figure). Thermodynamics does not describe the rate of reactions however -- this is left to the study of kinetics. For example, thermodynamics predicts that a piece of sugar in the presence of oxygen will be oxidized, releasing energy, but it does not state the rate or the route by which this will take place. In a room without a catalyst, the reaction will take place slowly, but with either a flame or a cell to release the energy, the reaction will be rapid. Thermodynamics states where things start and end up while kinetics states the path used to get from the start to the end.
The first law of thermodynamics is the conservation of energy. This law states that energy is never lost from the universe, or any closed system, but that it is simply converted from one form into another. For life, some energy is useful, such as the energy found in certain high-energy chemical bonds like those in glucose. Other forms of energy such as heat energy are not useful since they cannot be captured to drive essential activities. Heat energy when it is produced is lost to the exterior system and is no longer useful to drive biological reactions. Biological reactions are never 100% efficient in the transfer of energy, so that some energy is lost to the environment as heat during the reaction. Every living organism generates heat as a result of the reactions of life. Organisms extract as much energy as they can, losing a percentage to the environment as heat, with the total amount of energy at the end unchanged but in different forms.
The second law of thermodynamics states that (since no reaction or any other process in the universe can ever be 100% efficient in the conversion of energy) systems move over time toward a more disordered state with less useful energy. Entropy is the term used to describe the disorder of a system. An example of entropy is that molecules in solution favor a less-ordered state. Having many molecules of solute in one location in a solution is an ordered state. According to entropy, molecules will spontaneously assume a less ordered state, and so diffusion occurs, with molecules dispersing into a less ordered randomly spaced solution. Entropy dictates that over time large complex molecules will become smaller, less complex molecules. In any closed system, the amount of energy will remain the same over time (although it will change form), but the entropy will increase.
Living organisms at first glance may appear to contradict the second law, since life perpetuates a high degree of complexity in the face of entropy. Living organisms derive energy from an outside source however -- the sun. Living organisms use the energy from the sun to maintain the complex ordered state of the molecules of life. Considering the broader system of the sun and earth along with living organisms, the second law is upheld.
Entropy is denoted by the symbol "S" in thermodynamic equations. Another thermodynamic measure is enthalpy, "H." Enthalpy is the total thermodynamic heat content of a system. Changes in entropy are denoted by "DS" and changes in enthalpy are denoted by "DH." If DS>0 in a chemical reaction, then the product of a reaction has more entropy than the starting materials. If DH < 0, then the products have less heat energy than the reactants, having lost it to the environment as an exothermic reaction. Both DS and DH play a role in calculating whether a chemical reaction will proceed or not, but neither of these factors alone can determine this.
A factor that can be used to predict the spontaneity of a reaction is called the Gibbs Free Energy, denoted by the symbol "G." þG is the change in free energy of a reaction between reactants and products. If þG < 0 for a reaction, the reaction is favorable and will proceed spontaneously. If þG = 0 for a reaction, it is at equilibrium, with the forward and backward reactions occurring at the same rate and no net change in the concentrations of reactants or products occurring.
The free energy change (þG) for a reaction can be calculated from the change in enthalpy (þH) and the change in entropy (þS) during the reaction. The relationship between these values is given by the following equation, in which T is the temperature:
þG = þH - TDS
A decrease in enthalpy, releasing heat from the reaction into the environment, makes the reaction more favorable. Increases in entropy or temperature also make þG more negative and indicate a more favorable reaction. A reaction with a negative þG can be used by an organism to do work. Reactions with þG < 0 are called exergonic and reactions with þG>0 are called endergonic. These terms should not be confused with endothermic and exothermic, which refer to the enthalpy of a reaction.
If þG<0, then a reaction will spontaneously move forward to form product until equilibrium is achieved. At equilibrium the forward and backward reactions occur at the same rate, and þG = 0. It is important to remember that the free energy change of a reaction predicts only whether the reaction will spontaneously move forward; it says nothing of the rate. In biology, almost all reactions require enzymes as catalysts to allow the reaction to move forward at an appreciable rate. All that an enzyme (or any catalyst) can do is to increase the rate of a reaction that is favorable. A biological reaction catalyzed by an enzyme must still have a negative þG for it to move forward and a reaction with a positive þG will not occur even if an enzyme is present.
1.4 Enzymes
The chemical reactions required for life may be thermodynamically spontaneous, with a þG<0, but still occur at an extremely slow rate if the reactants are simply mixed together without a catalyst. Thermodynamics says nothing of the rate at which a reaction will occur. Even if a reaction is determined by thermodynamics to be favorable, it can take thousands of years to reach equilibrium without a catalyst. A factor that governs the rate of reactions is the activation energy.
In a reaction proceeding from reactants to products, with products at a lower free energy level than the reactants, the reaction is thermodynamically favorable and will occur spontaneously. The path of the reaction determines how rapidly it will occur. To get from reactants to products generally requires the reactants to go through a transient high-energy reaction intermediate, and the formation of the intermediate is the rate-limiting step in the reaction. The intermediate is chemically unstable, thus very short-lived, and will rapidly either fall back to the original reactants or go forward to form the products. The chemical instability of the intermediate also accounts for its high-energy state. Since the reaction intermediate is at a higher energy level than the reactants, energy must be put into the reactants for them to form the intermediate. Increasing the kinetic energy of molecules in solution by adding heat increases their energy, supplying the activation energy to form the intermediate, and increasing the reaction rate. This is one reason why heating a reaction will often make it go faster.
Another way to make a reaction go faster is to use a catalyst. A catalyst is a substance that increases the rate of a chemical reaction but is not itself consumed or altered in the reaction. A catalyst decreases the activation energy for the reaction by making it easier for molecules to form the transient reaction intermediate. The biological catalysts used by organisms to speed reactions are called enzymes.
Enzymes are specialized proteins that act as biological catalysts (although a few examples of RNAs that act as catalysts are known as well), speeding the rate of reactions by many orders of magnitude. By bringing reactants together in the right orientation to form the reaction intermediate and by stabilizing the reaction intermediate, enzymes reduce the activation energy and make biological reactions occur rapidly (see figure). Since enzymes are not catalysts, they are not altered or consumed at the end of each reaction cycle, and one enzyme can catalyze the reaction of many molecules of reactant, termed substrate in enzyme-catalyzed reactions.
Enzymes bring reactants together in the correct orientation in a region of the enzyme called the active site. The active site is generally a cleft or pocket in the enzyme structure that binds substrate in the correct orientation to catalyze the reaction. Specific amino acid residues in the enzyme's 3D structure fold together into precise locations in the active site to stabilize substrate binding, to interact chemically in the reaction process, or to stabilize the reaction intermediate. The interactions of substrate with the active site can be hydrophobic, ionic, and hydrogen bonds. The amino acids involved in catalysis at the active site are brought near each other in space in the tertiary structure of the folded enzyme, but are not necessarily near each other in the primary, linear structure of the enzyme. Since the active site requires specific residues in precise positions for the enzyme to catalyze its reaction, enzymes must fold correctly to catalyze a reaction (to have activity). Denaturation of an enzyme, which destroys the 3D structure of the enzyme, disrupts the active site structure along with the rest of the structure and eliminates enzyme activity.
An example of the importance of correct folding for enzyme activity is an experiment performed with the enzyme ribonuclease, which hydrolyzes RNA, breaking the RNA polymer into smaller pieces. The enzyme has 124 amino acids including 8 cysteines that form 4 disulfide bonds to stabilize the protein structure. Purified ribonuclease protein was subjected to several treatments, and then analyzed for enzyme activity. The treatments included reduction with b-mercaptoethanol (b-ME), or treatment with urea, a denaturing reagent that disrupts hydrogen bonds required for secondary and tertiary protein structure. The table below summarizes the findings of these experiments:
Step 1; Step 2; Observation
Condition 1: No reagents added; No reagents added; 100% activity
Condition 2: Urea and b-ME; Nothing removed; 0 % activity
Condition 3: Urea and b-ME; b-ME removed, then urea removed; 1% activity
Condition 4: Urea and b-ME; urea removed, then b-ME removed; 100% activity
What conclusions can be made based on these results? With urea and b-ME present, the secondary and tertiary structure of the enzyme are disrupted, the active site is not folded correctly, and the enzyme has lost all activity (Condition 2 compared to Condition 1). If the b-ME is removed first with urea still present, the enzyme regains only 1% of the original activity (Condition 3). In this condition, urea blocks correct protein folding during disulfide briþGe formation, and disulfide briþGes reform randomly. With 8 cysteines, the correct combination of disulfide bonds will form randomly about 1% of the time, correlating with the amount of active enzyme observed with condition. When the urea is removed, only those enzyme molecules that had randomly formed the correct disulfides are able to form the correct secondary and tertiary structure and regain enzyme activity. If the urea is removed first followed by the mercaptoethanol, however (Condition 4), then full enzyme activity is regained. In this circumstance, the enzyme will spontaneously form the correct secondary and tertiary structure when urea is removed. When b-ME is removed, the enzyme will be locked into the correct structure by the correct disulfides formed when the enzyme is folded correctly. This experiment demonstrates the importance of the correct enzyme folded structure for enzyme activity. It also demonstrates that the protein sequence alone is required for the protein to spontaneously fold into the active enzyme structure, since the enzyme correctly refolds after denaturation with no extra energy or information.
The three dimensional nature of the active site at which substrates bind leads to one of the key features of enzymatic catalysis -- the tremendous specificity of enzymes for a given reaction. The shape of the active site restricts the substrate that can bind, increasing the specificity of the reaction.
One model of substrate binding to the active site is termed the lock and key model, in which the substrate is like a key that binds in an active site with an exactly complimentary shape (the lock). It appears that a slightly more complicated model, the induced fit model, may more accurately represent enzyme function (see figure). In this model, the binding of substrate changes the structure of the enzyme and the active site. Changes in enzyme structure caused by substrate binding have been physically measured, supporting this model.
Enzymes do not alter the final energy of the reactants or products, and so do not change the equilibrium or change in free energy of the reaction, only the rate at which equilibrium is reached. In fact, enzymes will catalyze both the forward and backward reaction rates. In a model of enzyme action known as the Michaelis-Menten model, the activity of an enzyme is assumed to progress in several general steps. In the first step, the enzyme binds the substrate at the active site. This step is reversible, since the substrate can fall out of the active site in its original form. For enzymes with substrate bound to the active site, the other option is that the substrate is converted to the high energy reaction intermediate, from where it can go on to form product. Each step in the reaction model can be described by a rate constant.
Enzymes in this equation do not refer to enzyme molecules, but to the number of enzyme active sites, not exactly the same thing. As more substrate is added to a solution of enzyme, more of the active sites have substrate bound to them in ES (enzyme-substrate) complexes. The more ES complexes formed, the more product formed. When a high concentration of substrate is added, all of the active sites will have substrate bound and adding more substrate cannot increase the reaction rate any further, since the ES concentration is already maximal. This is another hallmark of enzyme catalyzed reactions -- they are saturable with increasing reactant (substrate) concentration. For an enzyme, once the active sites are full of substrate, adding more does not increase the rate further. For a non-enzymatic reaction, increasing the reactant concentration will continue to increase the rate since the formation of the reaction intermediate does not require a specific site and happens randomly in solution.
Based on the Michaelis-Menten model, an equation can be derived that describes the relationship of the reaction rate on the substrate concentration and the affinity of the enzyme for the substrate. This equation is called the Michaelis-Menten equation.
In this equation, Vmax is the maximal reaction rate that is achieved when 100% of the enzyme molecules in solution are in the ES form, occupied with substrate. Km is a measure of the affinity of the enzyme for the substrate. V is the reaction rate at a specific substrate concentration [S]. Practically speaking, Km is given in units of concentration and Km is the concentration of substrate requires to achieve 50% of the maximal possible reaction rate (1/2 Vmax).
Km and Vmax are often determined experimentally for an enzyme in experiments in which the concentration of enzyme is held constant while the substrate concentration is varied and the reaction rate measured. The reaction rate is measured by waiting a period of time, stopping the reaction, and then determining how much product has formed in a unit of time. When this is done, and the resulting data plotted with the substrate concentration on the x-axis and the measured reaction rate (V) is plotted on the y-axis, several of the features of en
