Metabolic reactions need activation energy to either build or break down molecules. Cells also use special proteins that aid metabolic reactions. These proteins, called enzymes, work by speeding up a chemical reaction. This chemical activity increases the reaction rate, or rate at which a reaction occurs, measured in terms of reactant used or product formed per unit time (while existing conditions remain unchanged). Some of the earliest studies on enzymes were performed in 1835 by Swedish chemist Jon Jakob Berzelius, who termed their chemical action “catalytic.”

Enzymes and the Catalytic Cycle

The acceleration of a chemical reaction by some substance, which itself undergoes no permanent chemical change, is called catalysis. The catalysts of metabolic reactions are enzymes, which are involved in almost all chemical reactions in living organisms. Without enzymes, metabolic reactions would proceed much too slowly to maintain normal cellular functions. Consider the hydrolysis of sucrose, an exothermic reaction. A solution of sucrose dissolved in water could sit for years without showing signs of hydrolysis. If the enzyme sucrase is added to the solution, the enzyme speeds up the reaction millions of times, so that all of the sucrose will be hydrolyzed in several seconds.
Enzymes speed up reactions by lowering the amount of activation energy needed. Thus, less energy is required for the reaction to begin. The action of an enzyme on an exothermic reaction is illustrated in Figure 2.4.
Cells carry out a large number of different biochemical reactions; many of these reactions require a specific enzyme in order to take place. Different sets of enzymes are responsible for catalyzing different chemical reactions. Oxidative
enzymes (oxidoreductases) work to catalyze oxidation-reduction reactions. Hydrolytic enzymes

(hydrolases) catalyze the addition of water in reactions and split molecules into simpler forms. These simpler molecules may be used to build other molecules or may be excreted from the cell. For example, the lysosomes of cells contain many hydrolytic enzymes. Tasks such as breaking down nucleotides, proteins, lipids, and phospholipids are each carried out by a specific hydrolytic enzyme. Other enzymes remove carbohydrate, sulfate, or phosphate groups from molecules.
Synthesis reactions that build structures such as proteins, nucleic acids, hormones, glycogen, and phospholipids all require the use of enzymes. The enzyme DNA polymerase, for example, is needed for DNA replication, which precedes mitosis. Each chemical reaction in cellular respiration requires a specific enzyme. Deaminases remove the amino
groups from amino acids so the remainder of the molecule can be used as an energy source. Enzymes also help to split long-chain fatty acids into smaller compounds, which are used as an energy source and broken down by the process of cellular respiration.
Blood clotting, the formation of angiotensin II to increase blood pressure, and the transport of carbon dioxide in the blood all require specific enzymes. Tables 2.1 and 2.2 show categories of enzyme specificity and modes of action.

A reactant in any given enzymatic reaction is called a substrate for that specific enzyme. Some enzymes catalyze one individual reaction; this is the case with peroxidase, an enzyme that decomposes hydrogen peroxide into water and
oxygen. Reactions within cells, however, are often part of a metabolic pathway (series of linked reactions), beginning with one substrate and ending with a product. Such metabolic pathways can involve many reactions, which often include other pathways. Each step of a metabolic pathway, or each constituent reaction of the pathway, needs its
own specific enzyme.

To understand how enzymes work, consider that the key to enzyme function is enzyme structure. Enzymes are globular proteins with depressions on their surfaces, as shown in Figure 2.5. These depressions are called active sites. Active sites are places where substrates fit and where catalysis occurs. Active sites are not static receptacles.
Substrates fit closely into active sites because enzymes can adjust their shapes slightly to accommodate the substrate. This process involves a subtle change in conformation, or three-dimensional shape, of the enzyme when the substrate binds to it. Multiple weak bonds between the enzyme and the substrate are involved in this process. The change in shape of the active site to accommodate the substrate is called induced fit. This process may bring specific amino acid functional groups on the enzyme into the proper orientation with the substrate to catalyze the reaction see Figure 2.5

The combination of the substrate and the enzyme itself forms a compound called an enzyme–substrate complex. Swedish chemist Svanté Arrhenius first hypothesized about the enzyme–substrate complex in 1888, proposing that
there must be a stage during catalysis when the enzyme and the substrate join together. Modern laboratory experiments have confirmed his hypothesis. In many cases, the enzyme–substrate complex is held together by such bonds as hydrogen bonds and weak ionic bonds. The polar and non-polar groups of the active site attract compatible groups on the substrate molecule.
These attractions effectively lock the substrate molecule in the active site. Once in the active site, the substrate is subject to necessary collisions, bond breaks, and bond formations that must take place to form the product molecule. This reaction can be anabolic or catabolic, depending upon the enzyme. Once the product molecule has been
formed, it is released from the enzyme–substrate complex. The enzyme is now able to accept another substrate, and begin the process anew. This cycle is known as the catalytic cycle. Figure 2.6 shows the catalytic cycle involving sucrose and the enzyme sucrase.
There are several methods by which enzymes reduce the activation energy needed to break the bonds in a substrate. In the enzyme–substrate complex, the substrate molecules experience

physical stress. The R-groups in the active site of an enzyme are able to stress the bonds of the substrate. There is bending and stretching of bonds that hold the molecule and the active site together. In this case, the activation energy is lowered because the bonds within the molecule have become weaker, reducing the amount of energy needed to break them.
Another way in which the active site of an enzyme may lower activation energy involves special amino acids that line the active site. These amino acids have reactive R-groups that can aid in the transfer of hydrogen ions to or from the substrate. For example, the active sites of hydrolytic enzymes, such as those within the lysosome, often provide
acidic and/or basic amino acid groups at precisely the correct orientations required for catalysis. The yeast enzyme, intertase (also known as betafructofuranosidase), is a hydrolytic enzyme that speeds up the breakdown of sucrose into the products glucose and fructose. Some other enzymes provide amino acid groups at their active sites that can accept electrons, while others are attracted to atomic nuclei of the substrate.
This process can form a temporary attraction with the substrate. In this state, the substrate is less stable and can more easily react to form the product. Some enzymes may facilitate the correct reaction by bringing two different substrates together in the appropriate orientation to each other.
An oxidative enzyme (such as cytochrome P450s) catalyzes the transfer of electrons from substrates to oxygen molecules. Substrates for these enzymes are often referred to as hydrogen donors because hydrogen ions along with electrons are taken from the substrate. Cytochrome P450s is most common in the endoplasmic reticulum of liver cells. In these cells, the enzyme helps to metabolize toxins, as well as fat-soluble vitamins such as A, D, and E.

Enzyme Activity

As you have learned, enzymes lower the activation energy required to start a chemical reaction. The activity of enzymes, however, can be influenced by environmental factors, such as pH and temperature.
The shape of an enzyme is determined by hydrogen bonds, which hold peptide chains in the enzyme in a specific orientation. As well, all enzymes contain segments that are hydrophobic. The hydrogen bonds in an enzyme and any hydrophobic interactions that parts of the enzyme may experience are easily affected by changes in temperature. Enzyme activity increases as temperature increases, but only up to a maximum point. If the temperature increases beyond a critical point, enzyme activity declines rapidly (see Figure 2.7). When this occurs the enzyme has been denatured. When an enzyme is denatured by excessive heat, its shape changes and it can no longer bind to its substrate.

Most human enzymes function best between 35°C and 40°C. Below this temperature range, enzymes are less flexible and therefore less able to provide an induced fit to substrates. Above this range, the bonds become weaker and less able to hold the peptide chains in the enzyme in the proper orientation. Some bacteria, however, can function at temperatures as high as 70°C. These bacteria live in and around hydrothermal vents, which are fissures in the Earth’s crust on the ocean floor that release hot water and gases. The bacteria are able to survive in these environments because the bonds between peptide chains in their enzymes are relatively strong and able to withstand the extreme temperatures. These enzymes are therefore called thermostable enzymes.
Thermostable enzymes could operate above the growth temperature for pathogens that otherwise can contaminate foods. Potential applications of this knowledge might include development of food products that could be processed at higher temperatures, and are more resistant to microbial contamination (such as E. coli). Thermostable enzymes may also be useful in drug synthesis.

Such enzymes may be able to catalyze reactions more effectively, affording higher productivity. They may also last longer and could possibly be re-used. In the next Thinking Lab, you will conduct research into the sources of enzymes in foods.

Each enzyme also works optimally (best) at a specific pH. Figure 2.8 shows the activity ranges for the enzymes pepsin and trypsin at different pH levels. At pH values where the enzymes work optimally, the enzymes have their normal
configurations. The bonds that hold peptides in position in the enzyme are sensitive to hydrogen ion concentrations. A change in pH can alter the ionization of these peptides and disrupt normal interactions. Under extreme conditions of pH, the enzyme will eventually denature. Most enzymes function best in the pH range of 6 to 8. Pepsin, which digests proteins in the human stomach, works best under very acidic conditions (pH of 2).
In the next investigation, you will design an experiment to study the effects of temperature and pH on enzyme activity.

Enzyme Inhibitors and Allosteric Regulation

In addition to the environmental factors of pH and temperature, various substances can inhibit the actions of enzymes. Inhibitors are chemicals that bind to specific enzymes. This results in a change in the shape of the enzyme that causes the enzyme to shut down its activity. In cells, enzyme inhibition is usually reversible; that is, the inhibitor is not
permanently bound to the enzyme. Inhibition of enzymes can also be irreversible. For example, hydrogen cyanide, a powerful toxin, is an inhibitor for the essential enzyme cytochrome c oxidase.
Toxins, such as hydrogen cyanide, typically bind (either covalently or non-covalently) so strongly with an enzyme that the enzyme cannot bind with its substrate. Some poisons that result in irreversible enzyme inhibition do not combine with the enzyme; instead, they destroy enzyme activity by chemically modifying critical amino acid R-groups.
Other toxins, such as venom from the Malayan it viper (Calloselasma rhodostoma) (shown in Figure 2.9 on the next page), are enzyme inhibitors that can help people overcome the effects of a stroke. Strokes are caused by blood clots in the brain, which can result in mental and physical debilitation. A substance called ANCROD, derived from this venom, contains enzyme inhibitors that prevent blood clots from forming. In 1999, pharmaceutical researchers found that more than 40% of stroke patients who received ANCROD recovered all of their mental faculties. Other venom, such as scorpion venom, is being used to treat autoimmune disorders.

There are two kinds of inhibition that can affect the activity of enzymes. In non-competitive inhibition, an inhibitor molecule binds to the enzyme at a site known as the allosteric site. As a result, the three-dimensional structure of the enzyme is altered, which prevents the substrate from binding to the active site (see Figure 2.10). Most metabolic
pathways are regulated by feedback inhibition. This is a type of non-competitive inhibition in which the end product of the pathway binds at an allosteric site on the first enzyme of the pathway. In this way, non-competitive inhibitors can play a key role in the normal functioning and regulation of metabolic pathways. Study Figure 2.11 to learn how a metabolic pathway is regulated by feedback inhibition.
Figure 2.10 Non-competitive inhibition

Molecules that promote the action of enzymes can also bind to the allosteric site. These molecules are known as activators. The activity of any enzyme can change, depending on the number of activators and inhibitors in its environment. The regulation of enzyme activity by inhibitors and activators is known as allosteric regulation.
Competitive inhibition involves chemical compounds that bind to the active site of the enzyme and inhibit enzymatic reactions. The compounds compete with the true substrate for access to the active site. This competition is possible because competitive inhibitors are very similar in shape and structure to the enzyme’s substrate. The metabolic pathway can only be restored if the substrate concentration is increased so that the substrate is more likely to enter the active sites than is the inhibitor. Penicillin is a commonly used competitive inhibitor. It works by bonding to the active site of transpeptidase, the enzyme involved in bacterial cell wall construction.
When penicillin transpeptidase inhibits, a bacterial cell cannot divide successfully, and infectionis prevented.
Protease inhibitors are a relatively new class of ompetitive inhibitors that interfere with the normal activity of protease enzymes. Molecular modelling played a major role in the research and design of effective protease inhibitor molecules. Figure 2.12 shows the general appearance and behaviour of protease and protease inhibitors. These inhibitors have been used to dramatically reduce the level of human immunodeficiency viruses (HIVs) in AIDS patients. HIVs infect host cells, such as the T-cells of the human immune system. The virus does this by injecting its genetic material into the host cell. The virus DNA then commandeers the cell’s cellular processes to make polyproteins. The protease HIV enzyme then cuts these polyproteins into smaller structural proteins and enzymes that will be used to make new HIVs. The snipping or cleavage of polyproteins involves a hydrolysis

reaction that uses a water molecule for every bond that is broken in the substrate molecule. HIV protease inhibitors are similar in chemical composition and structure to the HIV polyprotein. The inhibitor molecules bind tightly to the active
site of HIV protease enzymes. This process prevents the enzymes from cutting the actual HIV polyproteins to form new HIVs. The HIV protease enzyme is composed of two identical peptide halves. The enzyme’s active site is located in the
depression formed where the two halves join.

Cofactors and Coenzymes: Non-protein Helpers

The final manner in which enzymes are regulated comes in the form of cofactors. Cofactors are inorganic ions and organic, non-protein molecules that help some enzymes function as catalysts. The inorganic ions are metals such as copper, zinc, or iron. Located in the active sites of enzymes, these ions attract electrons from substrate molecules. For
instance, carboxypeptidase breaks down proteins using a zinc cofactor. This cofactor draws electrons away from bonds, which causes them to break. If cofactors are organic, non-protein molecules, they are also called coenzymes. Many vitamins, small organic molecules that the human body requires in trace amounts to function, are parts of coenzymes.

Table 2.3 shows vitamins necessary to the formation of specific coenzymes.
Deficiencies in any of these vitamins can affect the enzymatic reactions in cells. For example, lack of niacin may result in a lack of NAD+ (nicotinamide adenine dinucleotide), which can affect enzymatic reactions in cellular respiration. Niacin deficiency can cause a skin disease called pellagra. At one time this disease was often mistaken for leprosy, but in
the early 1900s American researcher Dr. Joseph Goldberger determined that pellagra is caused by a nutritional deficiency. To treat the disease, he recommended a diet that included meat, milk, fish, or a small portion of dried brewer’s yeast.

Both coenzymes NAD+ and FAD (flavin adenine dinucleotide) serve as electron acceptors in redox reactions. They carry electrons from one active site to another. Once the electrons have been released, the coenzymes return to the original enzyme for another complement of electrons.
The NAD+ coenzyme takes the energy from the oxidation of nutritive molecules digested by animals to form NADH, a molecule with more chemical energy. NADH is then oxidized into NAD+ again in order to collect more electrons.
NAD+ is the principal carrier of electrons in the oxidation of molecules that are used as an energy source in the cell. For example, NAD+ accepts electrons from the products of the breakdown of glucose in one stage of cellular metabolism, and then transports them to a metabolic pathway that reduces oxygen to water. During such reactions,
NAD+ accepts two electrons, but only one hydrogen ion, as shown in the following equation:

When NADH is oxidized back into NAD+, energy is released. Similar in function to NAD+, NADP+ (NAD+ plus an additional phosphate group) is a coenzyme in photosynthetic reactions.

Enzymes and Coenzymes for Human Health and Industry

Enzymes and coenzymes have proven useful in medical and industrial applications. Medical researchers have been conducting tests using NADH on patients with Alzheimer’s disease or Chronic Fatigue Syndrome (CFS). In a study conducted in the 1990s at Georgetown University Medical Center, CFS patients who received injections of NADH experienced only one quarter of the symptoms experienced by patients who were given a placebo (a substance with no medical value). At the end of the twentieth century, six out of 10 individuals who were taking NADH used it to
improve their energy level; two out of 10 used it to control Alzheimer’s symptoms; and one out of 10 took it to relieve CFS. Enzymes are also used in the process of DNA fingerprinting, which you will learn more about in Chapter 9. DNA fingerprinting has been used in a variety of circumstances, including paternity tests, murder trials, and identifying people. In one step of the DNA fingerprinting process, special enzymes called restriction enzymes are used to cut the
DNA at specific places. DNA restriction enzymes recognize short, specific sequences of DNA bases and make breaks in the sugar–phosphate backbone of the DNA molecule in the region of the recognized sequence. Without these enzymes, the process of DNA fingerprinting would be much more involved.
DNA fingerprinting also uses a process called PCR, polymerase chain reaction, which you will learn about in Chapter 9. DNA can play a role in determining whether or not an individual’s enzymes are functioning normally. For example, Hurler syndrome is a genetic disorder caused by a defective gene. A chil born with Hurler syndrome cannot anufacture
the enzyme alpha-L-iduronidase. This enzyme is one of 10 lysosomal enzymes responsible for breaking down complex carbohydrates called mucopolysaccharides (MPS). Mucopolysaccharides are largely responsible for building connective
tissues in the human body. If mucopolysaccharides cannot be broken down properly, they build up in body cells and form excess tissue. A child diagnosed with Hurler syndrome will become afflicted with various cardiac or respiratory ailments by the age of five and not survive long thereafter.

People have also found ways to exploit enzymes and coenzymes for industry and profit. One of the most obvious ways that enzymes can be used in industry is in wine-making. Before 1897, scientists believed that enzymes required living material to function. The first to discover that a cell-free, or non-living, extract of yeast could cause alcohol fermentation was the German chemist Eduard Buchner (shown in Figure 2.13). His experiments led to the use of enzymes in industries as diverse as wine production, leather tanning, food production, textiles, pulp and paper, and
pharmaceutical manufacturing.

Enzymes are essential to the pharmaceutical industry in making products — from chemotherapy treatments to common painkillers. Many of these products are composed of enzymes or make use of enzymatic reactions. As well, they often affect the activity of enzymes within the body. A new form of chemotherapy, Antibody-directed Enzyme Prodrug Therapy (ADEPT) uses enzymes to improve the efficiency of the drugs being used in the treatment of common solid tumours. This process involves using tumour-associated antibodies directed against tumour antigens. Doctors link the antibodies to enzymes and administer them to the patient. A prodrug is administered separately. A prodrug is an
inactive drug that is only converted into its active form in the body by metabolic activity. At the site of the tumour, the enzyme converts the prodrug into an active compound that is toxic to the tumour. Painkillers, for example, affect enzymes in order to relieve headaches, inflammation, or swollen tissues. Aspirin™ and similar painkillers reduce
inflammatory pain by inhibiting enzymes called cyclo-oxygenase (Cox) 1 and 2. Cox-1 is located in the stomach, protecting it from hydrochloric acid in the digestive juices. Cox-1 is also found in blood platelets, where it aids in clotting reactions. Cox-2 is produced in the skin or joints following inflammation. Cox-2 is necessary in catalyzing the
formation of prostaglandin E2 (PGE2), which increases the sensitivity of nerves to pain. Until recently, biochemists believed that inhibition of PGE2 at the site of inflammation accounted for both the anti-inflammatory and painkilling actions of Aspirin™ and similar painkillers. Although Cox-2 is produced at the inflamed site of the body, recent studies have shown that nerve cells in the spinal cord and brain also begin to produce it. This results in the production of PGE2 throughout the central nervous system. Biochemists revised their knowledge of how and where Aspirin™ works. Aspirin™ reduces inflammatory pain not only at the inflamed site but also in the entire central nervous system.
Because PGE2 increases nerve sensitivity to pain, its manufacture throughout the central nervous system accounts for the tenderness surrounding inflamed tissues. Researchers suspect that the presence of Cox-2 and PGE2 may explain why people with inflamed tissues experience aches and pains and even appetite loss and depression.

Recent studies on synthetic oligosaccharides carbohydrates composed of a relatively small number of monosaccharides) indicate they have great potential as therapeutic agents. These compounds, which interfere with carbohydrate– protein reactions, are difficult to create in the laboratory. However, a new technology has been discovered using glycosidases, which are produced by genetically altering DNA. These altered enzymes catalyze the synthesis but not the hydrolysis of oligosaccharides, making them easier and less expensive to construct. The altered enzymes have been termed glycosynthases and can be used to make anti-ulcer agents, therapeutic drugs for
middle-ear infections, and infant formula additives, to name a few. Dr. Stephen Withers, a scientist at the University of British Columbia, and his co-workers were the first to develop glycosynthases.

They continue to be in the forefront of developing new ways to use these enzymes and their substrates in industry and medicine. The “Canadians in Biology” profile on the previous page provides a more complete account of the work
accomplished by Dr. Withers and his team. By lowering the activation energy needed by cells to start metabolic reactions, enzymes allow biological systems to undertake necessary processes at the temperatures that exist inside the cell. People have learned a great deal about enzymes and taken them from such diverse sources as yeast and organisms living in hydrothermal vents in order to manufacture foods and pharmaceuticals. The following section discusses another aspect of enzyme function and metabolic reactions within cells — coupled reactions and the production of ATP.

In the summer of 2001, a forest fire that had been started by a lightning strike raged through Kootenay National Park in British Columbia. Park officials allowed the fire to progress because the area was scheduled for a prescribed burn. Fires are a natural part of forest ecology and are important in forest regeneration. For example, some species of pine, such as the jack pine, drop cones that need the heat from a fire to open them and release their seeds. The Kootenay fire quickly consumed the dry grasses
and trees; it soon spread beyond the area park officials could manage, threatening nearby communities.
Many firefighters risked their lives to control the spread of the flames. By the time the fire was contained and eventually extinguished, thousands of hectares of forest had burned.
The chemical reaction that occurred in the fire involved oxygen and the wood that formed the trees. While the forest fire was an example of a reaction that occurred with oxygen outside cells, reactions with oxygen also occur inside cells. Energy is necessary to perform all cellular reactions, including redox, hydrolysis, and condensation reactions. Enzymes aid reactions within cells. Enzymes are necessary because they speed up the synthesis of energy-rich molecules needed for cellular processes.
In this chapter, you will learn how chemical reactions within cells are used to make energy-rich molecules.
Energy from these molecules is used for various cellular processes. The bonds that hold atoms together store energy in molecules. This energy can be used by a cell to do work. You will explore various factors that influence how molecular bonds are formed and broken. You will also discover which molecules are involved in cellular processes and how the energy from one reaction can be used to drive another reaction.

Thermodynamics and Biology

Many reactions occur inside every cell. These reactions, collectively known as metabolism, have been at the centre of much scientific investigation. For example, manufacturers of dietary supplements for athletes seek to isolate chemicals that increase metabolic activity. Creatine phosphate is one such chemical — it is a nitrogenous molecule that is stored in muscle cells. Enhanced stores of creatine phosphate in muscles have been shown to increase muscle mass and efficiency. The compound was synthesized and used in the former Soviet Union by elite athletes in the 1960s to increase their metabolic activity and performance. What are metabolic reactions, and why are they important?
To understand this, you must first understand how energy flows through systems.

To survive, all living things require energy, which is the capacity for doing work. Energy comes in different forms. For instance, energy comes from the Sun as light, and thermal energy from a furnace can be used to heat a home. All moving objects, such as falling water and pistons in an internal combustion engine, have kinetic energy. Energy can also be stored as potential energy. A molecule of glucose has potential energy. The potential energy stored in the bonds of a molecule is called chemical energy. If a molecule of glucose is broken down into carbon dioxide and water, the energy released can be used to do work. If a phosphate group is removed from a molecule of ATP, the chemical energy can be used to fuel various cellular processes.
Energy continually flows through living and non-living systems. The study of this flow of energy is called thermodynamics. Physicists and chemists have studied thermodynamics since the days of Sir Isaac Newton. Biologists also apply thermodynamics when they study metabolic processes and the energy transformations that take place within living systems. Scientists use the term system to identify a process under study, and they refer to it in relation to the rest of the universe. For instance, a hot drink in a sealed vacuum bottle is considered a closed system because the liquid is isolated from its surroundings — thermal energy cannot move from the liquid to outside the bottle.
Removing the lid from the bottle results in an open system, because energy (thermal, in this case) can now move between the liquid and its surroundings — it moves from the liquid to outside the bottle. All living organisms are open systems; energy moves two ways, both in and out of cells. For example, a green plant absorbs energy from the Sun and uses this energy for building structures, transporting materials, growth, and reproduction. The plant also releases energy into the environment in the form of thermal energy when the plant is forming metabolic products, such as water and carbon dioxide.
How energy flows between organisms and the environment is governed by the laws of thermodynamics. You have already encountered these laws in previous studies. The first law, or law of conservation of energy, states that energy can neither be created nor destroyed, but can be transformed from one form to another. For example, during photosynthesis, a green plant absorbs light energy from the Sun. This energy is transformed into chemical energy, which is stored in bonds that hold together atoms in a molecule of sugar. An internal combustion engine converts the chemical energy stored in gasoline molecules into kinetic energy — the motion of the car. Some chemical reactions, such as burning a fuel, release energy. Some of this energy is useful because it is available to do work. The energy available to do work is known as free energy. Free energy can be used to do the work of building molecules in a cell. However, whenever energy is transformed from one form to another, some of it is lost. This lost energy is the portion that is not free energy and therefore is not available for useful work. The amount of free energy that can be harnessed by a green plant or car is much less than the total amount of light or chemical energy present in the sunlight or gasoline. This fact is the basis of the second law of thermodynamics, which states that energy cannot be transformed from one form to another without a loss of useful energy. The energy that is lost eventually escapes into the atmosphere largely as waste thermal energy. There are many transformations of energy that occur inside a cell.
During each transformation, some energy is lost as thermal energy. Eventually, all forms of useful energy are transformed into thermal energy. After thermal energy dissipates, it can never be transformed back into a useful form, such as chemical energy, that can be used to do work. Therefore, biological systems require a constant supply of energy from the Sun to function.
A measure of the tendency of a system to become unorganized is called entropy. Every transformation of energy creates more disorder in the universe. Therefore, we can restate the second law of thermodynamics as follows: every energy transformation increases the entropy of the universe.
The conversion of chemical energy into thermal energy does not violate the first law of thermodynamics. If thermal energy is produced during a chemical reaction, it is still a form of energy. Although some of this energy is not available to do work, energy is still conserved.

Consider the following example as a case study of thermodynamic principles. Stacked beside the fire pit at your campsite are a stack of newspapers and a bundle of kindling that you intend to ignite to start a fire. The stack of paper and the wood are composed of cellulose, which is made up of complex carbon-based molecules. These molecules contain potential chemical energy. When you light the paper, the chemical bonds in the molecules are broken in a reaction with oxygen. During the reaction, thermal energy and light are released.
Recall from your study of Chapter 1 that this is a redox reaction. Once the reaction begins, the paper quickly burns, forming the products of the oxidation of cellulose: carbon dioxide and water. If energy is released from the reaction of paper with oxygen, the paper and oxygen must contain more chemical energy than the products (see Figure 2.2).

During the reaction, the chemical energy stored in the paper and in the oxygen molecules is transformed into thermal energy and light energy. You can feel the thermal energy that is released if you reach toward the fire to warm your hands. Why does the paper require an initial input of energy to start the fire? Chemical bonds hold atoms and molecules together. These bonds maintain the chemical energy in the molecules. In order to destabilize the bonds, and thereby release the energy they hold, an initial input of extra energy is needed. This extra energy is known as activation energy.
Figure 2.2 shows the activation energy required to ignite paper. Different substances require different amounts of activation energy to start a reaction. The activation energy needed to start a reaction within cells is governed by special proteins. Without these proteins, metabolic processes could not occur. Next, you will examine two types of metabolic reactions that occur within cells.

Exothermic and Endothermic Metabolic Reactions

Recall that metabolic reactions encompass all the reactions that occur within cells, including anabolic reactions (such as condensation) and catabolic reactions (such as hydrolysis), and redox reactions.
Complex carbohydrates, fats, and proteins can be broken down in catabolic reactions, thereby forming molecules such as simple sugars and amino acids. Anabolic processes then join up these products and their functional groups to form various macromolecules needed by cells for maintenance and growth. A reaction can be classified based on whether it releases or uses energy. A reaction that is accompanied by a release of energy is called an exothermic reaction, as shown in Figure 2.3 on the next page. For example, recall the overall reactionfor cellular respiration:

For each molecule of glucose oxidized in cellular respiration, energy is released. Some of this energy is useful and available to do work and some is waste thermal energy. This means that the products (carbon dioxide and water) contain less energy than the reactants (glucose and oxygen).
In contrast, an endothermic reaction involves an input of energy. For example, the synthesis of glucose
by plants during photosynthesis is as follows:

endothermic reaction stores chemical energy in molecules, there is a gain in energy.
As you can see in the two equations above, oxidation and synthesis of glucose are two reactions that are the reverse of each other. If two reactions are the reverse of each other, one reaction is endothermic and the other is exothermic. Exothermic and endothermic reactions both involve energy transformations. How do cells control the flow of energy so that they do not overheat and destroy themselves? In the next
section, you will learn how cells are able to lower the amount of activation energy necessary to carry out a variety of metabolic reactions.

Large molecules can be broken down to release energy. Alternatively, they can be formed to build cellular structures or store information. In biological systems there are four major types of chemical reactions involved in breaking apart and
building molecules: acid-base or neutralization reactions, which transfer hydrogen ions between molecules, redox, or oxidation-reduction reactions, which transfer electrons between molecules, hydrolysis reactions, in which molecules react with H2O to form other molecules, and condensation reactions, in which molecules react to form H2O and other molecules.
These types of chemical reactions are described below.

Acids, Bases, and Neutralization Reactions

Acids and bases are compounds that may be inorganic or organic. Hydrochloric acid, found in the mammalian stomach, is an inorganic acid. Acetic acid and amino acids are examples of organic acids. Sodium hydroxide, a key component of oven cleaners, is an inorganic base. Purines and pyrimidines, the molecules that form part of the
subunits of nucleic acids, are examples of organic bases; they are often referred to as nitrogenous bases, because they include the nitrogen-containing amine group. What is it, however, that makes one substance an acid and another a base? In biology, acids and bases are understood in relation to their behaviour in water. Under normal conditions, pure water exists in the form of H2O molecules. A small number of these molecules dissociate, which means that they
break up into ions. When a water molecule dissociates, it forms a positively charged hydrogen ion, H+, and a negatively charged hydroxide ion, OH-. Since very few water molecules dissociate, the concentration of these ions is low. In pure water at 25°C, the concentration of each of these ions is the same: 1 × 10-7 mol/L. Because hydrogen and
hydroxide ions are very reactive, changes in their concentrations can drastically affect cells and the macromolecules within them. Acids and bases, and more specifically the concentrations of hydrogen and hydroxide ions within cells, determine how effectively cellular processes are carried out.

An acid is any substance that donates H+ ions when it dissolves or dissociates in water. Therefore, acids increase the concentration of H+ ions in water solutions. Bases, on the other hand, decrease the concentration of H+ ions in solution. Usually this occurs because bases attract H+ ions, thus reducing their concentration. As a result, the concentration of OH- ions increases when bases dissolve or dissociate in water. The pH scale, shown in Figure 1.15, is a means for ranking substances according to the relative concentrations of their hydrogen and hydroxide ions. Water, with equal concentrations of these ions, is considered neutral and has a pH of 7. Substances with a pH that is lower than 7 have higher concentrations of H+ ions (and lower concentrations of OH- ions), so they are acids. Substances with a pH that is higher than 7 have lower concentrations of H+ ions (and higher concentrations of OH- ions), so they are bases.
When acids and bases react, they produce two products: water and a salt (an ionic compound). This chemical process in which acids and bases react to product a salt and water is called a neutralization reaction. In such a reaction, the acid no longer acts as an acid and the base no longer acts as a base; their properties have been neutralized.

Buffers

Many biological processes require specific pH levels in order to function properly. For example, pH and the control of pH play an integral role in both photosynthesis and cellular respiration. Many proteins require a certain pH in order to take on their characteristic shapes. Therefore, it is important for pH in organisms to be maintained at specific levels. Certain chemicals or combinations of chemicals known as buffers minimize changes in pH. Buffers maintain pH levels by taking up or releasing hydrogen ions or hydroxyl ions in solution. You will investigate the effect of a buffer in living cells in the next investigation. In Chapter 4, you will see how buffers play an important role in maintaining blood pH.

Redox Reactions

Almost every element on Earth can react with oxygen. For instance, if oxygen combines with calcium, the oxygen receives electrons and forms negatively charged ions.

The addition of two electrons has decreased the charge of the oxygen atom by two. The gain of electrons is referred to as reduction. The calcium loses electrons and forms positively charged ions, as shown here:

The loss of electrons is called oxidation.

The terms “oxidation” and “reduction” are applied to many reactions involving ions whether or not oxygen is involved. For instance, in the reaction Na + Cl → NaCl, chlorine is reduced (gains an electron to form Cl-) and sodium is oxidized (Na loses an electron to form Na+). Because reduction and oxidation are both involved in the process, the entire reaction is called a redox reaction. Figure 1.16 is a generalized schematic representation of a redox reaction.

Cellular respiration is an important example of a redox reaction that takes place in biological systems. The overall reaction is:

In cellular respiration, high-energy electrons are removed from food molecules, which oxidizes them. These high-energy electrons are transferred to increasingly electronegative atoms, and help the cell manufacture energy-rich molecules used by cells to do work.

Hydrolysis and Condensation Reactions

Macromolecules in living systems are built and broken down by hydrolysis and condensation reactions (see Figure 1.17). In condensation (or dehydration synthesis), the components of a water molecule are removed to bond two molecules together. Because the organic molecule formed is bigger than the two organic molecules that reacted,
condensation is an anabolic process. In the process of hydrolysis, the components of a water molecule are added to a molecule to break it into two molecules. Because the organic molecules produced are smaller than the organic molecule that reacted, hydrolysis is a catabolic process. Read on to see how hydrolysis and condensation work to
break down and build carbohydrates, nucleic acids, proteins, and lipids.

Making and Breaking Carbohydrates

Carbohydrates are important macromolecules because they store energy in all organisms. Carbohydrates are groupings of C, H, and O atoms, usually in a 1 : 2 : 1 ratio. Often, carbohydrates are represented by the chemical formula (CH2O)n, where n is the number of carbon atoms in the carbohydrate.
Carbohydrates can be simple, such as the monomer glucose. Glucose is a hexose (six-carbon) sugar with seven energy-storing C-H bonds. If the number of carbon atoms in a carbohydrate molecule is low (from three to seven), then it is a
monosaccharide. Greek prefixes for the numbers three through seven are used to name these sugars.
For example a five-carbon sugar is a pentose, and a six-carbon sugar is a hexose. The glucose, fructose, and galactose isomers you studied in the previous section are all hexoses. Glucose is the primary source of energy used by cells.
Two monosaccharides can bond to form a disaccharide. For example, two glucose molecules can join to form the disaccharide maltose, as shown in Figure 1.18.
Organisms store energy in molecules known as polysaccharides. Polysaccharide molecules, such as starch and glycogen, are polymers made up of chains of linked monosaccharides. The long chains of glucose molecules, which make up starch, glycogen, and some other polysaccharides, are formed by a condensation reaction, which removes water from 2 –OH functional groups or neighbouring monosaccharides. Because of its chemical composition, cellulose (a polysaccharide found in all plants) is indigestible for animals. The bonds in cellulose are difficult to break by normal metabolic means. In contrast, other polysaccharides, such as the amylopectin found in potatoes, rice, and wheat,
serve as convenient and accessible forms of stored energy. The bonds that bind their high-energy glucose molecules together are easily broken and easily formed.
In living cells and tissues, polysaccharides and disaccharides can be broken into smaller units by the process of hydrolysis. The complete hydrolysis of most forms of starch produces a form of glucose, which is a simple sugar that cannot be decomposed by hydrolysis. In the investigation on page 24, you can determine the products of hydrolysis reactions.

Nucleotides and Nucleic Acids

Nucleic acids such as DNA and RNA are huge polymers of nucleotides. These are molecules composed of one, two, or three phosphate groups, a five-carbon sugar (deoxyribose or ribose), and a nitrogen-base (see Figure 1.19). DNA contains genetic information about its own replication and the order in which amino acids are to be joined to
form a protein. RNA is the intermediary in the process of protein synthesis, conveying information from DNA regarding the amino acid sequence in a protein. There are four different bases in DNA — adenine, thymine, guanine, and cytosine. In RNA, uracil replaces thymine as a base. Adenine not only helps code genetic material and build proteins, but it also has important metabolic functions. You will investigate the structure and functions of nucleic acids further in Unit 3.

ATP, adenosine triphosphate, is composed of adenosine (adenine joined to ribose, as in RNA) and three phoshate groups (see Figure 1.20). The hydrolysis of ATP results in the formation of ADP and a phosphate (Pi), and in the release of a large quantity of energy for cellular work. After ATP breaks down, it can be rebuilt by the addition of the phosphate to ADP by condensation.

Condensation Synthesis and Hydrolysis of Proteins

Proteins are important as structural components, sources of nutrition, and for their role in speeding up metabolic processes in the cell. Peptide bonds formed in condensation reactions link amino acids in proteins (see Figure 1.21). Each amino acid is composed of a carbon atom bound to a hydrogen atom and three additional groups — an amino
group, -NH2, a carboxyl group, –COOH, and an R-group that is different in each amino acid. When two amino acids join, they become a dipeptide. A chain of amino acids is called a polypeptide. Try the Thinking Lab to model a polypeptide. Polypeptides may join to form proteins. The sequence of these polypeptides, their particular orientations in space, and their three-dimensional shapes determine the type of protein they form. Enzymes, essential to metabolism (as you will see in Chapter 2), are proteins that are shaped in different ways depending

on their function. Some proteins are composed of many polypeptides. These polypeptides can be broken during metabolism by hydrolysis.

Breaking Lipids

Lipids include fats and phospholipids (such as those in the cellular membrane), steroids, and terpenes (lipid pigments that operate during photosynthesis). Fats are composed of glycerol and three fatty acids; steroids and terpenes are composed of carbon rings and carbon chains respectively.
Fat is usually of animal origin and is solid at room temperature. Within animal bodies it is used for long-term energy storage. Fat also insulates against external heat and cold and protects major organs. Oil, the plant equivalent to fat, is liquid a room temperature. Fats and oils are often called triglycerides because of their structure. Fats and oils are insoluble in water because they are non-polar.
Both fats and oils are composed of two types of molecules: glycerol and fatty acids. Glycerol is a three-carbon alcohol in which each carbon is attached to a hydroxyl group (–OH), as shown in Figure 1.22. This three-carbon molecule is the
core of the fat or oil molecule. In a condensation reaction, three fatty acids are attached to this core to form a fat. A fatty acid is a hydrocarbon chain that ends with the carboxyl group (–COOH). Most of the fatty acids in cells contain 16 or 18 carbon atoms per molecule. Saturated fatty acids have no double bonds between their carbon atoms; the carbon chain is “saturated” with as many hydrogen

atoms as it can hold. Saturated fatty acids are generally solid at room temperature. In contrast, unsaturated fatty acids have one or more double bonds between carbon atoms. Therefore, the fatty acid is not saturated with hydrogen atoms. Fat molecules are split by hydrolysis for use in cells.
Figure 1.23(a) shows another lipid macromolecule with a different function in cells.

Called a phospholipid, this molecule interacts with water in a way that spontaneously results in the structure shown in Figure 1.23(b). This phospholipid bilayer is the foundation for the semi-permeable membrane that surrounds cells.
Some molecules can pass freely through the membrane, while others require assistance to enter. The phospholipid bilayer is virtually impermeable to macromolecules, relatively impermeable to charged ions, and quite permeable to small, lipidsoluble molecules. Molecules that move through the membrane do so at differing rates, depending
on their ability to enter the hydrophobic interior of the membrane bilayer.
Many small, non-polar solute molecules, such as oxygen and carbon dioxide, pass through the bilayer of the cell membrane with least resistance. They enter by means of diffusion, a form of passive transport. As you learned in previous studies, in this method of cellular transport, molecules move from regions of high concentration to those of low concentration. Water, a small polar molecule, can travel through the cell membrane freely in the process of osmosis. This process involves the movement of the solvent water from an area of higher concentration of water to an area of lower concentration of water.
Some molecules are too large to diffuse unassisted across the cell membrane. These molecules enter the cell by means of specialized proteins called carrier proteins — they move and change shape to create an opening into the cell.
Large uncharged hydrophilic molecules such as glucose make use of these proteins in order to enter cells (see Figure 1.24). No cellular energy is required for this facilitated diffusion process, so it is a form of passive transport. Appendix 5 shows several other examples of passive transport through the cell membrane. In the next chapter, you will see how cells use energy to move larger molecules across the cell membrane.

Large molecules can be broken down to release
energy. Alternatively, they can be formed to build
cellular structures or store information. In
biological systems there are four major types of
chemical reactions involved in breaking apart and
building molecules:
acid-base or neutralization reactions, which
transfer hydrogen ions between molecules,
redox, or oxidation-reduction reactions, which
transfer electrons between molecules,
hydrolysis reactions, in which molecules react
with H2O to form other molecules, and
condensation reactions, in which molecules react
to form H2O and other molecules.
These types of chemical reactions are described
below.

The atoms of four elements make up roughly 99 percent of the mass of most cells: hydrogen, nitrogen, carbon, and oxygen. With only a few exceptions, molecules that contain carbon atoms are called organic compounds. There are millions of different organic compounds. Nearly all organic compounds contain hydrogen as well as carbon, and most of these also include oxygen. Pure carbon and carbon compounds that lack hydrogen — such as carbon dioxide and calcium carbonate — are considered inorganic. Inorganic compounds are, nevertheless, integral components of living systems. See Figure 1.9. For example, water — an inorganic compound — provides a medium in which various substances may be dissolved and transported within and between cells.

Figure 1.9 In what ways do living and non-living systems,
and organic and inorganic compounds interact?

The Central Atom: Carbon

The diversity of life relies greatly upon the versatility of carbon. Recall that a carbon atom in its most stable state has two occupied energy levels, the second of which contains four valence electrons. This means that, in covalent molecules, a carbon atom can form bonds with as many as four other atoms. In biological systems, these atoms are mainly hydrogen, oxygen, nitrogen, phosphorus, sulfur, and — importantly — carbon itself. Carbon’s ability to bond covalently with other carbon atoms enables carbon to form a variety of geometrical structures, including straight chains, branched chains, and rings. Figure 1.10 shows the shapes of several simple organic molecules that contain only carbon and hydrogen atoms. These molecules, called hydrocarbons, comprise the fossil fuels that serve as the main fuel source for much of the world’s industrial activities. Hydrocarbons are themselves not components of living systems. However, substantial portions of many biological molecules consist of bonded chains of carbon and hydrogen.

Molecular Isomers

Because carbon can form so many compounds with so many elements, it is common to encounter several organic compounds with the same molecular formula but different structures. Such compounds are known as isomers. For example, two isomers of glucose, a six-carbon sugar, are fructose and galactose. Glucose, fructose, and galactose all have the same molecular formula (C6H12O6). However, they differ in their molecular structures, as shown in Figure 1.11.

There are two main types of isomers. Structural isomers are two or more compounds with the same atoms bonded differently. Glucose and fructose, for example, are structural isomers. Notice that a glucose molecule contains a ring of five carbon atoms and an oxygen atom, whereas a fructose molecule contains a ring of four carbon atoms and an oxygen atom. Because their structures are different, glucose and fructose have different properties, and cells metabolize them differently.
Stereoisomers are two or more compounds with their atoms bonded in the same way, but with atoms arranged differently in space. Stereoisomers may be geometrical or optical. Geometrical isomers can have very different physical properties (such as different melting points), but they tend to have the same chemical properties. Glucose and galactose are examples of geometrical isomers.
Optical isomers, shown in Figure 1.12, are nonsuperimposable mirror images of each other. They usually have similar chemical and physical properties, but enzymes or proteins on the cell membrane can distinguish between them. Usually, one optical isomer is biologically active and the other biologically inactive. In some cases however, this is not always true. For example, sometimes one optical isomer of a drug is not as effective as the other or can even cause complications. In the early 1960s, many pregnant women were prescribed a drug called thalidomide for morning sickness.
Thalidomide is a mixture of two optical isomers; one produced the desired effect, but the other caused major birth defects. As the thalidomide example demonstrates, organisms can be very sensitive to minute variations in molecular geometry.

The Functional Groups

Chemical reactions involve breaking or forming chemical bonds. These processes can transform simple molecules such as glucose into complex molecules such as starch or cellulose. Many of these complex molecules contain groups of atoms with characteristic chemical properties. These groups of atoms, known as functional groups, include hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups, as shown in Figure 1.13 Many compounds have more than one functional group in their structure.

These functional groups are hydrophilic. Except for the phosphate group, they are polar and so they increase the solubility in water of the organic molecules to which they are attached. Each functional group also has capabilities to change the chemical properties of the organic molecules to which it bonds. For example, if a hydrogen atom in
ethane is replaced by a sulfhydryl group, the result is ethanethiol, also known as ethyl mercaptan. While ethanethiol in small amounts stabilizes protein structures, it is also a dangerous neurotoxin and respiratory toxin. Each functional group has a specific role in cell metabolism. Phosphates are essential to the metabolic processes of photosynthesis and cellular respiration. For example, the transfer of a phosphate group from ATP (adenosine triphosphate) begins the very important process of glycolysis — the first step in cellular respiration. You will discover more about this process in Chapter 3.
While amino and phosphate groups contribute to energy transactions in the cell, the sulfhydryl (–SH) group is essential to protein stabilization. Amino acids with –SH groups form bonds called disulfide bridges (S–S bonds) that help protein molecules to take on and maintain a specific shape.

Monomers and Macromolecules
As you know, atoms can join together — bond — to form small compounds called molecules. Similarly, molecules can join together to form large structures called macromolecules. The small, molecular subunits that make up macromolecules are called monomers. The macromolecules themselves are built up of long chains of monomers. These chains are called polymers.
Table 1.2 lists the main types of macromolecules and their monomer subunits. Figure 1.14 depicts the subunits that comprise carbohydrates, selected lipids, proteins, and nucleic acids. Chemical reactions in cells synthesize macromolecules from these subunits, and break the molecules apart to release their subunits. Refer to Figure 1.14 often as you examine these chemical reactions in the final
section of this chapter.