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Figure 2.1(A) shows raw fruit. The crisp, sharp-tasting fruit becomes soft and sweet when it is cooked. Figure 2.1(B) shows a chemist accelerating the tranformation of ethanol into ethanoic acid, by adding potassium
dichromate and sulfuric acid.
What do these reactions have in common? They are both examples of organic reactions. In this section, you will take a quick look at the main types of organic reactions. You will concentrate on simply recognizing these types of organic reactions. In the next section, you will examine the reactions of specific functional groups and learn how to predict the products of organic reactions.
Addition, Substitution, and Elimination Reactions
Addition reactions, substitution reactions, and elimination reactions are the three main types of organic reactions. Most organic reactions can be classified as one of these three types.
In an addition reaction, atoms are added to a double or triple bond. One bond of the multiple bond breaks so that two new bonds can form. To recognize an addition reaction, remember that two compounds usually react to form one major product. (Sometimes two isomers are formed.)
The product has more atoms bonded to carbon atoms than the organic reactant did. A general example of addition to an alkene is given below.
Addition reactions are common for alkenes and alkynes. Addition reactions can also occur at a CO bond. Some examples of addition reactions are shown on the next page.
In a substitution reaction, a hydrogen atom or a functional group is replaced by a different functional group. To help you recognize this type of reaction, remember that two compounds usually react to form two different products. The organic reactant(s) and the organic product(s) have the same number of atoms bonded to carbon.
Alcohols, alkyl halides, and aromatic compounds commonly undergo substitution reactions, as shown in these examples.
In an elimination reaction, atoms are removed from a molecule to form a double bond. This type of reaction is the reverse of an addition reaction. One reactant usually breaks up to give two products. The organic product
typically has fewer atoms bonded to carbon atoms than the organic reactant did.
Alcohols often undergo elimination reactions when they are heated in the presence of strong acids, such as sulfuric acid, H2SO4, which acts as a catalyst. (See the first example below.) Alkyl halides also undergo elimination reactions to produce alkenes. (See the second example.)
Oxidation and Reduction
An important type of organic reaction occurs when there is a change in the number of hydrogen or oxygen atoms that are bonded to carbon. In Unit 5, you will take a close look at oxidation-reduction reactions in terms of the transfer of electrons. As you will learn, oxidation and reduction always occur together. One reactant is oxidized while the other reactant is reduced. In this unit, however, you will focus on the organic reactant only. Therefore, you will deal with oxidation and reduction separately, as they apply to organic compounds. In organic chemistry, oxidation and reduction are defined by the changes of the bonds to carbon atoms in the organic reactant.
In organic chemistry, oxidation is defined as a reaction in which a carbon atom forms more bonds to oxygen, O, or less bonds to hydrogen, H. An oxidation that involves the formation of double CO bonds may also be classified as an elimination reaction. For example, alcohols can be oxidized to produce aldehydes and ketones. Oxidation occurs when an organic compound reacts with an oxidizing agent. Common oxidizing agents include acidified potassium
permanganate, KMnO4, acidified potassium dichromate, K2Cr2O7, and ozone, O3. The symbol [O] is used to symbolize an oxidizing agent, as shown below. Note that equations for the oxidation of organic compounds are often left unbalanced. The purpose of the equation is to show the changes in the organic reactant only.
To identify an oxidation, count and compare the number of C-H and C-O bonds in both the reactant and product. Try it for the following example.
In organic chemistry, reduction is defined as a reaction in which a carbon atom forms fewer bonds to oxygen, O, or more bonds to hydrogen, H. Often, a CO bond or CC bond is reduced to a single bond by reduction. A reduction that transforms double CC or CO bonds to single bonds may also be classified as an addition reaction. Aldehydes,
ketones, and carboxylic acids can be reduced to become alcohols. Alkenes and alkynes can be reduced by the addition of H2 to become alkanes. Reduction occurs when an organic compound reacts with a reducing agent. Common reducing agents are lithium aluminum hydride, LiAlH4, and hydrogen gas over a platinum catalyst, H2/Pt. The symbol [H] is used to symbolize a reducing agent. As is the case for oxidation, equations showing the reduction of organic compounds are often left unbalanced.
To identify a reduction, count and compare the number of C-H and C-O bonds in both the reactant and the product. Try it for the following example.
Other Important Organic Reactions
In this chapter, you will also encounter the following classes of organic reactions: condensation reactions and hydrolysis reactions. Condensation and hydrolysis reactions are both types of substitution reactions.
In a condensation reaction, two organic molecules combine to form a single organic molecule. A small molecule, usually water, is produced during the reaction. For example, a carboxylic acid and an alcohol can condense to form an ester.
In a hydrolysis reaction, water adds to a bond, splitting it in two. This reaction is the reverse of a condensation reaction. For example, water can add to an ester or amide bond. A carboxylic acid and an alcohol are produced if an ester bond is hydrolyzed, as shown in the example below. A carboxylic acid and an amine are produced if an amide bond is hydrolyzed.
The following Sample Problems show how to identify different types of organic reactions.
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.
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
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.
Some of the most interesting and useful organic compounds belong to families you are about to encounter. For example, the sweet taste ofvanilla and the spicy scent of cinnamon have something in common: a carbonyl group. A carbonyl group is composed of a carbon atom doublebonded to an oxygen atom. In this section, you will study the structures and properties of organic compounds that have the C═O group.
Aldehydes and Ketones
Aldehydes and ketones both have the carbonyl functional group. An aldehyde is an organic compound that has a double-bonded oxygen on the last carbon of a carbon chain. The functional group for an aldehyde is
The general formula for an aldehyde is R-CHO, where R is any alkylgroup. Figure 1.18 shows the first two aldehydes.
When the carbonyl group occurs within a hydrocarbon chain, the compound is a ketone. A ketone is an organic compound that has a double-bonded oxygen on any carbon within the carbon chain. The
functional group of a ketone is
The general formula for a ketone is RCOR′, where R and R′ are alkyl groups. Figure 1.19 shows the simplest ketone, propanone.
Like the other organic compounds you have encountered, the names of aldehydes and ketones are based on the names of the parent alkanes. To name an aldehyde, follow the steps below.
How to Name an Aldehyde
Step 1 Name the parent alkane. Always give the carbon atom of the carbonyl group the position number 1.
Step 2 Replace the -e at the end of the name of the parent alkane with -al. The carbonyl group is always given position number 1. Therefore, you do not need to include a position number for it.
To name a ketone, follow the steps on the next page. The Sample Problem that follows gives examples for naming both aldehydes and ketones.
How to Name a Keton
Step 1 Name the parent alkane. Remember that the main chain must contain the CO group.
Step 2 If there is one ketone group, replace the -e at the end of the name of the parent alkane with -one. If there is more than one ketone group, keep the -e suffix and add a suffix such as -dione or -trione.
Step 3 For carbon chains that have more than four carbons, a position number is needed for the carbonyl group. Number the carbon chain so that the carbonyl group has the lowest possible number.
Additional Characteristics of Aldehydes and Ketones
• In general, aldehydes have a strong pungent smell, while ketones
smell sweet. Aldehydes with higher molecular masses have a pleasant
smell. For example, cinnamaldehyde gives cinnamon its spicy smell.
(See Figure 1.20.) Aldehydes and ketones are often used to make
perfumes. The rose ketones (shown in Figure 1.21) provide up to 90%
of the characteristic rose odour. Perfumers mix organic compounds, such as the rose ketones, to obtain distinctive and attractive scents.
• Since aldehydes and ketones are polar, they can act as polar solvents.
Because of the non-polar hydrocarbon part of their molecules, aldehydes and ketones can also act as solvents for non-polar compounds. For example, 2-propanone (common name: acetone) is an important organic solvent in the chemical industry.
• Table 1.10 compares the boiling points of an alkane, an alcohol, and an aldehyde with the same number of carbon atoms. You can see that the boiling point of an alcohol is much greater than the boiling point of an alkane or an aldehyde.
You are already familiar with one carboxylic acid. In fact, you may sprinkle it over your French fries or your salad, as shown in Figure 1.22. Vinegar is a 5% solution of acetic acid in water. The IUPAC name for
acetic acid is ethanoic acid, CH³COOH.
A carboxylic acid is an organic compound with the following functional group:
This -COOH group is called the carboxyl group. The general formula for a carboxylic acid is RCOOH. Figure 1.23 shows some common carboxylic acids.
To name a simple carboxylic acid, follow the steps below. Figure 1.24 gives some examples of carboxylic acid names.
How to Name a Carboxylic Acid
Step 1 Name the parent alkane.
Step 2 Replace the -e at the end of the name of the parent alkane with
Step 3 The carbon atom of the carboxyl group is always given position number 1. Name and number the branches that are attached to the compound.
Table 1.12 lists some of the physical properties of carboxylic acids. Notice that carboxylic acids have even stronger hydrogen bonding than alcohols
Additional Characteristics of Carboxylic Acids
• Carboxylic acids often have unpleasant odours. For example, butanoicacid has the odour of stale sweat.
• The -OH group in a carboxylic acid does not behave like the basic hydroxide ion, OH-. Oxygen has a high electronegativity (attraction to electrons) and there are two oxygen atoms in the carboxylic acid
functional group. These electronegative oxygen atoms help to carry the extra negative charge that is caused when a positive hydrogen atom dissociates. This is why the hydrogen atom in a carboxylic acid is able to dissociate, and the carboxylic acid behaves like an acid.
• Figure 1.25 compares the melting and boiling points of a carboxylic acid with the melting and boiling points of other organic compounds. As you can see, the melting and boiling points of the carboxylic acid are much higher than the melting and boiling points of the other compounds. This is due to the exceptionally strong hydrogen bonding between carboxylic acid molecules.
Carboxylic Acid Derivatives
The strong-smelling compounds you prepared in Investigation 1-A do not fit into any of the organic families you have studied so far. According to their molecular formulas, however, they are isomers of carboxylic acids.
They are esters. Because an ester is obtained by replacing the -OH group of a carboxylic acid with a different group, it is called a derivative of a carboxylic acid. Carboxylic acids have several important derivatives.
In this section, you will study two of these derivatives: esters and amides.
An ester is an organic compound that has the following functional group:
The general formula for an ester is RCOOR′, where R is a hydrogen atom or a hydrocarbon, and R′ is a hydrocarbon. You can think of an ester as the product of a reaction between a carboxylic acid and an alcohol, as shown in Figure 1.26.
To name an ester, you must recognize that an ester can be thought of as having two distinct parts. The main part of the ester contains the -COO group. This part comes from the parent acid. When numbering the main chain of a carboxylic acid, the carbon atom in the carboxyl group is always given position number 1. The second part of an ester is the alkyl group. To name an ester, follow the steps below.
How to Name an Ester
Step 1 Identify the main part of the ester, which contains the CO group. This part comes from the parent acid. Begin by naming the parent acid.
Step 2 Replace the -oic acid ending of the name of the parent acid with -oate.
Step 3 The second part of an ester is the alkyl group that is attached to the oxygen atom. Name this as you would name any other alkyl group.
Step 4 Put the two names together. Note that esters are named as two words. (See Figure 1.27.)
Table 1.13, on the next page, describes some of the physical properties of esters. As you will see, esters have different physical properties than carboxylic acids, even though esters and carboxylic acids are isomers of each other.
Additional Characteristics of Esters
• Esters often have pleasant odours and tastes, so they are used to produce perfumes and artificial flavours. In fact, the characteristic tastes and smells of many fruits come from esters. (See Figure 1.28.)
An ester can be thought of as the combination of a carboxylic acid and an alcohol. Similarly, you can think of an amide as the combination of a carboxylic acid and ammonia or an amine. An amide is an organic compound that has a carbon atom double-bonded to an oxygen atom and single-bonded to a nitrogen atom.
Amides have the functional group below:
The general formula for an amide is R-CO-NR2. R can stand for a hydrogen atom or an alkyl group. Figure 1.29 gives some examples of amides.
How to Name an Amide
Step 1 Locate the part of the amide that contains the CO group. Name the parent carboxylic acid that this part derives from. Note: The carbon in the CO group is always given position number 1.
Step 2 Replace the -oic acid ending of the name of the parent acid with the suffix -amide.
Step 3 Decide whether the compound is a primary, secondary, or tertiary amide:
• If there are two hydrogen atoms (and no alkyl groups) attached to the nitrogen atom, the compound is a primary amide and needs no other prefixes.
• If there is one alkyl group attached to the nitrogen atom, the compound is a secondary amide. Name the alkyl group, and give it location letter N- to indicate that it is bonded to the nitrogen atom.
• If there are two alkyl groups, the compound is a tertiary amide. Place the alkyl groups in alphabetical order. Use location letter N- before each group to indicate that it is bonded to the nitrogen atom. If the two groups are identical, use N,N-.
Step 4 Put the name together: prefix + root + suffix.
Additional Characteristics of Amides
• An amide called acetaminophen is a main component of many
• Urea, another common example of an amide, is made from the reaction
between carbon dioxide gas, CO2, and ammonia, NH3. Urea was the first
organic compound to be synthesized in a laboratory. It is found in the
urine of many mammals, including humans, and it is used as a fertilizer.
Comparing Physical Properties
In this chapter, you have learned how to recognize many different types
of organic compounds. In the first section, you learned how to use polar
bonds and the shape of a molecule to determine its molecular polarity.
The following investigation allows you to apply what you have learned
to predict and compare the physical properties of various organic
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.
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.
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.
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
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
When you cut yourself, it is often a good idea to swab the cut with rubbing alcohol to disinfect it. Most rubbing alcohols that are sold in drugstores are based on 2-propanol (common name: isopropanol), C3H8O. You can also swab a cut with a rubbing alcohol based on ethanol, C2H6O. Often it is hard to tell the difference between these two compounds. Both have a sharp smell, and both evaporate quickly. Both are effective at killing bacteria and disinfecting wounds. What is the connection between these compounds? Why is their behaviour so similar?
Both 2-propanol and ethanol contain the same functional group, an OH (hydroxyl) group, as shown in Figure 1.12. Because ethanol and 2-propanol have the same OH functional group, their behaviour is similar.
The general formula for a family of simple organic compounds is R + functional group. The letter R stands for any alkyl group. (If more than one alkyl group is present, R′ and R′′ are also used.) For example, the general formula ROH refers to any of the following compounds: CH3OH, CH3CH2OH, CH3CH2CH2OH, CH3CH2CH2CH2OH, etc.
Organic compounds are named according to their functional group. Generally, the suffix of a compound’s name indicates the most important functional group in the molecule. For example, the suffix -ene indicates
the presence of a double bond, and the suffix -ol indicates the presence of a hydroxyl group.
Functional groups are a useful way to classify organic compounds, for two reasons: 1. Compounds with the same functional group often have similar physical properties. In the next two sections, you will learn to recognize various functional groups. You will use functional groups to help you predict the physical properties of compounds.
2. Compounds with the same functional group react chemically in very similar ways. In Chapter 2, you will learn how compounds with each functional group react.
Table 1.4, on the next page, lists some of the most common functional groups.
Physical Properties and Forces Between Molecules
Organic compounds that have the same functional group often have similar physical properties, such as boiling points, melting points, and solubilities. Physical properties are largely determined by intermolecular forces, the forces of attraction and repulsion between particles. Three types of intermolecular forces are introduced below. You will examine
these forces further in Chapter 4.
• Hydrogen bonding is a strong intermolecular attraction between the hydrogen atom from an NH, OH, or FH group on one molecule, and a nitrogen, oxygen, or fluorine atom on another molecule.
• The attractive forces between polar molecules are called dipole-dipole interactions. These forces cause polar molecules to cling to each other.
• Dispersion forces are attractive forces that occur between all covalent molecules. These forces are usually very weak for small molecules, but they strengthen as the size of the molecule increases.
The process that is outlined on the next page will help you to predict the physical properties of organic compounds by examining the intermolecular forces between molecules. As you progress through the chapter, referring back to this process will enable you to understand the reasons behind trends in physical properties.
In the following ThoughtLab you will use the process in the box above to predict and compare the physical properties of some organic compounds.
Compounds With Single-Bonded Functional Groups
Alcohols, alkyl halides, ethers, and amines all have functional groups with single bonds. These compounds have many interesting uses in daily life. As you learn how to identify and name these compounds, think about how the intermolecular forces between their molecules affect their properties and uses.
An alcohol is an organic compound that contains the OH functional group. Depending on the position of the hydroxyl group, an alcohol can be primary, secondary, or tertiary. Figure 1.13 gives some examples of alcohols.
Table 1.6 lists some common physical properties of alcohols. As you learned earlier in this chapter, alcohols are polar molecules that experience hydrogen bonding. The physical properties of alcohols depend on these characteristics.
Additional Characteristics of Alcohols
• Alcohols are extremely flammable, and should be treated with caution.
• Most alcohols are poisonous. Methanol can cause blindness or death
when consumed. Ethanol is consumed widely in moderate quantities, but it causes impairment and/or death when consumed in excess.
An alkyl halide (also known as a haloalkane) is an alkane in which one or more hydrogen atoms have been replaced with halogen atoms, such as F, Cl, Br, or I. The functional group of alkyl halides is RX, where X represents a halogen atom. Alkyl halides are similar in structure, polarity, and reactivity to alcohols. To name an alkyl halide, first name the parent hydrocarbon. Then use the prefix fluoro-, chloro-, bromo-, or iodo-, with a position number, to indicate the presence of a fluorine atom, chlorine atom, bromine atom, or iodine atom. The following Sample Problem shows how to name an alkyl halide.
Suppose that you removed the H atom from the OH group of an alcohol. This would leave space for another alkyl group to attach to the oxygen atom.
The compound you have just made is called an ether. An ether is an organic compound that has two alkyl groups joined by an oxygen atom.
The general formula of an ether is ROR. You can think of alcohols and ethers as derivatives of the water molecule, as shown in Figure 1.14.
Figure 1.15 gives two examples of ethers.
To name an ether, follow the steps below. The Sample Problem then shows how to use these steps to give an ether its IUPAC name and its common name.
How to Name an Ether
Step 1 Choose the longest alkyl group as the parent alkane. Give it an alkane name.
Step 2 Treat the second alkyl group, along with the oxygen atom, as an alkoxy group attached to the parent alkane. Name it by replacing
the -yl ending of the corresponding alkyl group’s name with -oxy. Give it a position number.
Step 3 Put the prefix and suffix together: alkoxy group + parent alkane.
Step 1 List the alkyl groups that are attached to the oxygen atom, in alphabetical order.
Step 2 Place the suffix -ether at the end of the name.
Table 1.7 describes some physical properties of ethers. Like alcohols, ethers are polar molecules. Ethers, however, cannot form hydrogen bonds with themselves. The physical properties of ethers depend on these characteristics.
An organic compound with the functional group -NH2, -NHR, or -NR2 is called an amine. The letter N refers to the nitrogen atom. The letter R refers to an alkyl group attached to the nitrogen. The general formula of an amine is R-NR′2. Amines can be thought of as derivatives of the ammonia molecule, NH3. They are classified as primary, secondary, or tertiary, depending on how many alkyl groups are attached to the nitrogen atom. Note that the meanings of “primary,” “seconday,” and “tertiary” are slightly different from their meanings for alcohols.
Figure 1.16 gives some examples of amines.
To name an amine, follow the steps below. The Sample Problem illustrates how to use these steps to name a secondary amine.
How to Name an Amine
Step 1 Identify the largest hydrocarbon group attached to the nitrogen atom
as the parent alkane.
Step 2 Replace the -e at the end of the name of the parent alkane with
the new ending -amine. Include a position number, if necessary, to
show the location of the functional group on the hydrocarbon chain.
Step 3 Name the other alkyl group(s) attached to the nitrogen atom. Instead
of position numbers, use the letter N- to locate the group(s). (If two
identical alkyl groups are attached to the nitrogen atom, use N,N-.)
This is the prefix.
Step 4 Put the name together: prefix + root + suffix.
Amines are polar compounds. Primary and secondary amines can form hydrogen bonds, but tertiary amines cannot. Table 1.8 lists some common physical properties of amines.
Additional Characteristics of Amines
• Amines are found widely in nature. They are often toxic. Many amines that are produced by plants have medicinal properties.
(See Figure 1.17.)
• Amines with low molecular masses have a distinctive fishy smell. Also, many offensive odours of decay and decomposition are caused by amines. For example, cadavarine, H2NCH2CH2CH2CH2CH2NH2, contributes to the odour of decaying flesh. This compound gets its common name from the word “cadaver,” meaning “dead body.”
• Like ammonia, amines act as weak bases. Since amines are bases, adding an acid to an amine produces a salt. This explains why vinegar and lemon juice (both acids) can be used to neutralize the fishy smell of seafood, which is caused by basic amines.
In this section, you will review the structure and names of hydrocarbons. As you may recall from your previous chemistry studies, hydrocarbons are the simplest type of organic compound. Hydrocarbons are composed
entirely of carbon and hydrogen atoms, and are widely used as fuels. Gasoline, propane, and natural gas are common examples of hydrocarbons. Because they contain only carbon and hydrogen atoms, hydrocarbons are
Scientists classify hydrocarbons as either aliphatic or aromatic. An aliphatic hydrocarbon contains carbon atoms that are bonded in one or more chains and rings. The carbon atoms have single, double, or triple bonds. Aliphatic hydrocarbons include straight chain and cyclic alkanes, alkenes, and alkynes. An aromatic hydrocarbon is a hydrocarbon based on the aromatic benzene group. You will encouter this group later in the section. Benzene is the simplest aromatic compound. Its bonding arrangement results in special molecular stability.
Alkanes, Alkenes, and Alkynes
An alkane is a hydrocarbon that has only single bonds. Alkanes that do not contain rings have the formula CnH2n + 2. An alkane in the shape of a ring is called a cycloalkane. Cycloalkanes have the formula CnH2n. An alkene is a compound that has at least one double bond. Straight-chain alkenes with one double bond have the same formula as cycloalkanes, CnH2n. A double bond involves two pairs of electrons. In a double bond, one pair of electrons forms a single bond and the other pair forms an additional, weaker bond. The electrons in the additional, weaker bond react faster than the electrons in the single bond. Thus, carbon-carbon double bonds are more reactive than carbon-carbon single bonds. When an alkene reacts, the reaction almost always occurs at the site of the double bond.
A functional group is a reactive group of bonded atoms that appears in all the members of a chemical family. Each functional group reacts in a characteristic way. Thus, functional groups help to determine the physical and chemical properties of compounds. For example, the reactive double bond is the functional group for an alkene. In this course, you will encounter many different functional groups. An alkyne is a compound that has at least one triple bond. A straightchain alkyne with one triple bond has the formula CnH2n – 2. Triple bonds are even more reactive than double bonds. The functional group for an alkyne is the triple bond.
Figure 1.7 gives examples of an alkane, a cycloalkane, an alkene, and an alkyne.
General Rules for Naming Organic Compounds
The International Union of Pure and Applied Chemistry (IUPAC) has set standard rules for naming organic compounds. The systematic (or IUPAC) names of alkanes and most other organic compounds follow the same pattern, shown below.
The Root: How Long Is the Main Chain?
The root of a compound’s name indicates the number of carbon atoms in the main (parent) chain or ring. Table 1.2 gives the roots for hydrocarbon chains that are up to ten carbons long. To determine which root to use, count the carbons in the main chain, or main ring, of the compound. If the compound is an alkene or alkyne, the main chain or ring must include the multiple bond.
The Suffix: What Family Does the Compound Belong To?
The suffix indicates the type of compound, according to the functional groups present. (See Table 1.4 on page 22.) As you progress through this chapter, you will learn the suffixes for different chemical families. In your previous chemistry course, you learned the suffixes -ane for alkanes, -ene for alkenes, and -yne for alkynes. Thus, an alkane composed of six carbon atoms in a chain is called hexane. An alkene with three carbons is called propene.
The Prefix: What Is Attached to the Main Chain?
The prefix indicates the name and location of each branch and functional group on the main carbon chain. Most organic compounds have branches, called alkyl groups, attached to the main chain. An alkyl group is obtained
by removing one hydrogen atom from an alkane. To name an alkyl group, change the -ane suffix to -yl. For example, CH3 is the alkyl group that is derived from methane, CH4. It is called the methyl group, taken from the root meth-. Table 1.3 gives the names of the most common alkyl groups.
Read the steps below to review how to name hydrocarbons. Then examine the two Sample Problems that follow.
How to Name Hydrocarbons
|Find the root: Identify the longest chain or ring in the hydrocarbon. If the hydrocarbon is an alkene or an alkyne, make sure that you include any multiple bonds in the main chain. Remember that the
chain does not have to be in a straight line. Count the number of carbon atoms in the main chain to obtain the root. If it is a cyclic compound, add the prefix -cyclo- before the root.
|Find the suffix: If the hydrocarbon is an alkane, use the suffix -ane. Use -ene if the hydrocarbon is an alkene. Use -yne if the hydrocarbon is an alkyne. If more than one double or triple bond is present, use the prefix di- (2) or tri- (3) before the suffix to indicate the number of multiple bonds.
|Give a position number to every carbon atom in the main chain. Start from the end that gives you the lowest possible position number for the double or triple bond, if there is one. If there is no double or triple bond, number the compound so that the branches have the lowest possible position numbers.
|Find the prefix: Name each branch as an alkyl group, and give it a position number. If more than one branch is present, write the names of the branches in alphabetical order. Put the position number of any double or triple bonds after the position numbers and names of the branches, just before the root. This is the prefix.
Note: Use the carbon atom with the lowest position number to give the location of a double or triple bond.
|Put the name together: prefix + root + suffix.
If you completed the Concept Check activity on page 12, you drew a possible structure for benzene. For many years, scientists could not
determine the structure of benzene. From its molecular formula, C6H6,
scientists reasoned that it should contain two double bonds and one triple
bond, or even two triple bonds. Benzene, however, does not undergo the
same reactions as other compounds with double or triple bonds.
We know today that benzene is a cyclic compound with the equivalent
of three double bonds and three single bonds, as shown in Figure 1.9(A).
However, the electrons that form the double bonds in benzene are spread
out and shared over the whole molecule. Thus, benzene actually has six
identical bonds, each one half-way between a single and a double bond.
These bonds are much more stable than ordinary double bonds and do
not react in the same way. Figure 1.9(B) shows a more accurate way to
represent the bonding in benzene. Molecules with this type of special
electron sharing are called aromatic compounds. As mentioned earlier,
benzene is the simplest aromatic compound.
Figure 1.10 illustrates some common aromatic compounds. To name
an aromatic compound, follow the steps below. Figure 1.11 gives an
Naming an Aromatic Hydrocarbon
Step 1 Number the carbons in the benzene ring. If more than one type of branch is attached to the ring, start numbering at the carbon with the highest priority (or most complex) group. (See the Problem Tip.)
Step 2 Name any branches that are attached to the benzene ring. Give these branches position numbers. If only one branch is attached to a benzene ring, you do not need to include a position number.
Step 3 Place the branch numbers and names as a prefix before the root, benzene.
Chemists do not always use position numbers to describe the branches CHEM that are attached to a benzene ring. When a benzene ring has only two branches, the prefixes ortho-, meta-, and para- are sometimes used instead
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.
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.
Early scientists defined organic compounds as compounds that originate from living things. In 1828, however, the German chemist Friedrich Wohler (1800–1882) made an organic compound called urea, CO(NH2)2, out of an
inorganic compound called ammonium cyanate, NH4CN. Urea is found in the urine of mammals. This was the first time in history that a compound normally made only by living things was made from a non-living substance. Since Wohler had discovered that organic compounds can be made without the involvement of a life process, a new definition was required.
Organic compounds are now defined as compounds that are based on carbon. They usually contain carbon-carbon and carbon-hydrogen bonds.
The Carbon Atom
There are several million organic compounds, but only about a quarter of a million inorganic compounds (compounds that are not based on carbon). Why are there so many organic compounds? The answer lies in the bonding properties of carbon.
As shown in Figure 1.1, each carbon atom usually forms a total of four covalent bonds. Thus, a carbon atom can connect to as many as four other atoms. Carbon can bond to many other types of atoms, including hydrogen, oxygen, and nitrogen.
In addition, carbon atoms can form strong single, double, or triple bonds with other carbon atoms. In a single carbon-carbon bond, one pair of electrons is shared between two carbon atoms. In a double bond, two pairs of electrons are shared between two atoms. In a triple bond, three pairs of electrons are shared between two atoms. Molecules that contain only single carbon-carbon bonds are saturated. In other words, all carbon atoms are bonded to the maximum number of other atoms: four. No more bonding can occur. Molecules that contain double or triple carbon-carbon bonds are unsaturated. The carbon atoms on either side of the double or triple bond are bonded to less than four
atoms each. There is potential for more atoms to bond to each of these carbon atoms.
Carbon’s unique bonding properties allow the formation of a variety of structures, including chains and rings of many shapes and sizes. Figure 1.2 on the next page illustrates some of the many shapes that can be formed from a backbone of carbon atoms. This figure includes examples of three types of structural diagrams that are used to depict organic molecules. (The Concepts and Skills Review contains a further review of these types of structural diagrams.)
Carbon compounds in which carbon forms only single bonds have a different shape than compounds in which carbon forms double or triple bonds. In the following ExpressLab, you will see how each type of bond affects the shape of a molecule.
the shape of a molecule depends on the type of bond. Table 1.1 describes some shapes that you must know for your study of organic chemistry. In Unit 2, you will learn more about why different shapes and angles form around an atom.
Three-Dimensional Structural Diagrams
Two-dimensional structural diagrams of organic compounds, such as condensed structural diagrams and line structural diagrams, work well for flat molecules. As shown in the table above, however, molecules containing single-bonded carbon atoms are not flat.
You can use a three-dimensional structural diagram to draw the tetrahedral shape around a single-bonded carbon atom. In a three-dimensional diagram, wedges are used to give the impression that an atom or group is coming forward, out of the page. Dashed or dotted lines are used to show that an atom or group is receding, or being pushed back into the page. In Figure 1.3, the Cl atom is coming forward, and the Br atom is behind. The two H atoms are flat against the surface of the page.
Molecular Shape and Polarity
The three-dimensional shape of a molecule is particularly important when the molecule contains polar covalent bonds. As you may recall from your previous chemistry course, a polar covalent bond is a covalent bond between two atoms with different electronegativities.
Electronegativity is a measure of how strongly an atom attracts electrons in a chemical bond. The electrons in a polar covalent bond are attracted more strongly to the atom with the higher electronegativity. This atom has a partial negative charge, while the other atom has a partial positive charge. Thus, every polar bond has a bond dipole: a partial negative charge and a partial positive charge, separated by the length of the bond.
Figure 1.4 illustrates the polarity of a double carbon-oxygen bond. Oxygen has a higher electronegativity than carbon. Therefore, the oxygen atom in a carbon-oxygen bond has a partial negative charge, and the carbon atom
has a partial positive charge.
Other examples of polar covalent bonds include CO, OH, and NH. Carbon and hydrogen attract electrons to almost the same degree. Therefore, when carbon is bonded to another carbon atom or to a hydrogen atom, the bond is not usually considered to be polar. For example, CC bonds are considered to be non-polar.
Predicting Molecular Polarity
A molecule is considered to be polar, or to have a molecular polarity, when the molecule has an overall imbalance of charge. That is, the molecule has a region with a partial positive charge, and a region with a partial negative charge. Surprisingly, not all molecules with polar bonds are polar molecules. For example, a carbon dioxide molecule has two
polar CO bonds, but it is not a polar molecule. On the other hand, a water molecule has two polar OH bonds, and it is a polar molecule.
How do you predict whether or not a molecule that contains polar bonds has an overall molecular polarity? To determine molecular polarity, you must consider the shape of the molecule and the bond dipoles within the
If equal bond dipoles act in opposite directions in three-dimensional space, they counteract each other. A molecule with identical polar bonds that point in opposite directions is not polar. Figure 1.5 shows two examples, carbon dioxide and carbon tetrachloride. Carbon dioxide, CO2, has two polar CO bonds acting in opposite directions, so the molecule
is non-polar. Carbon tetrachloride, CCl4, has four polar CCl bonds in a tetrahedral shape. You can prove mathematically that four identical dipoles, pointing toward the vertices of a tetrahedron, counteract each other exactly. (Note that this mathematical proof only applies if all four bonds are identical.) Therefore, carbon tetrachloride is also non-polar.
If the bond dipoles in a molecule do not counteract each other exactly, the molecule is polar. Two examples are water, H2O, and chloroform, CHCl3, shown in Figure 1.6. Although each molecule has polar bonds, the bond dipoles do not act in exactly opposite directions. The bond dipoles do not counteract each other, so these two molecules are polar.
The steps below summarize how to predict whether or not a molecule is polar. The Sample Problem that follows gives three examples.
Note: For the purpose of predicting molecular polarity, you can assume that CH bonds are non-polar. In fact, they have a very low polarity.
Step 1 Does the molecule have polar bonds? If your answer is no, see below. If your answer is yes, go to step 2.
If a molecule has no polar bonds, it is non–polar. Examples: CH3CH2CH3, CH2CH2
Step 2 Is there more than one polar bond? If your answer is no, see below. If your answer is yes, go to step 3.
If a molecule contains only one polar bond, it is polar. Examples: CH3Cl, CH3CH2CH2Cl
Step 3 Do the bond dipoles act in opposite directions and counteract each other? Use your knowledge of three-dimensional molecular shapes to help you answer this question. If in doubt, use a molecular model to help you visualize the shape of the molecule.
If a molecule contains bond dipoles that do not counteract each other, the molecule is polar. Examples: H2O, CHCl3
If the molecule contains dipoles that counteract each other, the molecule is non–polar. Examples: CO2, CCl4