2.4 Organic Compounds Essential to Human Functioning

Organic compounds typically consist of groups of carbon atoms covalently bonded to hydrogen, usually oxygen, and often other elements as well. Created by living things, they are found throughout the world, in soils and seas, commercial products, and every cell of the human body. The four types most important to human structure and function are carbohydrates, lipids, proteins, and nucleotides. Before exploring these compounds, you need to first understand the chemistry of carbon.

The Chemistry of Carbon

What makes organic compounds ubiquitous is the chemistry of their carbon core. Recall that carbon atoms have four electrons in their valence shell and that the octet rule dictates that atoms tend to react in such a way as to complete their valence shell with eight electrons. Carbon atoms do not complete their valence shells by donating or accepting four electrons. Instead, they readily share electrons via covalent bonds.

Normally, carbon atoms share with other carbon atoms, often forming a long carbon chain referred to as a carbon skeleton. When they share, however, they do not share all their electrons exclusively with each other. Rather, carbon atoms tend to share electrons with a variety of other elements, one of which is always hydrogen. Carbon and hydrogen groupings are called hydrocarbons. If you study the figures of organic compounds in the remainder of this chapter, you will see several with chains of hydrocarbons in one region of the compound.

Many combinations are possible to fill carbon’s four “vacancies.” Carbon may share electrons with oxygen or nitrogen or other atoms in a particular region of an organic compound. Moreover, the atoms to which carbon atoms bond may also be part of a functional group. A functional group is a group of atoms linked by strong covalent bonds and tending to function in chemical reactions as a single unit. You can think of functional groups as tightly knit “cliques” whose members are unlikely to be parted. Five functional groups are important in human physiology: the hydroxyl, carboxyl, amino, methyl and phosphate groups (Table 2.1).

Carbon’s affinity for covalent bonding means that many distinct and relatively stable organic molecules readily form larger, more complex molecules. Any large molecule is referred to as macromolecule (“macro-” meaning “large”), and the organic compounds in this section all fit this description. However, some macromolecules are made up of several “copies” of single units called monomer (“mono-” meaning “one”; “-mer” meaning “part”). Like beads in a long necklace, these monomers link by covalent bonds to form long polymers (“poly-” meaning “many”). There are many examples of monomers and polymers among the organic compounds.

Monomers form polymers by engaging in dehydration synthesis (Figure 2.4.1). As was noted earlier, this reaction results in the release of a molecule of water. Each monomer contributes; one gives up a hydrogen atom and the other gives up a hydroxyl group. Polymers are split into monomers by hydrolysis (“-lysis” meaning “rupture”). The bonds between their monomers are broken via the donation of a molecule of water, which contributes a hydrogen atom to one monomer and a hydroxyl group to the other.

Carbohydrates

The term carbohydrate means “hydrated carbon.” Recall that the root “hydro-” indicates water. A carbohydrate is a molecule composed of carbon, hydrogen, and oxygen; in most carbohydrates, hydrogen and oxygen are found in the same two-to-one relative proportions they have in water. In fact, the chemical formula for a “generic” molecule of carbohydrate is (CH₂O)_n.

Carbohydrates are referred to as saccharides, a word meaning “sugars.” Three forms are important in the body: monosaccharides, disaccharides, and polysaccharides. Monosaccharides are the monomers of carbohydrates. Disaccharides (“di-” meaning “two”) are made up of two monomers. Polysaccharides are the polymers and can consist of hundreds to thousands of monomers.

Monosaccharides

A monosaccharide is a monomer of carbohydrates. Five monosaccharides are important in the body. Three of these are the hexose sugars, so called because they each contain six atoms of carbon. These are glucose, fructose, and galactose, shown in Figure 2.4.1a. The remaining monosaccharides are the two pentose sugars, each of which contains five atoms of carbon. They are ribose and deoxyribose, shown in Figure 2.4.1b.

Disaccharides

A disaccharide is a pair of monosaccharides. Disaccharides are formed via dehydration synthesis, and the bond linking them is referred to as a glycosidic bond (“glyco-” meaning “sugar”). Three disaccharides (shown in Figure 2.4.2) are important to humans. These are sucrose, commonly referred to as table sugar; lactose, or milk sugar; and maltose, or malt sugar. As you can tell from their common names, you consume these in your diet; however, your body cannot use them directly. Instead, they are split into their component monosaccharides in the digestive tract via hydrolysis.

Polysaccharides

Polysaccharides can contain a few to a thousand or more monosaccharides. Three are important to the body (Figure 2.4.3):

• Starches are polymers of glucose. They occur in long chains called amylose or branched chains called amylopectin, both of which are stored in plant-based foods and are relatively easy to digest.
• Glycogen is also a polymer of glucose, but it is stored in the tissues of animals, especially in the muscles and liver. It is not considered a dietary carbohydrate because very little glycogen remains in animal tissues after slaughter. However, the human body stores excess glucose as glycogen, again, in the muscles and liver.
• Cellulose, a polysaccharide that is the primary component of the cell wall of green plants, is the component of plant food referred to as “fiber.” In humans, cellulose/fiber is not digestible; however, dietary fiber has many health benefits. It helps you feel full so you eat less, it promotes a healthy digestive tract, and a diet high in fiber is thought to reduce the risk of heart disease and possibly some forms of cancer.

Functions of Carbohydrates

The body obtains carbohydrates from plant-based foods. Grains, fruits, legumes, and vegetables provide most of the carbohydrates in the human diet, although lactose is found in dairy products.

Although most body cells can break down other organic compounds for fuel, all body cells can use glucose. Moreover, nerve cells (neurons) in the brain, spinal cord, and peripheral nervous system, as well as red blood cells, can only use glucose for fuel. In the breakdown of glucose for energy, molecules of adenosine triphosphate, better known as ATP, are produced. Adenosine triphosphate (ATP) is composed of a ribose sugar, an adenine base, and three phosphate groups. ATP releases free energy when its phosphate bonds are broken and thus supplies ready energy to the cell. More ATP is produced in the presence of oxygen (O2) than in pathways that do not use oxygen. The overall reaction for the conversion of the energy in glucose to energy stored in ATP can be written as follows:

C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + ATP

In addition to being a critical fuel source, carbohydrates are present in very small amounts in cells’ structure. For instance, some carbohydrate molecules bind with proteins to produce glycoproteins, and others combine with lipids to produce glycolipids, both of which are found in the membrane that encloses the contents of body cells.

Lipids

A lipid is one of a highly diverse group of compounds made up mostly of hydrocarbons. The few oxygen atoms they contain are often at the periphery of the molecule. Their nonpolar hydrocarbons make all lipids hydrophobic. In water, lipids do not form a true solution, but they may form an emulsion, which is the term for a mixture of solutions that do not mix well.

Triglycerides

A triglyceride is one of the most common dietary lipid groups, and it is the type found most abundantly in body tissues. This compound, which is commonly referred to as a fat, is formed from the synthesis of two types of molecules (Figure 2.4.4):

• A glycerol backbone at the core of triglycerides, consisting of three carbon atoms
• Three fatty acids, long chains of hydrocarbons with a carboxyl group and a methyl group at opposite ends, extending from each of the carbons of the glycerol

Triglycerides form via dehydration synthesis. Glycerol gives up hydrogen atoms from its hydroxyl groups at each bond, and the carboxyl group on each fatty acid chain gives up a hydroxyl group. A total of three water molecules are thereby released.

Fatty acid chains that have no double carbon bonds anywhere along their length and therefore contain the maximum number of hydrogen atoms are called saturated fatty acids. These straight, rigid chains pack tightly together and are solid or semisolid at room temperature (Figure 2.4.5a). Butter and lard are examples, as is the fat found on a steak or in your own body. In contrast, fatty acids with one double carbon bond are kinked at that bond (Figure 2.4.5b). These monounsaturated fatty acids are therefore unable to pack together tightly and are liquid at room temperature. Polyunsaturated fatty acids contain two or more double carbon bonds and are also liquid at room temperature. Plant oils such as olive oil typically contain both mono- and polyunsaturated fatty acids.

Whereas a diet high in saturated fatty acids increases the risk of heart disease, a diet high in unsaturated fatty acids is thought to reduce the risk. This is especially true for the omega-3 unsaturated fatty acids found in cold-water fish such as salmon. These fatty acids have their first double carbon bond at the third hydrocarbon from the methyl group (referred to as the omega end of the molecule).

Finally, trans fatty acids found in some processed foods, including some stick and tub margarines, are thought to be even more harmful to the heart and blood vessels than saturated fatty acids. Trans fats are created from unsaturated fatty acids (such as corn oil) chemically treated to produce partially hydrogenated fats.

As a group, triglycerides are a major fuel source for the body. When you are resting or asleep, a majority of the energy used to keep you alive is derived from triglycerides stored in your fat (adipose) tissues. Triglycerides also fuel long, slow physical activity (such as gardening or hiking) and contribute a modest percentage of energy for vigorous physical activity. Dietary fat also assists the absorption and transport of the nonpolar fat-soluble vitamins A, D, E, and K. Additionally, stored body fat protects and cushions the body’s bones and internal organs and acts as insulation to retain body heat.

Fatty acids are also components of glycolipids, which are sugar-fat compounds found in the cell membrane. Lipoproteins are compounds in which the hydrophobic triglycerides are packaged in protein envelopes for transport in body fluids.

Phospholipids

As its name suggests, a phospholipid is a bond between the glycerol component of a lipid and a phosphate group. In fact, phospholipids are similar in structure to triglycerides. However, instead of having three fatty acids, a phospholipid is generated from a diglyceride, a glycerol with just two fatty acid chains (Figure 2.4.6). The third binding site on the glycerol is taken up by the phosphate group, which in turn is attached to a polar “head” region of the molecule. Recall that triglycerides are nonpolar and hydrophobic. This still holds for the fatty acid portion of a phospholipid compound. However, the head of a phospholipid contains charges on the phosphate groups, as well as on the nitrogen atom. These charges make the phospholipid head hydrophilic. Therefore, phospholipids are said to have hydrophobic tails, containing the neutral fatty acids, hydrophilic heads, the charged phosphate groups, and nitrogen atom.

Steroids

A steroid compound (referred to as a sterol) has as its foundation a set of four hydrocarbon rings bonded to a variety of other atoms and molecules (Figure 2.4.6b). Although both plants and animals synthesize sterols, the type that makes the most important contribution to human structure and function is cholesterol, which is synthesized by the liver in humans and animals and is also present in most animal-based foods. Like other lipids, cholesterol’s hydrocarbons make it hydrophobic; however, it has a polar hydroxyl head that is hydrophilic. Cholesterol is an important component of bile acids and compounds that help emulsify dietary fats. In fact, the word’s root “chole-” refers to bile. Cholesterol is also a building block of many hormones, signaling molecules that the body releases to regulate processes at distant sites. Finally, like phospholipids, cholesterol molecules are found in the cell membrane, where their hydrophobic and hydrophilic regions help regulate the flow of substances into and out of the cell.

Prostaglandins

Like a hormone, a prostaglandin is one of a group of signaling molecules, but prostaglandins are derived from unsaturated fatty acids (Figure 2.4.6c). One reason that the omega-3 fatty acids found in fish are beneficial is that they stimulate the production of certain prostaglandins that help regulate aspects of blood pressure and inflammation, and thereby reduce the risk for heart disease. Prostaglandins also sensitize nerves to pain. One class of pain-relieving medications called nonsteroidal anti-inflammatory drugs (NSAIDs) works by reducing the effects of prostaglandins.

Proteins

You might associate proteins with muscle tissue, but in fact, proteins are critical components of all tissues and organs. A protein is an organic molecule composed of amino acids linked by peptide bonds. Proteins include the keratin in the epidermis of skin that protects underlying tissues, and the collagen found in the dermis of skin, bones, and the meninges that cover the brain and spinal cord. Proteins are also components of many of the body’s functional chemicals, including digestive enzymes in the digestive tract, antibodies, the neurotransmitters that neurons use to communicate with other cells, and the peptide-based hormones that regulate certain body functions (e.g., growth hormone). While carbohydrates and lipids are composed of hydrocarbons and oxygen, all proteins also contain nitrogen (N), and many contain sulfur (S), in addition to carbon, hydrogen, and oxygen.

Microstructure of Proteins

Proteins are polymers made up of nitrogen-containing monomers called amino acids. An amino acid is a molecule composed of an amino group and a carboxyl group, together with a variable side chain. Just 20 different amino acids contribute to nearly all of the thousands of different proteins important in human structure and function. Body proteins contain a unique combination of a few dozen to a few hundred of these 20 amino acid monomers. All 20 of these amino acids share a similar structure (Figure 2.4.7). All consist of a central carbon atom to which the following are bonded:

• A hydrogen atom
• An alkaline (basic) amino group NH2 (Table 2.1)
• An acidic carboxyl group COOH (Table 2.1)
• A variable group

Notice that all amino acids contain both an acid (the carboxyl group) and a base (the amino group) (“amine” meaning “nitrogen-containing”). For this reason, they make excellent buffers, helping the body regulate acid–base balance. What distinguishes the 20 amino acids from one another is their variable group, which is referred to as a side chain or an R-group. This group can vary in size and can be polar or nonpolar, giving each amino acid its unique characteristics. For example, the side chains of two amino acids—cysteine and methionine—contain sulfur. Sulfur does not readily participate in hydrogen bonds, whereas all other amino acids do. This variation influences the way that proteins containing cysteine and methionine are assembled.

Amino acids join via dehydration synthesis to form protein polymers (Figure 2.4.8). The unique bond holding amino acids together is called a peptide bond. A peptide bond is a covalent bond between two amino acids that is formed by dehydration synthesis. A peptide, in fact, is a very short chain of amino acids. Strands containing fewer than about 100 amino acids are generally referred to as polypeptides rather than proteins.

The body is able to synthesize most of the amino acids from components of other molecules; however, nine cannot be synthesized and have to be consumed in the diet. These are known as the essential amino acids.

Free amino acids available for protein construction are said to reside in the amino acid pool within cells. Structures within cells use these amino acids when assembling proteins. If a particular essential amino acid is not available in sufficient quantities in the amino acid pool, however, synthesis of proteins containing it can slow or even cease.

Clinical Connection – Thalidomide

In the 1950s, a new drug called thalidomide became available in some parts of Europe. The drug had been developed by Grünenthal, a West German pharmaceutical company. Thalidomide is a derivative of glutamic acid, one of the 20 amino acids used in protein production. Thalidomide was available over the counter and was promoted as an effective drug for sleep problems, anxiety, and morning sickness.

The structure of thalidomide is complex; when the molecule is formed, it will spontaneously and randomly form as one of two configurations called enantiomers (Figure 2.4.9). These enantiomers are like your left and right hands—while they contain the same structures, they are mirror images of one another that cannot be perfectly superimposed. This difference in structure gives the two versions of thalidomide different properties. One version, called the R-enantiomer, functions as a sedative; the other version, called the S-enantiomer, is a powerful teratogen that produces severe birth defects. In developing thalidomide, Grünenthal only performed minimal testing of the drug; as a result of this lack of testing, the risk of birth defects was not identified and the drug was promoted throughout Europe as a sedative without negative side effects.

In 1960, the drug company Merrell sought to distribute thalidomide in the United States. Like Gruenthal, Merrell did not perform adequate testing of the drug and entirely skipped testing the drug on animals. Despite the lack of safety testing, the company applied to the U.S. Food and Drug Administration (FDA) for approval to bring thalidomide to the U.S. market in September 1960. The new drug application (NDA) for thalidomide was reviewed by Dr. Frances Kelsey—it was her second NDA to review, as she had only recently joined the NDA division of the FDA. Dr. Kelsey found multiple omissions in the NDA and rejected it, prompting Merrell to submit more data, which was also incomplete. Over the course of two years, Dr. Kelsey repeatedly blocked approval for thalidomide, citing incomplete or inadequate data. By 1961, multiple reports of nerve damage, miscarriage, and severe birth defects came from Europe, where thalidomide had been available for years; thalidomide was removed from the European markets in 1961, but by this time over 10,000 children had died and thousands more had been born with severe birth defects due to the effects of thalidomide. Merrell finally withdrew their application in 1962, and Dr. Kelsey is credited with preventing the thalidomide crisis from reaching the United States.

Watch the video below for more information on Dr. Kelsey and the thalidomide crisis.

Video 2.1. How One Scientist Averted a National Health Crisis  – Andrea Tone by Ted-Ed

Shape of Proteins

Just as a fork cannot be used to eat soup and a spoon cannot be used to spear meat, a protein’s shape is essential to its function. A protein’s shape is determined, most fundamentally, by the sequence of amino acids of which it is made (Figure 2.4.10a). The sequence is called the primary structure of the protein.

Although some polypeptides exist as linear chains, most are twisted or folded into more complex secondary structures that form when bonding occurs between amino acids with different properties at different regions of the polypeptide. The most common secondary structure is a spiral called an alpha-helix. If you were to take a length of string and simply twist it into a spiral, it would not hold the shape. Similarly, a strand of amino acids could not maintain a stable spiral shape without the help of hydrogen bonds, which create bridges between different regions of the same strand (Figure 2.4.10b). Less commonly, a polypeptide chain can form a beta-pleated sheet, in which hydrogen bonds form bridges between different regions of a single polypeptide that has folded back upon itself or between two or more adjacent polypeptide chains.

The secondary structure of proteins further folds into a compact three-dimensional shape, referred to as the protein’s tertiary structure (Figure 2.4.10c). In this configuration, amino acids that had been very distant in the primary chain can be brought quite close via hydrogen bonds or, in proteins containing cysteine, via disulfide bonds. A disulfide bond is a covalent bond between sulfur atoms in a polypeptide. Often, two or more separate polypeptides bond to form an even larger protein with a quaternary structure (Figure 2.4.10d). The polypeptide subunits forming a quaternary structure can be identical or different. For instance, hemoglobin, the protein found in red blood cells is composed of four tertiary polypeptides, two of which are called alpha chains and two of which are called beta chains.

When they are exposed to extreme heat, acids, bases, and certain other substances, proteins will denature. Denaturation is a change in the structure of a molecule through physical or chemical means. Denatured proteins lose their functional shape and are no longer able to carry out their jobs. An everyday example of protein denaturation is the curdling of milk when acidic lemon juice is added.

The contribution of the shape of a protein to its function can hardly be exaggerated. For example, the long, slender shape of protein strands that make up muscle tissue is essential to their ability to contract (shorten) and relax (lengthen). As another example, bones contain long threads of a protein called collagen that acts as scaffolding upon which bone minerals are deposited. These elongated proteins, called fibrous proteins, are strong and durable and typically hydrophobic.

In contrast, globular proteins are globes or spheres that tend to be highly reactive and are hydrophilic. The hemoglobin proteins packed into red blood cells are an example (Figure 2.4.10d); however, globular proteins are abundant throughout the body, playing critical roles in most body functions. Enzymes, introduced earlier as protein catalysts, are examples of this. The next section takes a closer look at the action of enzymes.

Proteins Function as Enzymes

If you were trying to type a paper, and every time you hit a key on your laptop there was a delay of six or seven minutes before you got a response, you would probably get a new laptop. In a similar way, without enzymes to catalyze chemical reactions, the human body would be nonfunctional. It functions only because enzymes function.

Enzymatic reactions—chemical reactions catalyzed by enzymes—begin when substrates bind to the enzyme. A substrate is a reactant in an enzymatic reaction. This occurs on regions of the enzyme known as active sites (Figure 2.4.11). Any given enzyme catalyzes just one type of chemical reaction. This characteristic, called specificity, is due to the fact that a substrate with a particular shape and electrical charge can bind only to an active site corresponding to that substrate.

Binding of a substrate produces an enzyme–substrate complex. It is likely that enzymes speed up chemical reactions in part because the enzyme–substrate complex undergoes a set of temporary and reversible changes that cause the substrates to be oriented toward each other in an optimal position to facilitate their interaction. This promotes increased reaction speed. The enzyme then releases the product(s) and resumes its original shape. The enzyme is then free to engage in the process again, and it will do so as long as substrate remains.

Other Functions of Proteins

Advertisements for protein bars, powders, and shakes all say that protein is important in building, repairing, and maintaining muscle tissue, but the truth is that proteins contribute to all body tissues, from the skin to the brain cells. Also, certain proteins act as hormones and chemical messengers that help regulate body functions. For example, growth hormone is important for skeletal growth, among other roles.

As was noted earlier, the basic and acidic components enable proteins to function as buffers in maintaining acid–base balance, but they also help regulate fluid–electrolyte balance. Proteins attract fluid, and a healthy concentration of proteins in the blood, the cells, and the spaces between cells helps ensure a balance of fluids in these various “compartments.” Moreover, proteins in the cell membrane help to transport electrolytes in and out of the cell, keeping these ions in a healthy balance. Like lipids, proteins can bind with carbohydrates. They can thereby produce glycoproteins or proteoglycans, both of which have many functions in the body.

The body can use proteins for energy when carbohydrate and fat intake is inadequate and stores of glycogen and adipose tissue become depleted. However, since there is no storage site for protein except functional tissues, using protein for energy causes tissue breakdown and results in body wasting.

Nucleotides

The fourth type of organic compound important to human structure and function are the nucleotides (Figure 2.4.12). A nucleotide is one of a class of organic compounds composed of three subunits:

• One or more phosphate groups
• A pentose sugar (either deoxyribose or ribose)
• A nitrogen-containing base (adenine, cytosine, guanine, thymine, or uracil)

Nucleotides can be assembled into nucleic acids (DNA or RNA) or the energy compound adenosine triphosphate.

Nucleic Acids

The nucleic acids differ in their type of pentose sugar. Deoxyribonucleic acid (DNA) is nucleotide that stores genetic information. DNA contains deoxyribose (so called because it has one less atom of oxygen than ribose) plus one phosphate group and one nitrogen-containing base. The “choices” of base for DNA are adenine, cytosine, guanine, and thymine. Ribonucleic acid (RNA) is a ribose-containing nucleotide that helps manifest the genetic code as protein. RNA contains ribose, one phosphate group, and one nitrogen-containing base, but the “choices” of base for RNA are adenine, cytosine, guanine, and uracil.

The nitrogen-containing bases adenine and guanine are classified as purines. A purine is a nitrogen-containing molecule with a double ring structure, which accommodates several nitrogen atoms. The bases cytosine, thymine (found in DNA only), and uracil (found in RNA only) are pyrimidines. A pyrimidine is a nitrogen-containing base with a single ring structure

Bonds formed by dehydration synthesis between the pentose sugar of one nucleic acid monomer and the phosphate group of another form a “backbone” from which the components’ nitrogen-containing bases protrude. In DNA, two such backbones attach at their protruding bases via hydrogen bonds. These twist to form a shape known as a double helix (Figure 2.4.13). The sequence of nitrogen-containing bases within a strand of DNA form the genes that act as a molecular code instructing cells in the assembly of amino acids into proteins. Humans have almost 22,000 genes in their DNA, locked up in the 46 chromosomes inside the nucleus of each cell (except red blood cells, which lose their nuclei during development). These genes carry the genetic code to build one’s body and are unique for each individual except identical twins.

In contrast, RNA consists of a single strand of sugar-phosphate backbone studded with bases. Messenger RNA (mRNA) is created during protein synthesis to carry the genetic instructions from the DNA to the cell’s protein manufacturing plants in the cytoplasm and the ribosomes.

Adenosine Triphosphate

The nucleotide adenosine triphosphate (ATP) is composed of a ribose sugar, an adenine base, and three phosphate groups (Figure 2.4.14). ATP is classified as a high-energy compound because the two covalent bonds linking its three phosphates store a significant amount of potential energy. In the body, the energy released from these high-energy bonds helps fuel the body’s activities, from muscle contraction to the transport of substances in and out of cells to anabolic chemical reactions.

When a phosphate group is cleaved from ATP, the products are adenosine diphosphate (ADP) and inorganic phosphate (P_i). This hydrolysis reaction can be written as follows:

ATP + H₂O → ADP + P_i + energy

Removal of a second phosphate leaves adenosine monophosphate (AMP) and two phosphate groups. Again, these reactions also liberate the energy that had been stored in the phosphate-phosphate bonds. They are reversible, too, as when ADP undergoes phosphorylation. Phosphorylation is the addition of a phosphate group to an organic compound, in this case resulting in ATP. In such cases, the same level of energy that had been released during hydrolysis must be reinvested to power dehydration synthesis.

Cells can also transfer a phosphate group from ATP to another organic compound. For example, when glucose first enters a cell, a phosphate group is transferred from ATP, forming glucose phosphate (C₆H₁₂O₆—P) and ADP. Once glucose is phosphorylated in this way, it can be stored as glycogen or metabolized for immediate energy.

Glossary

amino acid

a molecule composed of an amino group and a carboxyl group, together with a variable side chain

carbohydrate

a molecule composed of carbon, hydrogen, and oxygen

denaturation

a change in the structure of a molecule through physical or chemical means, often resulting in a loss of function

deoxyribonucleic acid (DNA)

deoxyribose-containing nucleotide that stores genetic information

disaccharide

carbohydrate made of two monosaccharides

disulfide bond

a covalent bond between sulfur atoms in a polypeptide

enzyme

organic catalyst

functional group

a group of atoms linked by strong covalent bonds and tend to function in chemical reactions as a single unit

lipid

one of a highly diverse group of compounds made up mostly of hydrocarbons

macromolecule

a large, complex molecule often composed of multiple subunits or monomers

monosaccharide

monomer or building block of carbohydrates

nucleotide

one of a class of organic compounds composed of one or more phosphate groups, a five-carbon sugar, and a nitrogen-containing base

peptide bond

a covalent bond between two amino acids that is formed by dehydration synthesis

phospholipid

compound made of glycerol, two fatty acids, and a phosphate group

phosphorylation

the addition of a phosphate group to an organic compound

polysaccharide

carbohydrate made of more than two monosaccharides

prostaglandin

cell-signaling molecule derived from unsaturated fatty acids

protein

an organic molecule composed of amino acids linked by peptide bonds

purine

a nitrogen-containing molecule with a double ring structure; adenine (A) and guanine (G) in DNA and RNA

pyrimidine

a nitrogen-containing base with a single ring structure; cytosine (C) in DNA and RNA, thymine (T) in DNA, and uracil (U) in RNA

ribonucleic acid (RNA)

ribose-containing nucleotide that helps direct the production of protein

saturated fatty acid

fatty acid chain that contains no double bonds

steroid

compound made of four hydrocarbon rings

substrate

a reactant in an enzymatic reaction

triglyceride

compound made of glycerol and three fatty acids

unsaturated fatty acid

fatty acid chain that contains at least one double bond

Glossary Flashcards

Image Descriptions

Figure 2.4.1. A diagram showing three ways to represent a water molecule. Part (a) shows a planetary model with a central oxygen atom containing 8 protons and 8 neutrons, surrounded by electron shells with yellow electrons. Two hydrogen atoms (small white circles with + signs) are bonded to the oxygen. The diagram labels the oxygen end as ‘weakly negative’ (δ⁻) and the hydrogen ends as ‘weakly positive’ (δ⁺), showing water’s polar nature. Part (b) shows a 3D space-filling model where oxygen is a large pink sphere and the two hydrogen atoms are smaller white spheres attached at an angle, with the same δ⁻ and δ⁺ labels. Part (c) shows a simple structural formula with ‘O’ at the top connected by lines to two ‘H’ atoms below, illustrating the bent shape of the water molecule. [Return to Figure 2.4.1]

Figure 2.4.2. A diagram showing three common disaccharides formed by joining two simple sugars. Part (a) shows sucrose, made from glucose (a six-sided ring) and fructose (a five-sided ring) connected by an oxygen bridge. Part (b) shows lactose, made from galactose and glucose (both six-sided rings) connected by an oxygen bridge. Part (c) shows maltose, made from two identical glucose molecules (both six-sided rings) connected by an oxygen bridge. Each sugar ring is drawn as a light blue polygon with a black base, with chemical groups labeled around it: CH₂OH (hydroxymethyl groups), OH (hydroxyl groups), H (hydrogen atoms), and O (oxygen atoms). The oxygen bridges between rings represent glycosidic bonds where the sugars are joined together through dehydration synthesis. [Return to Figure 2.4.2]

Figure 2.4.3. A diagram comparing the molecular structures of four polysaccharides made from glucose. Amylose, shown at the top, is a simple unbranched chain of hexagonal glucose units in a wavy line. Amylopectin, below it, has a main chain with several short branches extending from it. These two structures together form starch. Glycogen, shown in the center, is heavily branched like a dense bush with many short branches radiating from a central core. Cellulose (fiber), on the right, shows glucose units arranged in straight, parallel rows forming a rigid, organized lattice structure. The diagram illustrates how the same glucose building blocks can be arranged differently to create polysaccharides with distinct functions: starch for plant energy storage, glycogen for animal energy storage, and cellulose for plant structural support. [Return to Figure 2.4.3]

Figure 2.4.4. A chemical reaction diagram showing how a triglyceride (neutral fat) is formed through dehydration synthesis. On the left side, glycerol is shown as a pink-shaded molecule with three carbon atoms, each bearing an OH group and hydrogen atoms. Next to it are three fatty acid chains (shown in tan/beige), each with a carboxyl group (HO-C=O) at one end and a long hydrocarbon chain (CH₂-CH₂···CH₂-CH₂-CH₃) extending to the right. A plus sign separates the reactants. A gray arrow points to the right side showing the product: a triglyceride molecule where the glycerol backbone (still pink-shaded) is now connected to all three fatty acid chains (tan/beige) through ester bonds (C-O-C=O linkages). The hydroxyl groups from glycerol and the carboxyl groups from the fatty acids have been removed and combined to form three water molecules, shown as ‘+ 3H₂O’ on the far right. The diagram illustrates that dehydration synthesis removes water to join the molecules together, creating the characteristic structure of a fat molecule used for energy storage in living organisms. [Return to Figure 2.4.4]

Figure 2.4.5.A diagram comparing the molecular structures of saturated and unsaturated fatty acids. Part (a) shows a saturated fatty acid with a carboxyl group (shown in blue: O=C-O-H) on the left end, followed by a straight chain of nine carbon atoms (C), each bonded to two hydrogen atoms (H) above and below, with the chain ending in a CH₃ group. All carbon-carbon bonds are single bonds (shown as single lines), allowing the chain to remain completely straight. Part (b) shows an unsaturated fatty acid with the same carboxyl group on the left, followed by six carbon atoms in a straight chain with single bonds, but then has a double bond (C=C, shown in red) between two carbon atoms. This double bond creates a kink or bend in the chain, causing the remaining carbon atoms to angle downward rather than continuing in a straight line. The presence of the double bond means these carbons have only one hydrogen atom each instead of two, making the fatty acid ‘unsaturated’ (not fully saturated with hydrogen). This structural difference explains why unsaturated fats are typically liquid at room temperature while saturated fats are solid—the bent chains cannot pack together as tightly. [Return to Figure 2.4.5]

Figure 2.4.6. A diagram showing three categories of lipids with their molecular structures. Part (a) shows phospholipids, described as having two fatty acid chains and a phosphorus-containing group attached to a glycerol backbone. The example given is phosphatidylcholine, with its structure displayed showing a phosphorus-containing group (polar ‘head’) in a blue-gray box on the left containing a choline group with CH₃ groups and N⁺, connected to a glycerol backbone (pink box) in the middle, which links to two fatty acid chains (nonpolar ‘tail’) shown in tan extending to the right. One fatty acid chain is straight while the other has a kink from a double bond. A simplified icon on the far right shows the phospholipid as a circular head with two wavy tails. Part (b) shows sterols, described as having four interlocking hydrocarbon rings. The example is cholesterol, depicted as four connected tan-colored rings (three six-membered rings and one five-membered ring) with various CH₃ groups attached and a branched hydrocarbon tail extending from the top right. An OH group is attached to the bottom left ring. Part (c) shows prostaglandins, with two examples: PGF₂ₓ and PGE₂. Both molecules feature a five-membered ring with two OH groups attached, and two hydrocarbon chains extending from the ring—one ending in COOH (carboxyl group) and the other containing double bonds. These molecules are signaling lipids involved in inflammation and other physiological processes. [Return to Figure 2.4.6]

Figure 2.4.7. A diagram showing the basic structure of an amino acid molecule. The molecule has four components attached to a central carbon atom (labeled ‘C’ in gray, also called the alpha carbon or α carbon). On the left side is the amino group (labeled at top), consisting of a blue nitrogen atom (N) bonded to two white hydrogen atoms (H). On the right side is the carboxyl group (labeled at top), consisting of a gray carbon atom (C) double-bonded to one pink oxygen atom (O) and single-bonded to another pink oxygen atom (O) that has a hydrogen atom (H) attached. At the top center, a single hydrogen atom (H) is bonded to the central carbon. At the bottom center is a white box labeled ‘R’ representing the side chain (also called the R group), which varies among different amino acids and determines their unique properties. The three sections are separated by gray dividing lines to show the three main functional groups: amino group, side chain, and carboxyl group. This basic structure is common to all amino acids, the building blocks of proteins. [Return to Figure 2.4.7]

Figure 2.4.8. A diagram illustrating how two amino acids join together to form a peptide bond. The top portion shows two separate amino acids before bonding, with their amino groups (N-H₂) on the left, central carbons with hydrogen atoms and R groups (side chains), and carboxyl groups (C=O-OH) on the right. Between them, highlighted in a blue box, are the components that will be removed: an OH from one carboxyl group and an H from the other amino group, which combine to form a water molecule (H₂O) during dehydration synthesis. The bottom portion shows the resulting dipeptide after the bond forms. The two amino acids are now connected by a peptide bond (C-N linkage, indicated by a bracket labeled ‘Peptide Bond’) where the water molecule was removed. The structure shows the characteristic backbone of a protein: N-C-C-N-C-C, with R groups attached to the central carbons, hydrogen atoms throughout, and free amino (N-H₂) and carboxyl (C=O-OH) groups at the ends. This peptide bond formation is the fundamental reaction that links amino acids together to build proteins. [Return to Figure 2.4.8]

Figure 2.4.9. A diagram showing two mirror-image molecules called enantiomers. On the left is labeled (R)-enantiomer and on the right is (S)-enantiomer. Both molecules have the same atoms and bonds but are arranged as non-superimposable mirror images of each other, like left and right hands. Each structure contains carbonyl groups (C=O), nitrogen atoms, and hexagonal ring structures. The spatial arrangement around certain atoms differs between the two forms, which is significant because enantiomers can have different biological effects despite being chemically similar. [Return to Figure 2.4.9]

Figure 2.4.10. A diagram showing the four levels of protein structure organization. Part (a) shows primary structure as a linear chain of eleven purple circles labeled A1 through A11, representing amino acids connected in sequence. Part (b) shows secondary structure, depicted two ways: on the left, an alpha-helix shown as amino acids arranged in a spiral pattern with dotted lines indicating hydrogen bonds between them; on the right, a pleated sheet shown as amino acids arranged in zigzag parallel strands with bonds between them, rendered as a folded pink surface. Part (c) shows tertiary structure as a compact, tangled mass of orange ribbon-like structures representing a single folded protein chain with purple disk-shaped heme units embedded within it. Part (d) shows quaternary structure using hemoglobin as an example—four separate protein subunits (orange ribbon structures) assembled together into a single functional complex, with multiple purple heme units visible within the overall structure. Gray arrows connect each level to show the progression from simple linear sequence to complex multi-subunit assembly. [Return to Figure 2.4.10]

Figure 2.4.11. A four-panel diagram illustrating how enzymes work through the induced-fit model. Part (a) shows two separate substrate molecules (S₁ and S₂, shown as beige irregular shapes) approaching a green enzyme with a depression called the active site (shown in orange-brown). Part (b) shows the substrates binding to the enzyme’s active site, which changes shape slightly to accommodate them, forming an enzyme-substrate complex. Part (c) shows the substrates being converted into a single product molecule (beige shape) while still bound to the enzyme. Part (d) shows the product detaching from the enzyme, which returns to its original shape and is ready to catalyze another reaction. An arrow from part (d) back to part (a) indicates the cycle can repeat. This diagram demonstrates that enzymes are biological catalysts that speed up reactions by binding substrates, facilitating their conversion to products, and then releasing the products while remaining unchanged themselves. [Return to Figure 2.4.11]

Figure 2.4.12. A diagram showing the building blocks and structure of nucleic acids (DNA and RNA). Part (a) on the right shows a polynucleotide chain structure with repeating units, each containing a pentose sugar (beige pentagon), a phosphate group (gray circle with P atom), and a nitrogenous base (hexagonal ring). The sugars are connected by phosphodiester linkages between their phosphate groups. Part (b) at top left shows the two types of nitrogenous bases: pyrimidines (single-ring structures) including cytosine (C), thymine (T, found in DNA), and uracil (U, found in RNA); and purines (double-ring structures) including adenine (A) and guanine (G). Each base is shown with its chemical structure. Part (c) at bottom left shows the two types of pentose sugars: deoxyribose (found in DNA) and ribose (found in RNA), both drawn as five-membered rings with attached hydroxyl (OH) and HOCH₂ groups. The key difference is that deoxyribose has an H at one position where ribose has an OH group. Gray arrows connect these components to show how they combine to form nucleotides, which then link together to create the polynucleotide chains of DNA and RNA. [Return to Figure 2.4.12]

Figure 2.4.13. A diagram of a DNA double helix structure showing two strands twisted around each other. The outer edges are formed by sugar-phosphate backbones (shown as light blue ribbons), and the interior contains pairs of nitrogenous bases connecting the two strands like rungs on a twisted ladder. The bases are color-coded and shown as horizontal bars: adenine (red) pairs with thymine (orange/tan), and guanine (dark blue) pairs with cytosine (green). A legend on the right identifies each base by color. Two labels point to key features: ‘Base pair’ indicates where complementary bases connect across the two strands, and ‘Sugar phosphate backbone’ identifies the outer structural framework. The diagram illustrates DNA’s characteristic double helix shape and the specific base-pairing rules that allow genetic information to be stored and replicated accurately. [Return to Figure 2.4.13]

Figure 2.4.14. A diagram showing the molecular structure of ATP (adenosine triphosphate) and its related compounds. On the left is adenine (shown as a green double-ring structure with NH₂ group) attached to ribose (a tan five-membered sugar ring with OH groups). Together, adenine and ribose form adenosine. On the right are three phosphate groups (shown as yellow-green circles) connected in a chain, with each phosphate containing a central P atom bonded to oxygen atoms. The bonds between the phosphate groups are labeled as ‘high-energy bonds’ and shown in red, indicating they store chemical energy. Below the structure, brackets show the progressive components: adenosine (base + sugar), adenosine monophosphate or AMP (adenosine + one phosphate), adenosine diphosphate or ADP (adenosine + two phosphates), and adenosine triphosphate or ATP (adenosine + three phosphates). ATP serves as the primary energy currency in cells, releasing energy when the high-energy phosphate bonds are broken. [Return to Figure 2.4.14]

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