Organic Compounds

Organic compounds are chemical substances that make up organisms and carry out life processes. All organic compounds contain the elements carbon and hydrogen. Because carbon is the major element in organic compounds, it is essential to all known life on Earth. Without carbon, life as we know it could not exist.

The Significance of Carbon

Why is carbon so important to organisms? The answer lies with carbon’s unique properties. Carbon has an exceptional ability to bind with a wide variety of other elements. Carbon atoms can form multiple stable bonds with other small atoms, including hydrogen, oxygen, and nitrogen. Carbon atoms can also form stable bonds with other carbon atoms. In fact, a carbon atom may form single, double, or even triple bonds with other carbon atoms. This allows carbon atoms to form a tremendous variety of very large and complex molecules.

Nearly 10 million carbon-containing organic compounds are known. Types of carbon compounds in organisms include carbohydrates, lipids, proteins, and nucleic acids. The elements found in each type are listed in Table 1. Elements other than carbon and hydrogen usually occur within organic compounds in smaller groups of elements called functional groups. When organic compounds react with other compounds, generally just the functional groups are involved. Therefore, functional groups generally determine the nature and functions of organic compounds.

This table lists the four types of organic compounds, the elements they contain, and examples of each type of compound.

Carbohydrates

Carbohydrates are organic compounds that contain only carbon, hydrogen, and oxygen. They are the most common of the four major types of organic compounds. There are thousands of different carbohydrates, but they all consist of one or more smaller units called monosaccharides.

Monosaccharides and Disaccharides

The general formula for a monosaccharide is:

$$(CH_2 O)_n$$

where n can be any number greater than two. For example, if n is 6, then the formula can be written: $$C_6 H_{12} O_6$$

This is the formula for the monosaccharide glucose. Another monosaccharide, fructose, has the same chemical formula as glucose, but the atoms are arranged differently. Molecules with the same chemical formula but with atoms in a different arrangement are called isomers. Compare the glucose and fructose molecules in Figure 1. Can you identify their differences? The only differences are the positions of some of the atoms. These differences affect the properties of the two monosaccharides.

Figure 1: Sucrose Molecule. This sucrose molecule is a disaccharide. It is made up of two monosaccharides: glucose on the left and fructose on the right.

If two monosaccharides bond together, they form a carbohydrate called a disaccharide. An example of a disaccharide is sucrose (table sugar), which consists of the monosaccharides glucose and fructose (Figure 1). Monosaccharides and disaccharides are also called simple sugars. They provide the major source of energy to living cells.

Polysaccharides

If more than two monosaccharides bond together, they form a carbohydrate called a polysaccharide. A polysaccharide may contain anywhere from a few monosaccharides to several thousand monosaccharides. Polysaccharides are also called complex carbohydrates. Their main functions are to store energy and form structural tissues. Examples of several polysaccharides and their roles are listed in Table 2.

These complex carbohydrates play important roles in living organisms.

Lipids

Lipids are organic compounds that contain mainly carbon, hydrogen, and oxygen. They include substances such as fats and oils. Lipid molecules consist of fatty acids, with or without additional molecules. Fatty acids are organic compounds that have the general formula \(CH_3 (CH_2 )_nCOOH\), where n usually ranges from 2 to 28 and is always an even number.

Saturated and Unsaturated Fatty Acids

Fatty acids can be saturated or unsaturated. The term saturated refers to the placement of hydrogen atoms around the carbon atoms. In a saturated fatty acid, all the carbon atoms (other than the carbon in the -COOH group) are bonded to as many hydrogen atoms as possible (usually two hydrogens). Saturated fatty acids do not contain any other groups except -COOH. This is why they form straight chains, as shown in Figure 2. Because of this structure, saturated fatty acids can be packed together very tightly. This allows organisms to store chemical energy very densely. The fatty tissues of animals contain mainly saturated fatty acids.

Figure 2: Saturated and Unsaturated Fatty Acids. Saturated fatty acids include arachidic, stearic, and palmitic fatty acids, shown on the left in this figure. Unsaturated fatty acids include all the other fatty acids in the figure. Notice how all the unsaturated fatty acids have bent chains, whereas the saturated fatty acids have straight chains.

In an unsaturated fatty acid, some carbon atoms are not bonded to as many hydrogen atoms as possible. This is because they are bonded to one or more additional groups, including double and triple bonds between carbons. Wherever these other groups bind with carbon, they cause the chain to bend - they do not form straight chains (Figure 2). This gives unsaturated fatty acids different properties than saturated fatty acids. For example, unsaturated fatty acids are liquids at room temperature whereas saturated fatty acids are solids. Unsaturated fatty acids are found mainly in plants, especially in fatty tissues such as nuts and seeds.

Unsaturated fatty acids occur naturally in the bent shapes shown in Figure 2. However, unsaturated fatty acids can be artificially manufactured to have straight chains like saturated fatty acids. Called trans fatty acids, these synthetic lipids were commonly added to foods, until it was found that they increased the risk for certain health problems. Many food manufacturers no longer use trans fatty acids for this reason.

Types of Lipids

Lipids may consist of fatty acids alone or in combination with other compounds. Several types of lipids consist of fatty acids combined with a molecule of alcohol:

• Triglycerides are the main form of stored energy in animals. This type of lipid is commonly called fat. A triglyceride is shown in Figure 3.

• Phospholipids are a major component of the membranes surrounding the cells of all organisms.

• Steroids (or sterols) have several functions. The sterol cholesterol is an important part of cell membranes and plays other vital roles in the body. Other steroids are male and female sex hormones.

Figure 3: Triglyceride Molecule. The left part of this triglyceride molecule represents glycerol. Each of the three long chains on the right represents a different fatty acid. From top to bottom, the fatty acids are palmitic acid, oleic acid, and alpha-linolenic acid. The chemical formula for this triglyceride is \(C_{55} H_{98} O_6\). KEY:H=hydrogen, C=carbon, O=oxygen

Lipids and Diet

Humans need lipids for many vital functions, such as storing energy and forming cell membranes. Lipids can also supply cells with energy. In fact, a gram of lipids supplies more than twice as much energy as a gram of carbohydrates or proteins. Lipids are necessary in the diet for most of these functions. Although the human body can manufacture most of the lipids it needs, there are others, called essential fatty acids, that must be consumed in food. Essential fatty acids include omega-3 and omega-6 fatty acids. Both of these fatty acids are needed for important biological processes, not just for energy. Although some lipids in the diet are essential, excess dietary lipids can be harmful. Because lipids are very high in energy, eating too many may lead to unhealthy weight gain. A highfat diet may also increase lipid levels in the blood. This, in turn, can increase the risk for health problems such as cardiovascular disease. The dietary lipids of most concern are saturated fatty acids, trans fats, and cholesterol. For example, cholesterol is the lipid mainly responsible for narrowing arteries and causing the disease atherosclerosis.

Proteins

Proteins are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and, in some cases, sulfur. Proteins are made of smaller units called amino acids. There are 20 different common amino acids needed to make proteins. All amino acids have the same basic structure, which is shown in Figure 4. Only the side chain (labeled R in the figure) differs from one amino acid to another. The variable side chain gives each amino acid unique properties. Proteins can differ from one another in the number and sequence (order) of amino acids. It is because of the side chains of the amino acids that proteins with different amino acid sequences have different shapes and different chemical properties.

Small proteins can contain just a few hundred amino acids. Yeast proteins average 466 amino acids. The largest known proteins are the titins, found in muscle, which are composed from almost 27,000 amino acids.

Figure 4: General Structure of Amino Acids. This model shows the general structure of all amino acids. Only the side chain, R, varies from one amino acid to another. For example, in the amino acid glycine, the side chain is simply hydrogen (H). In glutamic acid, in contrast, the side chain is \(CH_2 CH_2 COOH\). Variable side chains give amino acids acids different chemical properties. The order of amino acids, together with the properties of the amino acids, determines the shape of the protein, and the shape of the protein determines the function of the protein. KEY: H = hydrogen, N = nitrogen, C = carbon, O = oxygen, R = variable side chain

Protein Structure

Amino acids can bond together to form short chains called peptides or longer chains called polypeptides (Figure 5). Polypeptides may have as few as 40 amino acids or as many as several thousand. A protein consists of one or more polypeptide chains. The sequence of amino acids in a protein’s polypeptide chain(s) determines the overall structure and chemical properties of the protein. Primary protein structure is sequence of a chain of amino acids.

Figure 5: Polypeptide. This polypeptide is a chain made up of many linked amino acids.

The amino acid sequence is the primary structure of a protein. As explained in Figure 6, a protein may have up to four levels of structure, from primary to quaternary. The complex structure of a protein allows it to carry out its biological functions.

Figure 6: Protein Structure. Primary protein structure is the sequence of amino acids in a single polypeptide. Secondary protein structure refers to internal shapes, such as alpha helices and beta sheets, that a single polypeptide takes on due to bonds between atoms in different parts of the polypeptide. Tertiary protein structure is the overall three-dimensional shape of a protein consisting of one polypeptide. Quaternary protein structure is the shape of a protein consisting of two or more polypeptides.

Functions of Proteins

Proteins are an essential part of all organisms. They play many roles in living things. Certain proteins provide a scaffolding that maintains the shape of cells. Proteins also make up the majority of muscle tissues. Many proteins are enzymes that speed up chemical reactions in cells. Other proteins are antibodies. They bond to foreign substances in the body and target them for destruction. Still other proteins help carry messages or materials in and out of cells or around the body. For example, the blood protein hemoglobin bonds with oxygen and carries it from the lungs to cells throughout the body.

One of the most important traits of proteins, allowing them to carry out these functions, is their ability to bond with other molecules. They can bond with other molecules very specifically and tightly. This ability, in turn, is due to the complex and highly specific structure of protein molecules.

Proteins and Diet

Proteins in the diet are necessary for life. Dietary proteins are broken down into their component amino acids when food is digested. Cells can then use the components to build new proteins. Humans are able to synthesize all but eight of the twenty common amino acids. These eight amino acids, called essential amino acids, must be consumed in foods. Like dietary carbohydrates and lipids, dietary proteins can also be broken down to provide cells with energy.

Nucleic Acids

Nucleic acids are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. They are made of smaller units called nucleotides. Nucleic acids are named for the nucleus of the cell, where some of them are found. Nucleic acids are found not only in all living cells but also in viruses. Types of nucleic acids include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Structure of Nucleic Acids

A nucleic acid consists of one or two chains of nucleotides held together by chemical bonds. Each individual nucleotide unit consists of three parts:

• a base (containing nitrogen)

• a sugar (ribose in RNA, deoxyribose in DNA)

• a phosphate group (containing phosphorus)

The sugar of one nucleotide binds to the phosphate group of the next nucleotide. Alternating sugars and phosphate groups form the backbone of a nucleotide chain, as shown in Figure 7. The bases, which are bound to the sugars, stick out at right angles from the backbone of the chain.

Figure 7: Part of a Nucleic Acid. This small section of a nucleic acid shows how phosphate groups (yellow) and sugars (orange) alternate to form the backbone of a nucleotide chain. The bases that jut out to the side from the backbone are adenine (green), thymine (purple), cytosine (pink), and guanine (blue). Bonds between complementary bases, such as between adenine and thymine, hold the two chains of nucleotides together. These bonds, called hydrogen bonds.

RNA consists of a single chain of nucleotides, and DNA consists of two chains of nucleotides. Bonds form between the bases on the two chains of DNA and hold the chains together (Figure 7). There are four different types of bases in a nucleic acid molecule: cytosine, adenine, guanine, and either thymine (in DNA) or uracil (in RNA). Each type of base bonds with just one other type of base. Cytosine and guanine always bond together, and adenine and thymine (or uracil) always bond with one another. The pairs of bases that bond together are called complementary bases.

The binding of complementary bases allows DNA molecules to take their well-known shape, called a double helix. Figure 8 shows how two chains of nucleotides form a DNA double helix. A simplified double helix is illustrated in Figure 9. It shows more clearly how the two chains are intertwined. The double helix shape forms naturally and is very strong. Being intertwined, the two chains are difficult to break apart. This is important given the fundamental role of DNA in all living organisms.

Figure 8: Double-Stranded Nucleic Acid. In this double-stranded nucleic acid, complementary bases (A and T, C and G) form bonds that hold the two nucleotide chains together in the shape of a double helix. Notice that A always bonds with T and C always bonds with G. These bonds help maintain the double helix shape of the molecule.

Figure 9: Simple Model of DNA. In this simple model of DNA, each line represents a nucleotide chain. The double helix shape forms when the two chains wrap around the same axis.

Role of Nucleic Acids

The order of bases in nucleic acids is highly significant. The bases are like the letters of a four-letter alphabet. These “letters” can be combined to form “words.” Groups of three bases form words of the genetic code. Each code word stands for a different amino acid. A series of many code words spells out the sequence of amino acids in a protein (Figure 10). In short, nucleic acids contain the information needed for cells to make proteins. This information is passed from a body cell to its daughter cells when the cell divides. It is also passed from parents to their offspring when organisms reproduce.

Figure 10: The letters G, U, C, and A stand for the bases in RNA. Each group of three bases makes up a code word, and each code word represents one amino acid (represented here by a single letter, such as V, H, or L). A string of code words specifies the sequence of amino acids in a protein.

How RNA codes for Proteins

DNA and RNA have different functions relating to the genetic code and proteins. Like a set of blueprints, DNA contains the genetic instructions for the correct sequence of amino acids in proteins. RNA uses the information in DNA to assemble the amino acids and make the proteins.