Carbon

It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role.

Carbon Bonding

Figure 1. Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (CH₄), depicted here.

Carbon contains four electrons in its outer(valence)shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH₄), in which four hydrogen atoms bind to a carbon atom (Figure 1).

However, structures that are more complex are made using carbon. Any of the hydrogen atoms could be replaced with another carbon atom covalently bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure 2a). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 2b). The molecules may also form rings, which themselves can link with other rings (Figure 2c). This diversity of molecular forms accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to form multiple bonds with itself and other atoms.

Figure 2. These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various ways to other carbon atoms and the atoms of other elements. (a) This molecule of stearic acid has a long chain of carbon atoms. (b) Glycine, a component of proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of carbon atoms and one oxygen atom.

Carbohydrates

Carbohydrates are macromolecules with which most consumers are somewhat familiar.  Carbohydrates are a quick, short-term energy storage molecule.  Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have other important functions in humans, animals, and plants.

Carbohydrates can be represented by the formula (CH₂O)_n, where n is the number of carbon atoms in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbon atoms usually ranges from three to six. Most monosaccharide names end with the suffix -ose. Depending on the number of carbon atoms in the sugar, they may be known as trioses (three carbon atoms), pentoses (five carbon atoms), and hexoses (six carbon atoms).

The chemical formula for glucose is C₆H₁₂O₆. In most living species, glucose is an important source of energy. During cellular respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water by the process of photosynthesis, and the glucose, in turn, is used for the energy requirements of the plant. The excess synthesized glucose is often stored as starch that is broken down by other organisms that feed on plants.

Figure 3. Glucose, galactose, and fructose are isomeric monosaccharides, meaning that they have the same chemical formula but slightly different structures.

Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C₆H₁₂O₆), they differ structurally and chemically because of differing arrangements of atoms in the carbon chain (Figure 3).  For this reason, they are referred to as isomers.

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction. During this process, the hydroxyl group (–OH) of one monosaccharide combines with a hydrogen atom of another monosaccharide, releasing a molecule of water (H₂O) and forming a covalent bond between atoms in the two sugar molecules.

Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

A long chain of monosaccharides linked by covalent bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Polysaccharides may be very large molecules. Starch, glycogen, cellulose, and chitin are examples of polysaccharides, also referred to by many as “complex carbs”.

Starch is the stored form of sugars in plants.  Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. The starch that is consumed by animals is broken down into smaller molecules, such as glucose. The cells can then absorb the glucose.

Glycogen is the storage form of glucose in humans and other vertebrates, and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels decrease, glycogen is broken down to release glucose.

Cellulose is one of the most abundant natural polysaccharides. The cell walls of plants are mostly made of cellulose, which provides structural support to the cell. Wood and paper are mostly cellulose in nature. Cellulose is made up of glucose monomers that are linked by bonds between particular carbon atoms in the glucose molecule.

Every other glucose monomer in cellulose is flipped over and packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. Cellulose passing through our digestive system is called dietary fiber. While the glucose-glucose bonds in cellulose cannot be broken down by human digestive enzymes, herbivores such as cows, buffalos, and horses are able to digest grass that is rich in cellulose and use it as a food source because they secrete the enzyme, cellulase.  Cellulases can break down cellulose into glucose monomers that can be used as an energy source by herbivores.

Carbohydrates serve other functions in different animals. Arthropods, such as insects, spiders, and crabs, have an outer skeleton, called the exoskeleton, which protects their internal body parts. This exoskeleton is made of the polysaccharide, chitin, which is a nitrogenous carbohydrate. It is made of repeating units of a modified sugar containing nitrogen.

Thus, through differences in molecular structure, carbohydrates are able to serve the very different functions of energy storage (starch and glycogen) and structural support and protection (cellulose and chitin) (Figure 4).

Figure 4. Although their structures and functions differ, all polysaccharide carbohydrates are made up of monosaccharides and have the chemical formula (CH₂O)n.

Lipids

Figure 5. Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements. (credit: Ken Bosma)

Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water-fearing”), or insoluble in water, because they are nonpolar molecules.  Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane. Lipids include fats, oils, phospholipids, and steroids.

A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids.  Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18 carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond (Figure 6).

Figure 6. Lipids include fats, such as triglycerides, which are made up of fatty acids and glycerol, phospholipids, and steroids.

Fatty acids may be saturated or unsaturated. A fatty acid chain made up of only single covalent bonds forms a saturated fat.  Saturated fats are saturated with hydrogen.  The number of hydrogen atoms attached to the carbon skeleton is at the maximum number allowed. Saturated fats tend to get packed tightly and are solid at room temperature. Animal fats contained in meat and the fat contained in butter are examples of saturated fats. Mammals store fats in specialized cells called adipocytes, where globules of fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used as a source of energy during embryonic development.

A fatty acid chain that contains double bonds forms an unsaturated fat.  Due to the double bond, there are fewer hydrogens attached to the carbon skeleton.   Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).

Unsaturated fats or oils are usually of plant origin and contain unsaturated fatty acids. The double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to improve blood cholesterol levels, whereas saturated fats contribute to plaque formation in the arteries, which increases the risk of a heart attack.

Figure 7. During the hydrogenation process, the orientation around the double bonds is changed, making a trans-fat from a cis-fat. This changes the chemical properties of the molecule.

In the food industry, oils are artificially hydrogenated to make them semi-solid, leading to less spoilage and increased shelf life. Simply speaking, hydrogen gas is bubbled through oils to solidify them. The orientation of the double bonds affects the chemical properties of the fat (Figure 7).

Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans-fats. Recent studies have shown that an increase in trans-fats in the human diet may lead to an increase in levels of low-density lipoprotein (LDL), or “bad” cholesterol.  This may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently eliminated the use of trans-fats, and U.S. food labels are now required to list their trans-fat content.

Essential fatty acids are fatty acids that are required but not synthesized by the human body. Consequently, they must be supplemented through the diet. Omega-3 fatty acids fall into this category and are one of only two known essential fatty acids for humans (the other being omega-6 fatty acids). They are a type of polyunsaturated fat and are called omega-3 fatty acids due to the third carbon from the end of the fatty acid participating in a double bond.

Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 fatty acids are important in brain function and normal growth and development. They may also prevent heart disease and reduce the risk of cancer.

Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain. However, fats do have important functions. Fats serve as long-term energy storage. They also provide insulation for the body and protect our internal organs.  Therefore, “healthy” unsaturated fats in moderate amounts should be consumed on a regular basis.

Phospholipids are the major constituent of the plasma membrane. Like fats, they are composed of fatty acid chains attached to a glycerol or similar backbone. Instead of three fatty acids attached, one fatty acid is replaced with a phosphate group.  A phospholipid has both hydrophobic(nonpolar) and hydrophilic(polar) regions. The fatty acid chains are hydrophobic and repel water, whereas the phosphate is hydrophilic and interacts with water.  Cells are surrounded by a membrane, which has a bilayer of phospholipids. The fatty acids of phospholipids face inside, away from water, whereas the phosphate group can face either the outside environment or the inside of the cell, which are both aqueous.

Proteins

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules.  Functions of proteins (and examples) include:  (1)  structural = collagen; (2)  transport = hemoglobin;  (3)  metabolic = enzymes;  (4)  defense = antibodies; and (5)  regulatory = hormones.

Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. Regardless, proteins are all polymers composed of amino acids monomers.  There are only 20 total amino acids and these can be combined in any order.  All proteins are made up of different arrangements of the same 20 amino acids.

Figure 8. Amino acids are made up of a central carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), and a hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.

Proteins have different shapes.  Hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and chemical exposure may lead to permanent changes in the shape of the protein.  When a protein undergoes a change in shape a process known as denaturation has occurred.  Changes in shape can create changes in function.

Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH₂), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of atoms bonded to the central carbon atom known as the R(functional) group. The R group is the only difference in structure between the 20 amino acids. (Figure 8)

The chemical nature of the R group determines the chemical nature of the amino acid within its protein.   Is it an acid or base?  It is polar or nonpolar?

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid by a special covalent bond.  A peptide bond is a covalent bond between 2 or more amino acids formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water molecule.

The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used interchangeably. A polypeptide is technically a polymer of amino acids, whereas a protein is used for a polypeptide(s) that have combined together.

Protein Structure

As discussed earlier, the shape of a protein is critical to its function. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary (Figure 8).

The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every protein is ultimately determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution, causing a change in both the structure and function of the protein. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy—is a single amino acid of the 600.

Because of the change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or “sickle” shape, which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and abdominal pain for those who have this disease.

Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.

In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons, and extend above and below the folds of the pleat. The pleated segments align parallel to each other, and hydrogen bonds form between the same pairs of atoms on each of the aligned amino acids. The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins.

The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions.

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, hemoglobin is a combination of four polypeptide subunits.

Figure 9. The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National Human Genome Research Institute)

Each protein has its own unique sequence and shape held together by chemical interactions.  As mentioned earlier, if a protein is subject to changes in temperature, pH, or chemical exposure, the protein structure may change or denature.  Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible.  This change in shape leads to a loss or change of function.  An example is a chicken egg.  What happens if we take it away from the chicken and place in a pan of boiling water?  What result will I get?  Can I return the boiled egg back to the mother and get a baby chick?

Concept in Action

For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive animation.

Nucleic Acids

Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals.

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein synthesis and its regulation.

Figure 10. A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a phosphate group.

DNA and RNA are made up of monomers known as nucleotides.Each nucleotide is made up of three components: (1)   nitrogenous base;  (2)  pentose (five-carbon) sugar;  and (3) phosphate group (Figure 10). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group.

DNA Double-Helical Structure

Figure 11. The double-helix model shows DNA as two parallel strands of intertwining molecules. (credit: Jerome Walker, Dennis Myts)

DNA has a double-helical structure (Figure 11). It is composed of two strands of nucleotides.  A covalent bond joins the phosphate of one nucleotide to the 5C sugar of the neighboring nucleotide.

The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase.  These base pairs are held together by a hydrogen bond. The hydrogen bond is strong enough to hold the nitrogenous bases together but weak enough to twist.  Thus, the result is the double helix.  Within the DNA molecule, the 4 bases are adenine pairing with thymine, and guanine always pairing with cytosine.

RNA has some slight changes.  Unlike DNA, RNA is single stranded.  While the sugar are different in both DNA and RNA, they are still composed of five carbons.  The other notable change occurs within the nitrogenous bases.  Within RNA, thymine is replaced with uracil.  RNA has many functions, but ultimately is important in protein formation.

Section Summary

Living things are carbon-based because carbon plays such a prominent role in the chemistry of living things. The four covalent bonding positions of the carbon atom can give rise to a wide diversity of compounds with many functions.   Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to many organisms.  Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides.

Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, phospholipids, and steroids. Fats and oils are a stored form of energy and can include triglycerides. Fats and oils are usually made up of fatty acids and glycerol.

Proteins are a class of macromolecules that can perform a diverse range of functions for the cell.  The building blocks of proteins are amino acids. Proteins are organized at four levels: primary, secondary, tertiary, and quaternary. Protein shape and function are intricately linked. Any change in shape may lead to protein denaturation and a loss of function.

Nucleic acids are molecules made up of repeating units of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA.