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Self-Instructional on Biological Molecules


Organic Compounds

All living things are composed of organic compounds. Generally, organic compounds are distinguished from inorganic compounds by the presence of both carbon and hydrogen. We are referred to as carbon-based life forms, as is all life on earth. This means that carbon is a component of most of the chemical molecules that make up living organisms on this planet.

Why is carbon so ubiquitous in nature? Carbon's participation in organic chemistry is probably due to its relatively unique chemical bonding properties. These properties allow carbon to participate in the formation of an incredibly wide variety of chemical compounds and electron configurations. Carbon is also a relatively small, non-bulky atom so it can share electrons easily with other atoms.

Carbon, atomic number six, has six electrons. Two are in the first electron shell and four are in the second electron shell. Carbon must share four electrons with other atoms to fill its outermost electron shell and attain a stable configuration. Carbon atoms can share electrons with a wide variety of elements also commonly found in organic compounds, the most notable being other carbon atoms, hydrogen atoms and oxygen atoms. As a matter of fact, the simplest organic molecules are defined as being comprised of only carbon and hydrogen, and are therefore referred to as hydrocarbons.

Hydrocarbons are non-polar, hydrophobic compounds. The term hydrophobic comes from the Latin roots "hydro" (water) and "phobia" (fear). Literally speaking, a hydrophobic compound is afraid of water. The term non-polar is often used in conjunction with the term hydrophobic, because those compounds that have no charges on them will not mix with polar water. A non-polar compound repels a polar solvent and collects together in a film on top of the solvent, or forms a layer on the bottom of the container. Most oils, waxes, and fat compounds are hydrocarbons, as are the fossil fuels gasoline, kerosene, and similar compounds. Just think of how well these compounds mix with water and you'll easily grasp the concept of hydrophobicity.

Since we have introduced the concept of hydrophobicity we should discuss its complement, hydrophilicity. Hydrophilic comes from the Latin roots "hydro" (water) and "philia" (love). Hydrophilic compounds love water, and mix with it easily. These compounds are polar, and so dissolve easily in the polar solvent water.

Figure 1. Structural formulas of some simple hydrocarbons.

Methane CH4Ethane C2H6 Propane C3H8Ethylene C2H4

Now that you have seen the structures associated with the bonds around carbon, let's discuss how carbon can form so many different compounds. Carbon always needs to share four electrons to fill its outermost electron shell. Each straight line extending from the carbon in the diagrams represents one electron carbon is sharing with another atom.  In turn, that atom shares one of its electrons with carbon, forming a covalent bond. Each atom involved in the covalent bond has essentially gained an electron.  When carbon shares two electrons with another carbon or another atom a double covalent bond is formed. Two straight lines extending from the carbon to its electron-sharing partner represent a double bond. All structural formulas use the same characters to represent bonds. One line equals one shared electron from carbon, two lines equals two shared electrons, and three lines equals three shared electrons. These are called single bonds, double bonds, and triple bonds, respectively.  Single and double bonds are the most common and single bonds are the most stable (least likely to react with other molecules). Carbon is not the only element that can form double bonds, as you will see when you review the structural formulas of other compounds.

Now that you have some information about carbon and simple organic compounds, we must consider some of the other elements essential to more complex organic compounds. While the simplest organic compounds consist of carbon and hydrogen, many organic compounds also include one or more of the following elements:

Not all complex organic compounds contain every one of these elements. For example, sulfur is a component of protein but is never a component of nucleic acid.  Scientists have capitalized on this fact to differentiate between these two major biological molecules. Historically, the presence of phosphorus was used to determine that nucleic acid, and not protein, was the biological molecule of heredity!

Practice Round One

1. Please discuss the types of bonds that carbon forms and what implication this has for carbon based organisms.

2. What are hydrocarbons? What physical characteristics do they have in common? Give some examples of hydrocarbon containing compounds.

3. Define the terms hydrophobic and hydrophilic.

4. Draw and label the bonds of the hydrocarbons methane CH4 and ethylene C2H4.

5. List the six elements commonly found in organic compounds.

The Major Classes of Biological Molecules

Now that we have introduced two groups of biological molecules, let us discuss all four major groups of biological molecules:

These four types of biological molecules compose all life on earth.

Proteins have an incredible variety of functions in living organisms. The functions of proteins include but are not limited to:

Nucleic Acids consist of two distinct, but closely related chemical forms: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The main functions of these biomolecules include the storage of all heritable information of all organisms on earth and the conversion of this information into proteins.

Carbohydrates are the major source of food and the major form of energy for most living organisms. When carbohydrates combine together to form polymers they can function as long term food storage molecules, as protective coverings for cells and organisms, as the main structural support for land plants and constituents of many cells and their contents.

Lipids are the major constituents of all membranes in all cells. They also serve as food storage molecules. This class of biological molecules includes the hydrophobic fats, oils and waxes.

Often times students have difficulty remembering the four major classes of biological molecules, so I have a way to help. To recall the four major classes of biological molecules I want you to think of lunch at a hamburger joint. No endorsements intended! Take a hamburger, fries, and a milkshake and you have all the components of the four major classes of biological molecules.

Of all four classes which do you think is most abundant in this meal?

If you guessed LIPIDS you would be right! The hamburger is full of fat, and processors add fat to the hamburger bun. Mayonnaise is oil and egg yolk, which is mostly fat. Milk contains fat (if your shake has any milk product in it), and fat is added to nondairy shakes. As for the fries, we all know why they are called fries!

Okay - we know there are plenty of lipids, but where do the rest of the biological molecules come in?

The hamburger bun is made from wheat flour, which is full of starch, a carbohydrate. The sugar in your shake is the disaccharide sucrose, which is also a carbohydrate. As a matter of fact, the lettuce, onion and tomato on that burger all contain carbohydrates.

Meat is composed of muscle tissue, and muscle tissue is a structural form of protein. Also most of the formerly living things that we eat have some form of protein in them: wheat, milk, potatoes, and so on.

All cells contain DNA and RNA, except mature mammalian red blood cells, so DNA and RNA can be found in all organic matter. The lettuce, onion, and tomato contain nucleic acid, and the hamburger meat contains cow DNA.

Practice Round Two

1. List and describe at least one function of each of the four major classes of biological molecules.

Biological molecules: Structure and Function

Figure 2 shows the structural formula of a particular type of lipid (a phospholipid) which is the major component of cell membranes. Please notice the long hydrocarbon chains at one end of the molecule. This, as you should now realize, is a non-polar, hydrophobic, hydrocarbon structure. This part of the molecule is often referred to as the hydrophobic tail.

At the opposite end of the molecule you will see carbons attached to oxygen, nitrogen and phosphorus. These components make this end of the phospholipid hydrophilic and therefore water-soluble. This end of the phospholipid is called the hydrophilic head. The dual hydrophobic and hydrophilic nature of this phospholipid is essential to the structure of all cell membranes.

Figure 2, below. The Structural Formula of a Phospholipid Molecule.

Phospholipids will spontaneously form membranes in water because of their hydrophobic and hydrophilic ends. As hydrophobic elements try to avoid the polar water molecules they attract other hydrophobic molecules to them, excluding the water molecules.  Hydrophobic forces are very important to both membrane and protein structure, and therefore are very important to the functions of these biomolecules. The force that comes from the hydrophobic attraction for other hydrophobic molecules and the repulsion of water is as essential to the processes of life as chemical bonds.

Imagine millions of these lipid molecules dumped into aqueous surroundings. Their hydrophobic nature causes them to aggregate with all the hydrophobic tails clustered together and all the hydrophilic heads oriented toward the water-based medium. If this phospholipid cluster occurs in a single layer as seen in Figure 3, then a structure called a micelle is formed. If this occurs in a double layer as is seen in Figure 4, a bilipid layer membrane is formed.  The bilipid layer membrane is the primary structure of all cells. Because the function of membranes is to either exclude or retain components solubilized in aqueous solutions, you can see that lipids are structurally well suited for this role.

Figure 3. A micelle and bilipid layer.

Carbohydrates are a class of biomolecules composed of carbon, hydrogen and oxygen. They can be referred to as hydrated skeletons of carbon. Basically, carbohydrates are carbons covalently bonded to each other and covalently bonded to oxygens and hydrogens. The best way to understand carbohydrate structure is to examine the linear and cyclic structures of glucose. Glucose (C6H12O6) is the major food source for most cells.

Figure 4. The linear and cyclic structural formulas of glucose.

Not only is the glucose monomer the major source of energy for organisms, but it also has many polymeric forms. These include starch, the long-term glucose food storage molecule; and cellulose, the major structural support molecule in plants and chitin and a major component of animal exoskeletons. Monomer actually means "single unit," from the Latin "mono" (one) and "mer" (unit). Many chemical molecules exist as single units and may also chemically combine in a long string of repeating monomeric units called polymers. You've certainly heard of polyester - this is the polymer made of repeating ester units.

Just as artificial polymers are formed through the bonding of monomers, glucose monomers can covalently bond together to form naturally occurring biological polymers. Glucose can actually form several different polymers, as mentioned previously, which are quite different in their characteristics.  For example, starch and cellulose, both polymers of glucose, have quite different properties. Starch is easily broken down by organisms into the single glucose monomer and then taken up by cells for use as an energy source. Cellulose, however, resists digestion and breakdown by all organisms except a few unusual microbes. That is why the cellulose in plants is known as fiber, or the indigestible portion of plants. Fiber is still healthful to eat in moderate quantities because it facilitates the passage of materials through the digestive system.

Polymerization is an essential aspect of three of the four major biological molecules, so it is very important to understand this concept. Before we continue, lets review how monomers of biological molecules bond together to form polymers.

In the cases of carbohydrate, protein, and nucleic acid, polymers are formed through the chemical reaction called a dehydration reaction. A dehydration reaction can take place when the oxygen and hydrogen on one end of a molecule combine with a hydrogen on another molecule. When these monomers come together under the appropriate conditions, an oxygen and two hydrogens are lost from the two molecules and a covalent bond is formed between the two monomers. The byproduct of this reaction is water, formed by the oxygen and two hydrogens that were removed from the monomeric units. In a sense, the monomers are now dehydrated, because they have lost water. As the bond formation is continued between several more monomers, a polymer or multiunit structure is formed.

The dehydration reaction is a very common reaction inside cells. The companion reaction to the dehydration reaction is the hydrolysis reaction. This is exactly opposite of what occurs in dehydration. In the hydrolysis reaction a molecule of water is added across the covalent bond, breaking the bond and adding the oxygen and hydrogens back on the ends of the molecules. Remember, what is built up in the cell must be able to be broken down eventually. In this self-instructional you will be able to see examples of dehydration reactions between monomers of carbohydrates, proteins, and nucleic acids.

Figure 5. The dehydration reaction between glucose monomers to form amylose, a simple form of starch.

Practice Round Three

1. Draw the diagrammatic structure of a phospholipid and label the ends of the molecule.

2. Draw a diagram of a micelle and bilipid layer membrane.

3. Carbohydrates are composed of what elements?

4. Please give examples and functions for the three carbohydrate polymers of glucose.

5. Explain the concepts of monomers and polymers and give examples of each.

Proteins

Proteins are composed of repeating monomeric units called amino acids. These monomers are named for the presence of the functional groups common to all amino acids, the amine group at one end of the molecule and the carboxylic acid group at the other.  The amine functional group is NH2 and the carboxylic acid functional group is COOH. Although there are 20 different amino acids that compose all proteins, all amino acids have the amine and carboxylic acid ends. The ends of the amino acid monomer are essential in the formation of bonds between amino acids. The bond that links amino acids together is called the peptide bond, as seen below in Figure 6. Because of the peptide bond formation between all amino acids, the polymeric form of amino acids is called a polypeptide. Most people use the terms polypeptide and protein interchangeably; however, the term protein implies a functional, three-dimensional molecule while a polypeptide is simply a string of amino acids bonded together.

The 20 essential amino acids are quite different from each other. Biochemists usually categorize groups of amino acids together according to the types of functional characteristics they exhibit. These groups include the charged, or ionizable, amino acids; the non-polar amino acids; the polar, uncharged, amino acids; and those with unique structural properties.  The amino acids can be categorized in many different ways but the grouping itself is insignificant. The real significance in the structure of amino acids resides in the ability of the chemical groups on different amino acids to impart very important structural and functional information into the protein that they form.

All of the proteins in living systems perform essential functions for organisms, and the functions of proteins are defined by the characteristics of the amino acids that compose them. In particular, the sequence of amino acids in a protein determines the function of that protein. This explains how there can be seemingly limitless types of proteins from a mere 20 different amino acids.

Compare two polypeptides: one composed of a string of 99 glycine amino acids and a final asparagine amino acid on the end. The other composed of a string of 98 glycine amino acids, with one asparagine amino acid in the next position, and then a final glycine on the end. Are these two polypeptides different? Absolutely! One might make a functional protein and the other may not.  Change the amino acid sequence of any polypeptide or protein and the polypeptide or protein structure changes.

For example, consider the genetic condition called sickle cell anemia. People who have this condition make a hemoglobin protein (the oxygen carrying protein molecule of red blood cells) that has one different amino acid from normal hemoglobin. One charged aspartic acid amino acid is replaced with an uncharged glycine amino acid.  This amino acid replacement results in a drastic alteration in the structure and function of the hemoglobin protein. The sickle cell hemoglobin protein actually precipitates out of solution under low oxygen conditions and causes the red blood cell to become sickle shaped. This, as you may imagine, has devastating effects upon individuals who have only this type of hemoglobin and usually results in a greatly shortened life span. Never underestimate the power of the sequence of amino acids, for it determines the structure and function of all proteins.

Figure 6. Two glycine amino acids combining through the formation of a peptide bond to form a dipeptide.

Nucleic Acids

Nucleic Acids are truly the biomolecules that define life. You may think that this is a rather startling statement when one considers the power of proteins; however, the information for the manufacture of all proteins - indeed for all biological molecules - resides in the nucleic acid molecule.

Nucleic acids are polymers as are proteins and carbohydrates. The monomeric units of nucleic acids are called nucleotides. Nucleotides are made up of three parts covalently bonded together:

Each nucleotide is identical except for the specific nitrogenous base that is covalently bonded to the #1 carbon of ribose.

There are two main types of nucleic acid: deoxyribonucleic acid (DNA), and ribonucleic acid (RNA). These two types differ from each other in that the ribose of DNA lacks an oxygen on the #2 carbon, and the nitrogenous base thymine is replaced by uracil in RNA. DNA is normally double-stranded, or consists of two polymers wound up together, while RNA is normally single-stranded. RNA's function in the cell is to carry small pieces of information to various regions of the cell, while DNA functions as a storage for all genetic information.

Figure 7. Structural formula of one complete nucleotide found in DNA and one complete nucleotide found in RNA for comparison.

When the nucleotide monomers of nucleic acids covalently bond together through a dehydration reaction, a special kind of bond, called a phosphodiester bond, is formed.

Figure 8. Three nucleotides covalently bonded together through their phosphodiester bonds.

The four different bases of DNA are shown below in Figure 10.

Figure 9. The purines, Adenine and Guanine and the pyrimidines Cytosine and Thymine, as well as uracil.

The double-stranded structure of DNA is due to hydrogen bonds that form between the bases on one strand of DNA and the bases on a different strand.

The hydrogen bond, although one of the weakest chemical bonds, is absolutely essential to the structure and function of nucleic acids and proteins. The potential for hydrogen bond formation arises when two atoms are bonded together that have very different electronegativities. In the case of the hydrogen bond, hydrogen is the electropositive element developing a partial positive charge. Oxygen or nitrogen are both electronegative elements, and develop a partial negative charge. In nucleic acids, a hydrogen on one nitrogenous base will form a hydrogen bond with either an oxygen or nitrogen on another nitrogenous base. Hydrogen bonding occurs between bases on opposite strands. Adenine and Thymine (or Uracil) hydrogen bond together, as do Cytosine and Guanine. Hydrogen bonding cannot occur properly in any other combination of bases. The A and T bases share two hydrogen bonds, while C and G share three hydrogen bonds.

Figure 10. Hydrogen bonds formed between A and T or C and G.

The ability of the bases on one molecule of DNA to hydrogen bond to another molecule of DNA or RNA is called complementarity. This ability is the single most important feature of nucleic acid. Complementarity allows DNA to replicate or duplicate itself, and to be transcribed, or rewritten, in the RNA format. RNA travels through the cell to the organelles that translate its sequence of bases into the sequence of amino acids making up proteins. Complementarity also allows certain types of RNA molecules to fold up into 3-dimensional structures necessary for protein translation and a variety of cellular and regulatory processes.

Base Pairing Rules:

The sequence of the amino acids in a protein is critically important to the structure and thus the function of a protein, and protein sequence is ultimately determined by DNA sequence. Therefore the linear sequence of bases in DNA determines the linear sequence of the amino acids in a protein. Change the base sequence of a DNA molecule and you will alter the amino acid sequence in the protein molecule obtained from that DNA sequence.  The two critical features of nucleic acid function are the importance of the sequence of nucleotides, and complementarity, or the base pairing rules.

Practice Round Four

1. Proteins are composed of what monomeric unit? What functional groups are responsible for bond formation between these monomers? What is the name of this bond? What is the name for a string of these monomers bonded together?

2. What determines the structure and function of all proteins?

3. What are the monomeric units of nucleic acid, and what three parts compose this monomer?

4. What are the official names of DNA and RNA and how did they come by these names?

5. What types of bonds are formed between nucleic acid monomers?

POST TEST on Biological molecules

1. Silicon atomic number 14 has four electrons in its outer most electron shell just as carbon does. Speculate about why life on earth is based upon Carbon rather that Silicon.

2. Please explain how and why a membrane may form spontaneously when the appropriate phospholipids are placed in an aqueous medium.

3. Give an example of the monomeric forms and at least one polymer for each of the three classes of biological molecules that form polymers.

4. Write the molecular and structural formula for glucose.

5. Define and explain the types of reactions that build up and break down biological polymers.

6. Define complementarity.

7. In general, how does DNA hold the information necessary to manufacture proteins?

8. List the bases of the nucleotides for both DNA and RNA and state the base pairing rules.

9. List three ways in which RNA structurally differs from DNA.

copyright by Gretchen Kirchner 1996, 2001

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