The Chemistry of Life

What Is Organic Chemistry?

We are now leaving the study of water and ions to study molecules that are based on carbon.  This scientific discipline is called organic chemistry.  It is of utmost importance to biology, since all living matter is made from organic compounds. 

The first form of life originated from carbon-based molecules in the earth’s oceans.  So, what is special about carbon that makes it such a central element of living matter?  One answer is that carbon contains only 4 electrons in its outer shell.  Thus it cannot lose all 4 electrons or gain 4 more in order to obtain the stable number of 8—too much energy is required for this to be feasible.  So instead, carbon typically forms covalent bonds with 4 other molecules.  The 4 attachment sites provide places where other groups can attach, so many branched molecular forms are possible.  Since covalent bonds are the strongest type, the resulting molecules are very stable.  The organic molecule shown here is small, but carbon chains are stable enough to become quite long, and some organic molecules are so large that they are called macromolecules.  Note also that hydrogen is the most common element bound to carbon.

Four Covalent Bonds
Here are some small organic molecules.  Note the different ways that they can be drawn.  Structural formulas are most common, but other representations can give a more realistic view of the molecule.  For example, when a carbon is surrounded by 3 or 4 hydrogen atoms, that part of the molecule forms the shape of a tetrahedron.  This 3-dimensional shape can be visualized in ball-and-stick models.  When adjacent carbons form a double bond, the tetrahedron cannot form and the molecule is flat.  Note that in each case, the carbon atoms have formed 4 bonds with their neighbors.

Carbon Skeletons
The carbon backbones of organic molecules may vary in length and location of single and double bonds.  Molecules may be straight or branched and may even contain rings of atoms.  We will see all of these features as we study the biologically important groups of organic molecules.

Functional Groups
Here we see examples of the many functional groups that can attach to the carbon skeleton.  Hydroxyl groups  are found in alcohols such as ethanol.  They are not ionized, so do not confuse them with the hydroxide ions studied earlier.  Carboxyl groups and amino groups are quite important in biology, since they are crucial to the structure of proteins.  The carboxyl group can donate its hydrogen, which makes the molecule acidic.  For example, the organic molecule acetic acid is found in vinegar giving it a sour taste.  In cells, the carboxyl group often loses its hydrogen creating a negatively charged molecule.  Note that amino groups consist of nitrogen bonded to two hydrogens.  These functional groups can pick up an extra hydrogen as shown in the diagram.  The group thus acts as a base and acquires a positive charge. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen.  Two sulfhydral groups in different parts of a macromolecule can interact to stabilize molecular shape.  In phosphate groups, a phosphorus atom is surrounded by 4 oxygen atoms, one of which is attached to the carbon skeleton.  Two of the oxygen atoms typically carry a negative charge.  Phosphate groups are very important in biology because they can transfer energy between organic molecules.  You will learn more about phosphate groups in the topic “Enzymes and Energy”.

There are 4 major groups of biologically important organic molecules.  Three of these groups (carbohydrates, proteins and nucleic acids), are formed from small molecules called monomers that are linked together.  The resulting chains of monomers are called polymers.  Polymers can consist of just a few monomers or can become very long, containing hundreds of monomers.  The diagram shown here indicates how monomers can be connected to form polymers.  Monosaccharides are the monomers of carbohydrates, also called polysaccharides.  Amino acid monomers link together to form the polypeptide chains of proteins, and nucleotide monomers form nucleic acids, one of which is DNA.   The upcoming animation will illustrate how polymers are synthesized from monomers.

Which Organic Molecules Are Important For Life?

The first group of organic molecules that we will examine are the carbohydrates.  These molecules are familiar to us as nutrients and indeed they provide a source of energy for most living organisms.  There are two main types of carbohydrates.  Sugars are relatively small molecules made of one or two monomers.  They are found in plant material, especially fruits, sugar cane and sugar beets.

The other type of carbohydrate consists of long chains of monomers.  These are called complex carbohydrates.  We are most familiar with the complex carbohydrate starch, a plant product that is found in the foods shown here.

Lipids are the one large class of biological molecules that are not comprised of polymers.  Lipids are a diverse group with 3 main subdivisions:  the triglycerides (or fats), the phospholipids, and the steroids.  The one thing that all of these molecules have in common is that they are hydrophobic. Although some lipids do have polar regions, they are mostly composed of hydrocarbon chains. 

Phospholipids are similar to triglycerides with one important difference.  Instead of 3 fatty acid chains, a phospholipid has 2 fatty acids plus a phosphate group.  The phosphate group is negatively charged and thus the phospholipid has a polar end.  Since the other end is hydrophobic, this molecule is amphipathic.

What do you expect to happen if phospholipids are added to a container containing water and oil?  Remember that water is polar, but oil is not.

You can see that the phospholipids are oriented so that their hydrophobic regions are in the oil while their polar, hydrophilic heads are in the water.

What would happen if phospholipids molecules were trapped within water?  Here is one configuration that they could assume.  Note that all of the polar heads are exposed to water while the hydrophobic tails are in the center, where water is largely excluded.  This structure resembles the membranes of a living cell and cellular membranes do, in fact, contain phospholipids.  You will learn more about membranes later in the topics related to cells.

The last category of lipids are the steroids.  These molecules are characterized by a carbon skeleton of four fused rings.  The atom symbols have been omitted from this diagram for simplicity, but there is a carbon atom at every point of the rings.  Steroids differ from one another by the addition of various side groups to the rings. 

Sex Hormones
One important steroid is cholesterol.  It is a component of cell membranes and serves as a precursor for steroid hormones, including the sex hormones.  However, too much cholesterol can lead to plaque formation. In fact, the negative effects of saturated and trans fats are largely due to their actions on circulating cholesterol levels.  The two main sex hormones in humans are the female hormone estradiol and the male hormone testosterone.  As you can see, these hormones are quite similar—they differ only in two side groups.  Vitamin D which is essential for bone calcification is also a steroid. 

You have undoubtedly heard of steroid abuse by athletes and body builders.  To learn about these anabolic steroids and their side effects, read the article indicated below.

Living organisms must accomplish many tasks just to make it through each day.  We have seen that carbohydrates and lipids play important roles in providing energy and some structural support.  But proteins are involved in virtually every task that living things perform.  The importance of proteins is indicated by their name, which comes from the Greek word proteios, meaning first place.

The secondary and tertiary structure of proteins gives each protein a distinct, 3-dimensional shape. Here we see the shape of the protein insulin from several angles.

This model represents a small protein that binds to DNA. Certain 3-dimensional regions of a protein may have specific functions. Such regions are called domains and are usually composed of 25-500 amino acids. The DNA-binding domain of this protein is designated by the purple, pink and gold areas.

In this larger protein, the helical regions are represented by cylinders and the pleated sheet regions by the broad lines with arrows. Each domain has a specific 3-dimensional shape and a specific function.

As you learned earlier, the shape of biological molecules often determines their ability to function.  This is especially true of proteins.  Here we see computer-models of two macromolecules.  The one on the left is a molecule found on the surface of the influenza virus.  The one on the right is a portion of a human protein, called an antibody, which attacks invaders such as viruses.  Note that this specific antibody has a region that is designed to fit that of the virus.

Thus the antibody protein can attach to the virus using a hand-in-glove fit that is the prelude to destruction of the virus.

If a protein loses its precise 3-dimensional structure, it is said to be denatured.  Proteins will become denatured under conditions of high temperature or change in pH.  For example, boiling an egg denatures the proteins causing the egg white to coagulate.  This is also the reason why high fevers are dangerous—they can denature proteins in the blood.  In the “wrong” pH, the hydrogen and ionic bonds of a protein can be broken, allowing the protein to unfold. Alcohol is a good disinfectant because it denatures or alters the shape of bacterial proteins.

Proteins can also combine with lipids to form lipoproteins.  One use of lipoproteins in the human body is to serve as a “carrier” for fats within the blood.  The liver processes triglycerides from the diet and surrounds them with a protein shell.  This allows the hydrophobic lipids to be transported through the aqueous bloodstream to their destination in fat-storing cells or for use in muscle.  After “dropping off” the lipids, the protein portion returns to the liver and combines with more lipid.

In many cases, carbohydrate chains are attached to proteins to form glycoproteins.  Many of the proteins found in cell membranes are of this type.  The example shown here represents a glycoprotein embedded in the membrane of a cell’s surface.  The brown structure is the protein part of a glycoprotein and the green chains represent the carbohydrate parts.  Such glycoproteins often function as enzymes or as signal receptors on the surface of cells.

Information in Nucleic Acids
Nucleic acids are the final group of macromolecules with biological importance.  As we have seen, the human body contains a vast number of different proteins.  A single cell can have 4,000 different types of enzyme.  Nucleic acids contain the information that specifies how each of these proteins is made.  Each amino acid and its order in the polypeptide chain is “coded” by the type and order of monomers in a nucleic acid chain.  Thus these molecules are also very large.  Taken together, the nucleic acids of a cell control all of its structural and functional properties by specifying which proteins that cell will contain.  Thus nucleic acids are the information-bearing molecules of life.  In the photograph shown here, we see two researchers pointing to an early model of deoxyribonucleic acid (commonly called DNA).  These researchers, Watson and Crick ,  discovered the structure of DNA in the late 1950’s.  This initiated the intensive research in the field of molecular biology that continues today.