Compounds of Life

Molecules can be grouped as either inorganic or organic based on various properties.

• Inorganic: These types of molecules are usually formed through ionic bonding, have small numbers of atoms in them, and though they are important to living organisms primarily form nonliving matter.
• Organic: For a molecule to be considered organic is must contain carbon and hydrogen, usually forms through covalent bonding, is made up of many atoms in most cases, and forms the matter from which living organisms are formed.

We will be looking closer at the structure of various organic molecules important to living organisms. We will see repeating combination of atoms associated with the various organic molecules. These repeating units are known as functional groups and they give the organic molecule certain chemical and physical properties. If you go on to study organic chemistry in more detail you will need to learn these properties, however for biology all we need to know is the functional group’s structure and which types of organic molecules you would find them in.

The R component of the functional group is not the symbol for an atom; it refers to the rest or remainder of the organic molecule. Recall that functional groups are attached to organic molecules.

• Hydroxyl: R-OH this functional group is found in sugars.
• Carboxyl: A carbon double bonded to oxygen and single bonded to a hydroxyl it is found in fats and amino acids.
• Ketone: A carbon double bonded to oxygen, it is found in some sugars.
• Aldehyde: A carbon double bonded to oxygen and single bonded to hydrogen, it is found in some sugars.
• Amine: R-NH₂ this functional group is found in amino acids and proteins.
• Sulfhydryl: R-SH this functional group is found in some amino acids and proteins.
• Methyl: R-CH₃ this functional group is found in fats and some amino acids and proteins.
• Phosphate: Phosphorus double bonded to oxygen, single bonded to hydroxyl at two points and single bonded to oxygen, it is found in phospholipids, nucleotides, and nucleic acids.

When studying the structure of these functional groups keep things simple. The phosphate is the only one with phosphorus in it. Sulfhydryl is the only one with sulfur in it. Amine is the only one with nitrogen in it. By thinking of simple ways to remember the unique looking functional groups, you will have an easier time learning the more confusing ones.

The organic molecules that help form cells are described as macromolecules. Macromolecules are large organic molecules. These large organic molecules can also be described as polymers. A polymer is made by the joining of many smaller units known as monomers. Poly means many and Mono means one.

We will be studying four groups of macromolecules; we need to know their polymer name and the monomers that joined to form them.

• Polysaccharides are the polymer commonly referred to as carbohydrates or complex sugars. They are made by joining monosaccharide units commonly called carbohydrates or simple sugars.
• Proteins are the polymer formed by joining the monomers called amino acids.
• Triglycerides are the polymer commonly called fats or lipids. They are formed by joining glycerol and three fatty acids.
• Nucleic Acids are the polymers formed by joining the monomers called nucleotides.

We will be looking at each group of macromolecule in some detail in this unit.

Good news, the chemical reaction that joins each group of monomers to form the polymer is the same. So we only need to understand this one type of reaction to make polysaccharides, or proteins, or triglycerides, or nucleic acids.

In order to join monomers together to make a polymer you remove an OH from one monomer and an H from the other. OH + H = water so you are removing water in order to join the two monomers together. This type of reactions is called a dehydration synthesis reaction or a condensation reaction. You can figure out what is happening in the reaction by just looking at the reaction name. Dehydration means to remove water and synthesis means to make. So you are removing water to make a polymer. Condensation is another name for forming water as well.

Often our cells need to break the large polymers down to obtain monomers. This is just the opposite of dehydration synthesis. This type of reaction is called a hydrolysis reaction. Water will be split putting an OH back onto one monomer and the H onto the other. In doing this the bond holding the two monomers together is broken separating them.

The first group of organic molecules we will look at are the carbohydrates. They are used as a quick energy source for our cells.  Some carbohydrates have structural roles in the cell as well. We will learn more about this later.

The basic unit of a carbohydrate is known as a monosaccharide. The basic formula of a monosaccharide is (CH₂O)_n. This means there are always twice as many hydrogens as carbons and oxygens.

You need to be able to look at a structure of a carbohydrate and identify functional groups.

Glucose: When looking at the stick (linear) figure of glucose functional groups can easily be seen. You should be able to pick out many hydroxyl groups as well as an aldehyde group on the molecule. If you count up the number of carbons, hydrogens, and oxygens you should come up with the molecular formula as C₆H₁₂O₆ for glucose. This formula fits the profile of a monosaccharide.

Fructose: When looking at the linear figure of fructose you should see several hydroxyl functional groups as well as a ketone. If you count up the number of carbons, hydrogens, and oxygens you should come up with the molecular formula as C₆H₁₂O₆ for fructose. This formula fits the profile of a monosaccharide.

Why do glucose and fructose have the same molecular formula but different names? Well it all depends on the way the atoms are arranged in the molecule and the functional groups present. When molecules have the same molecular formula but are put together and function differently they are said to be isomers.

The molecules are shown in their ring structure form that is how they occur naturally. As the figure clearly shows, one monomer, fructose, will lose an OH while the other monomer, glucose, will lose a H. This forms water that is removed leaving the two molecules free to bond. You can see that an oxygen atom bonds the two molecules together.

The joining of two monosaccharides together forms what is known as a disaccharide. Sucrose, which is our common table sugar, is an example of a disaccharide. Two other disaccharides are lactose and maltose. Lactose is formed by joining glucose and galactose and is called a milk sugar because it is found in dairy products. Maltose is formed by joining two glucose molecules together. It is the first product produced when starch (a polysaccharides of glucose) is digested.

Polysaccharides are formed when many monosaccharides link up. We will consider four polysaccharides all based on the linkage of the same monosaccharide, glucose.

Starch vs. Glycogen: Both of these molecules are formed by joining many many glucose units together. They differ structurally with the fact that starch has few glucose side branch chains while glycogen has many. The function of each molecule is basically the same however they differ in the type of organism they are found in. Starch is the storage form of glucose in plants while glycogen is the storage form of glucose in animals. Both types of cells will store the excess glucose in the polysaccharides form that can quickly be broken down if the glucose monomers are need again.

Cellulose vs. Chitin: Both of the molecules are formed by joining many many glucose units together. They arrangement of the bond holding each glucose together is different then the type of bond in starch and glycogen. We do not have enzymes to break this bond so we cannot digest cellulose or chitin. Cellulose is the structural form of glucose in plants, it helps form their cell wall and is what we call fiber in our diet. It is formed when many long glucose chains hydrogen bond together. This bonding of chains produced a much stronger molecule, hence its function. Chitin forms the exoskeleton of insects, crabs, and lobsters. It is formed from a long chain of glucose with amino groups attached.

Lipids: This group of organic molecules is often referred to as fats. They have many functions. They provide a long term energy storage, can insulate organisms from extreme heat (camel’s hump) or extreme cold (whale blubber). They protect internal organs from damage and act a cushion or shock absorber. In plants they form a protective waxy coating to prevent water loss at the leaves.

Fats or oils are the common term for triglycerides. Recall that a triglyceride is formed by joining a glycerol molecule with three fatty acids. Triglyceride fats can be further categorized based on the type of bonding that occurs between the carbon atoms in the fatty acid tails.

• Saturated: A triglyceride is described as a saturated fat with only single bonds between carbons of the fatty acid tail. When there are single bonds between the carbons a lot of hydrogens will be present, the molecule is saturated with hydrogens. Saturated fats are solid at room temperature and examples would be butter or lard.

• Unsaturated: A triglyceride is described as  an unsaturated fat if one or more double bonds are present between carbons in the fatty acid tail. When these double bonds are present a lot less hydrogens will be present in the molecule. The molecule is not saturated with hydrogens (unsaturated). Unsaturated fats are liquid at room temperature, oil would be an example of an unsaturated fat.

Waxes: Waxes are long chain fatty acids with long chain alcohols. They are extremely hydrophobic (water hating) and make great waterproofers because of this. Plants have a waxy cuticle on the surface of leaves to prevent water loss. Aquatic animals, such as ducks, have a waxy coating over their feathers to protect the underlying down feathers from getting wet.

Phospholipids: We will learn a lot more about phospholipids later in this unit. They are unusual molecules because they have two personalities, one part is hydrophobic (water hating) and the other part is hydrophilic (water loving). They consist of glycerol bonded to two fatty acid tails and one phosphate group. In water they arrange themselves into a phospholipid bilayer which as we will see will become the backbone of all cell’s plasma membrane.

Steroids: Steroids are not made from long carbon chains, they are formed by carbon rings. They play an important role in stabilizing the animal cell plasma membrane. They also make up a class of hormones, chemical messages, in our body. They help our various organs communicate with each other.

Proteins: Proteins have many functions in our cells. They can be structural to help the cell keep its shape. Proteins also have many chemical roles including acting as organic catalysts to speed up chemical reactions in our cells.

The basic subunit of a protein is the amino acid. It consists of a central Carbon atom with an Amine group, Carboxyl group, Hydrogen, and R group attached. The R group stands for something unique for each amino acid. For living organisms there are 20 different kinds of amino acids each one is different because of the R group.

When two amino acid join up to form a protein they always react in a specific way. The amino end of one amino acid will react with the Carboxyl end of the other amino acid. Once the water is removed the two amino acids will be joined between the Carbon of one amino acid and the Nitrogen of the other. This type of covalent bond is given the special name of Peptide Bond. You should have noticed that the reaction joining the two amino acids was a condensation reaction. We remove water to join the two amino acids together.

Proteins are very complicated molecules. In order for them to function properly they must take on a specific three dimensional shape. There are various levels to the folding of the protein into its three dimensional shape.

• Primary: This first level of protein structure is just the order of the amino acids linked together into a long chain.
• Secondary: Regions of the long amino acid chain will form hydrogen bonds. This hydrogen bonding causes the protein to take on unique shape patterns known as the alpha helix or beta pleated sheet.

·         Tertiary: Due to R group interactions portions of the chain will be attracted to or repelled from other portions. This will cause the protein to fold further into a glob type of shape. This glob shape is not random and must be maintained in order to the protein to function.

• All proteins have the first three levels of structure, some proteins go on further to form a fourth level of structure known as Quaternary Structure. This level of protein folding occurs when more than one polypeptide chain (protein) bond together. For example the protein hemoglobin in your red blood cells is actually 4 proteins working together. If they did not bond to work as a unit your red blood cell would not be able to transport oxygen to your tissues.

What happens if the protein’s shape is changed?

When environmental conditions such as temperature or pH cause a change if protein shape to the extent that it can no longer function; it has been denatured. I am sure we have all witnessed this, for example the white of an egg is liquid and clear at room temperature. However, when we cook the egg (heat) the white turns solid and white. This change is due to changes in shape of the albumin (egg white protein) protein brought about by heating during cooking.

The last group of organic molecules is known as the nucleic acids. We will learn a lot more about this group of molecules in later units so we will just briefly mention them here.

Nucleic acids are very large organic molecule made by joining small subunits known as nucleotides. A nucleotide has three parts to it. A nucleotide always contains a sugar, at least one phosphate group, and a nitrogen containing base region. For our studies we will deal with only 5 possible nitrogen containing bases : adenine, guanine, cytosine, thymine, and uracil.

Some nucleotides function alone others join up to form nucleic acids.

ATP: This is a nucleotide named Adenosine Triphosphate. From its name you can probably guess that adenine is the nitrogen containing base and that three phosphate groups are present. We will learn a lot more about this molecule in unit two, it is the energy molecule for the cell.

Nucleotide Coenzymes: We will learn more about these in unit two also. They are organic molecules that help our enzymes function. Enzymes speed up chemical reactions in our cells and certain enzymes required helpers to get their job done. These helpers are the vitamins in our diet and are called nucleotide coenzymes.

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids from which our genetic material is formed. We will learn much about these two molecules in unit three and four. The DNA is the blueprint for making all of the proteins in our cells and the RNA functions as a disposable copy of the DNA blueprint. We will see how these two molecules interact and function at a later date.