Organic molecules are molecules that contain carbon and hydrogen.

All living things contain these organic molecules: carbohydrates, lipids, proteins, and nucleic acids. These molecules are often called macromolecules because they may be very large, containing thousands of carbon and hydrogen atoms and because they are typically composed of many smaller molecules bonded together. These four macromolecules will be discussed in the second half of this chapter.. 

Carbon has four electrons in its outer shell.

Hydrogen has one electron and one proton.

Carbon can bond by covalent bonds with as many as 4 other atoms.

The diagram above shows a molecule of methane. Lines can be used to represent bonds in the shorthand formula seen in the upper right side of the diagram.

Carbon can also form double covalent (shares 2 pairs of electrons) or triple covalent bonds (shares 3 pairs).

Carbon can form 4 covalent bonds because it has 4 electrons in its outer shell. It can form the following number of bonds. Notice that in each case below, there is a total of four bonds.

• 4 single bonds
• two double bonds
• one double bond and two single bonds
• one triple and one single bond

Long chains of carbon atoms are common. The chains may be branched or form  rings.

Polar and ionic molecules have positive and negative charges and are therefore attracted to water molecules because water molecules are also polar. They are said to be hydrophilic because they interact with (dissolve in) water by forming hydrogen bonds.

Nonpolar molecules are hydrophobic (means "water fearing"). They do not dissolve in water.

	Nonpolar molecules are hydrophobic.
	Polar and ionic molecules are hydrophilic.

Portions of large molecules may be hydrophobic and other portions of the same molecule may be hydrophilic.

Condensation

In order to bond the two molecules shown below together, you must first remove a hydrogen from each one. This is necessary because carbon has a maximum of 4 bonds and hydrogen can have only one.

In biological systems, macromolecules are often formed by removing H from one atom and OH from the other (see the diagram below). The H and the OH combine to form water. Small molecules (monomers) are therefore joined to build macromolecules by the removal of water. The diagram below shows that sucrose (a sugar) can be produced by a condensation reaction of glucose and fructose.

Sucrose:

This is called a condensation reaction.

Hydrolysis

This is a type of reaction in which a macromolecule is broken down into smaller molecules.

It is the reverse of condensation (above).

The general formula for carbohydrates is (CH₂O)_n.

Monosaccharides are simple sugars, having 3 to 7 carbon atoms. They can be bonded together to form polysaccharides. Glucose, fructose, and galactose are monosaccharides; their structural formula is C₆H₁₂O₆.

Monosaccharides function to store energy. Energy is needed to form the bonds when the molecules are made. This energy is released when the bonds are broken.

Monosaccharides also function as the building blocks for larger carbohydrates (discussed below).

Disaccharides are composed of 2 monosaccharides joined together. Sucrose (table sugar) is composed of glucose and fructose. Lactose is found in milk and contains glucose and galactose.

The digestion of carbohydrates typically involves hydrolysis reactions in which complex carbohydrates (polysaccharides) are broken down to maltose (a disaccharide). Maltose is then further broken down to produce two glucose molecules.

Monosaccharides may be bonded together to form long chains called polysaccharides. Starch and glycogen are polysaccharides that function to store energy. 

Animals store extra carbohydrates as glycogen in the liver and muscles. Between meals, the liver breaks down glycogen to glucose in order to keep the concentration of glucoses in the blood stable. After meals, as glucose levels in the blood rise, it is removed from and stored as glycogen.

Plants store energy in starch.

Lipids are compounds that are insoluable in water but soluable in nonpolar solvents. 

Some lipids function in long-term energy storage. Animal fat is a lipid that has six times more energy per gram than carbohydrates. 

Lipids are also an important component of cell membranes.

Fats and oils are composed of fatty acids and glycerol.

Fatty acids have a long hydrocarbon (carbon and hydrogen) chain with a carboxyl (acid) group. The chains usually contain 16 to 18 carbons.

Glycerol contains 3 carbons and 3 hydroxyl groups. It reacts with 3 fatty acids to form a triglyceride or fat molecule.

 

Fats are nonpolar and therefore they do not dissolve in water.

Saturated and Unsaturated Fat

Saturated fatty acids have no double bonds between carbons. Unsaturated fatty acids have at least one double bond. Each double bonds produces a "bend" in the molecule.

Double bonds produce a bend in the fatty acid molecule (see diagram above). Molecules with many of these bends cannot be packed as closely together as straight molecules, so these fats are less dense. As a result, triglycerides composed of unsaturated fatty acids melt at lower temperatures than those with saturated fatty acids. For example, butter contains more saturated fat than corn oil, and is a solid at room temperature while corn oil is a liquid.

Phospholipids have a structure like a triglyceride (see diagram above), but contain a phosphate group in place of the third fatty acid. The phosphate group is polar and therefore capable of interacting with water molecules.

Phospholipids spontaneously form a bilayer in a watery environment. They arrange themselves so that the polar heads are oriented toward the water and the fatty acid tails are oriented toward the inside of the bilayer (see the diagram below). 

In general, nonpolar molecules do not interact with polar molecules. This can be seen when oil (nonpolar) is mixed with water (polar). Polar molecules interact with other polar molecules and ions. For example table salt (ionic) dissolves in water (polar). 

The bilayer arrangement shown below enables the nonpolar fatty acid tails to remain together, avoiding the water. The polar phosphate groups are oriented toward the water.

Membranes that surround cells and surround many of the structures within cells are primarily phospholipid bilayers.

Steroids have a backbone of 4 carbon rings.

Cholesterol (see diagram above) is the precursor of several other steroids, including several hormones.   It is also an important component of cell membranes.

Saturated fats and cholesterol in the diet can lead to deposits of fatty materials on the linings of the blood vessels.

Proteins

Some important functions of proteins are listed below.

enzymes (chemical reactions)

hormones

storage (egg whites of birds, reptiles; seeds)

transport (hemoglobin)

contractile (muscle)

protective (antibodies)

membrane proteins (receptors, membrane transport, antigens)

structural

toxins (botulism, diphtheria)

Enzymes are proteins that speed up the rate of chemical reactions.

Example:

The presence of an enzyme in the chemical reaction diagrammed below causes hypothetical chemicals A and B to react, producing C.

Proteins are able to function as enzymes due to their shape. For example, enzyme molecules are shaped like the reactants, allowing the reactants to bind closely with the enzyme.

Amino acids are the building blocks of proteins.

Twenty of the amino acids are used to make protein. Each has a carboxyl group (COOH) and an amino group (NH2).

Each amino acid is different and therefore has its own unique properties.

Some amino acids are hydrophobic, others hydrophilic. The carboxyl or amino group may ionize (forming NH₃⁺ or COO^-). The "R" group of some amino acids is nonpolar and the "R" group of some others is polar or it ionizes.

Amino acids are joined together by a peptide bond. It is formed as a result of a condensation reaction between the amino group of one amino acid and the carboxyl group of another.

Polypeptides

Two or more amino acids bonded together are called a peptide. A chain of many amino acids is referred to as a polypeptide.  The complete product, either one or more chains of amino acids, is called a protein.

There is unequal sharing of electrons in a peptide bond. The O and the N are negative and the H is positive.

The large number of charged atoms in a polypeptide chain facilitates hydrogen bonding within the molecule, causing it to fold into a specific 3-dimensional shape.

The 3-dimensional shape is important in the activity of a protein.

The following is the list of amino acids in one of the polypeptide chains of hemoglobin.

val his leu thr pro glu glu lys ser ala val thr ala leu tyr gly lys val asn val asp glu val gly gly glu ala leu gly arg leu leu val val tyr pro try thr gln arg phe phe glu ser phe gly asp leu ser thr pro asp ala val met gly asn pro lys val lys ala his gly lys lys val leu gly ala phe ser asp gly leu ala his leu asp asp leu lys gly thr phe ala thr leu ser gln leu his cys asp lys leu his val asp pro glu asn phe arg leu leu gly asn val leu val cys val leu ala his his phe gly lys glu phe thr pro pro val gln ala ala tyr gln lys val val ala gly val ala asp ala leu ala his lys tyr his

The chain of amino acids folds into a complex shape that often includes coils and sheet-like structures.

Some proteins contain two or more polypeptide chains.Hemoglobin, for example, contains four polypeptide chains.

Denaturation occurs when the normal bonding patterns are disturbed causing the shape of the protein to change.  This can be caused by changes in temperature, pH, or salt concentration. For example, acid causes milk to curdle and heat (cooking) causes egg whites to coagulate bacause the proteins within them denature.

 If the protein is not severely denatured, it may regain its normal structure.

Other Kinds of Proteins

Some proteins contain only amino acids. Other proteins contain other kinds of molecules. For example, glycoproteins contain carbohydrates, nucleoproteins contain nucleic acids, and lipoproteins contain lipids. 

DNA (deoxyribonucleic acid) is the genetic material. It functions by storing information regarding the sequence of amino acids in each of the body’s proteins. This "list" of amino acid sequences is needed when proteins are synthesized. Before protein can be synthesized, the instructions in DNA must first be copied to another type of nucleic acid called messenger RNA.

Nucleic acids are composed of units called nucleotides, which are linked together to form a larger molecule. Each nucleotide contains a base, a sugar, and a phosphate group. The sugar is deoxyribose (DNA) or ribose (RNA). The bases of DNA are adenine, guanine, cytosine, and thymine. Notice that the carbon atoms in one of the nucleotides diagrammed below have been numbered.

The diagram below shows how nucleotides are joined together to form a "chain" of nucleotides.

DNA is composed of two strands in which the bases of one strand are hydrogen-bonded to the bases of the other. The sugar-phosphate groups form the outer part of the molecule while the bases are oriented to the center. 

The strands are twisted forming a configuration that is often referred to as a double helix. The photograph below is of a model of DNA.

The adenine of one strand is always hydrogen-bonded to a thymine on the other. Similarly, Guanine is always paired with Cytosine.

A-T

G-C

The end of a single strand that has the phosphate group is called the 5’ end. The other end is the 3’ end.

The two strands of a DNA molecule run in opposite directions. Note the 5’ and 3’ ends of each strand in the diagram.

Codons

One strand of the double-helix contains the three-letter (three-base) codes, the other is a non-coding strand. For example, in the diagram above, CAC is the code for valine. The sequence of codes in DNA determines the sequence of amino acids in the protein.

Click here for details on how information is stored in DNA.

Each three-letter code is a codon. It is the code for one amino acid.

RNA

RNA (ribonucleic acid) is similar to DNA and is also involved in protein synthesis. The table below lists differences between DNA and RNA.

	DNA	RNA
# strands	2	1 (see diagram below)
sugar	deoxyribose	ribose
bases	A, T, G, C	A, U, G, C

RNA is single-stranded as shown below.

ATP (adenosine triphosphate) is a nucleotide that is used in energetic reactions for temporary energy storage.

Energy is stored in the phosphate bonds of ATP. When the bonds are broken, the energy is released. Normally, cells use the energy stored in ATP by breaking one of the phosphate bonds, producing ADP. Energy is required to convert ADP + P_i back to ATP.

ATP is continually produced and consumed as illustrated below.

Review

Use the symbols below to draw a dissacharide, polysaccharide, triglyceride, phospholipid, protein, and DNA. Use short, straight lines to represent covalent bonds.

Additional Reading and Help

The Visionlearning website contains good summaries of the material presented in this class. Do Chemistry CHE 1.1 - 1.4, 1. 6, 1.7, 2.1, 2.2, 2.4 - 2.6.