QUIZ YOURSELF!

a. carbohydrate b. lipids c. protein d. nucleic acids

1. contains adenine and thymine

2. lactose

3. chains of amino acids

4. long term energy storage

5. cholesterol

6. chains of fatty acids and glycerol

7. plant cell walls

Introduction

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

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.

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.

Hydrophilic and Hydrophobic

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.

Functional Groups

Organic molecules may have functional groups attached. A functional group is a group of atoms of a particular arrangement that gives the entire molecule certain characteristics. Functional groups are named according to the composition of the group. For example, COOH is a carboxyl group.

Organic chemists use the letter "R" to indicate an organic molecule. For example, the diagram below can represent a carboxylic acid. The "R" can be any organic molecule.

Some functional groups are polar and others can ionize. For example, if the hydrogen ion is removed from the COOH group, the oxygen will retain both of the electrons it shared with the hydrogen and will have a negative charge. The hydrogen that is removed leaves behind its electron and is now a hydrogen ion (proton).

Isomers

Different molecules that are composed of the same number and kinds of atoms are called isomers. Glucose and fructose (shown below) are both C6H12O6 but the atoms are are arranged differently in each molecule. Three kinds of isomers are described below.

Structural isomers differ in their overall construction as shown above for glucose and fructose.

Geometric isomers maintain the same carbon skeleton but a double bond occurs between carbon atoms. The location of atoms bonded to a double-bonded carbon atom differs. The two molecules below are geometric isomers because the double bond cannot rotate. If the bond between the two carbon atoms below were a single bond, they would not be isomers because atoms attached by single bonds can rotate. The carbon atoms would be able to rotate from one orientation to another if the bond were a single bond.

Enantiomers are molecules that are mirror images of each other. The molecules shown below are enantiomers.

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. This is called a condensation or dehydration reaction.

Energy is required to form the bond.

Hydrolysis

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

It is the reverse of condensation (above).

Macromolecules and Monomers

Many of the common large biological molecules (macromolecules) are synthesized from simpler building blocks (monomers). Each of the types of molecules listed in the table are discussed below.

Example of a Macromolecule Monomer

polysaccharide (complex carbohydrate) monosaccharide (simple sugar)

fat (a lipid) glycerol, fatty acid

protein amino acid

nucleic acid nucleotide

Proteins

Importance of 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.

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. The diagrams below show that the enzyme matches the shape of the substrate molecules. The enzyme is therefore able to hold the substrate molecules in the correct orientation needed for the chemical reaction to proceed. The enzyme does not participate in the reaction and is not changed by the reaction.

Amino Acids

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.

Levels of structure

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.

Primary Structure

Primary structure refers to the sequence of amino acids found in a protein. The following is the primary structure of one of the polypeptide chains of hemoglobin.

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Secondary structure

The oxygen or nitrogen atoms of the peptide bond are capable of hydrogen- bonding with hydrogen atoms elsewhere on the molecule. This bonding produces two common kinds of shapes seen in protein molecules, coils (called alpha helices) and beta pleated sheets. The alpha helices and beta pleated sheets are referred to as a proteins secondary structure.

Tertiary structure

Tertiary structure refers to the overall 3-dimensional shape of the polypeptide chain.

Hydrophobic interactions with water molecules are important in creating and stabilizing the structure of proteins. Hydrophobic (nonpolar) amino acids aggregate to produce areas of the protein that are out of contact with water molecules.

Hydrophilic (polar and ionized) amino acids form hydrogen bonds with water molecules due to the polar nature of the water molecule.

Hydrogen bonds and ionic bonds form between R groups to help shape the polypeptide chain.

Disulfide bonds are covalent bonds between sulfur atoms in the R groups of two different amino acids. These bonds are very important in maintaining the tertiary structure of some proteins.

The shape of a protein is typically described as being globular or fibrous. Globular proteins contain both coils and sheets.

Quaternary structure

Some proteins contain two or more polypeptide chains that associate to form a single protein. These proteins have quaternary structure. For example, hemoglobin contains four polypeptide chains.

Denaturation

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 because the proteins within them denature.

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

Nucleic Acids

DNA

DNA (deoxyribonucleic acid) is the genetic material. An important function of DNA is top store 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.