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Chemistry 23: 1-2

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Main Lecture

Most high school courses in chemistry offer very little introduction to organic chemistry. Those of you who have had biology will find some of this material already familiar; if not, pay particular attention to the chapter, since the concepts will reappear in any good biology course, and in organic chemistry itself if you continue your chemical studies into college.

Note that because of their fuel properties, messing about with hydrocarbons is not encouraged. The first organic chemistry lab of the college year always involves a practical drill in the use of the fire extinguisher.

Carbon Characteristics

Carbon has two characteristics which make it ideal as the basis of organic molecules. The first is that it can bond with four different units simultaneously, in three dimensions, giving it the maximal number of combinations and structures possible for a single element. While other members of the Group 4A family also share this ability, carbon is the only non-metal to do so.

For example, carbon can bond to itself in one dimension, forming sheets of hexagnoal units we call graphite and use as pencil "lead"; this is a soft, easily broken solid. It can also bond to itself in three dimensions, forming one of the hardest natural substances known, diamond. These elemental forms are allotropes. Carbon sheets can form complex lattices, both naturally and through atomic-level manipulations in the lab.

The second characteristic of carbon is that its bonds are primarily covalent, the strongest type of chemical bond, requiring the greatest amount of energy to break. This makes all carbon compounds fairly strong in comparison with other bond pairs, increases the activation energy required to start a chemical reaction, and slows down the reaction once it starts. This is especially true with hydrocarbon bonds, where the electronegativity of the two elements is similar and the bonds mostly non-polar.


Isomers are molecules which have the same chemical formula, but different structures. This is equivalent to having one set of Brio train tracks, from which you can make several different track patterns. Sometimes the patterns are wildly different, sometimes they have one section of track switched with another, and sometimes the track patterns are mirror images of each other. Because the hydrocarbon bonds are equivalent in terms of energy, the same combination of hydrogen and carbon atoms can combine to form several molecules with the same chemical formula, but different structures. There are two primary sorts of isomers in organic chemistry:

Thus carbon compounds are both stable and diverse in structure. These two characteristics make it a sound basis for organic molecules which must withstand trivial changes while performing a variety of complex functions.

Visit the Isomers of Organic Compounds site (requires Java capability) to view and minpulate structural and steriosimers.

Classes of Organic Molecules

Carbon-based organic molecules fall into several categories: simply hydrocarbons, and hydrocarbon chains with specific groups attached. These groups are called functional groups because this is the part of the molecule that usually reacts with other substances, while the remainder of the attached molecule remains inert. The hydrocarbon types and functional groups are summarized in the following table, and discussed in more detail through the rest of the unit lectures.

Group Formula Class Example
Hydrocarbons CnH2n+2 Alkanes (single bonds) Butane, propane, octane
CnH2n Cycloalkanes (single bonds, ring) Cyclohexane
CnH2n Alkenes (one double bond) Ethylene
CnH2n Alkene rings (multiple double bonds) Benzene, toluene
CnH2n-2 Alkynes (one triple bond) Acetylene (ethyne)
Hydroxyl R-OH Alcohols Ethanol
Amino R-NH2 Amines Amino acids
Carboxyl R-COOH Carboxylic acids Amino acids
Ester R-COOR Esters Methyl Acetate
Carbonyl R-COH Aldehydes O=C-H and Ketones O=C-R Formaldehyde and Acetone
Methyl R-CH3 Many organic compounds Methane
Phosphate R-PO4H2 Phosphates Glycerol Phosphate
Sulfhydryl R-SH Thiols Cysteine (an amino acid)

Notice that structure and type of bond must be considered as well as formula to distinguish between some of the combinations.

Hydrocarbons: alkanes, alkenes, alkynes

Alkanes, alkenes, and alkynes are all simple hydrocarbons: their structures involve no other elements. Almost all hy6drocarbons can exist as isomers, with several possible structures. Alkanes have the most diversity of structure, since all carbon bonds in alkanes are single bonds, so each carbon has the maximum number (four) of bonded groups.

All hydrocarbons burn in oxygen to form carbon dioxide and water:

CnH2n+2 + (3n+1)/2 O2 —> n CO2 + (n+1) H2O

C8H18 + 25/2 O2 —> 8 CO2 + 9 H2O

Alkanes have the formula CnH2n+2. The simplest alkanes are the familiar fuel compounds methane, ethane, propane, butane, and octane (gasoline). In the linear form of the molecule, each interior carbon is attached to two carbons and two hydrogens. The end carbons are attached to a third hydrogen rather than another carbon. In "planar" and three-dimensional structures, the carbons may be linked to form branches rather than chains. A special form of alkanes are the cycloalkanes, which have lost their end hydrogen atoms, bent to form a circle, and bonded the now-available end carbons to each other.

In analyzing the chemical properties of the different isomers, we must take into account these differences in bonds, since they will affect the energy required to break the molecule apart, and the energy released by that reaction.

Alkenes are alkanes which have lost two hydrogen atoms so that two carbons can form a double bond. Hence the general alkene formula is CnH2n. Again, these molecules can exist in linear, planar, or three-dimensional isomers. As with alkanes, there are ring-shaped variations, and some molecules with multiple double bonds (called -dienes, so butadiene). The latter are usually combinations of two or more alkene units which have lost end hydrogens to form yet another C=C bond and join together.

Alkynes are similar to alkenes, except that they have lost a second set of hydrogens and contain triple bonds. Obviously, this triple bond can be difficult to break, but also the source of a tremendous amount of energy. The most common alkyne is ethylene, more commonly known as the acetylene that powers metal-working torches at extremely high temperatures.

Aromatic Compounds

Most aromatic hydrocarbons have as their basis a ring of carbon atoms. The most common aromatic base is the "benzene ring", in which six carbons are joined by alternating single and double bonds, so that each carbon has a single C-C bond, a double C=C bond, and a single remaining bond with which to attach some other element. In benzene itself, the extra bonds all attach hydrogen, so benzene has the formula C6H6. By replacing one or more hydrogens in this structure with other elements or groups, we can create a variety of aromatic compounds with different chemical characteristics.

Moreover, we can create different molecular structures simply by altering the particular hydrogen replaced. Two different naming conventions developed for substitions to base hydrogen identifies not only the new element, but its location on the benzene ring, and aromatic compound names often reflect both. One uses numbers for the carbons in the ring two which the non-hydrogen group is attached, the other uses prefixes ortho (next to the first carbon), meta (two over from the first carbon), and para (opposite to the first carbon). The compound C6H4CH3CH3 is known both as1, 3-dimethylbenzene, showing that it has two (di) methyl groups attached to the 1st and 3rd carbons in benzene ring, and also as m-xylene, showing that the two methyl groups are 2 carbons apart on the ring.

Organic Chemistry: Alcohols and Amines


In an alcohol, one of the hydrogens in the hydrocarbon chain has been replaced with a polar OH group, making the normally non-polar molecule polar. (Another way to look at this is to consider an alcohol the replacment of one of the H atoms in water with an organic group). This changes certain properties of the base alkane considerably. Because the OH group is polar, alcohols will mix with water, where the alkanes themselves do not. Alcohols have low boiling points, allowing them to evaporate quickly. On the other hand, the presence of the carbon chains in the rest of the molecule still provide the materials for efficient fuels: alcohols, like alkanes, combust with oxygen.

Both methanol and ethanol can be produced from petroleum by-products, as a side industry to gasoline production. Ethanol is also produced by anaerobic fermentation of sugars and is the "alcohol" in wine and beer. The rapid evaporation of propanol compounds explains why they are used as solvents and drying agents.

MethanolFuel, formaldehyde and acetic acid manufacturing
EthanolBeverages, solvent
PropanolSolvents, rubbing alcohol
Ethylene glycolAntifreeze

Ethers (not to be confused with esters) are formed by alcohol dehydration synthesis. If two alcohol molecules lose the equivalent of a water molecule (an OH group from one, an H from the other), the symmetrical components will bond on the remaining O atom to form a molecule with the structure R - O - R, where R is the base alcohol.


Amines are important as the base groups for all proteins. Proteins are the builders of cells: they are to regulate growth, repair damage. They are the basic components of the enzymes which act as catalysts to most biological processes. Amines occur when one or more of the H atoms in NH3 is replaced with an organic group (hydrocarbon chain).

Proteins are built from amino acids, of which there are 20 commonly found in earth life. All amino acids have the same basic structure: an amine group (NH2) and a carboxyl group (COOH —see next unit!) attached to the same carbon, which in turn is attached to a hydrogen atom and an R-molecule. Only the R-molecule changes from amino acid to amino acid. The common amino acids break down into three groups by the way they combine: polar, non-polar, and ionic (electrically charged).

Essential amino acids are the ones your body can't make from raw materials, and which you have to get from the environment. The ability to make amino acids differs from species to species. In Jurassic Park, the assumption was that the dinosaurs couldn't make lysine. If it wasn't available for them to eat (and the builders of the park had left it out of the food chain on purpose), the dinos would die. For the record, humans cannot synthesize phenylalanine, valine, leucine, isoleucine, threonine, tryptophan, or lysine. Indequate amounts of these in the diet lead to retarded growth, mental apathy, and various physical deformities.

All essential amino acids are readily available from animal products; so if you eat meat, you probably don't have to worry much about amino-deficiency problems. Vegetarians who will eat cheese and eggs are usually able to compensate for the lack of amino acids in plants, but strict vegans can run serious health risks unless they eat specific vegetables in sufficient quantity.

Carbonyl Group Compounds

Carbonyl groups differ from alcohols because their carbon-oxygen group has a double bond rather than a single bond. They are often created by oxidizing alcohols, and the product depends on the type of alcohol. alcohol to be classified by the number of methyl groups (CH3) and single hydrogens associated with the central carbon atom. By definition, the central carbon atom always has an -OH group attached by a single bond; that's what makes it an alcohol.

In each reaction, two hydrogens are lost from the central carbon, and an additional or remaining oxygen forms a double bond to replace the missing bonds. Note that tertiary alcohols do not undergo dehydration and do not react with air.

PrimaryCH3-CH2-OHTwo step process with aldehyde intermediaryCarboxylic acidWine (ethanol) + air = wine vinegar (acetic acid)
Secondary(CH3)2-CH-OHSingle-step processKetoneBenzene + air = acetone
Tertiary(CH3)3-C-OHNo ReactionNoneNone

The five major groups of carbonyl compounds are aldehydes, ketones, carboxylic acids, esters, and amides (see table in lecture 10a). Both aldehydes and ketones are based on hexagonal rings (benzene rings) and share the aromatic characteristics of the structure. Carboxylic acids include acetic acid (the sour component of vinegar and sourdough bread), citric acid (found in citrus fruits like oranges and lemons), lactic acid (found in sour milk), and a oleic acid (found in vegetable oils). as we've already seen, acids or proton donors, and the OAH group which characterized the original alcohol provides the hydrogen for the acid reaction.

When carboxylic acid and alcohols react through dehydration synthesis, they form esters, so the name of the Esther comes from the name of the hydrocarbon group in the alcohol and the carboxylate group. For example, acetic acid combining with ethanol forms ethyl acetate. Esters often take the shape of benzene rings, which makes some aromatic: they give bananas and roses their characteristic scents.

Amides form in a similar manner, when acid reacts with an amine in dehydration synthesis. This amide formation has a special name: a peptide bond, and is characteristic of proteins.

Polymers in Living Organisms

So far, we have been studying individual molecular structures. We've seen how dehydration synthesis can link two molecules together, such as a carboxylic acid and alcohol to form an ester. Dehydration synthesis is a means whereby organic forms combine monomers to create polymer molecules of hundreds to thousands of components.

Organic MoleculeMonomerPolymer
LipidMethyl groupFatty Acid
Amino AcidAmino groupProtein
Nucleic AcidNucleic baseDNA

Polypeptide organization

A polypeptide molecule is just a string of amino acids (joined by dehydration). Its backbone is not -C-C-C-, as with the polymers, but H2-N-C-C-N-C-C-COOH. One of the two internal carbons has some R-group and a hydrogen attached, the other has a double-bonded oxygen atom. Each protein is a long polypeptide chain with a particular sturcutre. The simple chain (primary structure) can be thousands of amino acids long. The chain coils like a phone cord (secondary structure), which itself twists about (tertiary structure). The kinks are held in place by H bonds, hydrogen atoms in polar bonds, where the hydrogen's electron spends all its time between the hydrogen and the bonded atom, leaving the hydrogen's positive nucleus "bare" to the rest of the world, and able to form weak bonds with negative areas of its own protein chain, orthose of other polar molecules. When multiple polypeptide chains are combined together (quaternary structure), the result is an enzyme with a specific function, dictated by a unique sequence of amino acids.

Polymers Classification

in modern chemistry, polymeres are classified by how they are made: through direct addition of monomers, or through dehydration synthesis. Many commercial polymers, such as polyethylene, or byproducts of petroleum refining. Most are stable, and nonreactive, which makes them highly useful in a number of practical applications, but also poses a problem for their eventual disposal.

Putting it all together: Organic Chemistry "mind map".

Practice with the Concepts

Identifying hydrocarbons

What type of hydrocarbon is ethylene, C2H4?

Hydrocarbon characteristics

Which is more likely to be a liquid, CH4 , C6H14, or C20H42?

Organic compound types

A simple molecule containing a C-N bond is most likely to be what kind of organic molecule?

Functional Groups

What is the functional group of an an alcohol? What does the functional group do?

What is the functional group of an amine?

Discussion Questions