An
Introduction
to
Organic
Chemistry
A beginners' guide to the chemistry of Carbon compounds
What is Organic Chemistry?
The word Organic is one of the most overused in the English language.
People use it as a derogatory term in phrases like Don't eat that; it's not organic. Of
course, there is a precise scientific definition of the word. In science, Organic can be a
biological or chemical term. In Biology it means any thing that is living or has lived. The
opposite is Non-Organic. In Chemistry, an Organic compound is one containing Carbon
atoms. The opposite term is Inorganic.
It's the chemical meaning we are going to explore.
Molecules
All substances are made up of molecules which are collections of atoms. All the molecules
in existence are made up of about a hundred different kinds of atoms.
For example, a water molecule is composed of two atoms of Hydrogen and one atom of
Oxygen. We write its formula as H2O.
A molecule of Sulphuric Acid contains two atoms of Hydrogen, one atom of Sulphur and
four atoms of Oxygen. Its formula is H2SO4.
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These are simple molecules containing only a few atoms. Most Inorganic molecules are
small. Below are a few common inorganic substances with their formulas.
Name of Substance
Formula
Carbon Dioxide
CO2
Salt
NaCl
Nitric Acid
HNO3
Laughing Gas
N2O
Ammonia
NH3
Saltpetre
(used in gunpowder)
Carbon Monoxide
KNO3
CO
Potassium Permanganate
(used in labs)
KMnO4
Calcium Carbonate
(chalk)
CaCO3
All of these molecules have less than a dozen atoms.
The symbols Ca, K, Mn, Na and Cl stand for calcium, potassium, manganese, sodium and
chlorine.
Molecules With Carbon
Most atoms are only capable of forming small molecules. However one or two can form
larger molecules.
By far and away the best atom for making large molecules with is carbon. Carbon can
make molecules that have tens, hundreds, thousands even millions of atoms! The huge
number of possible combinations means that there are more carbon compounds that those
of all the other elements put together!
A single carbon atom is capable of combining with up to four other atoms. We say it has a
valency of 4. Sometimes a carbon atom will combine with fewer atoms.
The carbon atom is one of the few that will combine with itself.
In other words carbon combines with other carbon atoms.
This means that carbon atoms can form chains and rings onto which other atoms can be
attached.
This leads to a huge number of different compounds. Organic Chemistry is essentially
the chemistry of carbon. Biochemistry is a branch of organic chemistry.
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Carbon forms four bonds with other atoms (each bond consisting of one of carbon's
electrons and one of the bonding atom's electrons). Every valence electron participates in
bonding, thus a carbon atom's bonds will be distributed evenly over the atom's surface.
These bonds form a tetrahedron (a pyramid with a spike at the top), as illustrated below:
Carbon forms 4 bonds
Questions to check understanding:
1. What is the difference between organic and inorganic chemistry?
2. Why can organic molecules be so much larger than inorganic molecules?
3. Why carbon so good at making large molecules?
4. What is the basic shape of a single carbon-based compound?
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Classifying Organic Hydrocarbon Compounds
Organic (carbon-based) compounds are classified according to how the carbon atoms are
arranged and what other groups of atoms are attached.
Hydrocarbons
The simplest Organic compounds are made up of only Carbon and Hydrogen atoms only.
Even these run into thousands! Compounds of Carbon and Hydrogen only are called
Hydrocarbons.
Please note that the molecule structure images below show the structure of three
dimensional molecules in two dimensional format.
Alkanes
The simplest Hydrocarbon is methane, CH4. This is the simplest member of a series of
hydrocarbons. Each successive member of the series has one more Carbon atom than the
preceeding member. This is shown in the table below. Make ethane and propane, butane
and pentane with your molecular modeling kits and draw the molecules in the chart below.
(You may need to combine several kits to make the larger molecules.)
Formula
Structure
Name /
Uses
CH4
Methane
- gas
used for
cooking.
C2H6
Ethane
C3H8
Propane
- heating
fuel.
3-D Shape
4
C4H10
Butane lighter /
camping
fuel.
C5H12
Pentane
C6H14
Hexane
There is a series of these compounds with this general formula:
CnH2n+2
This series of compounds are called alkanes. The lighter ones are gases and used as fuels.
The middle ones (7 Carbons to 12 Carbons) are liquids used in petrol (gasoline). The higher
ones are waxy solids. Candle wax is a mixture of alkanes.
After Butane, the names of these compounds are from the Greek for the number of Carbon
atoms followed by the suffix -ane. So, Decane would have the formula
C10H22.
In the alkanes, all four of the Carbon valency bonds are taken up with links to different
atoms. These types of bonds are called single bonds and are generally stable and resistant
to attack by other chemicals. Alkanes contain the maximum number of Hydrogen atoms
possible. They are said to be saturated. (This connects to saturated fats – their long
carbon chains have only single bonds and are saturated with hydrogen atoms.)
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Alkane Naming Basics:
Carbon
Atoms
Prefix
Alkane
Chemical
Structural
Name
Formula
Formula
1
Meth
Methane
CH 4
CH4
2
Eth
Ethane
C2H6
CH3CH3
3
Prop
Propane
C3H8
CH3CH2CH3
4
But
Butane
C4H10
CH3CH2CH2CH3
5
Pent
Pentane
C5H12
CH3CH2CH2CH2CH3
6
Hex
Hexane
C6H14
...
7
Hept
Heptane
C7H16
8
Oct
Octane
C8H18
9
Non
Nonane
C9H20
10
Dec
Decane
C10H22
The alkanes are not the only hydrocarbons.
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Alkenes
Another series of compounds is called the alkenes. These have a general formula:
CnH2n.
Alkenes have fewer hydrogen atoms than the alkanes. The extra valencies left over occur as
double bonds between a pair of Carbon atoms. The double bonds are more reactive than
single bonds making the alkenes chemically more reactive.
The simplest alkenes are listed in the table below.
Make propene, butane, and pentene with your molecular modeling kits and draw the
molecules in the chart below. (You may need to combine several kits to make the larger
molecules.)
Formula
Structure
Name / Uses
C2H4
Ethene - used as an
industrial starter
chemical.
C3H6
Propene
C4H8
Butene
C5H10
Pentene
3-D Shape
These compounds are named in a similar manner to the alkanes except that the suffix is ene.
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Alkynes
A third series are the alkynes. These have the following formula:
CnH2n-2.
Alkynes have two carbon atoms joined by a triple bond. This is highly reactive making these
compounds unstable.
Single Bonding (alkanes)
Double-bonding (alkenes)
Triple-bonding (alkynes)
Examples of alkynes are:
Formula
Structure
Name / Uses
C2H2
Ethyne - better known as acetylene
which is used for welding underwater.
C3H4
Propyne
C4H6
Butyne
C5H8
Pentyne
These highly reactive substances have many industrial uses.
Again the naming of these compounds is similar to the alkanes except that the suffix is yne.
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Carbon Rings
Alkanes, alkenes and alkynes all contain Carbon atoms in linear chains. There are also
hydrocarbons arranged in rings. Some examples follow:
Formula
C6H12
Structure
Name / Uses
Cyclohexane - a saturated hydrocarbon with
the atoms arranged in a hexagonal ring. In
organic chemistry, the presence of Hydrogen
atoms is often assumed and this compund can
be reprsented by a hexagonal ring:
Benzene - an industrial solvent.
C6H6
The Benzene Ring is one of the most important
structures in organic chemistry. In reality, its
alternate double and single bonds are "spread
around" the ring so that the molecule is
symetrical. This structure is represented by a
hexagon with a circle:
Toluene - an important solvent and starter
chemical.
Using the Benzene Ring, this molecule can also
be depicted as:
C7H8
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Naphthalene - used in moth balls.
C10H8
This can be depicted as two fused Benzene
Rings:
When rings are combined with chains, the number of hydrocarbons is virtually infinite.
And we are still using only two types of atoms (Carbon and Hydrogen). We will now add a
third.
Questions to check understanding:
1. What two atoms are basic organic molecules made of?
2. Draw ethane, ethane and ethyne in 3-D.
3. What is the difference between alkanes, alkenes, and alkynes?
4. Which cyclical hydrocarbon is the most important in organic chemistry? Why?
5. Use the attached sheet to make flashcards to help you learn/study.
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Saturated hydrocarbon
CnH2n+2
e.g. CH3CH3
(i.e. C2H6 , where 2n+2 = 2(2) + 2 = 6)
Alkene
Alkyne
Butene
11
12
Ethane
CH3(CH2)4CH3 or C6H14
Propene
Ethyne
13
14
C10H22
Organic molecule made
of only carbon and
hydrogen
Carbon molecule
Valency = 4
tetrahedral shape
15
16
Adding Functional Groups to Hydrocarbon
Building Blocks
Carbon, Hydrogen and Oxygen
When Oxygen atoms are added, the variety of compounds grows enormously. In the table
below, each row discusses a series of compounds.
General
Formula
Series
Name
CnH2n+1OH Alcohols
Details
Examples
Alcohols
have the
OH
(hydroxyl)
group in
the
molecule.
CH3OH
Methanol
wood alcohol
A group of
atoms that
gives an
organic
series its
distinctive
character is
called a
functional
group.
Structures
C2H5OH
Ethanol
drinking
alcohol
C6H5OH
Phenol
carbolic acid used as
disinfectant
(CnH2n+1)2O Ethers
(CH3)2O
Dimethyl
Ethers have
Ether
an O atom
a gas
attached to
two
(C2H5)2O
hydrocarbo
Diethyl Ether
n chains (or
a liquid used
rings).
as an
anaesthetic)
(CnH2n+1)2C
Ketones
O
Ketones
have a CO
group
attached to
two
hydrocarbo
n chains (or
CH3COCH3
Dimethyl
Ketone
Also known as
acetone: nailvarnish
remover
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rings).
Aldehydes
have a CHO
group
Aldehyde attached to
CnH2n+1CHO
s
a
hydrocarbo
n chain (or
ring).
CnH2n+1CO2 Fatty
H
Acids
RCO2R'
(R, R' are
Esters
Hydrocarbo
n chains or
rings).
HCHO
Formaldehyd
e
preservative in
labs
CH3CHO
Acetaldehyde
HCO2H
Formic Acid
Fatty Acids in ant bites
contain the and stinging
nettles
CO2H (or
COOH)
CH3CO2H
group
attached to Acetic Acid
vinegar
a
hydrocarbo
n chain or
C2H5CO2H
ring.
Butyric Acid
the rancid
butter smell
Esters are
similar to
Fatty Acids
except that
the H in the
COOH
group is
another
hydrocarbo
n chain.
They are
usually
very sweet
smelling
liquids used
in
perfumes.
CH3CO2CH3
Methyl
Methoate
essence of
pear drops
In the above examples, each molecule has a single functional group.
It is possible to have two or more functional groups on a molecule. These can be the same
group (as in Oxalic Acid - a poison found in rhubarb leaves - which has two fatty acid
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groups) or different (as in Hydroxymethanoic Acid - which has a hydroxyl group and a
fatty acid group):
(COOH)2 : Oxalic Acid
CH2OHCOOH : Hydroxymethanoic Acid
The most famous compounds containing Carbon, Hydrogen and Oxygen are the
Carbohydrates. An example is the common sugar, Sucrose (C12H22O11).
This shows how varied and complex even simple organic compounds can be. Sucrose has a
pair of rings: one hexaganol, the other pentaganol. Each ring contains an Oxygen atom. The
rings are joined by an Oxygen (Ether) link. The entire compound contains several Hydroxyl
(OH) groups.
Sucrose
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Isomerism
An interesting phenomenon with organic molecules is called isomerism. Let us look at two
compounds introduced earlier.
Dimethyl Ether: (CH3)2O and Ethanol: C2H5OH.
The first is a gas which will knock you out if inhaled. The second is common alcohol drunk in
spirits. The two molecules are shown below.
Dimethyl Ether
Ethanol
Notice that both compounds contain 2 Carbon atoms, 6 Hydrogen atoms and 1 Oxygen
atom.
Even though the atoms are the same, they are arranged differently. This yields two different
compounds with the same number of atoms. These compounds are isomers and the
phenomenon is called Isomerism.
In this example, the two molecules have different functional groups. They are structural
isomers. Other types of isomers exist.
Isomerism increases the number of Organic compounds. The more Carbon atoms in a
compound, the more ways of arranging the atoms and the larger number of isomers.
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Adding Nitrogen
Many very important organic compounds contain Nitrogen. This produces more series of
compounds.
General
Formula
Series
Name
Details
Examples
Structures
Amines have one
or more of the
Hydrogen atoms
in Ammonia (NH3)
replaced by a
Hydrocarbon chain
or ring.
Primary Amines
have the formula
RNH2
CnH2n+1NH2
Amines
Secondary
Amines have the
formula RR'NH
CH3NH2
Methylamine
a pungent,
water soluble
gas
Tertiary Amines
have the formula
RR'R''N.
(R, R', R'' are
Hydrocarbon
chains or rings).
CnH2n+1CN
CnH2nNH2COOH
Cyanides
CH3CN
Cyanides have the
Methyl
CN group.
Cyanide
Amino
Acids
Amino Acids have
two functional
groups: the amine
(HN2) group and
the fatty acid
(COOH) group.
CH2NH2COOH
Glycine
the simplest
Amino Acids
combine together amino acid.
to form proteins
which are an
important
component of
living organisms.
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A famous compound containing Nitrogen is Trinitro Toluene (C6H2CH3(NO2)3 - usually
abbreviated to TNT). This is an artificially made explosive. Its structure is shown below:
Trinitro Toluene (TNT)
There are six isomers of this compound as the three NO2 groups can be placed in six
different arrangements on the ring. These are known as positional isomers.
Other Atoms
The vast majority of organic compounds contain Carbon, Hydrogen, Oxygen and Nitrogen.
Other types of atoms can be included to form even more compounds. These can contain
atoms like Phosphorus, Sulphur (e.g. Thiamine, Vitamin B1), Magnesium (e.g.
Chlorophyll) and Iron (e.g. Haemoglobin).
As can be imagined, these additions increase the number of compounds. Apart from the
naturally occurring Organic compounds, millions more can be synthesised. These can
include atoms like Chlorine (used in pesticides). Examples of organic compounds
containing Chlorine are shown below.
There is no difference between the same substance extracted from living organisms and
made in a laboratory.
Formula
Structure
Name / Uses
CHCl3
Chloroform - a human-made
anaesthetic.
C14H9Cl5
Dichloro Diphenyl Trichloro
Methane - DDT an insecticide.
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Connection to Biochemistry
Biochemistry is just one branch of organic chemistry. Another branch would be plastics, for
example. Biochemistry’s molecules can be divided into 4 basic categories: carbohydrates,
lipids, proteins, and nucleic acids.
1. Carbohydrates (sugars and starches)
The carbohydrates are the compounds which provide energy to living cells. They are
compounds of carbon, hydrogen and oxygen with a ratio of two hydrogens for every
oxygen atom. The carbohydrates we use as foods have their origin in the
photosynthesis of plants. They take the form of sugars, starches, and cellulose.
The name carbohydrate means "watered carbon" or carbon with attached water
molecules. Many carbohydrates have empirical formuli which would imply about
equal numbers of carbon and water molecules. For example, the glucose formula
C6H12O6 suggest six carbon atoms and six water molecules.
2. Lipids (fats)
Fats, oils, waxes, and sterols are collectively known as lipids. Like the carbohydrates,
the true fats contain only carbon, hydrogen, and oxygen. The molecules of such a
lipid are made up of a glycerol molecule with three fatty acid molecules attached to
it. This kind of lipid is also called a triglyceride.
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An important class of lipids is composed of the phospholipids that make up cell
membranes. The class of compounds called steroids are also lipids, and cholesterol is
one of the steroids.
3. Proteins (made of amino acids)
Proteins are the "workhorse" molecules of life, taking part in essentially every
structure and activity of life. They are building materials for living cells, appearing in
the structures inside the cell and within the cell membrane. While many of the
proteins are structural proteins, many are regulatory proteins called enzymes.
They contain carbon, hydrogen, and oxygen like the carbohydrates and lipids, but
they also contain nitrogen and often sulfur and phosphorus.
Protein molecules are often very large and are made up of hundreds to thousands of
amino acid units. The 20 amino acids are combined in different ways to make up the
100,000 or so different proteins in the human body. Some of these proteins are in
solution in the blood and other fluids of the body, and some are in solid form as the
framework of tissue, bone and hair. Shipman, et al. suggests that they make up
about 75% of the dry weight of our bodies.
Proteins can be characterized as extremely long-chain polyamides. The amides
contain nitrogen, and nitrogen composes about 16% of the protein atomic content.
These proteins are created in the body by condensation of amino acids under the
influence of enzyme catalysts, using patterns or direction from the nucleic acids in
the cells.
The amino acid units in a protein molecule are held together by peptide bonds, and
form chains called polypeptide chains. The sequencing of the 20 amino acids forms a
kind of alphabet for expression of the type of protein, leading to a very large number
of types of proteins.
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In the cell, the DNA directs or provides the master blueprint for creating proteins,
using transcription of information to mRNA and then translation to actually create
proteins.
A comment from Miller "Living things, after all are constructed by the execution of a
series of genetic messages encoded in DNA. Genes, the functional units of that
genetic program, generally encode proteins, which are the workhorses of the cell. As
our exploration of the genomes of humans and other organisms expands, it becomes
clear that those proteins can do just about everything required to produce an
organism ..."
4. Nucleic Acids (e.g. DNA – deoxyribonucleic acid)
Nuclei acids control the processes of heredity by which cells and organisms
reproduce proteins. The key nucleic acids are DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid). A molecule of a nuclei acid consists of a long chain of units called
nucleotides. The type, location, and sequencing of the nucleotides governs the
biological activity of the nucleic acid.
All of these are built on the basic carbon-chains of hydrocarbons!
I hope this introduction to Organic Chemistry indicates just how vast and interesting the
subject is.
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Questions to check for understanding:
1. List the 6 types(“series names”) of organic compounds that can be created when
adding oxygen to a hydrocarbon. Also give at least one example for each type.
2. What is isomerism? Give an example .
3. List the 2 types of organic compounds that can be created when adding ONLY
nitrogen to a hydrocarbon. Also, give at least one example for each type.
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4. What is an amino acid? What do they combine together to form?
5. What are the 4 major categories of biochemical compounds and what are their basic
functions?
Sources:
http://www.krysstal.com/organic.html;
http://www.visionlearning.com/library/module_viewer.php?mid=60;
http://hyperphysics.phy-astr.gsu.edu/hbase/hframe.html
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