Applied Organic
Chemistry
Theory Manual
Written by Judy Gordon & Lara Passlow
Table of Contents
Carbohydrates .....................................................................................................................
3
Lipids ...................................................................................................................................
13
Fats And Oils ......................................................................................................................
14
Waxes ...................................................................................................................................
19
Soaps and Detergents .........................................................................................................
20
Amino Acids and Proteins .................................................................................................
21
Nucleic Acids ......................................................................................................................
34
Plastics .................................................................................................................................
42
Pesticides and Herbicides ..................................................................................................
46
Applied Organic Chemistry
Carbohydrates
Carbohydrates are alkanals or alkanones that contain many alkanol groups. They are common
components of foods, both as additives and as natural products. They have a great variety of
molecular structures and shapes, and exhibit many different physical and chemical properties.
They are commonly chemically modified to improve their properties, particularly in foods.
The word carbohydrate is derived from the fact that glucose (the first carbohydrate to be
purified) has the molecular formula C6H 12O6 and was originally thought to be a “hydrate of
carbon” i.e. C6(H2O)6. The great majority of natural carbohydrates are large molecules made
up of many smaller units (which are normally called monosaccharides).
The Importance of Carbohydrates
Carbohydrates are the chemical intermediaries by which solar energy is stored and used to
support life. Green plants manufacture them during photosynthesis. When broken down in the
cell they provide a major source of energy for living organisms. Photosynthesis essentially
involves the conversion of CO2 and H2O to glucose and O2 as in the following equation.
6CO 2
+
6H2O
light
C6H 12O6
+ 6O2
starch & cellulose
When ingested as food, glucose can be metabolised in the body to provide energy or it can be
stored in the liver in the form of glycogen for later use. As most mammals lack the enzymes
to digest cellulose (cows and other ruminants are an exception), they must use starch as their
main source of dietary carbohydrate.
Another very important carbohydrate is cellulose. It is the most abundant organic chemical on
the earth. Ten billion tons of cellulose is synthesised daily by plants. It is the main chemical
constituent of such diverse items as paper, cotton, wood, and dietary fibre.
Classification of Carbohydrates
Essentially carbohydrates are classified (this has nothing to do with naming
systems) according to:
1. The number of sugar (saccharide) units
2. The number of C atoms per sugar unit
3. Whether they are alkanals or alkanones
Chem. Natural Substances
p3
Applied Organic Chemistry
1. The Number of Sugar Units
Monosaccharides are simple sugars such as glucose and fructose, which cannot be
hydrolysed (broken down) into smaller units. Monosaccharides can be linked together by
acetal bonds to form disaccharides (two sugar units) or even polysaccharides (many sugar
units).
Sucrose is a disaccharide made up of a glucose molecule linked to a fructose molecule.
Cellulose and starch are polysaccharides made up of several thousand glucose molecules.
Another term, oligosaccharide is also occasionally used to describe carbohydrate molecules
with a small number of saccharide units (generally from about three to ten).
Hydrolysis can break up disaccharides and polysaccharides into their constituent
monosaccharides. This involves the reaction of the disaccharide or polysaccharide unit with
water and an acid or enzyme to yield monosaccharide units. The equation below demonstrates
this.
disaccharide
+
water
polysaccharide +
water
acid or enzyme
two monosaccharides
acid or enzyme
many monosaccharides
2. The number of Carbon Units
Carbohydrates may also be classified according to the number of carbon units which they
posses, and whether they are alkanals or alkanones. Additionally when naming an organic
compound the ending -ose means that a substance is a sugar.
Generally monosaccharides are only found with three to seven carbon units commonly occur in nature.
These are given the following names:
Classification of sugar
unit
triose
tetrose
pentose
hexose
heptose
Number of carbons
Molecular formula
3
4
5
6
7
C3H6O
C4H8O
C5H10O
C6H12O
C7H14O
Table 13: Naming of monosaccharides.
3. Alkanal or Alkanone?
An aldose is a carbohydrate which contains an alkanal group
A ketose is a carbohydrate which contains an alkanone group
Chem. Natural Substances
p4
Applied Organic Chemistry
For example the molecule below contains five carbons, and is an alkanal.
H
C
O
H
C
H
H
C
OH
H
C
OH
As it contains five carbons it is a pentose.
As it is an alkanal it is an aldose.
These two are combined and the carbohydrate is referred to as an
aldopentose.
CH2OH
Class Exercise. Classify the following molecules according to the systems listed on the
previous page.
O
CH2OH
H
C
O
C
O
HO
C
H
H
C
OH
CH
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
CH2OH
glucose
CH2OH
fructose
CH2OH
ribose
Monosaccharides
Even though there are many thousands of monosaccharides only a few are of any great
biological significance. Of these glucose (see structure above) is by far the most important. It
is found in reasonable concentration in both plant and animal tissue, and is used to provide a
ready source of metabolic energy. It is also commonly known as dextrose and is carried
throughout the body by the blood. Typical concentrations are 800-1000mg/L of blood. It is a
lack of glucose that triggers the hunger response in humans. When the blood glucose level
drops below normal, you feel hungry. As glucose needs no processing in the body it may be
administered directly into the blood of patients who cannot eat.
Fructose (see structure above) is another important monosaccharide. It is along with glucose
one of the components of table sugar (see section on disaccharides). It is the sweetest of all
sugars (about 2x that of glucose) and is responsible for the extreme sweetness of honey.
Another common name for fructose is levulose.
Chem. Natural Substances
p5
Applied Organic Chemistry
Galactose is one of the monosaccharides that combine to make up lactose (see section on
disaccharides), and is also a major component of many of the polysaccharides that make up
glues and gums and also an important constituent of cell membranes. It is produced in the
mammary glands. Galactose intolerance is a fairly common disease where people cannot
metabolise galactose due to the lack of an enzyme. This leads to pain and bloating of the
stomach. Infants who suffer from this condition must be given milk supplements.
The Cyclic Form of Sugars
There are several ways of drawing the structures of carbohydrates. The two that are of most
importance are the Fischer Projection for straight chain representations (discussed in the
fats and oils notes and shown in the diagrams above), and the Haworth Projection for the
cyclic form of the sugars. Cyclic sugars are also sometimes referred to as pyranose (six
membered ring) or furanose (five membered ring) forms.
The straight or open chain form of glucose is extremely reactive and it readily rearranges its
bonds to form one of two new structures. Here the C=O and -OH groups on a sugar molecule
can react with each other to produce a ring structure closed by an oxygen bridge (referred to
as a Haworth structure).
alkanal
+
alkanone +
-OH
-OH
is known as a hemi-acetal
is known as hemi-ketal
In general
OH
O
HO
HO
O
OH
OH
HO
HO
OH
CH2OH
CH2OH
These groups are recognised by a C attached to two O‟s.
Chem. Natural Substances
p6
Applied Organic Chemistry
When numbering the carbons for naming purposes the anomeric carbon (the C atom attached
to two O‟s) is always carbon number 1 and the other carbons are named clockwise around the
ring. The C atom above the ring is number 6.
Reducing Sugars
A reducing sugar is one that reacts with Fehlings solution i.e. it turns Fehling‟s from blue to
red. This reducing ability is used to classify sugars. In general this means that the sugar
possesses a
C
C
HO
O
C
or a
an α-hydroxyalkanone
C
O
H
group.
an alkanal
This means all monosaccharides, but only some disaccharides. As the cyclic forms of sugars
continuously open and close to form alkanals and α hydroxyalkanones they are quite reactive
to Fehling‟s solution.
This test is commonly used for determining the amounts of reducing sugars in foods and other
biological materials.
Fehling‟s solution is an alkaline solution of Cu 2+ ions. Another reagent, Benedict‟s solution,
which is not alkaline – reacts only with aldoses, but not ketoses.
Glycosides
When a monosaccharide reacts with an alkanol (such as glucose reacting with methanol) the
product is called a glycoside.
Disaccharides
Single sugar units (monosaccharides) can condense with one another to give disaccharides
and polysaccharides. In this reaction the elements of H 2O are lost between two -OH groups
one of which must be the hemi-acetal or hemi-ketal -OH (remember this is always C no. 1).
e.g.
+
OH HO
+ H2O
O*
* NOTE: this is not an ether link. It is very stable and requires boiling in acid (hydrolysis) to break it.
As both of the -OH groups in this diagram point down (α - configuration) this is referred to as
a α-glycosidic link. If one of the bonds points up then it is said to be a β-glycosidic link
A glycosidic bond between C1 of the first sugar and C4 of the second sugar is particularly
common and is called a 1,4‟-link (the superscript „ indicates that the 4 position is on a
different sugar to the 1 position). Another very common link is the 1,6‟-link.
Some of the most important disaccharides are listed below.
Chem. Natural Substances
p7
Applied Organic Chemistry
Sucrose is made up of α-D-glucose and β-D-fructose joined via their hemi-acetal or hemiketal -OH. It has the following properties.
doesn’t mutarotate
and
is not a reducing sugar
It is commonly known as table sugar and is one of the most abundant pure organic chemicals
on this planet. The average human consumes 160g of sucrose per day. It has many
applications in both the food industry including fermentation, sweetening and colouration.
α-D-glucose
CH2OH
O
OH
1
O
HO
HO
β-D-fructose
HOCH2 O
2'
HO
CH2OH
HO
Sucrose - note this has an α-1,2‟ glycosidic
link
Sucrose is often prepared as a highly concentrated solution in water, which due to its high
osmotic strength needs no preservatives. This works because any bacterium that comes near
the solution loses all of its water through osmosis and therefore dies. This is also why sugar
coated foods need no preservatives.
Lactose - β-D-galactose and α-D-glucose joined together in a β-1,4‟- link. Lactose occurs
commonly in both human and cow‟s milk and is widely used in baking and commercial infant
milk formulas. It is sometimes called milk sugar. Typical concentrations of lactose in milk
are from 2 – 8.5%, with human milk containing about 7%. Most non-fermented dairy foods
are rich sources of lactose. Fermented dairy foods such as yogurt and cheese contain less
lactose as it is consumed in the fermentation process. Lactose has the following properties:
reducing sugar and
exhibits mutarotation.
α-D-glucose
CH2OH
O
HO
OH
4'
O
CH2OH
O
OH
1
1'
OH
HO
HO
β D-galactose
β-1,4‟-glycosidic link
Maltose - Two α-D-glucose units joined in an α-1,4‟- link. It occurs in germinating seeds
from the breakdown of starch. It is a reducing sugar, and is sometimes used as a mild
sweetening agent in foods.
Chem. Natural Substances
p8
Applied Organic Chemistry
CH2OH
O
CH2OH
O
1
OH
4'
O
HO
1'
OH
HO
OH
HO
Cellobiose - Two glucose units joined in a β-1,4‟- link. Formed by the breakdown of
cellulose. It is a reducing sugar.
CH2OH
O
OH
HO
CH2OH
O
4'
1
O
1'
OH
OH
HO
HO
Cellobiose - note the only difference between this and maltose is the orientation of the
glycosidic link
Chem. Natural Substances
p9
Applied Organic Chemistry
Polysaccharides
These are naturally occurring polymers of simple sugars that are linked together through
glycosidic bonds. They are not reducing sugars and do not mutarotate. They have many
important roles in nature and industrial processes some of which are listed below.



They act as a food store - e.g. starch in plants and glycogen in animals.
They act as structural material - e.g. cellulose in trees and plants.
Other commercial polysaccharides include;
i. pectins- available from fruit and set as jelly.
ii. alginates (agar)- derived from seaweed and used in cosmetics and food.
iii. gum arabic and gum acacia- exuded by trees for protection against wounds.
By far the most important of the polysaccharides are starch, cellulose and glycogen.
All of these polysaccharides are made from glucose monomers and yield glucose upon
hydrolysis. The general reaction for this process is;
polymeric substance
acid or enzyme
glucose units
Starch is a polymer of glucose with the units linked as in maltose. It is found in plants
mainly in seeds, roots and tubers (potatoes) and is the main reserve for carbohydrate storage.
Starch and starch products account for 70-80% of the calories consumed worldwide by
humans (rice and bread are the main sources). It occurs naturally as granules, which are not
very water soluble, but which greatly change their chemical properties upon cooking at
temperatures above 80C. It has many roles in food production processes, but is mostly used
to produce pastes and gels that give food the correct texture and consistency.
Starch can be separated into a cold water-soluble fraction called amylopectin and a cold
water insoluble fraction called amylose (20 - 25% of starch).
Chem. Natural Substances
p10
Applied Organic Chemistry
Cellulose - consists simply of D-glucose molecules linked by β-1,4‟ - glycosidic bonds. It
is the most abundant organic compound on the earth. It is a major constituent of wood (more
than 50% of dry weight), cotton (almost 100%) and all products derived from these such as
paper and textiles. It is also known as dietary fibre when found in foods as humans cannot
digest cellulose, as they lack the appropriate enzymes. Only ruminoid bacteria found in the
gut of some animals (cows, termites and grass eating mammals) are able to hydrolyse
cellulose and hence obtain glucose from it. Cellulose is used to produce reduced calorie foods
– which are liberally dosed with cellulose powder. This often has the effect of making the
product stay moist and fresh for longer periods of time.
CH2OH
O
OH
CH2OH
O
4'
1
O
OH
HO
CH2OH
O
O
OH
CH2OH
O
4'
1
O
1'
OH
OH
HO
HO
HO
HO
n
Cellulose
Some Applications of Carbohydrates
Protection of Foods during Freezing
High and low molecular weight carbohydrates protect food products stored in freezers from
destructive changes in texture and structure. This occurs because high concentrations of
carbohydrate greatly restrict ice crystal growth.
Blood Groups
The human ABO blood groups which are of primary importance to blood transfusions are
determined by the presence of certain carbohydrate molecules on their surface. For example
group B has a α-D-Galactose unit connected to a α-L-fructose unit. If a red blood cell is
spotted by the immune system and it does not contain these groups then the body‟s immune
system destroys it. Different carbohydrate groups are used to identify the other blood groups.
Blood Clotting
The clotting of blood in response to exposure to the atmosphere can be prevented by the
addition of an anti-clotting agent. Heparin is one of the most common of these and is found in
body tissues such as the lungs, intestine, etc. In these tissues it serves to prevent the blood
from clotting. Blood sucking animals such as mosquitoes also use this to allow them to
Chem. Natural Substances
p11
Applied Organic Chemistry
obtain blood from the body of other animals. Heparin is a polysaccharide, where the
individual monosaccharide units vary, but are all joined by α-1,4‟-glycosidic links.
Textiles
Cotton is 95% cellulose. It is normally obtained from the cotton plant, but in this form is too
crystalline and does not have the correct properties for use in garment manufacture. It is
normally processed by soaking in strong base (18% NaOH) to decrease the crystallinity (this
is referred to as mercerisation), then washing. The processed fibre is more amenable to
dying and washing than that obtained directly from the plant.
Construction
Cellulose is a major constituent of wood, which serves as an important material in the
construction industry.
Explosives
Cellulose can be modified by nitration of OH group attached to carbon 2 on the monomeric
units to produce Nitrocellulose that is used as an explosive. This was formerly referred to as
gun cotton.
Chem. Natural Substances
p12
Applied Organic Chemistry
Lipids
These are simply a group of substances classified according to their solubility characteristics.
They may be defined as water insoluble substances that can be extracted by non-polar organic
solvents (e.g. ether or benzene). More simply these are just the fatty materials that are
produced by or from living organisms.
Classification of Lipids
Lipids can be broadly classified into four classes according to their molecular structure.
1. Simple Lipids
This includes:


Fats & Oils - examples of these include. the lard and dripping found in animals, and the
oils found in plants. These fats and oils are in used in the production of soaps. Synthetic
fats are used in the production of detergents.
Waxes - these are generally found as coatings on leaves and berries.
2. Compound Lipids


Phospholipids - these are those substances made from fats and phosphates found in
structures such as cell membranes. One example is lecithin used in the manufacture of
many foods e.g. chocolate.
Glycolipids - these are substances made from fats, and carbohydrate.
3. Steroids - examples of these include cholesterol, adrenal cortex hormones, sex
hormones and bile acids.
4. Miscellaneous Lipids - this includes other important fat-soluble substances such as
the prostaglandins, fat-soluble vitamins and lipoproteins.
The Role of Lipids
Lipids have a number of biological roles such as:

energy storage

membrane components

nerve and brain tissue

protective coating on skin and cuticles.
Chem. Natural Substances
p13
Applied Organic Chemistry
Fats And Oils
Structure
Fats & oils are esters formed between glycerol (the alkanol part of the ester) and various long
chained carboxylic acids (the acid part of the ester). Glycerol has 3 -OH groups and
therefore forms three ester bonds. The product of the triesterification of glycerol is called a
triglyceride. Monoglycerides and diglycerides (you should be able to deduce what these are)
do exist, but are far less common than triglycerides.
Triglycerides
Typically these have the following structure:
H
C
O
O
C
H C
O
C
C
O
C
O
H
H
H
O
and are made by the following general reaction:
H
H
HO
O
C
COH
HO
C
COH
HO
C
O
COH
H
H
H
the alkanol part
+
O
the acid part
triglyceride
The alkanol part is always 1,2,3-propanetriol (commonly referred to as glycerol).
Chem. Natural Substances
p14
Applied Organic Chemistry
The acid part usually has the following properties:





long chained fatty acid (more than 10C‟s and less than 20)
contains an even number of C atoms
any double bonds are oriented cis- and are not conjugated
contain virtually no branching
have no extra functional groups except for the carboxyl group and some alkene
groupings.
Only even numbers of carbons are found in these molecules as they are produced in the body
from ethanoic acid units. Most triglycerides contain three different acid molecules, however
it is possible to see two or even three of the same acids being used to construct the
triglyceride.
Class Exercise.
Consult a suitable reference text and complete the table below.
Fatty Acid Number
Source
Formula / Structure
(common
of C
name)*
Atoms
butanoic
Melting
Point C
lauric
myristic
palmitic
stearic
arachidic
palmitoleic
oleic
linoleic
linolenic
arachidonic
Table 14: Table of fatty acids.
Common names are provided due to their unfortunate widespread use. Give each of these a correct
systematic name.
Chem. Natural Substances
p15
Applied Organic Chemistry
Melting Points of Fats and Oils
Definition: Fats melt above room temp and oils melt below room temp.
The melting points of these substances are generally low. Melting points depend upon:


the length of the carbon chain
the degree of unsaturation of the carbon chain
In general, long chains mean high molecular weight and melting point. Hence any triglyceride
made up from predominately long chain fatty acids will most likely have a high melting point
and will therefore be a fat. Saturated chains pack in a uniform fashion, and lead to highly
crystalline dense material. Once again any triglyceride formed from saturated fatty acids will
produce a dense solid material and will most likely produce a fat.
By contrast, unsaturated chains have kinks at each double bond and pack poorly. These have
poor crystallinity and produce materials of much lower densities such as oils or deformable
solids. This situation is demonstrated in the diagram below that shows a comparison of the
shapes of saturated and unsaturated triglycerides.
O
CH2 - O - C
O
CH - O - C
O
CH2 - O - C
saturated triglyceride
O
CH2 - O - C
O
CH - O - C
O
CH2 - O - C
unsaturated triglyceride
Chem. Natural Substances
p16
Applied Organic Chemistry
To summarise;


Fats such as butter, lard and dripping contain a small percentage of short-chained
unsaturated acids
Oils such as safflower and coconut oil contain a large percentage of short chained and
unsaturated acids
Chem. Natural Substances
p17
Applied Organic Chemistry
Other important triglycerides include;
Castor Oil - is used to “open the sluices at both ends” by people such as your grandma. It
contains the bowel irritant ricinoleic acid, which is the active component.
Linseed Oil - protects wooden surfaces. It contains a high proportion of unsaturated acids
that undergo free radical cross-linking on exposure to air. This forms an impervious barrier.
Rancidity
Rancidity refers to the process by which fresh oils on exposure to air/moisture/heat /light are
oxidised into a smelly putrid oil. An example of this is the so-called rancid butter. This is
thought to be due to breaking down of the oils to yield oxidised species such as alkanals,
alkanones, alkanoic acids and other associated by products.
In part this is attributed to slight hydrolysis of the triglyceride into lower molecular weight
fatty acids (in the case of butter this is butanoic which is responsible for the “sick” smell). It
is thought that O2 from the atmosphere further reacts with unsaturated regions of the
triglyceride or low molecular weight fatty acids to yield the other products of hydrolysis (such
as alkanals, alkanones etc.).
Chem. Natural Substances
p18
Applied Organic Chemistry
Waxes
These are esters of high molecular weight alkanols and fatty acids. They have the general
formula
O
R' C
O R.
Typically the alkanol portion of the molecule would have approximately 30-40 carbons and
the fatty acid group about the same. This makes these substances extremely non-polar, and
they are one of the most hydrophobic groups of lipid molecules. It is this that makes them
ideal as coatings for leaves, fruits and other parts of plants, which need to be impervious to
water.
Waxes are extensively used in industry as polishes. The fact that they have extremely long
unsaturated groups means that they form highly crystalline, very hard coatings.
Chem. Natural Substances
p19
Applied Organic Chemistry
Soaps and Detergents
Each year tonnes of soaps and detergents are discharged into the waterways. To assess the
environmental impact of this discharge it is essential to understand the chemistry of soaps and
detergents, and what type of degradation processes, if any, they undergo in the environment.
Soaps
Soaps are the sodium salts of long-chain fatty acids. They have the general formula of
RCOO-Na+, where R is a long chain hydrocarbon, CH 3 (CH2)10-16. There preparation by
boiling animal fat with potash (a mixture of potassium carbonate and potassium hydroxide) is
one of the most ancient organic reactions known. These salts can be made by the reaction of
the corresponding acid with base.
O
O
R - C - OH
+
NaOH
R - C - O-Na+
+
H2O
The most common source of these fatty acids is animal fats and certain vegetable oils, which
are found in the ester form. The reaction of these esters with base is called saponification.
O
O
R - C - OR
+
NaOH
R - C - O-Na+
+
ROH
Beef tallow provides sodium stearate CH 3(CH2 )16COO-Na+, which is the most common soap.
Palm oil provides sodium palmitate CH3(CH2)14COO-Na +.
Soap has a cleansing action due to its ability to act as an emulsifying agent. Because the long
hydrocarbon chains are non-polar and so insoluble in water, they tend to cluster in such a way
as to minimise their contact with the surrounding water. The polar carboxylate groups tend to
remain in contact with water. This results in the formation of structures called micelles; in
these structures the charged carboxylate groups are on the outside in contact with water,
whilst the non-polar hydrocarbon chains are hidden inside the structure, away from water.
Dirt mainly consists on non-polar substances such as grease, oils and fats. When soaps are
mixed with the dirt, the non-polar portion of the micelle dissolves the dirt (like dissolves like),
which can then be washed away with water.
Soaps have a limited impact on the environment; moreover they are produced from a
renewable source. In addition, soaps are also biodegradable as they are readily broken down
by bacteria, and so do not pollute rivers. Unfortunately, there are some disadvantages in their
use, which promoted the search for alternatives. These include:


deterioration on storage,
lack of cleaning power,
Chem. Natural Substances
p20
Applied Organic Chemistry

soap cannot be designed to tackle specialist cleaning tasks,
Precipitation in areas of hard water (water that contains lots of calcium and magnesium).
The precipitation arises from the sodium of the fatty acid salts being replaced by magnesium
or calcium; these new salts are insoluble in water.
These disadvantages led to the development of detergents. Detergents are distinguished from
soaps only by the fact that they are fully synthetic. The structure of one of the first detergents,
alkylbenzene sulfonate is shown below.
-
S O3 N a
+
This type of detergent is much more soluble than soap, and the calcium and magnesium salts
are also soluble, so that hard water is no longer a problem. However, they are more stable
than soaps and so persist in the waterways for large periods of time. The consequence of this
was the fouling of the sewerage works and waterways with large amounts of froth.
The increased stability of these detergents arose from the greater stability of the sulfonate
group, and the fact that the long carbon chains used were branched, in contrast to the straight
chains of animal and plant fats. Bacteria digest branched chains much slower than straight
chains.
This led to the development of biodegradable detergents, obtained by reducing the amount of
branching found in the long chain. The sulfonate portion of the detergent was also replaced
by a sulfate, which is attacked by water to give the corresponding alkanol. These alkanols do
not act as detergents and so reduce foaming in the waterways.
O
O
S
-
O Na
+
O
Sodium dodecylbenzene sulfonate: a common detergent
Amino Acids and Proteins
Proteins are large biological compounds that occur in all living tissue and are key elements in
almost all life processes. They serve many diverse roles in both plants and animals. There
are many examples of this diversity. These include the function of proteins as enzymes to
catalyse biological reactions: their roles in the formation of living structural materials (hair,
skin and muscle tissue), hormones, the immunological system, the nervous system and the
Chem. Natural Substances
p21
Applied Organic Chemistry
reproductive systems of both plants and animals. They also have more unusual roles in some
species such as acting as antifreeze in fish that are specially adapted for life in very cold
water.
Protein molecules are constructed by joining many amino acid molecules together into long
polymeric chains. An individual protein molecule may be constructed of one of these chains
or several chains that are associated by intermolecular bonding.
The Role of Proteins in Organisms
Food and Nutrition- Proteins are one of the three major food groups along with
carbohydrates and fats. The role of proteins in our food is totally different however to the
carbohydrates and fats. The latter are used to provide and store energy, whilst proteins are
used as sources of amino acids that are used to produce new proteins for growth and
maintenance of living tissue. A lack of protein in the diet leads to a gradual breakdown in
body tissue (known as Kwashiorkor) and eventually death.
Structural Material - The body is capable of making many different proteins, which can be
used in construction and maintenance of quite diverse types of body tissue. These range from
skin, hair and fingernails (which are constructed of a tough protein known as keratin) to
delicate tissues in the lungs that are used to absorb oxygen. Even though these materials show
vastly different physical behavior, and have different biological roles they are chemically very
similar in that they are just chains of amino acids linked together. Changing the amino acid
sequence greatly changes the properties of the protein produced.
Enzymes - These are proteins that are used by living organisms to catalyse chemical reactions
in the body. They are discussed in more detail later in this chapter.
Transport - Proteins are vital components in the transport of components across cell
membranes, and the delivery of oxygen to body tissues. Haemoglobin is the essential protein
component of blood that allows oxygen to be moved from the lungs to other areas of the
body.
Storage - Some proteins such as casein (milk) and albumin (eggs) are used to store energy.
Hormones - Many of the hormones (chemical messengers) found in plants and animals are
made from proteins. Some examples of this include human growth hormones and insulin,
which is vital to the processing of food in the body (people who cannot produce insulin are
suffering from the disease diabetes.
Protection - Much of the immune system of animals is composed of proteins. Examples of
this include antibodies produced by the body to fight invading organisms. Additionally
proteins act in other protective roles such as acting as blood clotting agents (an example of
which is fibrinogen) to prevent blood loss.
Amino Acids
All proteins, regardless of their biological function are structurally similar. They are
polymers made up of amino acids. Amino acids are organic compounds that contain both an
amino group and a carboxylic acid group,
Chem. Natural Substances
p22
Applied Organic Chemistry
e.g.
H
R
C
NH2
O
C
OH
Hundreds of amino acids are known, but only 20 of these occur naturally in proteins. These
are called α- amino acids because the amino group is attached to the  carbon (the one next
to the COOH group). Each amino acid has its own characteristic side chain which may
contain different structural features such as aromatic groups, extra amino groups, extra acid
groups, hydroxyl groups, I etc.
This variety in side chains is responsible for the differences in properties of the individual
amino acids and the proteins that they make up. The nature and polarity of the side group
(R group in the above example) is important and is used to classify α-amino acids into four
groups.
Classification of Amino Acids
Essentially amino acids can be classified as belonging to one of the following four groups.
 acidic
 basic
 neutral polar
 neutral non-polar
Acidic amino acids have an extra carboxylic acid group located on their side chain (the R
part of the molecule). An example of this is aspartic acid.
H
HOOC CH2
C
COOH
NH2
Aspartic acid
Chem. Natural Substances
p23
Applied Organic Chemistry
Basic amino acids have an extra amine group located on their side chain.
An example of this is lysine -
H
NH2CH2CH2CH2 CH2
C
COOH
NH2
Neutral polar amino acids have only one amino group and one carboxylic acid group
connected to the -carbon. The side chain (the R part of the molecule) contains a polar group
such as -OH or -SH.
An example of a neutral polar amino acid is serine -
H
HO CH2
C
COOH
NH2
Neutral non-polar amino acids have only one amino group and one carboxylic acid group
connected to the -carbon. The side chain contains a nonpolar group such as an aromatic ring
or long carbon chain.
An example of a neutral polar amino acid is phenylalanine H
CH2
C
COOH
NH2
Class Exercise: Classify the amino acids below into one of the groups listed above.
H
HO
CH2
C
COOH
CH3
H
CH3CHCH2
C
NH2
COOH
NH2
H
H
HOOC CH2 CH2
C
N
COOH
NH2
Chem. Natural Substances
CH2
N
C
COOH
NH2
H
p24
Applied Organic Chemistry
Essential Amino Acids
Chemicals present in the human body allow us to manufacture some of the naturally occurring
amino acids to produce proteins. The body is not capable of manufacturing all of the
naturally occurring amino acids however, so some must be procured in the diet. These amino
acids are designated as being “essential”. There are ten essential amino acids.
They are isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, valine,
arginine, histidine, and lysine.
Nutritionists often describe the type of protein obtained in the diet as being complete or
incomplete. The term complete protein refers to one that contains all of the essential amino
acids. Many proteins, particularly those of plant origin are incomplete proteins (do not
contain all of the essential amino acids) and hence should not be used as the sole source of
protein in the diet of an individual. This is currently an area of intensive research for genetic
engineers who are seeking to produce plant proteins that are nutritionally complete.
Physical and Chemical Properties of Amino Acids
All amino acids:



are colourless crystalline solids
have high melting points (>200°C)
are usually relatively insoluble in organic solvents such as benzene and ether, but are
moderately soluble in water with the exception of cystine and tyrosine.
The explanation for these particular physical properties lies in the fact that amino acids do not
exist in their free acid/base form, but rather as zwitterions.
Zwitterion Formation
All amino acids possess a carboxylic acid group and an amino group. These two groups
cannot exist together in their free form (i.e. NH2 and COOH) as the carboxyl group is a
moderately weak acid and the amino group is a moderately weak base, hence the two will
react with each other. In aqueous solution the -COOH group donates a proton to the -NH2
group so that the amino acid actually has the structure shown below.
H
R
C
COO +
NH3
This structure is known as a zwitterion. Amino acids are zwitterions not only in aqueous
solution, but in the solid state as well. This accounts for their high melting points, as they are
ionic in nature. It also accounts for the general water solubility.
Amino acids are amphoteric as they can either accept a proton from strong acids or donate
one to a strong base. Hence the net charge on an amino acid is a function of the acidity of the
Chem. Natural Substances
p25
Applied Organic Chemistry
solution.
The pH at which an amino acid exists in its dipolar form (or zwitterionic form) is called the
isoelectric point (which means it has no net charge). Each amino acid has its own
characteristic isoelectric point. This usually lies between 5 and 8, but if there are acid or base
side chains in the molecule it can be as low as 3 or as high as 11. It is because of this
zwitterionic properties that amino acids have different solubilities in solutions of different pH.
This can be used as a means of purification as different amino acids will precipitate at
different pH values.
Amino Acid
glycine
alanine
asparagine
glutamine
cysteine
isoleucine
leucine
methionine
phenylalanine
proline
Isoelectric Point
5.97
6.00
5.41
5.65
5.07
6.02
5.98
5.74
5.48
6.30
Amino Acid
serine
threonine
tyrosine
tryptophan
valine
aspartic acid
glutamic acid
arginine
histidine
lysine
Isoelectric Point
5.68
5.60
5.66
5.89
5.96
2.77
3.22
10.76
7.59
9.74
Table 15: The isoelectric points for the 20 naturally occurring amino acids.
Tests for Amino Acids and Proteins
Many tests are commonly used to allow detection of amino acids and proteins. Only the most
common will be discussed here.
Ninhydrin test
Ninhydrin is a specific test for amino acids. This gives each amino acid spot a purple colour
(except for proline and hydroxyproline which give a yellow colour). It is extremely sensitive
and can detect as little as one microgram of amino acid.
O
OH
OH
O
Ninhydrin
Biuret Test
This uses a dilute alkaline solution of copper (II) sulfate. It produces a violet colour with
substances containing at least two peptide bonds. This means it gives a positive reaction to
proteins and polypeptides, but does not react with amino acids or simple dipeptides.
Proteins and Polypeptide Formation
Amino acids can join together in long chains via intermolecular amide bonds (known as
Chem. Natural Substances
p26
Applied Organic Chemistry
peptide bonds) to form polypeptides. The amino group of one amino acid links to the
carboxylic acid group of another amino acid. A molecule of water is eliminated in the
process, and a new amide bond formed. This is demonstrated in the reaction scheme below.
R
H
C
OH
H
C
NH2
N - C - COOH
+
O
R
H
H
R
H
N - C - COOH
C
C
H
R
NH2
+
H2
H
O
Peptides can be formed from as few as two amino acids (this is referred to as a dipeptide), up
to many thousands. In general, if less than about 50 amino acids are joined together the
molecule is referred to as a peptide (or sometimes an oligopeptide), and a molecule with more
than 50 amino acids is known as a protein.
There are many simple peptide molecules with important biological functions. One of the
more interesting is the enkephalins, and the endorphins. These are the so-called “natural
opiates” of the human body that are thought to have a role in pain reduction in the body. They
are also known to produce a sense of well being in the body. They are synthesised by peptide
formation of 5-10 amino acids. The simplest example is leu-enkephalin that has the following
amino acid sequence:
tyrosin-glycine-glycine-phenylalanine-leucine.
Making even very simple changes to the amino acid sequence of a peptide results in great
changes to the biological properties of the molecule produced. An example of this may be
found in the human hormones oxytocin and vasopressin. These two peptides have an almost
identical amino acid sequence, except for one amino acid unit, yet vasopressin affects blood
pressure and water retention in the body, whilst oxytocin is used to induce childbirth.
Class Exercise: Aspartame is an important sweetening agent in the food industry. It is a
dipeptide formed from aspartic acid and phenylalanine. Give an equation for the preparation
of the dipeptide formed from this reaction.
Chem. Natural Substances
p27
Applied Organic Chemistry
Protein Structure and Shape
Because of the immense size of many protein molecules, special descriptors of their chemical
structures have been developed. Additionally, because of the intimate link between their
shape and their function a great deal of effort has been directed toward finding the factors
which influence the general shape of a protein molecule, and how this shape may be
destroyed. In general loss of the special shape of any protein molecule renders it biologically
inactive.
Protein shapes are determined by four factors:




The R group present in the amino acids
pH
The availability of H and O for hydrogen bonding
The length of the R chain
Chem. Natural Substances
p28
Applied Organic Chemistry
Proteins have many functions in the organisms that produce them. In order to understand
these functions, we need to look at the four levels of organisation in their structures.
Primary Structure
In simple terms the primary structure of a protein consists of the sequence of amino acids
that makes up the chain. Each of the very large number of peptide and protein molecules in
biological organisms has a different sequence of amino acids, and it is this sequence that
allows the protein to carry out its function, whatever that may be. The primary structure of a
protein determines to a large extent the native (most frequently occurring) secondary, tertiary
and quaternary structure of a protein. Primary structure of a protein can only be broken down
by hydrolysis.
Secondary Structure
Proteins can fold or align themselves in such a manner that certain patterns repeat themselves.
These repeating patterns are referred to as secondary structures. The two most
commonly encountered secondary structures are the α- helix and the pleated sheet. Those
protein conformations that do not exhibit a repeating pattern are referred to as random coils.
In the α-helix form, a single protein chain twists in such a manner that its shape resembles a
coiled spring. The shape of this helix is maintained by numerous intermolecular hydrogen
bonds that exist between the backbone -C=O and H-N- groups. The pleated sheet structure is
likewise held in shape by intermolecular H-bonds.
Tertiary Structure
The coils and pleated sheets of proteins can be further folded and rearranged in threedimensional space (much in the same manner as a coiled telephone cord can become knotted).
It is often difficult to distinguish between the secondary and the tertiary structure of a protein,
but an easy way of doing this is to note that in all secondary structures the H-bonding is
between the backbone -C=O and H-N groups, whereas in the tertiary structure the
intermolecular bonding is between the R groups on the side chains.
Essentially there are four ways of stabilising the tertiary structure of a protein:
1. Covalent crosslinks - the most common of these is the disulfide bridge between two
cysteine residues. This binds together two chains or two parts of the same chain (this
is how hair perming works - see section on applications of proteins).
CH2CH2S
SCH2CH2
protein
protein
covalent crosslink
Chem. Natural Substances
p29
Applied Organic Chemistry
2. Hydrogen bonding - tertiary structures may be stabilised by H-bonding between
polar groups on side chains.
OH
CH2CH2C
O
HO-
protein
protein
H-bond
3. Salt bridges - These occur between two amino acids with ionised side chains that are
between an acidic amino acid and a basic amino acid each in its ionised form. The
two are held together by simple ion-ion attraction.
H
O
CH2CH2C
-
O
+
N
H
CH2CH2CH2CH2
H
protein
protein
salt bridge
4. Hydrophobic interactions - In aqueous solution globular proteins usually turn their
polar groups outward toward the aqueous solvent, and their non-polar groups inward
toward away from the water molecules. The non-polar groups tend to interact with
each other, excluding water from these regions. This is referred to as a hydrophobic
interaction. Although this type of interaction is generally far weaker than H-bonding,
it occurs over a very large area so often these interactions are strong enough to
stabilise a loop.
CH3
CHCH2CH3
protein
CH2
protein
hydrophobic interaction
Chem. Natural Substances
p30
Applied Organic Chemistry
Quaternary Structure
This only applies to complex proteins with more than one polypeptide chain and basically
refers to how the two or more protein chains in a unit fold around each other. Quaternary
structure is held together by non-covalent bonds (most commonly hydrogen bonds,
hydrophobic interactions and ionic interactions). It is important in large proteins that are
involved in metabolic processes. A good example is haemoglobin, a very large protein
involved in oxygen transport in the blood. This molecule consists of four smaller protein
chains (known as myoglobins) that are twisted around each other in a helical pattern. The
quaternary structure allows far more efficient binding of oxygen, as one haemoglobin
molecule is a much better oxygen carrier than four myoglobin molecules.
Note: Possibly the easiest way to remember the difference between primary, secondary,
tertiary and quaternary structure of proteins is to use the telephone cord analogy. Here
primary structure would refer to the straight cord, secondary structure, a coiled cord,
tertiary structure would refer to a knot in the coiled cord, and quaternary structure would
refer to two (or more) coiled telephone cords tied in another knot.
Denaturation of Proteins
Changing the shape of a protein without breaking the chain is called denaturation (i.e. we
destroy the secondary, tertiary and quaternary structure). Some of the factors that cause
denaturation are:
 heat
 heavy metals
 reducing agents
 acids, bases and salts
 ethanol
 detergents.
Heat breaks H-bonds, so boiling destroys the α-helical structure. This is what happens when
an egg is boiled, the tertiary structure of the albumin is destroyed causing the protein to
precipitate as a white solid. Most other cooking procedures also cause denaturation of
proteins
.
Detergents open up hydrophobic regions and allow emulsification of the protein chain.
Reducing agents break up disulfide linkages (this is of major importance in the hair perming
process).
Acids, bases and salts affect both salt bridges and H-bonds. This is basically what occurs in
the marinating process used prior to cooking. The marinade is usually an acid (such as
vinegar, wine or lemon juice) which dentures the proteins in the meat and makes them softer
(this is why they may appear cooked, because essentially the same chemical process is
occurring as is found in cooking).
Heavy metals form precipitates with many protein components. This is how simple topical
ointments such as mercurochrome work.
Note: Denaturation does not affect the primary structure of a protein.
Hydrolysis
Chem. Natural Substances
p31
Applied Organic Chemistry
Hydrolysis refers to the breaking up of the primary structure of a protein (i.e. the amino acid
sequence). Complete hydrolysis will reduce a protein to its component amino acids. This is
normally accomplished by boiling in HCl or NaOH, but is achieved in the body under much
more gentle conditions through the use of special enzymes (called proteolytic enzymes). This
latter reaction is of vital importance to the breakdown of foods in the stomach. None of us
would be too keen to have boiling concentrated HCl in our stomachs!
Enzymes
These are protein catalysts developed by organisms to:





process food
fight infection
prevent bleeding
build new structural materials for living organisms
regulate levels of chemicals in the body e.g. hormones and detoxification.
Enzymes accelerate chemical reactions in the body (sometimes up to thousands of times the
uncatalysed rate). They are specific catalysts in that they only perform one function; hence it
is necessary to have thousands of enzymes per organism. This specificity arises because their
shape will only allow them to attack one molecule. A lack of certain enzymes leads to
diseases in organisms such as diabetes, and lactose intolerance.
An enzyme can normally be identified by the fact that its name ends in the suffix “ ase”.
Chem. Natural Substances
p32
Applied Organic Chemistry
How an Enzyme Works
Enzymes catalyse chemical reactions by binding to a molecule. The binding takes place at the
so called active site which is a small crevice or pocket in the enzyme which has a highly
specific shape and will only allow one molecule to bind (this molecule is known as the
substrate). This type of binding is referred to as the lock and key mechanism in that only one
key (substrate) will fit the lock (enzyme binding site). The following general equation and
diagram illustrate this process.
enzyme + substrate
enzyme substrate complex
enzyme + product
This process is extremely sensitive to both pH and temperature, and any conditions that vary
from those found in the bodies of organisms generally greatly reduce the performance of an
enzyme.
Class Exercise. Suggest a reason why alteration of pH or temperature might affect enzyme
performance.
Chem. Natural Substances
p33
Applied Organic Chemistry
Nucleic Acids
In order for life to go on for generations, organisms need to transmit genetic material to the
next generation. Somehow this information needs to be stored somewhere, and be easy to
duplicate during reproduction.
The nucleic acids, DNA and RNA, have the perfect structure for governing the cell (telling it
what molecules to make and how) and are practical to duplicate. Thus nucleic acids function
is the storage, replication and transmission of genetic information.
Nucleic acids, like proteins, are large polymers made up of a small number of different
building blocks. The building blocks are called nucleotides and these are joined together by
phosphodiester bonds.
RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) are the 2 types of nucleic acids
found in every living organism.
Nucleotides
Nucleotides are the monomers of nucleic acids. In the structure of DNA and RNA, the order
of the different nucleotides stores the genetic code.
They are made up of three parts:
1. inorganic phosphate
2. a simple five carbon sugar
3. a nitrogenous base
The simple sugar can be either ribose or deoxyribose.
Ribose is present in RNA
Ribose
Deoxyribose is present in DNA.
Chem. Natural Substances
p34
Applied Organic Chemistry
deoxyribose
The nitrogenous base can be either purine or pyrimidine.
Purine
The only purines that occur in nucleic acids are adenine and guanine and they have two
nitrogen-containing rings. They are called purines because of their similarity to the molecule
purine.
NH2
O
H
N
N
N
adenine (A)
N
N
N
H2N
N
N
H
N
N
N
N
H
H
purine
guanine (G)
In a nucleoside either ribose or deoxyribose replaces the hydrogen atom shown in bold.
Pyrimidines
Nucleic acids can contain cytosine, uracil (only in RNA) and thymine (only in DNA). These
are referred to as pyrimidines due to their similarity to pyrimidine.
NH2
H
H
N
O
0
0
N
H
cytosine (C)
O
CH3
N
N
N
O
N
H
H
uracil (U)
thymine (T)
N
N
pyrimidine
In a nucleoside either ribose or deoxyribose replaces the hydrogen atom shown in bold.
DNA(deoxyribonucleic acid)
Chem. Natural Substances
p35
Applied Organic Chemistry
DNA is a double stranded nucleic acid. It is a chemical instruction manual for everything a
plant or animal does: grow, divide, even when and how to die. It is very stable and has error
detection and repair mechanisms. It stays in the cell nucleus and can make good copies of
itself.
The nucleotides bond together at the phosphate group and the sugar, so the backbone is a
chain of alternating phosphate and sugar.
The two nucleic acid chains are associated with one another by means of hydrogen bonds
which always occur between thymine and adenosine; cytosine and guanine. The structure of
DNA therefore is as follows:-
P
P
S
T ................. A
S
P
P
S
T ................. A
S
P
P
S
C ................. G
S
P
P = phosphate
S = deoxyribose
A = adenine
T = thymine
C = cytosine
G = guanine
....hydrogen bondine
P
S
G ................. C
P
S
P
The DNA molecule is extremely long and therefore there are many hydrogen bonds. This
gives the DNA molecule a great degree of stability.
The DNA molecule is not flat (as shown above) but in fact is coiled in a double helix. This is
called the Watson and Crick model of DNA after the two scientist who originally proposed its
structure.
Chem. Natural Substances
p36
Applied Organic Chemistry
The double-helix shape of DNA.
A molecule of DNA
RNA (ribonucleic acid)
Chem. Natural Substances
p37
Applied Organic Chemistry
The structure of RNA differs from DNA in three major areas.
1. It contains the sugar RIBOSE in its structure and not DEOXYRIBOSE as does DNA
2. RNA contains the base URACIL instead of THYMINE as does DNA.
3. It is single stranded and shorter.
There are three types of RNA:a. Messenger RNA (mRNA), a single uncoiled strand that carries single pages of
instructions out of the nucleus to places they‟re needed throughout the cell. It has no
error detection or repair and therefore makes flawed copies of itself. It evolves ten
times faster the DNA
b. Transfer RNA (tRNA), a single folded strand that helps translate the mRNA message
into chains of amino acids in the ribosomes.
c. Ribosomal RNA (rRNA), a globular form that helps the translation of the mRNA go
smoothly.
These are all involved in protein synthesis and will be discussed later.
Nucleic Acids and Protein Synthesis
Nucleic acids function is replication, storage and transmission of genetic information. DNA
also directs all cellular activity.
How does DNA, which is located in the nucleus manage to control activities occurring
throughout the cellular cytoplasm?
Answer: - By controlling protein synthesis.
Proteins are long strings of amino acids joined together. Proteins may be structural or may be
involved in chemical reactions – these proteins are called enzymes.
How does the nucleus instruct the cell as to which proteins to make?
All DNA contains inorganic phosphate and deoxyribose sugar, but what makes DNA unique
is the variable sequence of nitrogen bases which occurs along the length of the DNA. This
sequence of bases is unique for every living individual.
As we have previously discussed, there are four nitrogen bases occurring in DNA, adenine,
cytosine, guanine and thymine. The sequence of these bases along the length of DNA must be
able to code for 20 different amino acids.
How can four different bases code for 20 different amino acids?
Chem. Natural Substances
p38
Applied Organic Chemistry
If a base coded for an amino acid then there would be only 4 amino acids possible as there are
only 4 bases. If 2 bases coded for 1 amino acid then there would only be 16 different amino
acids. If 3 bases code for 1 amino acid then there would be 4 x 4 x 4 = 64 possible
combinations.
This is the most likely possibility – a sequence of 3 bases coding for 1 amino acid. This
group of bases is called a CODON and this theory is called the BASE TRIPLET Hypothesis.
These triplets do not overlap. e.g. for one strand of nucleic acid.
ACG = amino acid 1
ACC = amino acid 2
GGC = amino acid 3.
As there are 64 possible codons it follows that for each amino acid there is more than 1 codon.
Protein Synthesis
There are two phases:1. Transcription
2. Translation.
1. Transcription
As DNA does not leave the nucleus but somehow is able to direct protein synthesis in the
cytoplasm there must be another “carrier” molecule involved. This molecule is messenger
RNA (mRNA)
The mRNA must carry an exact copy of the base sequence of the DNA. This in turn
designates the amino acid sequence in the protein. This is achieved by the DNA unzipping
and the mRNA molecules in the nucleus aligning themselves opposite one of the DNAs.
The mRNA once assembled peels off its DNA template and moves out of the nucleus through
the pores in the nuclear membrane into the cytoplasm. Meanwhile the DNA rezips. This
represents the end of the TRANSCRIPTION phase of protein synthesis.
2. Translation
Once in the cytoplasm the mRNA attaches itself to the surface of the ribosome where it
directs the formation of the protein. This involves another intermediate molecule, Transfer
RNA (tRNA).
tRNA is a short molecule, single stranded like mRNA but the strand is doubled back on itself
and twisted to form a clover type helix. One part of the molecule has 3 unpaired bases and
the other end has a corresponding amino acid attached. Each tRNA has its own special
anticodon which recognises specific codons. The diagram below shows the concept of codon
and anticodon.
Chem. Natural Substances
p39
Applied Organic Chemistry
In translation the 3 bases on the tRNA attach to the corresponding codes on the mRNA. The
amino acids which are on the end of the tRNA then link up in order and this corresponds to
the sequence specified by the mRNA.
Once the amino acids are linked up peptide bonds are formed between adjacent amino acids
and a protein is formed. The protein peels away from the tRNA, the tRNA detaches from the
mRNA and returns from the cytoplasm.
During active protein synthesis ribosomes generally occur in small clusters – called
polyribosomes or polysomes. These are a strand of mRNA with a group of attached ribosomes
like a string of pearls. Each ribosome travels the whole length of the mRNA and then drops
off. This means that several ribosomes can be producing copies of the same protein at the
same time each working on a different portion of the message.
Chem. Natural Substances
p40
Applied Organic Chemistry
DNA is transcribed into mRNA which is translated into amino acids.
This is
Chem. Natural Substances
p41
Applied Organic Chemistry
Plastics
Polymers
A polymer is a large organic compound, made up of chains of small building blocks, known
as monomers – which are recognisable compounds in their own right – joined together by
covalent bonds (as shown below).
Monome
r
Monome
r
Monome
r
Monome
r
Monome
r
Monome
r
For example, cellulose – the structural material in plants – is a polymer made up of thousands
of glucose molecules joined by covalent bonds in a particular way.
If a protein is also a natural polymer, what are its monomers?
The properties of polymers are determined by: the constitution of the monomers, the structure
of the polymer chains, and the way the chains interact.
Polymers can be classified as naturally occurring or man-made, which is not normally a very
useful system, but in this case, distinguishes between natural substances, like those mentioned
above, and plastics, which are man-made polymers.
Plastics
Plastics must rank as perhaps the most important chemical invention of the twentieth century.
The first commercial true plastic - Bakelite – was invented by Leo Baekeland, a Belgian
chemist, in the 1910s from phenol and methanal (formaldehyde). (Other materials of similar
properties were made in the late 19 th century from modified natural materials, such as
cellulose and milk protein, and so don‟t really count as true plastics.)
Since then, hundreds of different plastics have been produced with vastly different properties.
In fact, the only things plastics have in common are they‟re large repeating organic structure
and those they are not found in nature.
What are some plastics that you are familiar with? What properties and uses do you associate
with them?
Classification of plastics
The most useful classification method for plastics is not what their monomers are, but the
effect of heat on the plastic. The two basic types of plastics are:
 thermoplastic – which means that the product will soften when heated, and
 thermoset – which means that the plastic has actually formed by the heating
of the
monomers, and once formed, is unaffected by all but direct flame or extreme heating
Chem. Natural Substances
p42
Applied Organic Chemistry
Thermoplastics include polyethylene, PVC, PET, polystyrene, nylon and polyester while
thermosets include the various formaldehyde resins with phenol, melamine and urea.
The difference in behavior is caused by the molecular structure of the polymer. If the
polymer is linear (that is it is made up of a straight chain), when it is heated the energy
supplied to the chains causes them to move past each other independently, resulting in
melting. This is the basis behind thermoplastic polymers.
In contrast, thermoset polymers are cross-linked. This means that they have many links
between the chains. So when these plastics are heated, the chains can‟t move past each other,
so melting can‟t occur. Instead when heated at a high enough temperature, they blister (due to
the release of gases) and finally char.
Plastics in the environment
The great problem associated with plastics is their slow breakdown rate in the environment,
which causes pollution, uses up valuable landfill space and can kill animals and birds that eat
or become entangled by discarded plastic products.
Which plastics are most easily recycled in a form similar to their initial one (eg milk
containers reprocessed into new milk containers)? Why?
Some Common Plastics
Polyethylene
Monomer
ethene
Basic structure
CH2CH2 CH2 CH2
Uses
cling wrap (low density)
milk and juice containers (high density)
Polyethylene Terephthalate (Pet)
Monomers
Ethanediol (HOCH2CH2OH)
1,4-benzenedicarboxylic acid (terephthalic acid)
Basic structure
HO
C
O
Chem. Natural Substances
O
C H 2C H 2
O
C
O
C H 2 C H 2 OH
O
p43
Applied Organic Chemistry
Uses
Soft drink bottles
Nylon
Monomers
Diamine, eg NH2 (CH2)6NH2
Diacid, eg COOH(CH 2)4COOH
Basic structure
H
C (C H 2 )4 C
O
H
H
N (C H 2 )6 N
O
H
C (C H 2 )4 C N (C H 2 )6 N
O
O
Uses
fibre for fabrics
engineering materials
Polystyrene
Monomer
Phenylethene (styrene)
Basic structure
B
B
B
B
where B = benzene ring
Chem. Natural Substances
p44
Applied Organic Chemistry
Uses
insulation
foam drinking cups
packing material
UV/VIS cells
Bakelite
Monomers
phenol
methanal (formaldehyde)
Basic structure
OH
OH
OH
OH
OH
Uses of thermoset resins in general
Hard moulded products required to withstand heat and physical stress eg kettles, telephones,
fiberglass
Chem. Natural Substances
p45
Applied Organic Chemistry
Pesticides and Herbicides
The development of agriculture was a major step forward for mankind, as it freed us from the
need to roam the land as hunter-gatherers. Food became more readily available through the
development of crops, allowing storage through bad seasons that greatly decreased the
number of persons who starved. Agriculture has also been of great benefit to other animals
such as small mammals and particularly insects.
Mans concentration of large amounts of food sources in small areas has allowed insects to
proliferate at enormous rates. This means that often insects get more of the food than do
humans, and so chemists have developed chemicals which allow us to kill insects and
undesirable plants, without harming food or humans (in the perfect example). These are the
pesticides and herbicides.
What is a Pesticide?
The general definition of a pesticide is a substance that is capable of selectively killing one or
a group of animas (generally insects) without harming the rest of the biological community.
Desirable Properties for Pesticides.
An ideal pesticide should have the following properties:
 low toxicity to mammals and non-target species.
 Very high toxicity to target species.
 Persistence
 Easy degradation to harmless products.
 Low allergenic effects.
If a pesticide is to perform it should ideally kill only the pest and have no effect on any other
species. This is most commonly referred to as selectivity. It should also remain in the
environment for only as long as necessary (persistence), and then be readily biodegradable to
non-toxic substances after completing its task. Almost no pesticide fulfils these criteria,
although some of the newer substances perform well.
Problems Associated with the use of insecticides.
These are obviously closely linked with the desirable properties in that basically this is a list
of how current pesticides fall short of being ideal. These include:

Environmental persistence and contamination.

Killing of non-target species.

Selection of resistant species.
Chem. Natural Substances
p46
Applied Organic Chemistry
Of greatest concern is the fact that most of the current insecticides (and those used in the
recent past) have great environmental persistence. This can be good in that pesticides
performance can be extended for many years and so places such as underneath houses may be
treated with residual poisons to protect them from insects for twenty years or more, but the
down side is that after the house is knocked down or rebuilt many years later the pesticide will
still remain tin the soil.
Additionally the great persistence of older pesticides means that they accumulate in the fatty
tissues of animals and are passed up the food chain. Hence larger animals such as human
beings tend to accumulate them in the liver and brain, and many of these have shown to be
carcinogenic upon long-term exposure. Thus they may be responsible for an increase in the
rate of disease among humans in recent years, although it is hard to substantiate this face.
The other major problem associated with pesticide use is that many friendly (and often
environmentally desirable) insect species are killed by them. These so called non-target
species often improve the environment.
The use of large amounts of insecticide means that we kill all but the strongest insects. Hence
we select the insects best able to survive our pesticides, and then these go on to breed and
produce more insects that are equally resistant to our current pesticides. In the long term this
means our pesticides become less effective and new, often more powerful ones needed to be
developed.
Major Groups of Pesticides
In general pesticides may be classified into groups according to their chemical structure and
physiological action. These groups are:
 inorganic pesticides.

organochlorine compounds

organophosphorus compounds

carbamates

plant extracts

pheromones
Each is considered in more detail in the following sections.
Inorganic Pesticides
This category includes substances such as copper, lead, arsenic and borax (sodium
tetraborate), which when ingested or absorbed by insects interfere with the function of
enzymes or other metabolic processes in the insect body, resulting in death. An example is
the use of borax to kill cockroaches (an old method is to mix borax and honey), or the
treatment of pine logs with arsenic when they are used in fences.
Chem. Natural Substances
p47
Applied Organic Chemistry
Organochlorine Pesticides
These were very popular during the middle of the twentieth century, but their low
biodegradability and they‟re suspected role in causing cancer has led to most of them being
banned or greatly restricted in use in many western countries. Some such as DDT (short for
dichlorodiphenyltrichloroethane) are still extensively used in parts of Africa, as they are
inexpensive and highly effective against locust plagues.
Some of the more important organochlorine insecticides include DDT, Lindane (also called
BHC and Gammaxane), methoxychlor, heptachlor, dieldrin, aldrin and chlordane. All of
these are of course trade names. Their correct chemical names and structures are listed on
following pages. All have specific applications, but in general we may take DDT and study it
as a typical example of an organochlorine pesticide.
DDT
DDT first came to prominence near the end of World War II, where its use on mosquito
infected swamps reduced malaria deaths by up to 50%. By the early 1960‟s extensive
spraying of DDT had, almost eradicated malaria, but this was discontinued in the late 1960‟s
and since then malarial deaths have dramatically increased.
DDT is highly toxic to insects by both ingestion and contact, and of very low acute toxicity to
mammals. It is chemically very inert and has no taste or odour. All of this should make it an
ideal pesticide, but its lack of biodegradability and long biological half-life has lead to its
bioaccumulation in the fatty tissues of mammals. Studies have shown that chronic exposure
to DDT may be involved in causing cancers in tissues such as the liver. Hence its use is now
greatly restricted.
Additionally insects have become increasingly resistant to DDT, developing enzymes which
allow it to be degraded to a far less toxic (to them) substance called DDE.
Cl
Cl
H
Cl
Cl
Cl
DDT (1,1-bis(4-chlorophenyl)-2,2,2-trichloroethane)
In an attempt to make DDT more biodegradable chemists developed the pesticide
Methoxychlor. This substance is far less toxic to mammals and far less fat soluble due to the
presence of more polar methoxy groups in the molecule. Its greater water solubility means
that it is more readily excreted by mammals and hence is not readily retained in the tissues.
Chem. Natural Substances
p48
Applied Organic Chemistry
CH3O
CH3O
H
Cl
Cl
Cl
Methoxychlor
DDT acts on insects by permeating the cell wall, and causing the sodium and potassium ions
to leak out. This means the insect dies of paralysis.
DDT is prepared by the reaction of chlorobenzene with 1,1,1-trichloro-2,2-thandiol (which is
commonly called chloral – and used to be used as knock out drops by spies). It is a simple
inexpensive one step reaction that uses heat and sulfuric acid as reagents.
Cl
Cl H
Cl
Cl - C - C - OH
+
Cl
OH
Cl
H
heat
H2SO4
Cl
Cl
Cl
Preparation of DDT.
Lindane
This substance is also known by the trade names Gammaxane and BHC (short for benzene
hexachloride). It is not a pure organic substance, but rather a mixture of the 9 isomers of
1,2,3,4,5,6-hexachlorobenzene. Only the so-called γ-lindane isomer is active as an
insecticide. In the past it was used as a veterinary wash to remove fleas. It is produced by the
reaction of benzene with chlorine in the presence of light.
light
+
Cl
Cl
Cl
3Cl2
Cl
Cl
Cl
Preparation of γ-Lindane.
Chem. Natural Substances
p49
Applied Organic Chemistry
Aldrin, Chlordane and Dieldrin
These insecticides are closely related in structure and properties and have proved very
effective against pests such as termites. Unfortunately they are toxic to mammals as well as
insects (this type of action is commonly referred to as being broad spectrum) and are very
persistent in the environment. They cause death by acting on the central nervous system of
the target animal.
Organophosphorus Pesticides
The term organophosphorus pesticide refers to a very broad range of substances with greatly
differing selectivity, activity, environmental persistence and modes of action. They all have
the general formula given below however, and this allows them to be linked together for the
purpose of examination.
O
P
R
R1
Y
In this formula both R and R1 are short chain hydrocarbon or substituted hydrocarbons, and Y
is a group built into the molecule to increase its biodegradability. Sometimes the O is
replaced by an S.
Some of the more important commercially used organophosphorus pesticides include
parathion, malathion, dichlorvus, rogor (dimethoate) and TEPP (tetraethylpyrophosphate).
All are inexpensive to produce, and most are still commercially available. Dichlorvus, which
used to be a major component of surface sprays such as Baygon (© Samuel Taylor Pty. Ltd.)
and in the old Shelltox pest strips, is no longer used in this country, as it is a suspected
carcinogen.
Parathion
This is a so called contact poison that means that it is absorbed through the insect‟s
exoskeleton and then acts on its body. It is quite toxic to both insects and mammals and
hence should be handled with great caution. It is one of the most persistent of
organophosphorus pesticides. It has been responsible for more deaths than any other
insecticide.
Chem. Natural Substances
p50
Applied Organic Chemistry
S
CH3CH2O - P - O
NO2
OCH2CH3
Parathion
Malathion
Is similar to parathion, but has far lower mammalian toxicity. Hence it is more commonly
used.
TEPP and Dimethoate (Rogor)
These are commonly used in areas such as crop spraying. This is possible because they are
rapidly broken down in the environment to low or non-toxic substances. TEPP has a
biological half-life of only 7 hours, and is 99% removed from the environment in less than 2
days. This means they can be sprayed on a crop to kill insects, and then the crop harvested
and consumed several days later without any danger to consumers.
S
CH3O - P - S - CH2CONHCH3
O
O
CH3CH2O - P - O - P - OCH2CH3
OCH3
Dimethoate (Rogor)
CH3CH2O
OCH2CH3
TEPP
Mode of Action of Organophosphorus Pesticides
These substances act by deactivating acetylcholinesterase enzymes. They are responsible for
removing the acetylcholine (a compound which carries nerve impulses between individual
nerves, and is called a neurotransmitter) from the tissues. This means the nerves fire
uncontrollably causing the victim to die of nervous exhaustion.
Chem. Natural Substances
p51
Applied Organic Chemistry
Carbamate Pesticides
These substances are manufactured from carbamic acid (or its derivatives), and act in a very
similar manner to the organophosphorus pesticides.
This group converted to an ester
H replaced with short
hydrocarbon groups
O H
HO - C - N - H
Carbamic acid
Chemists have developed these pesticides in a similar fashion to drugs in that many are now
manufactured (more than 300), with each having a specific target organism. One of the best
examples is Pirimicarb (© ICI) that is a highly selective killer for aphids and does not harm
other closely related insects.
CH3
CH3
N
N
CH3
N
CH3
O - C - N - CH3
O
CH3
Pirimicarb.
Pesticides Derived from Natural Products
There is a growing trend in the pesticide industry towards the use of substances derived from
natural products. The most important of these are the pyrethrins (originally extracted from
an African chrysanthemum plant) and rotenone’s (often called derris dust). These substances
have the advantage of being extremely toxic to insects, but of very low toxicity to
mammals
In addition they have short biological half lives (they are not persistent – you might call this
environmentally friendly) which means they do not accumulate in the tissues of animals. This
can also be a disadvantage in some instances however, as in the case of surface sprays where
they must be applied regularly. A disadvantage is that they are expensive to produce although
new techniques are lowering costs. Most pyrethrins are now produced synthetically.
Chem. Natural Substances
p52
Applied Organic Chemistry
Pyrethrins are now the most extensively used of all house hold pesticides due to their very
low mammalian toxicity. A whole range of pyrethrin type synthetic insecticides are now
available, with many companies mixing several different pyrethrins and a synergist in their
products.
Some of the more important synthetic pyrethrins include permethrin,
tetramethrin and allethrin.
Synergists.
Many pesticides (particularly DDT, and the pyrethrins) are much more toxic to insects if a
synergist is added to them. The synergist is almost always piperonly butoxide (once again a
common trade name). It is thought to work by deactivating enzymes in the insects that would
otherwise remove the pesticide from the insect‟s body.
O
O
O
O
O
Piperonyl butoxide
Future Trends in Pest Control
A no current pesticide cold be described as being anywhere near perfect, new directions in
pest control have taken different approaches rather than just trying to poison a species with a
chemical agent. These techniques are far more specific, but in general slower acting. Some
of the more interesting techniques include:

use of insect pheromones

use of hormones

use of sterilization

use of biological agents.
These techniques have the added advantage of not allowing the development of resistant
species as occurs with the use of conventional pesticides.
Chem. Natural Substances
p53
Applied Organic Chemistry
Insect Pheromones
These are organic substances naturally exuded by insects in very minute amounts to allow
them to communicate. Pheromones are produced to warn other insects of danger (alarm
pheromones), to attract insects of the opposite sex for mating (sex pheromones), and even to
tell other insects when an individual is dead. One of the most common alarm pheromones is
citronellal, which may explain why it is a successful insect repellent.
Insect pheromones have a very wide range of different structures and functional groups, but
one group (probably the most important), the sex pheromones, are in general long chain esters
or alkanols that contain one or more double bonds. These are used to kill insects by luring the
unsuspecting male or female (each sex responds to a different pheromone) into a trap that
either contains insecticide or glue. Many environmentally friendly cockroach traps now use
this technique. Traps have many advantages, the most important of which is that they can be
placed in and near food without fear of contamination.
O
The sex pheromone of the silk worm.
Hormones
Insects use hormones to control their body functions in exactly the same way as do other
animals (such as human beings). Hormones that control growth are now being used on
insects to prevent them from reaching maturity. This technique is best suited to insects that
are pests at the adult stage.
One common application of this technique is cockroach bombs, which spray a juvenile
hormone in the infested area. This prevents the juvenile cockroaches from growing to adults,
causing them to die before they can reproduce and continue the infestation. This technique is
extremely specific, only acting on the target species.
Sterilistion
This technique employs a sterilizing agent (either chemical or radiation source) on the male of
the species. These sterile males are then released in large numbers to mate with females,
which subsequently produce no offspring.
Biological Agents
These vary greatly in nature so only one example will be given here. Dipel is a special
pesticide for caterpillars. It contains a bacterium that infests the gut of the caterpillar, causing
ulceration and ultimately death.
Chem. Natural Substances
p54
Applied Organic Chemistry
Insect Repellents
These are substances that are applied to the body (or any other surface which seems apt) to
prevent insects from landing and staying on it. In general they do not kill the insect, and do
not prevent momentary landing of insects to test the site to bite. Instead they prevent the
insect from tucking down to a hearty meal on the exposed surfaces of the unsuspecting.
Very few substances are effective insect repellents. People have used citronella (active
component citronellal) and lavender oils for centuries, and these do have some effect (see
section on pheromones), but for personal application by far the most effective (and most
commonly used) repellent is DEET (common name Diethyltoluamide), whilst DMP (common
name dimethylphthalate) runs a distant second.
CH3
Citronellal
O
O
H3C
C-N
O
CH2CH3
C - OCH3
CH2CH3
C - OCH3
DEET
DMP
O
Herbicides
These are substances that are used to kill plants, or prevent plant growth in areas where this is
undesirable. Common terms used to describe these substances are weed killers and
defoliants. They are most commonly used in house hold gardens, although they have been
(and still are) employed for many other purposes including those of the military in wars.
Important terms used to classify herbicides include:

total herbicides

selective herbicides and

residual herbicides.
Chem. Natural Substances
p55
Applied Organic Chemistry
Total herbicides are also known as defoliants in that they kill all plant growth. Examples of
this include substances such as the notorious 2,4,5-T and 2,4-D used in the Vietnam War.
Selective herbicides kill only a target species. An example of this would be herbicides that
act on broad-leafed weeds, or Bindi killer.
Residual herbicides remain in the ground for long periods and prevent plant regrowth.
Properties of a Good Herbicide
These are very similar to those of a good pesticide. They include:
 low toxicity to mammals and non target species.
 Very high toxicity to target species
 Easy degradation to harmless products
 Low allergenic effects
Persistence may or may not be a desirable property depending on whether the herbicide is
residual or not. Obviously if growth prevention is desired it would be desirable.
Important Classes of Herbicides.
In this course we will only examine two types of herbicides.
 The hormone weed killers and
 The paraquat/diquat family
Hormone Weed Killers.
These function by mimicking the natural growth hormones of plants, but they are very
selective in how they promote growth. In general exposure of plants to these substances leads
to disproportionately large growth of stems and branches, with little or no associated root
growth. Leaf growth is also retarded, or leaves with inadequate chlorophyll are produced.
Ultimately this leads to the death of the plant. Examples of hormone weed killers are 2,4-D,
2,4,5T and MCPA (all common names).
Chem. Natural Substances
p56
Applied Organic Chemistry
Cl
Cl
Cl
OCH2C=O
Cl
OCH2C=O
OH
OH
Cl
2,4-D
2,4,5-T
Cl
OCH2C=O
OH
MCPA
Usage of these herbicides has been greatly restricted in this country due to the implication of
several of them as carcinogens (Agent Orange which was used in the Vietnam War was a
mixture of these). They are not directly stated as being carcinogenic, but a by-product of their
production (which is found in 2,4,5-T in small amounts), dioxin, is a potent mutagen and
suspected carcinogen.
Diquat and Paraquat Type (total herbicides)
These families of substances (of which paraquat and diquat are the best known examples)
totally prevent leaf growth in plants. They are contact weed killers in that only a small
amount of these herbicides needs to touch the plant to kill it. They find application in devices
such as “weed sticks and guns” where a wick is used to touch the plant you wish to destroy.
Other plants around are not harmed (unless you accidentally touch them). They may also be
used if you wish to totally eradicate all plant growth in an area. Hence they are total
herbicides.
These substances act by preventing the plant from producing cellular energy. They interfere
with electron transport in the cell that is an important part of the mechanism for energy
production.
+
N
Diquat
Chem. Natural Substances
+
N
+
+
H3C N
N
CH3
Paraquat
p57