applied organic chemistry - cffet.net organic chemistry chem. natural substances p3 ... an aldose is...

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

Chem. Natural Substances p3

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 C6H12O6 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

C6H12O6 + 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



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 acid or enzyme

two monosaccharides

polysaccharide + water 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

Number of carbons Molecular formula

triose 3 C3H6O

tetrose 4 C4H8O

pentose 5 C5H10O

hexose 6 C6H12O

heptose 7 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



For example the molecule below contains five carbons, and is an alkanal.

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.

Class Exercise. Classify the following molecules according to the systems listed on the

previous page.

glucose fructose 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.

C

CH

O

H

CH2OH

OH

OHC

C OH

C HHO

H

H

H

HO HC

C OH

OH

CH2OH

H C

CH2OH

C O

H

H C

C OH

OH

CH2OH

H C

C O

H

OH

H

H C

C OH

OH

CH2OH

H C

C O

H

H



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 + -OH is known as a hemi-acetal

alkanone + -OH is known as hemi-ketal

In general

O

O

O

O

O

O

O

OH

OH

H

H

H

HH

CH2OH CH2OH

HO

These groups are recognised by a C attached to two O‟s.



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

group.

an α-hydroxyalkanone 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 Cu2+

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 H2O 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.

+ + H2O

OH HO 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.

C C

OHO or a

C C

O

H



Sucrose is made up of α-D-glucose and β-D-fructose joined via their hemi-acetal or hemi-

ketal -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

β-D-fructose

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

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.

2'

1

CH2OH

HO

CH2OH

HO

HO

HO

O

OHO

OHOCH2

1

CH2OH

O

CH2OH

HOHO

HO O

OH

O

OHOH

4' 1'



1

CH2OH

O

CH2OH

HOHO

HO

O

OH

O

OHOH

4' 1'

Cellobiose - Two glucose units joined in a β-1,4‟- link. Formed by the breakdown of

cellulose. It is a reducing sugar.

1

CH2OH

O

CH2OH

HO

HO

HO

O

OH

O

OHOH

4' 1'

Cellobiose - note the only difference between this and maltose is the orientation of the

glycosidic link



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 80C. 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).



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.

1

C H 2 O H

O

C H 2 O H

H O

H O

H O

O

O H

O

O H 4 '

1

C H 2 O H

O

C H 2 O H

H O

H O

O

O H

O

O H OH

4 ' 1 '

O

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



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.



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.



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:

C

C

C

HH

H

H

H

O

O

O

C

O

CO

C

O

and are made by the following general reaction:

the alkanol part + the acid part

triglyceride

The alkanol part is always 1,2,3-propanetriol (commonly referred to as glycerol).

H

H

H

O

O

O

C

O

CO

C

O

COH

COH

COH

HH

H

H

H



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

(common

name)*

Number

of C

Atoms

Source Formula / Structure Melting

Point C

butanoic

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.



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.

CH2 - O - C

CH2 - O - C

CH - O - C

O

O

O

saturated triglyceride

CH2 - O - C

CH2 - O - C

CH - O - C

O

O

O

unsaturated triglyceride



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



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.).



Waxes

These are esters of high molecular weight alkanols and fatty acids. They have the general

formula

.

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.

R' O R

O

C



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, CH3(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.

R - C - OH + NaOH R - C - O-Na+ + H2O

O O

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.

R - C - OR + NaOH R - C - O-Na+ + ROH

O O

Beef tallow provides sodium stearate CH3(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,



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.

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.

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

SO3-Na

+

O S

O

O

O-Na

+



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,



e.g.

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.

Aspartic acid

C C

NH2 OH

H

R

O

COOH

NH2

C

H

HOOCCH2



Basic amino acids have an extra amine group located on their side chain.

An example of this is lysine -

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 -

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 -

Class Exercise: Classify the amino acids below into one of the groups listed above.

COOH

NH2

C

H

CH2CH2CH2CH2NH2

COOH

NH2

C

H

CH2HO

COOH

NH2

C

H

CH2

COOH

NH2

C

H

CH2HO COOH

NH2

C

H

CH2CH3

CH3

CH

COOH

NH2

C

H

CH2CH2HOOC

COOH

NH2

C

H

CH2N

N

H



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.

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

COO -

NH3+

C

H

R



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 Isoelectric Point Amino Acid Isoelectric Point

glycine 5.97 serine 5.68

alanine 6.00 threonine 5.60

asparagine 5.41 tyrosine 5.66

glutamine 5.65 tryptophan 5.89

cysteine 5.07 valine 5.96

isoleucine 6.02 aspartic acid 2.77

leucine 5.98 glutamic acid 3.22

methionine 5.74 arginine 10.76

phenylalanine 5.48 histidine 7.59

proline 6.30 lysine 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.

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

OH

OH

O

O



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.

CC

O

OH

HR

NH2

CC

O

HR

NH2

+N - C - COOH

R

H

H

N - C - COOH

R

HH

H+ H2

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.



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



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 three-

dimensional 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).

protein protein

covalent crosslink

CH2CH2S SCH2CH2



2. Hydrogen bonding - tertiary structures may be stabilised by H-bonding between

polar groups on side chains.

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.

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.

protein protein

hydrophobic interaction

CH2CH2C

OH

HO-O

CH2CH2C

O

O- +

N

H

H

H

CH2CH2CH2CH2

CHCH2CH3 CH2

CH3



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



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”.



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.



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.



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.

N

NN

NN

NN

NN

NN

N

NH2

Hadenine (A)

H

O

H

H2N

guanine (G)

H

purine

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.

N

N

N

N

N

N

N

N

H H H

O OO

NH2

CH3

0 0

H H

cytosine (C) uracil (U) thymine (T) pyrimidine

In a nucleoside either ribose or deoxyribose replaces the hydrogen atom shown in bold.

DNA(deoxyribonucleic acid)



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

S

P

S

P

S

P

S

P

P

S

P

S

P

S

P

S

P

T ................. A

T ................. A

C ................. G

G ................. C

P = phosphateS = deoxyriboseA = adenineT = thymineC = cytosineG = guanine....hydrogen bondine

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.



The double-helix shape of DNA.

A molecule of DNA

RNA (ribonucleic acid)



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?



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.



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.



DNA is transcribed into mRNA which is translated into amino acids.

This is



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).

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 19th

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

Monomer

Monomer

Monomer

Monomer

Monomer

Monomer



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

CH2CH2CH2CH2

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

C

O

HO O CH 2CH 2 O C

O

O CH 2CH 2OH



Uses

Soft drink bottles

Nylon

Monomers

Diamine, eg NH2(CH2)6NH2

Diacid, eg COOH(CH2)4COOH

Basic structure

Uses

fibre for fabrics

engineering materials

Polystyrene

Monomer

Phenylethene (styrene)

Basic structure

where B = benzene ring

C(CH2)4C N(CH2)6N

OO

H

C(CH2)4C

H

O

HH

N(CH2)6N

O

B B B B



Uses

insulation

foam drinking cups

packing material

UV/VIS cells

Bakelite

Monomers

phenol

methanal (formaldehyde)

Basic structure

Uses of thermoset resins in general

Hard moulded products required to withstand heat and physical stress eg kettles, telephones,

fiberglass

OH OH OH OH OH



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.



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.



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.

H

Cl

Cl

Cl

ClCl

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.



H

Cl

Cl

Cl

CH3O CH3O

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.

H

Cl

Cl

Cl

ClCl

Cl

+ Cl - C - C - OH

Cl

Cl

OH

H

heat

H2SO4

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.

+ 3Cl2

light ClCl

Cl

Cl ClCl

Preparation of γ-Lindane.



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.

P

O

R YR1

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.



NO2OCH3CH2O - P -

S

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.

CH3O - P - S - CH2CONHCH3

S

OCH3

Dimethoate (Rogor)

CH3CH2O - P - O - P - OCH2CH3

OO

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.



Carbamate Pesticides

These substances are manufactured from carbamic acid (or its derivatives), and act in a very

similar manner to the organophosphorus pesticides.

HO - C - N - H

O H

This group converted to an ester

Carbamic acid

H replaced with shorthydrocarbon groups

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.

N

N CH3

CH3 CH3

CH3

CH3

N O - C - N - CH3

O

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.



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

OO

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.



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.



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.

O

CH3

C - N

OCH2CH3

CH2CH3H3C

Citronellal

DEETDMP

C - OCH3

C - OCH3

O

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.



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).



Cl

Cl

OCH2C=O

OH

2,4-D

Cl

Cl

Cl

Cl

OCH2C=O

OH

OCH2C=O

OH

2,4,5-T

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 N

+ +

Diquat

N NH3C CH3

++

Paraquat

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