BIOLOGICAL & ORGANIC CHEMISTRY

TOPIC 5: ORGANIC AND BIOLOGICAL CHEMISTRY

Most chemicals are compounds of carbon with other elements, mainly hydrogen, oxygen, and nitrogen, with
many more being synthesised each year. The variety and importance of carbon compounds are so great that
there is a specific branch of chemistry known as ‘organic chemistry’. In this topic students are introduced to
the chemistry of the more common organic compounds.
Biological chemistry is one of the growing areas of research, including medical technology, genetic
engineering, and the development of pharmaceuticals. In this topic students are introduced to the major
groups of compounds of biological significance.
The reactions of the larger macromolecules can often be explained by referring to the reactions and
properties of smaller molecules with the same functional groups.
Subtopic 5.1: Systematic Nomenclature
Key Ideas Intended Student Learning
The presence or absence of functional groups in an Identify the functional groups in the structural
organic compound determines its physical and formulae of alcohols, aldehydes, ketones,
chemical properties. carboxylic acids, amines, esters, and amides.
Organic compounds are named systematically to State, given its structural formula, the systematic
provide unambiguous identification. name of an organic compound containing:
• up to eight carbon atoms arranged as either a
straight chain or a branched chain;
• one or more of the same functional groups
(with these limited to hydroxyl, aldehyde,
ketone, carboxyl, or primary amino groups).
The structural formula of an organic compound can be Draw, given its systematic name, the structural
deduced from its systematic name. formula of an organic compound containing:
• up to eight carbon atoms arranged as either a
straight chain or a branched chain;
• one or more of the same functional groups
(with these limited to hydroxyl, aldehyde,
ketone, carboxyl, or primary amino groups).
Esters are named as derivatives of a carboxylic acid. State the systematic names of methyl and ethyl
esters of straight-chain acids containing up to
eight carbon atoms.
The structural formula of an ester can be deduced from Draw, given its systematic name, the structural
its systematic name. formula of an organic methyl or ethyl ester of a
straight-chain acid containing up to eight carbon
atoms.

Introduction
Organic compounds are carbon-containing compounds. Carbon has the following unique properties:
• It has a covalence of four
• Carbon atoms can bond to each other to form straight chains, branched chains and rings.
• Carbon atoms can form sing, double and triple covalent bonds with each other and other atoms.
As a consequence, there are thousands of different organic molecules containing carbon atoms.
Terminology
Term Meaning Example
Molecular formula represents the number of atoms in a molecule C3H8

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Term Meaning Example

Empirical formula the simplest ratio of atoms in a compound C4H8 → CH2
Structural formula represents the arrangement of atoms in a CH3-CH=CH-CH3
molecule
Structural isomers molecules with the same molecular formula, but CH3-CH=CH-CH3
different structural formulae CH2=CH-CH2-CH3
Homologous series a series of organic compounds which conform to Alkanes
a general formula, which have the same CnH2n+2
functional group, which behave similarly in
chemical reactions but have slightly different
physical properties
Saturated compounds have no double bond between C atoms alkanes
Unsaturated have at least one C=C or C≡ C bond in a chain or Alkenes and alkynes
compounds ring
Aromatic compounds a benzene ring forms part of the molecule

OR
H

H H
C
C C

C C
H
C
H

Systematic Naming Of Organic Compounds

There is a set of rules established by IUPAC (the International Union of Pure and Applied Chemistry) to
name this compounds. eg alkanes
Find the longest continuous chain of carbon atoms and assign the parent name by combining the prefix from
the table below with the suffix –ane.
Number of C’s 1 2 3 4 5 6 7 8
Prefix meth- eth- prop- but- pent- hex- hept- oct-
The longest continuous chain in this molecule has 6 carbons so the parent name hexane:
CH3 CH CH2 CH2 CH2 CH3

CH3

Locate any side chains (alkyl groups) and name them according to the number of carbons in them:
-CH3 : methyl -C2H5 : ethyl etc

CH3 CH CH2 CH2 CH2 CH3

CH3 methyl group

Thus the molecule above is methylhexane.

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The position of the branching alkyl group in the continuous chain is then indicated by a number that is the
number of the carbon atom in the main chain to which the chain is attached. The chain is numbered
from the end which gives the lower of the two possibilities.

1 2 3 4 5 6
CH3 CH CH2 CH2 CH2 CH3

CH3

Thus the molecule above is 2-methylhexane.

Note:
• Numbers are only required when other isomers are possible.
• Numbers in a name are separated from each other by commas and from the words by hyphens.
If a compound contains two or more identical branches, the following prefixes are used:
Number of branches 2 3 4
Prefix di- tri- tetra-
This molecule has 2 methyl groups and so is a dimethyl-, with the methyl groups attached to the
second and third carbons this the name is 2,3-dimethylhexane.

CH3 CH CH CH 2 CH 2 CH3

CH 3 CH 3

If a molecule has two or more different branching alkyl groups, they are placed in alphabetical order in the
name, hence the molecule below is 3-ethyl-2-methylhexane.

CH3 CH CH CH 2 CH 2 CH3

CH 3 C2H5

Each homologous series has an associated functional group which is named as a suffix or prefix.
○ For suffixes, e is removed and the suffix added eg –ol, oic acid. The number of the carbon can
be before the parent name or before the suffix eg 2-propanol or propan-2-ol.
○ For prefixes it is added to the start of the parent name eg 2,2-dichloropropane.
For aldehydes, ketones, carboxylic acid and carboxylate ions, the longest carbon chain includes the carbon
that is part of the functional group eg CH3-CH2-COOH is propanoic acid.
Esters are formed from the reaction between a carboxylic acid and an alcohol, the names of which are
components of the name. The carboxylic acid gaines the –oate suffix instead of –oic acid and the
alcohol gets the name of the alkyl group it contains. Example – propanoic acid and methanol make
methyl propanoate.

propanoate from
propanoic acid
O

CH 3 CH 2 C

methyl from
O CH3
methanol

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Common Functional Groups

Homologous series Functional group General formula Naming

alkane C-C CnH2n+2 - ane
alkene C=C CnH2n - ene
alkyne C≡ C CnH2n-2 - yne
alcohol R − OH CnH2n+1OH - ol
aldehyde R C H CnH2n+1CHO - al
O
ketone R C R' CnH2nO - one
O
carboxylic acid CnH2n+1COOH - oic acid

oleObject1

carboxylate salt CnH2n+1COO- - oate ion

oleObject2

ester CnH2nO - oate

oleObject3

amine R - NH2 CnH2n+1NH2 - amine

Amindes R – CONH2 CnH2n+1CONH2 -amide
ASSIGNMENT 5.1 : SYSTEMATIC NOMENCLATURE
1. Write systematic names and give the molecular formulae (first 4only ) of the following molecules and
ions:

Name Name
Molecular formula Molecular formula

Name Name
Molecular formula Molecular formula

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2. Draw the structure of the following compounds

3–methylbutan–2–ol

3–methylpentan–3–ol

2,2–dimethylpentane– 1,3–diol

3 ,3–dimethylbutanal

3–methylhexane–1,6–dial

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2,4–dimethylpentan–3–one
heptan–2,4–dione
3–methylbutanoic acid
octan–1,8–dioic acid
methylpropanamine
N–ethylbutanamine
heptane–1,7–diamine
Subtopic 5.2: Physical Properties
Key Ideas
The melting-points and boiling-points of organic
compounds that contain the same functional group
increase with the length of carbon chain.
The boiling-points of organic compounds that display
hydrogen bonding between molecules are higher than
those of compounds of similar molar mass that do not
display hydrogen bonding.
The boiling-points of esters are lower than those of
isomeric acids because of the absence of hydrogen
bonding between molecules of the ester.
Organic compounds are generally insoluble in water.
Hydrogen bonding between functional groups and
water can explain the solubility in water of some
smaller organic compounds.
The solubility in water of an organic compound
depends on its molar mass and the functional groups
present.
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Intended Student Learning
Predict and explain the melting-points and
boiling-points of an organic compound in
comparison with those of other compounds that
contain the same functional group.
Predict and explain the boiling-points of alcohols
in comparison with those of aldehydes and
ketones of similar molar mass.
Predict and explain the boiling-points of esters in
comparison with those of isomeric acids.
Explain the insolubility in water of most organic
compounds.
Predict and explain the solubility in water of the
smaller amino acids, carboxylic acids, alcohols,
aldehydes, and ketones.
Predict and explain the relative solubilities in
water of two organic compounds, given their
structural formulae.
 BIOLOGICAL & ORGANIC CHEMISTRY

Important physical properties of organic compounds

Three important physical properties of organic compounds, which relate to their structure and bonding are
melting point, boiling point and solubility in water. The size of the hydrocarbon chain and the polarity of the
functional group(s) that make up a molecules structure influence each one of these properties.
Effect of carbon chain length on melting and boiling points
For compounds with identical functional groups, the boiling points increase as the length of the carbon chain
increases. The secondary bonding forces operating between non-polar hydrocarbon chains are dispersion
forces. The strength of the dispersion forces increases with molar mass (which is proportional to chain
length). The trend for melting points is similar but not as clear cut, because melting also involves the
complete separation of molecules.
Name Formula Molecular mass Melting Point (ºC) Boiling Point (ºC)
Methane CH4 16 -183 -162
Ethane C2H6 30 -172 -89
Propane C3H8 44 -190 -42
Butane C4H10 58 -135 -1
Pentane C5H12 72 -130 36
Hexane C6H14 86 -94 69
Heptane C7H16 100 -90 98
Octane C8H18 114 -57 126
Nonane C9H20 128 -51 151
Decane C10H22 142 -30 174

Melting & Boiling Point vs Molecular Mass

for the Alkanes
200

150

100
Temperature

50

0
melting point
0 20 40 60 80 100 120 140 160
-50 boiling point

-100

-150

-200

-250
Molecular Mass

Effect of functional group on melting and boiling points

The polarity of the functional group affects the strength of the secondary bonding and hence the melting and
boiling points. The most polar have the highest boiling point (keeping atomic mass about the same. The table
below compares the boiling points of compounds containing different functional groups in molecules
containing three carbons and about the same molecular mass.
Compound Molecular mass Boiling point (ºC)
Propanol 60 97.2

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Propanal 58 47.9
Propanone 58 56.1
Propanoic acid 74 140.8
Ethyl methanoate 74 54.5
propanamine 59 48.5
This suggests that the order of polarity amongst the functional groups is:
carboxylic acid > alcohol > aldehydes and ketones > amines
Solubility of organic compounds in water
Non-polar organic compounds, such as hydrocarbons, are not soluble in water because they cannot form
hydrogen bonds with polar water molecules. Molecules with polar functional groups, but long carbon chains
(of 6 or more carbon atoms) are also classified as non-polar because the non-polar carbon chain is the
dominant structural feature of these molecules.
Polar groups with the capacity to form hydrogen bonds with water, can render an organic compound soluble
in water, if the carbon chain is not too long. A molecule with more than one such polar functional group has
increased solubility. The effect of chain length and polar functional groups is shown in the table below.
Solubility (g/100g water)
Carbon chain Alcohol Aldehyde Ketone Carboxylic amine
acid
methan- ∞ very - ∞ ∞
ethan- ∞ ∞ - ∞ ∞
propan- ∞ 16 ∞ ∞ ∞
butan- 8 7 26 ∞ ∞
pentan- slightly slightly 6 4 very
octan- insoluble insoluble insoluble insoluble insoluble
It can be seen from inspection of the data table above that the lower members of each homologous series are
very soluble in water. As the non-polar carbon chain length increases, the molecules take on greater non-
polar character overall, with a consequent decrease in solubility.
The diagram below shows the hydrogen bonding between:.

ethanoic acid and water methanal and water

ASSIGNMENT 5.2 : PHYSICAL PROPERTIES

1. The alkanes have the general formula CnH2n+2. The melting and boiling points for the first ten
members of this homologous series are given in the table.

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Name Formula Melting Point (oC) Boiling Point (oC)

Methane CH4 -183 -162
Ethane C2H6 -172 -89
Propane C3H8 -190 -42
Butane C4H10 -135 -1
Pentane C5H12 -130 36
Hexane C6H14 -94 69
Heptane C7H16 -90 98
Octane C8H18 -57 126
Nonane C9H20 -51 151
Decane C10H22 -30 174
(a) Draw a graph with the boiling point temperatures on the vertical axis against the number of
carbon atoms in each molecule.
(b) How is the trend explained?
(c) How would the graph for the first ten alcohols differ from the one drawn. Explain why.
1. You have just extracted a substance from a plant and you suspect that you may have been the first
chemist to do so. After purifying it you examine its physical properties:
Your results: Tb = 78oC
Conductivity – non-conductor
Solubility – completely miscible with water
Solution conductivity - nil
pH of solution – 6.9
(a) What can you deduce from this information?
(b) How could you test your substance to show that it is not a mixture?
(c) What might be some of the analytical techniques you could use to find out more about your
discovery?
1. (a) Name the following
(i) (ii) (iii) (iv) (v)
H H H H H H H H H
O O

H C C C H H C C C H H C C OH H C C H C C

H O H
H OH H H O H H H H H

(a) Which substance has:

(i) the lowest boiling point?
(ii) the highest boiling point?
(b) Give reasons for your choices in part (b).
O

1. With esters you have to be careful to get the O group the right way round.

For example, ethyl ethanoate is very different to its isomer methyl

propanoate
(a) In what way would they differ?
(b) However, their Tb and lack of solubility in water are similar. Explain why.

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1. Draw diagrams to show hydrogen bonding between water molecules, between alcohol molecules and
between water and alcohol.
2. This table shows the solubility of some alcohols in water:
Name Formula Solubility (g/100g H2O)
Methanol CH3OH ∞
Ethanol CH3CH2OH ∞
Propan-1-ol CH3CH2CH2OH ∞
Butan-1-ol CH3CH2CH2CH2OH 8.0
Pentan-1-ol CH3CH2CH2CH2CH2OH 2.7
Hexan-1-ol CH3CH2CH2CH2CH2CH2OH 0.6
(a) Explain the observed trend.
(b) Butan-1-ol has a boiling point of 117.7oC, whereas butane boils at –0.5oC. Explain this
difference. (Diagrams must be used in your explanation.)
1. The table below shows information about some alcohols which form part of an homologous series.
Name Formula Boiling Point (°C) Molecular Mass
Methanol CH3OH 65 32
Ethanol C2H5OH 78 46
Propan-1-ol C3H7OH 97 60
Butan-1-ol C4H9OH 74
Pentan-1-ol C5H11OH 138
Hexan-1-ol C6H13OH 158 102
(a) (i) Identify the functional group common to all alcohols.
(i) What is the general formula for these alcohols?
(a) What is the formula of the next alcohol in the series?
(b) Calculate the relative molecular mass of pentan-1-ol, using only the information given in the
table. Explain your working.
(c) (i)Plot a graph of boiling point against number of carbon atoms in a molecule of the alcohol.
Use the graph to estimate the boiling points of:
(1) butan-1-ol
(2) C8H17OH
(d) State the connection between boiling point and the relative molecular mass of these alcohols.
1. Amino acids are the building blocks of proteins and contain both amine and carboxylic acid
functional groups. Three amino acids are shown in the diagrams below:
H O
H O H O
N CH C
N CH C N CH C
H O H
H O H H O H CH
H CH3
H3C CH3

glycine alanine valine

(a) Which would have the highest boiling point? Why?
(b) Which would be most soluble in water? Why?

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SUBTOPIC 5.3: ALCOHOLS

Key Ideas
Ethanol is produced by fermentation of glucose, which
can be derived by hydrolysis of complex
carbohydrates.
Alcohols are classified as primary, secondary, or
tertiary.
Primary and secondary alcohols can be distinguished
from tertiary alcohols by their reaction with acidified
dichromate solution.
The type of product obtained by oxidising an alcohol
depends on whether the alcohol is primary or
secondary.
Intended Student Learning
Describe the conditions, and write equations, for
the hydrolysis of polysaccharides and the
production of ethanol by fermentation of glucose.
Identify a hydroxyl group in an alcohol as
primary, secondary, or tertiary, given the
structural formula.
Describe how primary and secondary alcohols
can be distinguished from tertiary alcohols by
their reaction with acidified dichromate solution.
Predict the structural formula(e) of the product(s)
of dichromate oxidation of a primary or
secondary alcohol, given its structural formula.

Ethanol Production
On an industrial scale, ethanol is produced in two ways:
• Synthetic ethanol – produced from ethene from crude oil or natural gas
• Fermentation – produced from glucose (monosaccharide) in grape or sugar (disaccharide) in fruits or
starch (polysaccharide) in vegetables and grains.
Fermentation
If grain is used for the production of ethanol, the starch has to be converted to glucose before fermentation.
To do this they are firstly soaked in water, which causes the grains to germinate. Enzymes in the grain then
hydrolyse the starch to glucose in two steps.
Step 1 Hydrolysis of the polysaccharides to disaccharides
(C6H10O5)n + H2O → C12H22O11

oleObject4 oleObject5

Step 2 Hydrolysis of the disaccharides to glucose

C12H22O11 + H2O → 2C6H12O6
Some fruits contain disaacharides (like sucrose – cane sugar) so only the second step is needed.
Grape juice already contain glucose.
Step 3 The glucose is then fermented using yeast.
C6H12O6 → 2C2H5OH + 2CO2
Conditions needed
• Temperature - 20°C to 30°C. Outside this range, the enzymes are less effective. The reaction is
exothermic, so cooling is sometimes necessary to keep the temperature in the optimal range.
• Exclusion of oxygen – fermentation is an anaerobic process and needs little oxygen. Too much oxygen
causes oxidation of the alcohol to ethanoic acid (vinegar).
Primary, secondary and tertiary alcohols
Alcohols are classified as primary, secondary or tertiary according to the position of the hydroxyl (alcohol)
group in the molecular structure.
• Primary alcohols – the OH group is on the end of a chain eg CH3-CH2-CH2-OH

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• Secondary alcohols – the OH group is bonded to a carbon inside a chain, that is bonded to 2 other
carbons eg propan-2-ol
H H H

H C C C H

H OH H

• Tertiary alcohols – the OH group is bonded to a carbon that is in turn bonded to 3 other carbons eg
methyl propan-2-ol.
OH

CH 3 C CH 3

CH 3

Oxidation of alcohols
The type of product, if any, formed by the reaction of an alcohol with and oxidising agent such as acidified
potassium dichromate depend on whether the alcohol is primary, secondary or tertiary,
A primary alcohol is oxidised first to the corresponding aldehyde, and, if there is continued contact with the
oxidising agent, then the aldehyde is oxidised to the corresponding carboxylic acid. eg
H H H H H H H
O O
H C C C OH H C C C H C C C

H H H H H H H H OH
oleObject6 oleObject7

propan-1-ol propanal propanoic acid

A secondary alcohol is oxidised to the corresponding ketone.
H H H H H

H C C C H H C C C H

H OH H H O H
oleObject8

propan-2-ol propanone
A tertiary alcohol is not oxidised by acidified dichromate ions.
These tests can be use to distinguish between the alcohols. During the reaction, the orange dichromate is
reduced to the green chromium (III) ion.
Note
The reaction is slow at room temperature and needs heating.
The alkyl group is not involved in the reaction, only the functional group.

ASSIGNMENT 5.3 : ALCOHOLS AND ALDEHYDES

1. Alcohols are organic compounds with an --OH group. It is called a hydroxyl group, not a hydroxide
group. Why?
2. (a) Give systematic names for these alcohols:
(i) (ii) (iii)

CH 3 CH 2 CH OH CH 3 CH 2 CH CH 2 OH
CH 3 CH 2 CH 2 CH 2 OH
CH 3 CH 3

Classify each as a primary, secondary or tertiary alcohol.

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 BIOLOGICAL & ORGANIC CHEMISTRY

1. Glucose solution was fermented under anaerobic conditions. The glucose solution was boiled and
then cooled before the yeast was added.

Glucose and
yeast solution

(a) Why was the glucose solution boiled and cooled before the yeast was added?
(b) What does anaerobic mean?
(c) Explain the role of the S-shaped section of the tubing.
1. Ethanol is the starting material for a range of important organic chemicals. The reactions, which
produce some of these, are summarised below. The reagents and conditions for the reactions have not
been included.
CH3CHO CH3COOC2H5

B
A

C
C2H5OH CH3COOH

State the reagents and conditions needed to bring about each of the reactions A – C above.
2. Propan-1-ol, C3H7OH, is refluxed with an acidified solution of potassium dichromate (VI) to produce
propanoic acid. The acidified potassium dichromate (VI) acts as an oxidising agent.
(a) Explain what is meant by the term reflux.
(b) State what colour change takes place in the reaction mixture.
(c) Write a balanced equation for the oxidation of propan-1-ol to propanoic acid.
1. The production of body odour often begins with secretions from glands called apocrine glands which
are most numerous in the armpits. Skin bacteria, which live in the armpits, use these secretions to
produce energy and many different waste products. Scientists have isolated one of these products,
compound E, which is shown below. Compound E can be oxidised to form compounds F and G.
CH3 CH2OH CH3 COOH
C C Compound F C C
CH2CH2CH3 H CH2CH2CH3 H

Compound E Compound G
(a) Compound E contains two functional groups. Identify both functional groups and state how you
could test for each.
(b) Suggest the structural formula of compound F.

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1. Compound A is an alcohol, that has several structural isomers.

The molecular formula of A is C5H12O. Give and name a structural formula which is:
(a) a primary alcohol
(b) a secondary alcohol that has a branched carbon chain
(c) a tertiary alcohol.
(d) Each of these alcohols reacts differently with a solution of potassium dichromate which has
been acidified with sulfuric acid. For each example in (a), give the structure of the organic
product from this treatment. If there is no product, say so.
1. Before the introduction of IR spectroscopy to determine blood alcohol content of drivers, gas liquid
chromatography (GLC) was used.
The chromatogram shown gives the results of a GLC analysis of the first five straight chained primary
alcohols. The more volatile a compound the less its retention time.

(a) Record in table form, the name, the formula and retention time for each alcohol analysed.
(b) Estimate a retention time for hexan-1-ol.
In GLC analysis for BAC a doctor takes a blood sample and an exact amount of blood is mixed with a
known amount of a standard solution of propan-1-ol. Here is a chromatogram from such an analysis.

(c) What is meant by the term, a standard solution?

(d) Why is a standard amount of propan-1-ol added to the blood?
(e) If the concentration of the propan-1-ol was 60 mg per 100 mL of solution, what was the
approximate concentration of the ethanol?
1. (a) What is an aldehyde and what is a ketone?
(a) What is a carbonyl group?
1. (a) Aldehydes and ketones cannot form intermolecular hydrogen bonds. Explain why.
(a) What is a consequence of this?
1. Give the systematic name to each of the following:
(a) (b) (c) (d)

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 BIOLOGICAL & ORGANIC CHEMISTRY

O O
CH3CH2CH2CHO CH3CH2CH2CH2CHO
H3 C CH2 CH2 C CH2 CH3 CH3 C CH2 CH3

2. Compound A (butanal) and compound B (butanone) have the same molecular formula, C4H8O.
(a) What term is used to describe compounds with the same molecular formula?
(b) Name the functional group common to both A and B.
1. Three different compounds A, B, and C have the same molecular formula, C3H6O. Tests show that A is
an unsaturated alcohol, B is an aldehyde and C a ketone.
(a) Write structures for A, B and C.
(b) When compound B was added to a solution of silver nitrate in aqueous ammonia (Tollen’s
Reagent), metallic silver is formed.
(i) What is the name for this test?
(ii) Write an equation for the reaction.
(c) Another test used to distinguish between aldehydes and ketones uses acidified dichromate
solution.
(i) What would you observe when this solution is added to B and then C?
(ii) Write the equation for the reaction with B.
1. Compound C4H10O, is oxidised in two steps to 2-methylpropanoic acid.
CH3
CH COOH
CH3
Write the structure of the original compound.
2. Write the full structural and molecular formula of each of the following molecules
(a)
O OH
HO

HO OH
OH
(b)
OH OH
H
HO
O
OH OH

Subtopic 5.4: Aldehydes and Ketones

Key Ideas Intended Student Learning
Aldehydes and ketones are produced by the oxidation Draw, given the structural formula of the
of the corresponding primary and secondary alcohols aldehyde or ketone, the structural formula of the
respectively. Aldehydes are readily oxidised, and so alcohol from which it could be produced by
must be distilled off from the reaction mixture as they oxidation, and describe the necessary reaction
are formed. conditions.
Aldehydes can be oxidised to form carboxylic acids or, Draw the structural formula of the oxidation
in alkaline solutions, carboxylate ions. product of a given aldehyde in either acidic or
alkaline conditions.
Ketones cannot readily be oxidised. This difference in Describe how acidified dichromate solution and
properties can be used to distinguish aldehydes from Tollen’s reagent (ammoniacal silver nitrate
ketones. solution) can be used to distinguish between

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 BIOLOGICAL & ORGANIC CHEMISTRY

Key Ideas Intended Student Learning

aldehydes and ketones.

C O
Aldehydes and ketone molecules contain the carbonyl group . For aldehydes, the carbonyl group is in
a terminal position, while it is in a non-terminal position for ketones.
Aldehydes and ketones are widely used as solvents, flavourings, and fragrances.
Examples
C 3H7 C 3H7 CH3 O
O
C O C O
H3C CH2 C C C H3C CH 2 C CH CH 2
H C 2H5
H
butanal hexan-3-one 2-methylpent-2-enal (grassy) pent-1-en-3-one (mustard)
Preparation of aldehydes and ketones
Aldehydes are prepared by the controlled oxidation of primary alcohols.
A solution of the oxidising agent is dropped into the acid-alcohol mixture as it is heated. The aldehyde boils
off immediately it forms, preventing the further oxidation to the carboxylic acid. The aldehyde is the lowest
boiling point component of the mixture and consequently distils off at the lowest temperature.
O
R-CH2-OH R C
oleObject11 H

Ketones are prepared by the oxidation of secondary alcohols. Unlike aldehydes, they do not oxidise further.
Thus the ketone product does not have to be distilled off as it forms. Heating of the mixture is required to
increase the rate of the reaction.
R' R'
C OH C O
R oleObject12 R

Apparatus used for the production of an aldehyde from a primary alcohol

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Oxidation of aldehydes
When aldehydes are heated with acidified solution of dichromate. They undergo oxidation to carboxylic
acids. The oxidising agent is the orange dichromate ion which is reduced to the green chromium (III) ion.
H H H H
O O
H C C C H C C C

H H H H H OH
oleObject13

propanal propanoic acid

Under alkaline conditions, aldehydes also undergo oxidation to carboxylate ions for example when they are
heated with ammoniacal silver nitrate (Tollen’s Reagent). The oxidising agent is the silver diamine ion
which is reduced to metallic silver. Under favourable conditions, the silver can be made to deposit on the
inside walls of the reaction vessel as a silver mirror. This is used as a test for aldehydes. Note that the
carboxylate ion is formed rather than carboxylic acid, because of the alkaline conditions produced by the
ammonia.
Distinguishing between an aldehyde and a ketone
Ketones do not undergo oxidation when heated with acidified dichromate solution or Tollen’s reagent.
Acidified dichromate Tollen’s Reagent
aldehydes Turns green Silver mirror
ketones No reaction No reaction

Subtopic 5.5: Carboxylic Acids

Key Ideas Intended Student Learning
Carboxylic acids can be produced by the oxidation of Identify the aldehyde or primary alcohol from
aldehydes or primary alcohols. which a carboxylic acid could be produced by
oxidation, given its structural formula.
Carboxylic acids are weak acids and ionise, to a small Write an equation for the ionisation of a
extent, in water. carboxylic acid in water.
Carboxylic acids react with bases to form ionic Write equations for the reactions of carboxylic
carboxylate salts. acids with hydroxides, carbonates, and hydrogen
carbonates, and describe changes that accompany
these reactions.
The salts of sodium and potassium carboxylates are Explain why some drugs with carboxyl groups
soluble in water because of the ion–dipole attraction are usually taken in the form of their salts.
between the ions and water.
Carboxylic acid contain the carboxyl group –COOH δ −
O
δ +
C δ − δ +
O H
Preparation
Carboxylic acids can be prepared by heating primary alcohols or aldehydes with excess acidified dichromate
solution.
H O O
R C R C
R C OH
H OH
H oleObject14 oleObject15

primary alcohol aldehyde carboxylic acid

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 BIOLOGICAL & ORGANIC CHEMISTRY

Ionisation of carboxylic acids in water

Carboxylic acids are weak acids that partially ionise in water to form hydronium and carboxylate ions.
RCOOH(s) or (l) + H2O +
oleObject16

oleObject17 oleObject18

Neutralisation of carboxylic acids

Carboxylic acids are neutralised by hydroxide ions, carbonate ions and hydrocarbonate (bicarbonate) ions.
These reactions are fast and exothermic.
Neutralisation by hydroxide ions
RCOOH(s) or (l) + → +

oleObject19 oleObject20 oleObject21

Neutralisation by carbonate ions

2RCOOH(s) or (l) + →2 + + CO2(g)

oleObject22 oleObject23 oleObject24

Neutralisation by hydrogencarbonate ions

RCOOH(s) or (l) + → + + CO2(g)

oleObject25 oleObject26 oleObject27

The carboxylate salts are ionic and soluble in water, especially if the cation is sodium or potassium.
The solubility of the carboxylate salts
The solubility of the carboxylate ion is due to the strong ion-dipole bond (note - new type of bond) that forms
between the negatively charged carboxylate ion and water molecules. This bond is stronger than the
hydrogen bonds that form between hydroxyl groups and water in carboxylic acids.

Drugs with carbonyl groups as part of their molecular structure

Two commonly used drugs are pain-relieving drugs are aspirin and ibuprofen. Both have carboxyl groups,
but because of their size they are insoluble in water. They normally contain sodium hydrogencarbonate and
when they are added to water, the carboxylic acid and the hydrogencarbonate react with each other to
produce the soluble carboxylate ion. In this form, the drug is easier to administer and faster acting.
O O

C O C OH CH3 O
CH3 CH CH2 CH2 C
CH3
OH

Aspirin (acetyl salicyclic acid) Ibuprofen

(4-isobutyl-α -methylphenylacetic acid)
Once in the stomach, where it is acidic, it is converted back to the carboxylic acid

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 BIOLOGICAL & ORGANIC CHEMISTRY

Subtopic 5.6: Amines

Key Ideas
Owing to the presence of an unbonded electron pair,
amines are able to act as bases and accept H+ ions.
Amines are classified as primary, secondary, or
tertiary.
The salts of amines are soluble in water because of the
ion–dipole attraction between the ions and water.
Intended Student Learning
Draw the protonated form of an amine, given its
structural formula.
Identify an amino group in an amine as primary,
secondary, or tertiary, given the structural
formula.
Explain why some drugs with amine groups are
usually taken in the form of their salts.

Amines
Amines are derivatives of ammonia where one or more of the hydrogens have been substituted with and
alkyl group. Depending on the number of replacements, they are classified as primary (for 1), secondary (for
2) and tertiary (for 3), although we mainly consider the primary amines.

ammonia primary amine secondary amine tertiary amine

All amines contain an unbonded pair of electrons on the nitrogen. Because of this, they can behave as bases
and accept a proton and become protonated amines.

Solubility of amine salts

The protonated amine salts are soluble in water because of the ion-dipole attraction between the ions and
water.

Many amine containing drugs are taken in the form of the salt, because they dissolve better and are therefore
more easily absorbed.

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 BIOLOGICAL & ORGANIC CHEMISTRY

procaine protonated form of procaine

Note that only the tertiary amine is protonated. The primary amine, because it is connected directly to the
benzene ring, is difficult to protonate.

Assignment 5.4, 5.5, 5.6 : Carboxylic Acids and Amines

1. (a) (i) What is a carboxylic acid?
(i) Give the name and structure for the acid containing four carbon atoms
(a) Draw the carboxylic acid functional group, and show how the bonds are polarised in this
group.
(b) Why are the carboxylic acids weak acids? Give an equation to illustrate that methanoic acid is
a weak acid.
(c) How can carboxylic acids be prepared? Give an example with equations.
(d) Write the equation for the reaction of a carboxylic acid with a solution of sodium bicarbonate.
(e) Solid carboxylic acids do not react with solid carbonates. Why?
2. (a) Why would you expect the compounds CH3COOH and C3H7COOH to have similar chemical properties?
(a) Give, with equations, the reactions of both these compounds with:
(i) Sodium bicarbonate solution
(ii) Sodium hydroxide solution
(iii) Ethanol with concentrated sulfuric acid under reflux
(b) How would you expect the physical properties (ie. MPt and solubilities in water) to differ?
2. Ethanoic acid, CH3COOH, forms a weak acid when added to water.
Some reactions of ethanoic acid are shown:

oleObject28

(a) Explain what is meant by a weak acid.

(b) Name the substance A that is added to ethanoic acid.
(c) Substance B is formed when ethanoic acid reacts with ethanol. What type of substance is B?
(d) Draw a structural formula for salt C.
(e) Write a balanced equation for the reaction between magnesium and ethanoic acid.

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 BIOLOGICAL & ORGANIC CHEMISTRY

3. (a) A series of compounds called ‘prostaglandins’ are produced in the bodies of people who suffer from
inflammatory diseases such as arthritis. An example of a prostaglandin is shown below:
O

COOH

OH

Draw the structure of the organic product obtained when samples of prostaglandin are treated
in the following ways:
(i) Warmed with acidified potassium dichromate.
(ii) Refluxed with methanol and a small amount of concentrated sulfuric acid.
(b) A more recent mining technique is to react the required ore with sulfuric acid using
underground pipes. The ‘dissolved’ ore is then pumped to the surface and treated. An
environmental concern with this method is that excess sulfuric acid may leak into water
supplies. To remove this acid the use of sulfate-reducing bacteria is being researched. One of
the reactions that then occurs is shown by the following equation:
2CH3CHOHCOOH(aq) + SO42-(aq) → 2CH3COOH(aq) + 2CO2(g) + H2S(g) + 2OH-(aq)
(i) Give a reason for the resulting increase in pH.
(ii) The equation above suggests that these bacteria are anaerobic decomposers. Give a
reason to support this statement.
4. The more complex the carboxylic acid the less soluble it is.
(a) Why is this?
However, many complex carboxylic acids are useful medicines. If they are not soluble they cannot be
absorbed into the body.
(b) How can these acids be made into the more useful soluble compounds?
(c) Using a diagram, explain how the increase in solubility occurs.
(d) Many analgesics (pain-relieving medicines) contain aspirin.
OH

C
O

O C CH3

O
Suggest a formula for ‘soluble aspirin’.
5. A plant known to the Chinese as Ma Huang provided them with a medicine which was described in
2760 BC as a valuable remedy for coughs and as a cardiac stimulant. The active ingredient of this
plant is ephedrine. In 1933 during an attempt to find a synthetic analogue to ephedrine the compound
amphetamine was found to have similar properties. Amphetamine was widely used as a nasal
decongestant but later it was used, and now dangerously abused by some, as a stimulant.
Ephedrine Amphetamine

OH H H H
CH3
C C N C C NH2
H
H CH3 H CH3

2-(methylamino)-1-phenylpropan-1-ol 1-phenylpropan-2-amine

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 BIOLOGICAL & ORGANIC CHEMISTRY

(a) Both react with acids, eg. HCl(aq). Write equations to show the protonated form of these
compounds.
(b) Comment on their solubility both before and after protonation.
6. The relative basicities of some nitrogen-containing compounds are as follows:
NH3>C2H5NH2>C6H5NH2
(a) Explain why these compounds behave as bases.
(b) Explain the variation in basicity.
7. Adrenalin is a hormone which raises blood pressure, increases the depth of breathing and delays
fatigue in muscles, thus allowing people to show great strength under stress.
Benzedrine is a pharmaceutical that stimulates the central nervous system in a similar manner to
adrenalin.
Benzedrine Adrenalin
HO
H H H H
H
C C NH2 HO C C N
CH3
H CH3 OH H

1-phenylpropan-2-amine 4-(1-hydroxy-2-
(methylamino)ethyl)benzene-1,2-diol

(a) Suggest why adrenalin is more soluble in water than is Benzedrine.

(b) Give the structural formulae of the organic products obtained when Benzedrine reacts with an
aqueous acid such as dilute hydrochloric acid.
8. Consider the chemistry of love. The chemicals providing a romantic high are phenylethylamine (lots
found in chocolate), dopamine and norepinephrine. The release of these is triggered by genetics,
psychological experiences and even smells. These chemicals are related to epinephrine (also called
adrenalin) which is secreted by the adrenal gland in times of stress.
Circle and name all of the functional groups in these molecules.

Dopamine Phenylethylamine
HO
H H H H
H H
HO C C N C C N
H H
H H H H
4-(2-aminoethyl)benzene-1,2-diol 2-phenylethanamine
Adrenalin
Norepinephrine HO
HO
H H
OH H H
H
HO C C N
HO C C N
CH3
H OH H
H H
4-(1-hydroxy-2-
4-(2-amino-1-hydroxyethyl)benzene-1,2-diol
(methylamino)ethyl)benzene-1,2-diol

Subtopic 5.7: Esters

Key Ideas
An ester can be produced by a condensation reaction
between an alcohol and a carboxylic acid.
The production of an ester from the reaction of an
alcohol and a carboxylic acid is slow at 25°C.
Esters may be hydrolysed under acidic or alkaline
Intended Student Learning
Draw the structural formula of the ester that
could be produced by the condensation reaction
between an alcohol and a carboxylic acid, given
their structural formulae, and write an equation
for the reaction.
Explain the use of heating under reflux and the
presence of a trace of concentrated sulfuric acid
in the laboratory production of esters.
Identify the products of hydrolysis of an ester,

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 BIOLOGICAL & ORGANIC CHEMISTRY

Key Ideas Intended Student Learning

conditions. given its structural formula.

Esters
Esters contain the ester functional group

Commonly occurring esters include fragrances of flowers and fruits (with short carbon chains) and fats and
oils (with long carbon chains).

Preparation of esters
An ester is prepared by reacting, under reflux, an alcohol with a carboxylic acid in the presence of
concentrated sulfuric acid as a catalyst. These reactions are called esterifications. Water is the other product
and so it is also called a condensation reaction.
H H H
H H O H H O
H C C C + HO C C C H H C C C + H 2O
H H OH H H O C3 H 7
H H H
oleObject29

Propanoic acid propan-1-ol propylpropanoate

These reactions are slow and so an extended period of heating is required to achieve a satisfactory yield.
Reflux is a process by which a mixture of reactants is boiled for a prescribed period of time. The reactant and
product vapours pass into a condenser where they are condensed to liquid drops that then fall back into the
reaction mixture. The reflux process allows extended heating (to speed up the reaction) of the reaction
mixture without loss of volatile reactants and products by evaporation.

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 BIOLOGICAL & ORGANIC CHEMISTRY

The reactions are slow and reversible and so an equilibrium is established. It is pushed to the reactant side,
by using excess alcohol.
Hydrolysis of esters
Esters undergo hydrolysis when refluxed with aqueous acid or base. Hydrolysis can be considered to be the
reverse of esterification – water is consumed as a reactant during hydrolysis.
In acidic conditions, the products of the hydrolysis are a carboxylic acid and an alcohol. The acid is acting as
a catalyst. Because the reaction is slow, the mixture is heated under reflux.
O O
R C + H2O R C + R’- OH
O R' oleObject30
O H

In basic conditions, such as with sodium hydroxide solution, the products of hydrolysis are a carboxylate salt
and an alcohol. Refluxing is necessary to bring about a reaction at a reasonable rate.
O O
R C + OH -
→ R C + R’- OH
O R' O-
Note the formation of water soluble carboxylate salts under alkaline conditions.To convert this salt to a
carboxylic acid a solution of a strong acid such as hydrochloric acid is needed.
SUBTOPIC 5.8: AMIDES
Key Ideas Intended Student Learning
An amide can be produced by a condensation reaction Draw the structural formula of the amide that
between an amine and a carboxylic acid. could be produced by the condensation reaction
between an amine and a carboxylic acid, given
their structural formulae.
Amides may be hydrolysed under acidic or alkaline Identify the products of hydrolysis of an amide,
conditions. given its structural formula.

Amides
Amides have the following functional group

While small amides are not very common in nature, larger ones in polymetric forms are in proteins.

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 BIOLOGICAL & ORGANIC CHEMISTRY

Some simple amides of commercial importance:

Propenamide (polymer manufacture) Glutamine (infusion solution)

Caprolactum (polymer manufacture) Tick repellant

Preparation of amides
Theoretcially amides can be prepared from a condensation reaction between ammonia or an amine with a
carboxylic acid:

In practice, when a carboxylic acid is reacted with ammonia or an amine, an acid base reaction occurs
forming carboxylate and ammonium ions.

It usually requires refluxing to produce an amide.

Hydrolysis of amides
Amides are much more difficult than esters to hydrolyse and require extended refluxing.
Alkaline hydrolysis
Alkaline hydrolysis, with concentrated sodium hydroxide solution produces ammonia (or and amine) and a
carboxylate salt.

Acid hydrolysis
Acid hydroysis, with concentrated hydrochloric acid, produces an ammonium (or protonated amine) ion and
a carboxylic acid.

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 BIOLOGICAL & ORGANIC CHEMISTRY

Assignment 5.7, 5.8 : Esters and Amides

1. Here are some ester fragrances:
ethyl methanoate - raspberries
3-methylbutyl ethanoate – pears
ethyl 2-methylbutanoate - apples
(a) Write the names of the alcohols and acids from which they are derived.
(b) Draw structures for these alcohols, acids and esters.
(c) How are 3-methylbutyl ethanoate and ethyl 2-methylbutanoate related?
2. Ethanol and acetic acid were heated with a little concentrated sulfuric acid in the flask of the
apparatus shown:
(a) Name the organic product expected from the reaction.
(b) Write the equation for the reaction.
(c) State the function of the sulfuric acid.
(d) Explain why the condenser is used as shown in the diagram.
(e) Explain why the reactants must be heated for some time to
obtain a satisfactory yield of product.
3. (a) Name the following compounds
(i) O (ii) O

H C O CH2CH3 H3C(H2C)3 C O CH3

(a) Describe the expected odour of ethyl butanoate.

(b) Write an equation for its preparation.
(c) What is the catalyst used?
(d) Compare the water solubility of the reactants with that of ethyl butanoate and hence explain
which components of the reaction mixture are mainly in the ‘organic’layer and which are
mainly in the aqueous layer, when isolating the ester from the reactions in the separating
funnel.
4. Consider the instructions below (1 – 9) and then answer the questions.
AIM : To hydrolyse the ester, ethyl benzoate, under alkaline conditions, and test product
qualitatively.
INSTRUCTIONS.
1.Place about 5 mL of ethyl benzoate, 1rg of pumice (or boiling chips) and 25 mL of 10% sodium
hydroxide solution (bench strength) in a flask and reflux for 30 – 40 minutes.
2.Set the condensor for distillation and collect 5 – 10 mL of distillate. Allow the residue to cool.
3.Add fused CaCl2 to the distillate – enough to cover the bottom of the container. Leave for 5 minutes and
then
4.Test some of the liquid with acidified dichromate solution (warm). Note colour changes.
5.Test some for flammability. (A drop on a spatula in the Bunsen flame should ignite)
6.If time permits, determine the boiling point.
7.Acidify the cooled residue with concentrated sulfuric acid (CARE)
8.If time permits, filter, wash and dry the acidified residue.
9.Determine its melting point.
(a) Write a balanced equation for the reaction.
(b) Explain what reflux is and why it is necessary.

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 BIOLOGICAL & ORGANIC CHEMISTRY

(c) Explain the purpose of the distillation.

(d) Explain the purpose of the fused calcium chloride.
(e) Explain the colour changes with the help of an annotated equation.
(f) Write an equation for the combustion.
(g) Write an equation for the acidification step. Explain why the residue does not distill.
(h) Explain why filtration of the acidified product is possible.
5. Ethyl ethanoate is an example of an ester.
(a) State three important commercial uses of esters.
(b) Fats and vegetable oils contain naturally occurring esters. Give the general formula of these
esters and explain why they are important commercially.
(c) Describe, giving outline practical details, reaction conditions and equations, how you could
produce a sample of ethyl ethanoate using ethanol as the only organic starting material.
(d) Esters may be hydrolysed by warming them with dilute aqueous acid or base. There are two
possible bonds that could be broken in the ester as shown in the diagram below.
O
Y
R C

X O R'

To identify which bond, (X) or (Y), is broken in the reaction, water enriched with oxygen-18,
H218O, is used. After hydrolysis the oxygen-18 appears in the ethanoic acid and not in the
ethanol.
O O
+ 18
H2 O C2H5 OH +
C2H5 O C CH3 H 18O C CH3
oleObject31

(i) Use this information to identify which ester bond is broken during hydrolysis of the ester.
(ii) Suggest why it is this bond that is broken in preference to any other bond.
6. (a) Write a structural formula for the amide functional group.
(a) Complete the following equation:
H O
(i) + →
R N H HO C R'

(i) Why is this called a condensation reaction?

(a) Write the structural formula for ethanamide and identify the type of amide.
2. The C-N bonds in amides can be broken by hydrolysis.
(a) What is hydrolysis?
(b) This reaction requires reflux of the amide with either aqueous acid or alkali.
Complete these reactions with the appropriate structural formulae.
O
(i)
H3C C NH2
oleObject32

O
(ii)
C2H5 C NHCH3 oleObject33

O
(iii)
H3C C NHC2H5 oleObject34

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 BIOLOGICAL & ORGANIC CHEMISTRY

3. Nutrasweet, or aspartame, was discovered by accident in 1965. The patent expired in 1987 and sales
world wide are now worth millions. It is 200 times sweeter than sucrose (cane sugar) so can be used
in small quantities. It is hydrolysed in water or in the body.
Using structural formulae, complete this equation:

O CH2

H2 N + H 2O →
C CH
O
CH NH
C CH3
HO
CH2
O
C

O
Aspartame
Subtopic 5.9: Proteins
Key Ideas
Amino acids contain a carboxyl group and an amino
group.
Amino acids can self-ionise to produce an ion.
Proteins are large molecules in which amide groups
link monomer units.
Proteins are polyamides consisting of covalently
bonded long chains of amino acid units.
In proteins the amide group is called a ‘peptide link’ or
‘peptide bond’.
Proteins have sites that allow hydrogen bonding
between sections of chains and between the chain and
water.
The biological function of a protein is a consequence
of its unique spatial arrangement.
Changes in pH and temperature disrupt the secondary
interactions, and hence the spatial arrangements, of a
protein chain.
Intended Student Learning
Determine whether or not a compound is an
amino acid, given its structural formula.
Draw the structural formula of the product
formed when an amino acid self-ionises.
Identify the amide group and the repeating unit
and deduce the structural formula(e) of the
monomer(s), given the structural formula of a
section of a polyamide.
Write the general formula of amino acids and
recognise their structural formulae.
Identify the amide groups in a protein.
Identify where hydrogen bonding can occur
between protein chains or between the chain and
water, given the structural formula of a section
of the chain.
Explain why the biological function of a protein
(e.g. an enzyme) is altered if its spatial
arrangement is altered.
Explain why proteins are sensitive to changes in
pH and temperature.

Amino acids
Amino acids are the building blocks of proteins. They consist of small molecules with at least one amine
functional group and one carboxyl functional group, a ‘R’ group. They have a central carbon that is bonded
to:
• One hydrogen atom;
• One amine functional group;
• One carboxyl functional group;
• One other atom or group of atoms as R.

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 BIOLOGICAL & ORGANIC CHEMISTRY

Some examples of R groups

R
group

amino aspartic
glycine valine tyrosine
acid acid
Zwitterions
In a neutral environment, amino acids undergo self-ionisation whereby a proton is transferred from the
carboxyl group to the amine group in the same molecule. The product of this self ionisation is a dipolar ion,
called a zwitterion. Note it has no net charge.

H H O H H O

N C C O H H N+ C C O-

H R H R

Interesting point - The word zwitter in German means hermaphrodite.

Proteins
While condensation reactions involving carboxylic acids and amines is difficult to achieve in the laboratory,
condensation reactions between the carboxyl group from one amino acid can undergo a condensation
reaction with an amine group from another amino acid with the aid of specific enzymes. The product of such
a condensation is a dipeptide. The amide group that forms is called a peptide link. In the example below,
there are two possibilities. (note water is also formed)

The continuation of this type of condensation process involving more amino acid molecules leads to the
formation of along chain molecule called a polypeptide with many peptide links. These polypeptides are
proteins that have the following general structural formula:

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 BIOLOGICAL & ORGANIC CHEMISTRY

Hydrogen bonding within the protein chains

The peptide links within protein chains are polar. Hydrogen bonding between these links can occur both
within a protein chain and between protein chains as shown in the diagrams below.

The polar peptide links in protein chains can also from hydrogen bonds with water molecules.

This hydrogen bonding can explain the amount of water in proteins like muscle tissue (eg moisture of fresh
meat) and the ability of natural protein fibres like wood and silk to absorb water.

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 BIOLOGICAL & ORGANIC CHEMISTRY

The structure and function of proteins

The structure of a protein and its biological function are inextricably linked. A protein enzyme has a
structure that is compatible with the molecular structure of the substance that is undergoing an enzyme-
catalysed conversion. Thus specific proteins can only do certain conversions.
The structure of proteins is described at four levels.
Primary structure is the sequence in which the amino acids are linked together by peptide bonds to form the
polypeptide chain. eg DNA
Secondary structure refers to the shape that that the polypeptide chain folds or twists into. One example is
the α - helix shown below. The chains are held in these configurations by hydrogen bonds between peptides
groups. In this case the amino groups are pointing up and the carbonyls down and the hydrogen bonding
between them holds them together.

Tertiary structure refers to the folding of the structure onto itself. This structure is stabilised by different
types of bonding between different R groups along the coils.

Quaternary structure Some protein consist of a number of polypeptide chains packed together. Quaternary
structure refers to the 3-D arrangement in which chains pack together. It is mainly dispersion forces that hold
these together.
Denaturation of proteins
If the normal secondary, tertiary or quaternary structure of a protein is altered, it loses its capacity to perform
biological functions. The protein is said to be denatured.
Structural changes are commonly cause by changes in the temperature or pH of the environment of the
protein. These changes can break the secondary bonds holding these structures in their normal shapes. eg
setting of egg white or curdling of milk
Effect of pH
Changes in pH have the greatest effect in ionic bonding between –NH3+ and –COO- side groups. Increasing
the pH (with concentrated NaOH) converts the –NH3+ to molecular –NH2 and decreasing the pH (with

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 BIOLOGICAL & ORGANIC CHEMISTRY

concentrated H2SO4) concerts the –COO- to the molecular –COOH. Thus ionic bonds cannot form and the
structure is destabilised.
Effect of heat
Raising the temperature of a protein to above about 50°C is sufficient to break secondary bonds - dispersion
and hydrogen bonds. The protein structure then unravels as in the diagram below.

ASSIGNMENT 5.9: Proteins

1. The general structure of an α -amino acid is:
R

H2N CH COOH

Write equations for the following reactions:

(a) alanine (R = CH3) with hydrochloric acid.
(b) serine (R = CH2OH) with sodium hydroxide solution.
(c) lysine (R = (CH2)4NH2) with hydrochloric acid
(d) aspartic acid (R = CH2COOH) with sodium hydroxide solution.
(e) when alanine self ionises.
1. Amino acids are examples of bifunctional compounds, compounds with two functional groups. In
alanine
CH3

H2N C COOH

(a) Circle and name the two functional groups present.

(b) Which group is the proton donor?
(c) Which group is the proton acceptor?
(d) Draw the zwitterion that forms from alanine.
1. Supply the missing words in this paragraph.
When amino acids combine to form a protein like insulin the __________ group from one amino acid
joins into the _________ group on the next, and a molecule of __________ is lost from between them.

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 BIOLOGICAL & ORGANIC CHEMISTRY

This process is called ______ and the –CONH- group which links the amino acid residues in the
protein is called the __________ link.
2. Two amino acids joined by the –CONH – group make a dipeptide.
Use these structures to show the formulation of a dipeptide.
R R' OH
OH H
H2C C N CH C
O H O

3. Look at the structure of the polymer shown below:

O H O H O

(CH2)5 C N (CH2)5 C N (CH2)5 C

(a) Redraw it to show the repeating unit.

(b) Draw the structures of the monomers used to make the polymers above.
1. Proteins are polymers made up of amino acids.
(a) Write the general formula of an amino acid.
(b) The structure of a protein molecule is shown below.
O O

NH CH C NH CH C NH CH

CH2 CH2 CH2

OH OH OH

(i) Draw the structure of the peptide group.

(ii) Describe the type of bonding that is likely to occur between two of these protein
molecules.
(iii) Draw a sketch to show how they are attracted to each other.
1. Amino acids are components of proteins. Draw diagrams to show the two dipeptides that may be
formed between the amino acid glycine, H2NCH2CO2H, and alanine, H2NCH(CH3)CO2H.
2. Phenylketonuria (PKU) is a potentially lethal inherited disease. Babies suffering from PKU lack the
ability to break down the surplus phenylalanine that is present in their diet. Excess phenylalanine is
toxic and causes mental retardation. Its structural formula is given below:
H H

C C COOH

H NH2

(a) (i)Draw the structural formula of the zwitterion present in an aqueous solution of phenylalanine.
(i) Explain why the addition of small quantities of acid or alkali to an aqueous solution of
phenylalanine causes little change to the pH of the solution.
(a) Another amino acid, alanine, has the following structural formula:
CH3

H2N CH COOH

(i) Draw structural formulae for the two different dipeptides which can be formed when
phenylalanine and alanine join to each other.
(ii) On your formulae, draw a circle around the peptide link.
(iii) What reagent and conditions are usually used in the lab to break the peptide link?

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 BIOLOGICAL & ORGANIC CHEMISTRY

1. Explain why the biological function of a protein is altered if its special arrangement is altered.
2. Why do proteins often not work properly if there is a change in:
(a) Temperature
(b) pH
1. Proteins are made up of amino acid units joined together. The structural formula of a fragment of a
plant protein made up of three different amino acid units is shown below:

S
P
H 2C H O CH3 H O

CH N C CH N C CH2
N C CH2 N C CH N C

H O H O CH2 H O

S Q

O H CH3 O H H2C O H

HC N CH C N CH C N
CH C N CH2 C N CH2

CH2 O H O H

(a) Circle and label an amide group in the protein fragment shown above.
(b) The unit P is derived from the amino acid alanine. Draw the structural formula of alanine.
(c) The two protein strands shown are cross linked by two different types of bonds in two different
ways: by a disulfide link and by a hydrogen bond. On the structure above:
(i) Indicate the polarity of the hydrogen bond by using delta notation.
(ii) Indicate another hydrogen bond by using the same notation.
(iii) Circle the disulfide link and name the type of bond between the sulfur atoms.
(d) The amino acids represented by the units P and Q could bond together to from a polymer.
(e) Draw the structural formula of the resulting polymer, using two units each of P and Q
alternating along the chain.
(f) Write the formula for the small molecule that will be released when the amino acids condense
to form the polymer.

Subtopic 5.10: Triglycerides

Key Ideas Intended Student Learning
Edible oils and fats are esters of propan-1,2,3-triol Draw the structural formula of an edible oil or
(glycerol) and various carboxylic acids. The carboxylic fat, given the structural formula(e) of the
acids are unbranched and usually contain an even carboxylic acid(s) from which it is derived.
number of carbon atoms between twelve and twenty.
Triglycerides can be hydrolysed to produce propan- Identify the alcohol and the acid(s) from which a
1,2,3-triol and various carboxylic acids. triglyceride is derived, given its structural
formula.
Edible oils are liquids at 25°C and are commonly Identify the most likely source of a triglyceride,
obtained from plants and fish. Edible fats are solids at given its state at 25°C.
25°C and are commonly obtained from land animals.

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Key Ideas Intended Student Learning

Most liquid triglycerides contain a larger proportion of
unsaturated carbon chains than solid triglycerides
contain.
Liquid triglycerides can be converted into triglycerides
of higher melting-point by a process that involves the
addition of hydrogen, under pressure, at increased
temperature, and in the presence of a catalyst.
Describe the use of a solution of bromine or
iodine to determine the degree of unsaturation of
a triglyceride.
Explain the role of pressure, temperature, and a
catalyst in the hydrogenation of liquid
triglycerides.

Triglycerides
Triglycerides are edible fats and oils derived from plants and animals. They are esters of propan-1,2,3-triol
(glycerol) and various carboxylic acids. The general structural formula of a trigylceride is as follows:

These carboxylic acids are often referred to as fatty acids. Almost without exception they contain an even
number of carbon atoms (commonly from 12 to 22) In the carbon chain, including the carbon atom of the
carboxyl group. The chains are both saturated and unsaturated. If more than one C = C bond is present in the
carbon chain, it is described as polyunsaturated.
The structural formulae of some of the more common fatty acids are given in the table below. It should be
noted that these structural formulae are usually written in condensed form as in the following examples:
CH3CHCH2CH2CH2CH2CH2CH2CH2CH2CH2COOH is written as CH3(CH2)10COOH
CH3CH2CH2CH2CH2CH2CH = CHCH2CH2CH2CH2CH2CH2CH2COOH
is written as CH3(CH2)5CH = CH(CH2)7COOH
Fatty acid
common name systematic name
structural formula
(…… acid) (…….. acid)
lauric dodecanoic CH3(CH2)10COOH
palmitic hexadecanoic CH3(CH2)14COOH
stearic octadecanoic CH3(CH2)16COOH
palmitoleic hexadec-9-enoic CH3(CH2)5CH = CH(CH2)7COOH
oleic octadec-9-enoic CH3(CH2)7CH = CH(CH2)7COOH
linoleic octadec-9,12-dienoic CH3(CH2)4CH = CHCH2CH = CH(CH2)7COOH
Naturally occurring triesters of propane–1,2,3–triol nearly always have three different fatty acids forming the
ester linkages as shown In the following example in which linoleic, stearic and oleic acids have formed ester
links with the propane–1,2,3–triol:

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Hydrolysis of triglycerides
Fats and oils are highly concentrated stores of energy. The first stage in the use of fats as an energy source is
the hydrolysis of the triglyceride molecules catalysed by enzymes called lipases. The products of the
hydrolysis of each fat molecule are one molecule of glycerol and three fatty acid molecules as shown by the
following general equation:

Without the aid of these lipases, extreme conditions are needed to perform this hydrolysis. This usually
involves extended heating with concentrated acids or alkalis.
Edible fats and oils
Edible oils are liquids at 25°C and are commonly obtained from plants and fish. Edible fats are solids at
25°C and are commonly obtained from land animals. Some examples are shown below:
fat or oil mol % of saturated mol % of unsaturated
fatty acids fatty acids
beef fat 55 45
pig fat 45 55
corn (maize) oil 15 85
olive oil 15 85
cod liver oil 20 80
coconut oil 95 5
Note - melting point:
• Increases with chain length
• Decrease as the degree of unsaturation increases. This is due to the less ordered structure of the
unsaturated chains which cannot then pack together as closely, weakening the dispersion forces.

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The ordered and compact structure of a The disordered and loose structure of an
saturated triglyceride unsaturated trigyceride
Determining the degree of unsaturation of a triglyceride
Alkanes which contain the C=C group can undergo addition reactions with diatomic molecules like the
halogens and hydrogen. The general reaction can be represented as:

Fats and oils which contain unsaturated groups will also undergo these addition reactions if mixed with a
solution containing bromine or iodine in a saturated hydrocarbon solvent such as cyclohexane. The colour of
the solution disappears as the products of the addition reaction are colourless.
The degree of saturation can be be determined by measuring the volume of bromine solution required to
react with a solution of a fat or oil in cyclohexane eg by titration.
Hydrogenation of fats
Liquid oils can be converted to solid fats by a process called hydrogenation – the process of adding hydrogen
across a C=C bond. To do this a vegetable oil is heated with hydrogen under pressure in the presence of a
nickel catalyst. Sufficient hydrogen is added to form a product that is a solid at room temperature, but still
retain a degree of unsaturation.

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Subtopic 5.11: Carbohydrates

Key Ideas
Carbohydrates are naturally occurring sugars and their
polymers. They usually have the general formula
CxH2yOy. They are defined more precisely as either
polyhydroxy aldehydes or polyhydroxy ketones, or
their polymers.
Carbohydrates can be classified as monosaccharides,
disaccharides, or polysaccharides.
Polysaccharides are produced by the condensation of
many monosaccharide units linked in chains by
covalent bonds.
Glucose molecules can occur in either a chain form or
a ring form. There is equilibrium between the two
structures. In the chain form an aldehyde group is
present.
Many simple carbohydrates are soluble in water
whereas polysaccharides are insoluble in water.
Intended Student Learning
Determine, given its structural formula, the
molecular formula of an organic compound, and
whether or not it is a carbohydrate.
Write molecular formulae for glucose, and
disaccharides and polysaccharides based on
glucose monomers.
Identify the repeating unit and draw the
structural formula of the monomer, given the
structural formula of a section of a
polysaccharide derived from one monomer.
Explain the ability of glucose to react as an
aldehyde when in chain form but not when in
ring form.
Explain the differences in solubility in water of
simple carbohydrates and polysaccharides in
terms of the size of the molecules and the
number of hydroxyl groups.

Carbohydrates
Carbohydrates are naturally occurring sugars and their polymers. They usually have the general formula
Cx(H2O)y where x is often equal to y, and can be considered hydrates of carbon. They are defined more
precisely as either polyhydroxy aldehydes or polyhydroxy ketones, or their polymers. They are also
classified as monosaccharides, disaccharides and polysaccharides depending on the number of simple sugar
units that comprise the molecular structure.
Monosaccharides
These are the monomers from which all disaccharide and polysaccharide molecules are constructed. The
following generalisations can be applied to monosaccharides:
• their general formula is CXH2XOX with x having values from 3 to 8;
• they are water-soluble compounds (they have a low ratio of carbon to hydroxyl groups - almost 1:1);
• they have the name ending …ose. For example, glucose and fructose.
• they are sweet to taste and are often called simple sugars;
• structurally the molecules of six carbon polyhydroxyketones and five and six carbon
polyhydroxyaldehydes can exist in chain or cyclic (ring) form. The two forms exist in equilibrium with
each other. In aqueous solution the equilibrium lies very much in favour of the cyclic form.
• they are solids at room temperature (extensive hydrogen bonding).
Name and molecular
Chain structure Cyclic structure
formula

Glyceraldehyde
N/A
C3H6O3

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Erythose
N/A
C4H8O4

Ribose
C5H10O5

Ribulose
N/A
C5H10O5

Glucose
C6H12O6

Fructose
C6H12O6

Disaccharides
These are water-soluble carbohydrates, with two monosaccharide units per molecule. A disaccharide
molecule is formed by a condensation reaction of two monosaccharide molecules with the elimination of a
water molecule. Hydrolysis of disaccharides reverses the formation process to produce monosaccharides. In
nature, these condensation and hydrolysis reactions are catalysed by enzymes.
There are several disaccharides comprised of glucose monomers. They differ in the positions in which the
glucose units are linked and in the relative positions of H atoms and OH groups in the ring structures. Most
of them only occur as hydrolysis products of polysaccharides. Maltose is an example of a disaccharide.

Polysaccharides
These are insoluble in water (due to their very large molecular size) but do absorb water and are virtually
tasteless. They are formed by successive condensation reactions of monosaccharides. Partial hydrolysis
produces di- and tri-saccharides. Complete hydrolysis of a polysaccharide produces monosaccharides such as
glucose. Four of the most common and biologically most important polysaccharides are all composed of
glucose units. They are:
• cellulose - the main structural material of plants;
• glycogen - the main storage polysaccharide in animals;
• amylose - one of the two polysaccharides that make up starch;
• amylopectin - the other polysaccharide that makes up starch.

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Cellulose and amylose are straight chain polysaccharides whereas glycogen and amylopectin are branched
chain polymers.
Cellulose
On average, each cellulose molecule is made up of about 3,000 glucose units linked as shown below.

Glucose as a reducing agent

Glucose exists in both chain and cyclic forms, which in aqueous solution are in equilibrium. The aldehyde
functional group that is present in the chain form can be oxidised by Tollen's Reagent. The silver ion in the
Tollen's Reagent is reduced to silver metal in the form of a mirror, while at the same time the aldehyde group
is oxidised to a carboxylate group. There is no aldehyde group present in the cyclic form and consequently
this form does not react with Tollen's Reagent. However, consumption of the chain form by Tollen's Reagent
upsets the chain - cyclic equilibrium driving it towards the formation of more of the chain form (Le
Chatelier's Principle).

The interaction of carbohydrates with water

Carbohydrate molecules can undergo extensive hydrogen bonding with polar water molecules because of the
presence of hydroxyl groups as part of their molecular structure. However, only the mono- and di-
saccharides have molecules small enough in size to actually mix with the water molecules to form aqueous
solutions.

Assignment 5.10 & 5.11 : Triglycerides and Carbohydrates

1. (a) What structural feature of a molecule identifies a compound as an ester?
(a) Write down the full structural formula of the triester made from glycerol and ethanoic acid.
(a) Give an equation to show what happens when this ester is heated with sodium hydroxide
solution.
1. Below is the structure of a triester present in a naturally occurring substance.
O

H2C O C (CH2)7CH CH(CH2)7CH3

O

HC O C (CH2)7CH CHCH2CH CH(CH2)4CH3

O

H2C O C (CH2)7CH CH(CH2)7CH3

(a) What is the name given to this tiester and similar triesters?
(b) Is this triester likely to be a fat or an oil? Give reasons for your answer.
(c) The triester was hydrolysed by heating with sodium hydroxide solution, and the resulting
solution was neutralised by addition of hydrochloric acid.
(i) Draw structural formulae for the hydrolysis products formed. Use short form as above.
(ii) Name the alcohol formed.

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(d) How many moles of each product would be obtained from one mole of the triester?
1. Explain the difference between the following terms, which often appear on food labels.
(a) Saturated fat
(b) Monounsaturated fat
(c) Polyunsaturated fat
1. Animal fat is made up almost entirely of saturated fats. One compound present in sheep fat produces
only glycerol and stearic acid, CH3(CH2)16COOH, on hydrolysis. Draw out the structural formula of
this compound. (use the short form as in question 2)
2. A food company buys a vegetable oil and converts it to margarine by treatment with hydrogen in the
presence of a metal catalyst. During the process some of the double bonds in the oil are
hydrogenated.
(a) Name a suitable catalyst and give conditions under which the hydrogenation could be carried
out.
(b) Assume that the oil contains only the triester shown in question 2. 1 tonne (1,000 kg) of the oil
requires 4.90 kg of hydrogen to make margarine. What percentage of the double bonds in the
oil have been hydrogenated?
1. The ester spermaceti is a soft wax that in the past was obtained from the head of the sperm whale. It is
used in skin lotions and has the following formula:
O

C15H31 C O C10H22

Write the formula of the carboxylic acid and the alcohol from which spermaceti can be prepared.
2. Oleic acid is an unsaturated carboxylic acid obtained from the hydrolysis of soya bean oil. The
structure of oleic acid is shown below:
CH3(CH2)7CH=CH(CH2)2COOH
(a) Write the structural formula of a triglyceride that would give oleic acid on hydrolysis.
(b) When heated, liquid oils may be converted into solid fats, as shown below:

OIL + A FAT
oleObject36

Identify the required reagent A, the substance B and the condition C necessary for the
conversion to occur.
1. Trehalose, aspartame, and cyclamate are three substances used as sweeteners.
Trehalose Aspartame cyclomate
O
HOH2C O O CH2OH
C C C C
H H H H
H H H H
C H C C H C
HO C OH HO C OH
O CH2 NH
OH OH
H2N
C CH SO3H
O
CH NH
C CH3
HO
CH2
O
C

(a) Which one is the carbohydrate and why?

(b) Write down the molecular formula of this carbohydrate.
(c) State the conditions needed to convert the carbohydrate to ethanol.

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(d) Glucose burns in air above 500°C. Explain how it is possible for living organisms to carry out
this reaction swiftly and efficiently at 37°C.
(e) Write the equation for the conversion of the carbohydrate, glucose, to ethanol.
1. Sucrose is a natural sweetener derived from sugar cane. The structure of sucrose is shown below:
O CH2OH
HOH2C O O CH2OH
C C C C
H H H
C H C C C
HO C OH HO H H OH
H H
OH

Sugars may be classified as monosaccharides, disaccharides, or polysaccharides.

(a) State the type of saccharide that sucrose belongs to.
(b) A crushed sample of sucrose is warmed with ammoniacal silver nitrate solution. State the
observation you would expect. Give a reason for your answer.
(c) Sucrose can be hydrolysed to produce a mixture of fructose (F) and Glucose (G). The structure
of F and G are shown in open-chain forms below:

F G
(d) State the saccharide classification to which both fructose and glucose belong.
(e) The mixture of F and G is warmed with ammoniacal silver nitrate solution. State the
observation you would expect and name the functional group responsible for it.
1. Sucrose, C12H22O11, is so soluble in water that a saturated solution at room temperature is only one
third solvent by weight. The solubility of sucrose in several solvents at 20oC is given.
Solvent Solubility of sucrose
Water 1 g/0.5 mL water
Methanol 1 g/100 mL methanol
Ethanol 1 g/170 mL ethanol
Petrol insoluble
Explain these differences in solubility.
2. Glucose exists in equilibrium between a cyclic form and an open chain form shown below:

(a) Name the functional groups present in open form.

(b) (i)What would you observe if a sample of the above mixture was shaken and warmed with some
Tollen’s reagent?
(i) What type of reaction has the glucose undergone?
(i) Describe the changes to the above equilibrium resulting from the addition of Tollen’s
reagent.

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1. The structural formulae of glucose and fructose are shown below:

(a) (i) Circle and name the functional groups in the two structures above.
(i) Write down the molecular formula for both these sugars.
(i) Explain the high solubility of glucose in water.
(b) Glucose units can chemically bond together to form long chain molecules. Give two examples.
(c) Glucose, which is found in fruit and honey, is the most abundant sugar found in nature. Why do
athletes consume glucose, rather than other sugars, as a source of ‘instant’ energy? Support
your answer with a chemical equation.
(d) What would you observe if glucose was treated with:
(i) acidified dichromate ions?
(ii) ammoniacal silver nitrate solution?
(e) Can fructose undergo the two reactions in d) above? Explain.
(f) (i)Draw the structure of the compound formed when fructose is treated with some acetic acid, in the
presence of a few drops of concentrated sulfuric acid.
(i) Name the new functional group produced.
(i) What name is given to the reaction?
(ii) What is the function of the concentrated sulfuric acid?

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