H2 A-level Chemistry

Organic Nitrogen Compounds

Amino Acids and Proteins (H2 ONLY)

LECTURE OUTLINE
A) Amino acids
1) What are amino acids?
2) Types of amino acids
3) Acid-base nature of amino acids
4) Physical properties of amino acids

B) Polypeptides
1) What are polypeptides?
2) Properties of peptide bond/amide bond

C) Proteins
1) What are proteins?
2) Functions of proteins in the body
3) Digestion of proteins (hydrolysis)
4) Protein structures
5) Destruction of protein structures what is denaturation of proteins?
6) Factors that cause denaturation of proteins

REFERENCES
1) Introduction to Organic Chemistry by GI Brown
2) Principles of Organic Chemistry by Peter RS Murray
3) Organic Chemistry by Morrison and Boyd
4) Organic Chemistry by TW Graham Solomons

SYLLABUS
Amino acids (exemplified by aminoethanoic acid)
(i) Their acid and base properties
(ii) Zwitterion formation

Proteins
(i) Protein structure: primary; secondary; tertiary; quaternary structures
(ii) The hydrolysis of proteins
(iii) Denaturation of proteins

Learning Outcomes
Candidates should be able to:
1
2
3
4
5

6
7

8
9
10

describe the acid-base properties of amino acids and the formation of zwitterions
describe the formation of peptide (amide) bonds between amino acids and, hence, explain protein formation

list the major functions of proteins in the body & describe the hydrolysis of proteins
explain the term primary structure of proteins
recognise that the twenty amino acids that make up all the proteins in the body are -amino acids with the
general formula RCH(NH2)CO2H, and be able to interpret the properties of -amino acids in terms of the
nature of the R group
describe the secondary structure of proteins: -helix and -pleated sheet and the stabilisation of these
structures by hydrogen bonding
state the importance of the tertiary protein structure and explain the stabilisation of the tertiary structure with
regard to the R groups in the amino acid residues (ionic linkages, disulfide bridges, hydrogen bonds and van
der Waals forces, i.e. induced dipole-induced dipole attractions)
describe the quaternary structure of proteins & the protein components of haemoglobin
explain denaturation of proteins by heavy metal ions, extremes of temperature and pH changes
apply the knowledge of the loss and formation of secondary and tertiary structures to interpret common
everyday phenomena

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H2 A-level Chemistry

Organic Nitrogen Compounds

A) AMINO ACIDS
1. WHAT ARE AMINO ACIDS?

Amino acids are organic molecules containing both amine and carboxylic
acid groups.
They are classified as -amino acids and -amino acids.
Only -amino acids (i.e. 2-aminocarboxylic acid) occur naturally.

H
H
|
|

H2N C C COOH
|
|
H
R

The general formula of -amino acids is

Except for glycine where R = H, all other -amino acids are optically active.
Amino acids are the basic building block of proteins.
Animals can synthesise 10 amino acids and obtain the rest by way of food
chains and food webs. The ingested proteins are then hydrolysed into
amino acids by enzymes in the digestive system.
There are a total of 20 naturally occurring -amino acids which made up all
proteins.

ENRICHMENT NOTES ON AMINO ACIDS

Essential amino acids
Humans can produce 10 of the 20 amino acids. The others must be supplied in the food.
Failure to obtain enough of even 1 of the 10 essential amino acids, those that we cannot
make, results in degradation of the body's proteinsmuscle and so forthto obtain the one
amino acid that is needed. Unlike fat and starch, the human body does not store excess amino
acids for later usethe amino acids must be in the food every day. The 10 amino acids that
we can produce are alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine,
glycine, proline, serine and tyrosine.

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H2 A-level Chemistry

Organic Nitrogen Compounds

2. TYPES OF AMINO ACIDS

4 types
The 20 naturally occurring amino acids can be classified into 4 groups
according to the nature of their alkyl (R) group.

a) Neutral amino acids with Non-polar/ Hydrophobic R groups

Egs: Alanine (ala)
2-aminopropanoic acid
H
|
H2N C CO2H
|
CH3

Valine (val)

Leucine (leu)

H
|
H2N C CO2H
|
CH(CH3)2

H
|
H2N C CO2H
|
CH2
|
CH(CH3)2

b) Neutral amino acids with Polar/ Hydrophilic R groups

Egs: Serine (ser)
H
|
H2N C CO2H
|
CH2
|
OH

Cysteine (cys)
H
|
H2N C CO2H
|
CH2
|
SH

c) Acidic amino acids with Acidic/ Anionic R groups

Egs: Aspartic acid (asp)

Glutamic acid (glu)

H
|
H2N C CO2H
|
CH2
|
CO2H

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H
|
H2N C CO2H
|
CH2
|
CH2
|
CO2H

H2 A-level Chemistry

Organic Nitrogen Compounds

d) Basic amino acids with Basic/ Cationic R groups

Eg:

Lysine (lys)
H
|
H2N C CO2H
|
CH2CH2CH2CH2NH2

Figure: 20 -amino acids

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H2 A-level Chemistry

Organic Nitrogen Compounds

3. ACID-BASE NATURE OF AMINO ACIDS

Amino acids are amphoteric as they contain acidic COOH and basic
NH2 groups which can react with each other giving rise to dipolar ions, also
known as zwitterions.
Zwitterion is a dipolar ion with a positive and a negative charge, and
thus is electrically neutral.

Depending on the pH of the aqueous medium, amino acids can exist as

cationic, zwitterionic or anionic.

Eg: Aminoethanoic

H
|
H3N+ - C - CO2H
|
H
Cationic

acid (Glycine)

H+
As base
OH-

H
|
H3N+ - C - CO2|
H
Zwitterionic

H+

H
|
H2N - C - CO2- + H2O
|
OHH
As acid
Anionic

The pH at which ALL amino acids exist as Zwitterions is called

Isoelectric point. At this pH, the amino acids will NOT migrate in the
presence of an electric field as they are electrically neutral.
Isoelectric point of amino acids with acidic R groups < 7 so that only one
acidic group is deprotonated for the amino acid to be zwitterionic.
Isoelectric point of amino acids with basic R groups > 7 so that only one
basic group is protonated for the amino acid to be zwitterionic.
Isoelectric point of amino acids with neutral R groups 7

Isoelectric Points of amino acids can be predicted based on nature of their R group:
Nature of R group
Isoelectric point
Examples
Glycine = 6.0; Alanine = 6.0
Neutral
6-7
Aspartic acid = 3.0; Glutamic acid = 3.2
Acidic
<7
Lysine = 9.7; Arginine = 10.8
Basic
>7

Gel Electrophoresis A technique for

separation of mixture of amino acids using
electric current. In the presence of an electric
current, the amino acids will migrate towards
the electrodes and the rate of movement is
inversely proportional to the mass of the
amino acid.

Cationic amino acids will migrate towards

cathode (negative electrode)

Anode (+)

Anionic amino acids will migrate towards anode (positive electrode)

Neutral amino acids do not move.

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Cathode (-)

H2 A-level Chemistry

Organic Nitrogen Compounds

3.1) Titration Curve of a fully protonated neutral amino acid

Glycine, H3N+CH2COOH

Fully protonated glycine is a dibasic acid as it has 2 acidic groups.

The 2 acidic groups are____________________ and ____________________
The graph below shows the titration curve when NaOH is added to a solution of
H3N+CH2COOH of the same molar concentration.
There are ________ equivalence points in the titration curve since a fully
protonated glycine is _____________________.
Equivalence point is a stoichiometric point of the titration where the number of
moles of acid is the same as number of moles of NaOH added.

H3N+
|
CH2
|
CO2H

H3N+
|
CH2
|
CO2-

Consider at weak acid, HA

HA(aq) H+(aq) + A-(aq)
+
Ka = [H ] [A-]
[HA]
At mid-way of titration, [HA] = [A-]
Hence, Ka = [H+]
-lg Ka = - lg [H+]
So at mid-point of titration , pKa = _________

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H2N
|
CH2
|
CO2-

pI = Isoelectric point
= pH at 1st equivalence point of titration
= mid-point of pK1 and pK2
= (pK1 + pK2)
= ( ________ + ________)
= 6.1

H2 A-level Chemistry

Organic Nitrogen Compounds

THINK

Questions
1) There are two acidic groups in the fully protonated Glycine:
...
-carboxylic acid and protonated -amine
Based on the titration curve, which one is the stronger acid (i.e. has a larger Ka value)?

Addition of OH- to the fully protonated glycine led to neutralization of

_________________ rather than the ____________________________.

Hence ____________________is more acidic than ______________________, thus

the former has a larger Ka value.

-carboxylic acid is ____________ acidic than protonated -amine due to resonance

stabilisation of the carboxyl ion produced.
2) Draw the structure of amino acid present in the titration mixture at pH 6.1, i.e. the
isoelectric point, pI of glycine.

3.2) Titration Curve of a fully protonated acidic amino acid

Glutamic acid, H3N+CH(CH2CH2CO2H)CO2H
Fully protonated glutamic acid is a tribasic acid as it has 3 acidic groups.
The 3 acidic groups are____________________, ____________________ and
____________________
The graph below shows the titration curve when NaOH is added to a solution of
fully protonated glutamic acid, Glu+ of the same molar concentration.

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H2 A-level Chemistry

THINK

Organic Nitrogen Compounds

Questions
1) Fully protonated Glutamic acid has 3 acidic groups: -carboxylic acid, alkylcarboxylic acid and protonated -amine
Based on the titration curve, arrange them in order of decreasing Ka value:

Carboxylic acids are ___________ acidic than protonated amines due to resonance
stabilisation of the carboxyl ion produced.

-carboxylic acid is more acidic than the alkyl-carboxylic acid as it is closer to the
protonated -amine which exerts an electron-withdrawing inductive effect, leading
to ________________ of negative charge on the carboxyl group produced, thus
stabilising it.
2) From the graph, what is the approximate isoelectric point of Glutamic acid?

Enrichment notes:
Different approaches when comparing acid strength of carboxylic acid & protonated
amine
We use stability of carboxyl ion ______________ to compare its acid strength
RCO2H

RCO2- + H+
More stable => _______________easily formed => ___________________ acidic

We use stability of protonated amine to compare acid strength

RNH3+

RNH2 + H+
Less stable => ________________ to react => ____________________ acidic

3.3) Titration Curve of a fully protonated basic amino acid

Lysine, H3N+CH(CH2(CH2)3NH3+)CO2H
Below is the titration curve obtained on addition of NaOH to a solution of
Lys2+ of the same molar concentration.
A fully protonated lysine is tribasic as it has 3 acidic groups, namely
______________________, _______________________ and
_________________________________

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H2 A-level Chemistry

Organic Nitrogen Compounds

THINK
Questions
1) Fully protonated Lysine has 3 acidic groups: -carboxylic acid, protonated amine and protonated alkyl-amine
Based on the titration curve, arrange them in order of decreasing Ka value:

Carboxylic acid is __________ acidic than protonated amine due to resonance

stabilisation of the carboxyl group produced.

Protonated -amine group is more acidic than protonated alkyl-amine as it is closer to

the -carboxyl group which exerts an electron-withdrawing inductive effect,
leading to _______________________ of the positive charge on the protonated
-amine, thus destabilising it.
2) From the graph, what is the approximate pI of lysine?

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H2 A-level Chemistry

Organic Nitrogen Compounds

Self-test
Below is the titration curve when 1 mol dm-3 NaOH is added to 1 mol dm-3 of fully
protonated lysine which is a basic amino acid.

Give the structure of the species present when the following amount of NaOH is added
to one mole of fully protonated lysine, suggesting a value for the pH of the resulting
solution and stating the electrode each will migrate towards during electrophoresis.
Amount of NaOH
added

1 mol

2 mol

3 mol

pH of resulting
solution
Structure of species

Direction of
migration during
electrophoresis

(After youve answered this question, please refer to last page to check your answer)
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Organic Nitrogen Compounds

4. PHYSICAL PROPERTIES OF AMINO ACIDS

High melting point and exist as crystalline solids.
In dry solid state, amino acids are zwitterionic. They have giant ionic structures
containing dipolar ions held together by strong ionic bonds. The ions are arranged in a
regular manner giving to a crystalline structure. A lot of energy is needed to separate
the dipolar ions leading to a high melting point.

Soluble in polar solvents but insoluble in non-polar solvents.

The ionic nature of amino acids allows it to attract water molecules strongly through the
formation of ion-dipole bonds thus releasing large amount of hydration energy to
overcome the ionic bonds between amino acids and the hydrogen bonds between
water molecules.
Amino acids are insoluble in non-polar solvents as the energy released from ioninduced dipole attractions between the dipolar ions and non-polar solvent molecules is
insufficient to overcome the ionic bonds between the dipolar ions.

Question 1
Some aminoethanoic acid is dissolved in a buffer solution of pH 9.0. Which one of the
following gives the structure of the two main forms of aminoethanoic acid at this pH?
+NH CH CO H and NH CH CO H
A
3
2
2
2
2
2
B
NH2CH2CO2 and NH2CH2CO2H
+NH CH CO H and +NH CH CO C
3
2
2
3
2
2
+
D
NH3CH2CO2H and NH2CH2CO2
E
NH2CH2CO2- and +NH3CH2CO2-

Question 2
Which reagent reacts only with the acid group of the amino acid H2NCH2CO2H?
A HCl(aq)
B HNO2(aq)
C C2H5OH
D C6H5COCl

Question 3
Which sequence shows the correct order of increasing pH in aqueous solution?
A

C6H5COCl C6H5CONH2 C6H5NH2 C6H5NH3Cl

C6H5COCl C2H5NH3Cl C2H5CONH2 C6H5NH2

C2H5CO2H CH3CHNH2 CO2H C2H5 2 NH C2H5NH2

C2H5CO2H C6H5NH2 CH3CHNH2 CO2H C2H5NH2 CH3 2 NH

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Question 4
GABA is a neurotransmitter released by red algae which encourages shellfish larvae
to settle on the ocean bed.
H2NCH2CH2CH2CO2H
GABA
Which statements about GABA are correct?
1. It is a 2-aminocarboxylic acid.
2. It is soluble in water due to zwitterion formation.
3. It migrates to the anode of an electrolytic cell at pH 12.
A 1, 2 & 3 only
B 1 & 2 only
C 2 & 3 only
D 3 only

B) POLYPEPTIDES
1. WHAT ARE POLYPEPTIDES?

Polypeptides are formed when amino acids undergo nucleophilic acyl

substitution with each other to form a polymeric chain.
The reaction involves the -NH2 of an amino acid combining with the COOH group of another amino acid.
The reaction is also known as condensation as it involves combination of
two molecules to form a single molecule with elimination of a small molecule
of water.
The linkage formed is called peptide bond/linkage or amide bond.

Dipeptides formed by linking 2 amino acids.

Tripeptides formed by linking 3 amino acids.
Polypeptides formed by linking 10 to 100 amino acids.

+ H2O

2. PROPERTIES OF PEPTIDE/AMIDE BOND

We normally use peptide bond when the molecule is a protein or polypeptide. It

is also alright to refer to the linkage as amide bond.
The peptide or amide bond is rigid and cannot be rotated about the C-N bond.
This is caused by delocalisation of electrons in the peptide bond leading to
double bond character in the C-N bond. Due to delocalization, the N atom is
sp2 hybridised so that the lone pair of electrons on N is in a p-orbital which is
then able to overlap sideways with the p-orbital of C.

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Organic Nitrogen Compounds

The peptide bond can be split by hydrolysis. The reaction can be catalyed by
suitable enzymes such as pepsin (in stomach) or trypsin (in intestine) or acid
or alkali.
Heat is needed for acidic or alkaline hydrolysis.

Hydrolysis of peptide/amide bond:

Acid hydrolysis

+ H2O + H+

Alkali hydrolysis

+ OH-

Enzyme
hydrolysis

+ H2O

Question 5
Aspartic acid and glutamic acid can react with each other to form peptide linkages.
If two molecules of glutamic acid react with two molecules of aspartic acid, what is the
maximum number of different tetrapeptides that can be formed?
A 2
B 4
C 6
D 8

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Organic Nitrogen Compounds

Question 6
Aspartic acid and glutamic acid can react with each other to form amide linkages.
If one molecule of glutamic acid reacts with one molecule of aspartic acid, what is the
maximum number of different compounds (each containing one amide linkage) that
can be formed?
A 2
B 4
C 6
D 8

C) PROTEINS
1.

WHAT ARE PROTEINS?

Proteins are polypeptide chains twisted and folded to give a threedimensional structure.

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2. FUNCTIONS OF PROTEINS IN THE BODY

The functions of proteins depend on the arrangement of their polypeptide

chains which is determined by their primary structures.

There are 2 types of proteins.

a) Fibrous proteins
These proteins have thin and thread-like arrangement. They serve as
structural molecules, providing mechanical support to structures in living
organisms.
Examples: Keratin (present in hair, horns, nails and wool);
Collagen (present in skin; Collagen is the most abundant protein in the
body. It makes up 75% of the skin and about one-third of the body's total
protein. As a structural protein, it creates support for bones, skin tendons,
ligaments and blood vessels.)
b) Globular proteins
These proteins have conjugated, compact and rounded
arrangement. They serve as functional molecules to facilitate metabolism
in living organisms.
Egs: Enzymes, hormones, pigments (melanin), blood-transport molecules
(haemoglobin & myoglobin) and blood-clotting agents.

3. DIGESTION OF PROTEINS (HYDROLYSIS)

Proteins are broken into shorter polypeptides or amino acids by hydrolysis

of the peptide linkages.
The reaction is catalysed by proteolytic enzymes such as pepsin or trypsin
present in the human digestive system.
In the laboratory, proteins can be broken down by boiling it with aqueous
acid or alkali to hydrolyse the peptide bonds.

Eg: Enzyme hydrolysis

pepsin
H2NCHRCONHCHRCONHCHRCO2H + 2H2O 2H2NCHRCO2H + H2NCHRCO2H

Eg: Acid hydrolysis

H2NCHRCONHCHRCO2H

+ H2O

+ H+

Eg: Alkali hydrolysis

H2NCHRCONHCHRCO2H

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+ OH-

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4. PROTEIN STRUCTURES

A polypeptide chain can be arranged to give 4

levels of structure.

Level 1

..

Level 2

..

Level 3

..

Level 4

..

4.1) Primary structure of proteins

A polypeptide chain is made up of a repeating backbone of peptide bonds,

with a free amine group ( also known as N-terminal, written on the LEFT side)
on one end and a free carboxylic acid group (also known as C-terminal, written
on the RIGHT side) on the other end.

COOH

H2N

Definition: The primary structure refers to the sequence of amino acids in the
polypeptide chain.
asp lys lys phe tyr ala gly
lys ala tyr met ala gly phe

Egs:

Due to the interactions between R groups of amino acid residues, the primary
structure determines what the protein is, how it folds and hence its functions.

Each polypeptide chain may contain several hundred amino acid residues,
hence the number of ways /sequences in which these can be arranged in the
chain is astronomical giving rise to huge number of primary structures.

Example 1
The primary structure of a tetrapeptide A was found to be

met lys - phe tyr

The primary structure was determined by analyzing the fragments obtained from
different enzymic hydrolysis
The structure of polypeptide A can be represented as:
H

N
|
H

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MET

C
||
O

N
|
H

LYS

C
||
O
16

N
|
H

PHE

C
||
O

N
|
H

TYR

CO2H

H2 A-level Chemistry

Organic Nitrogen Compounds

a) A sample of A was hydrolysed using enzyme chymotrypsin which digests

(hydrolyses) proteins at carboxylic acid end of phenylalanine, phe.
Give the primary structure of the fragments obtained.

N
|
H

MET

C
||
O

LYS

N
|
H

C
||
O

N
|
H

PHE

C
||
O

N
|
H

TYR

CO2H

Cleavage by chymotrpsin

The fragments are

___________________________ and ____________________________

b) Another sample of A was hydrolysed using enzyme pepsin which digests at

amino end of lysine, lys. Give primary structure of the fragments obtained.

N
|
H

MET

C
||
O

N
|
H

LYS

C
||
O

N
|
H

PHE

C
||
O

N
|
H

TYR

CO2H

Cleavage by pepsin

The fragments are

___________________________ and ____________________________

Example 2:
Deduce the primary structure of a hexapeptide from the following peptides obtained
from hydrolysis experiments of the hexapeptide.
lys-tyr
lys glu
asp-arg
arg - lys
lys glu - asp
Note: Do not reverse the given
sequence of amino acids
in the fragments.

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4.2) Secondary structure of proteins

Definition: It refers to the regular repeating arrangement of the

polypeptide chain, stabilized by hydrogen bonds between C=O and N-H
groups of the peptide bonds. The 2 common types of secondary structure
are:

a)

..

b)

....

a) -helix (like a stretched telephone cord)

It is a regular coiled (spiral) polypeptide chain
held in place by intra-chain hydrogen bonds between
C=O group of a peptide bond and the N-H group of the
4th peptide bond further down the chain.
Consists of 3.6 amino acids per helical turn.
Intramolecular hydrogen bonds are linear,
so maximally stable.
Hydrophobic R-groups on their respective -carbon
all point towards the outside of the helix and are
perpendicular to the main axis of the helix. Hence,
proteins with -helix structures have low solubility in
water or polar solvents.
Each hydrogen bond is weak but the total binding
effect is strong.
The -helix is flexible and elastic.

Figure : -helix

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Example of -helix: -keratin

Elastic/ Stretchable. Found in hair, hooves, wool, claws, etc.

Stretchability & hardness of keratin depends on degree of cross-linking by

disulfide bridges between neighbouring chains.

Insoluble in water at room temperature since it is rich in hydrophobic R groups

which are exposed to the outside of the fibre.
Enrichment: What happens when you perm your hair?

Human hair, made of keratin, has high % of cysteine, cys

Straight or curly hair depends on the disulfide bonds between cys.

Curly hair arises when disulfide bonds are formed between cys.

During hair perming, the reducing agent breaks -S-S- bonds, molecules become
more flexible, hair can be set into desired shape/ curls.

By applying an oxidising agent, the disulfide bonds are reformed and as a

result hold the molecules in the desired positions giving rise to permanent curves.
A permanent wave treatment has three steps:
1. Break the disulphide bonds with a reducing agent.
2. Shape the hair into the desired configuration, usually with curlers; the size of the
curler will determine the tightness of the resulting curl.
3. Reform the disulfide bonds in new positions, using an oxidizing agent.

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b) -pleated sheet (Like the galvanized zinc sheet)

Formed most readily by polypeptides with repeating sequences of amino acids
with compact, bulky R groups/ side chains (eg. Tryptophan) or intra-chain
disulfide linkages, which disrupts formation of a smooth -helix.
Consists of polypeptide chains arranged in a parallel fashion running in same
or opposite directions to each other, with hydrogen bonds formed between the
chains (inter-chain hydrogen bonds).
The hydrogen bonds are formed between N-H and C=O groups of peptide
linkages.
The R groups project above or below the sheet.
Flexible but inelastic.
Eg: -keratin or fibroin present in silk fibres, nails, horns, scales and feathers.
Figure : -pleated sheet

Figure:
2-dimensional diagram showing Beta-pleated sheet of 2 polypeptide chains in same
or opposite directions, with hydrogen bonding between strands.

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Figure: Beta-pleated sheet formed by

a folded polypeptide chain

Exercise: Draw a beta-pleated sheet showing 3 strands of polypeptide chains in

opposite directions.

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4.3) Tertiary structure (Discussion applies chiefly to globular proteins)

Definition: Tertiary structure of protein refers to the precise complex and

somewhat rigid three-dimensional structure formed when a polypeptide chain
folds or coils extensively giving rise to a globular/ compact/ spherical shape
which is stabilized by interactions between the R groups.
The polypeptide chain folds up into different patterns depending on the type
of R groups present in the amino acid residues of the polypeptide chain.
The interactions between R groups stabilised the tertiary structure and the type
of R group interactions depend on the nature of the R group.
Globular proteins are soluble in water due to hydrophobic interactions as
well as the folding pattern of the protein chains resulting in the hydrophilic R
groups being located on the outer surface and the hydrophobic R groups
being internally located, hence out of contact with water, and the folding is
compact with little or no room for water molecules in the interior.

Note:

Hydrophilic groups
Polar groups or charged groups which attract water molecules readily.
Egs: -CO2- (carboxylate group); -NH3+ (ammonium group); -CONH2 (amide).

Hydrophobic groups
Non-polar groups which do not attract water molecules readily.
Egs: Hydrogen; alkyl ; phenyl.
Figure: Folding of polypeptide chain in Myoglobin
A iron-containing polypeptide chain found in muscle fibers, structurally similar to a
single subunit of hemoglobin and having a higher affinity for oxygen than hemoglobin
of the blood.

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Types of R group interactions

a) .... (electrovalent bonds or salt bridges)
between charged R groups.
Eg:
Ionic bond is formed between charged groups such as CH2COO- group
of anionic Aspartic acid and (CH2)4NH3+ group of cationic Lysine.
b) ..... between polar R groups with N-H, OH and C=O bonds.
Eg:
Serine has a CH2OH group which can form hydrogen bond with amine
group such as (CH2)4NH2 group of Lysine.
c) ... between non-polar R
groups.
Eg:
Instantaneous dipole-induced dipole (id-id) attractions exist between
non-polar alkyl groups such as CH3 of of Alanine and CH(CH3)2 of
Valine.
d) . which are formed when two
R groups with S-H groups undergo oxidation.
Eg:

Cysteine has a CH2SH group, hence 2 cysteine residues present in

different parts of a peptide strand can be oxidised to give Cystine which
has a S-S bond.

Formation of Cystine

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4.4) Quaternary structure

Definition: Quaternary structures found in highly complex or oligomeric

proteins. It refers to the precise arrangement of 2 or more polypeptide chains
(also known as sub-units) held together by R group interactions such as Van
der Waals forces, ionic bonds and hydrogen bonds.

Eg: Haemoglobin (oxygen-carrying pigment in red blood cells)

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H2 A-level Chemistry

It is a globular protein with a quaternary structure. It has 4 polypeptide chains/

sub-units (2 -sub-units and 2 -sub-units) which are fitted together tightly to
form a stable compact globular structure.
The and chains contain different number of amino acid residues.
Each sub-unit is bonded to a haem residue which contains a six-coordinated
Fe(II) ion.
Each sub-unit is irregularly folded in which lengths of pure -helical regions are
separated by bends.
Both and chains have about 70% -helical regions.
There is little contact between similar sub-units but the R-groups of adjacent
and sub-units have considerable interactions similar to those that
stabilize a tertiary structure.
Fe(II) in the haem can undergo ligand-exchange reaction with oxygen.
(You can refer to your notes on Transition metals for more details.)

Haemoglobin

Organic Nitrogen Compounds

4O2

_________________________

+ 4H2O

Hemoglobin which is present in blood carries O2 from the lungs to the cells to
support metabolic processes.

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Organic Nitrogen Compounds

Definitions and Summary of Protein Structures

1. Primary structure
- It refers to the sequence of amino acids in a polypeptide chain.
- It is important as it determines type, shape/ folding and function(s) of protein.
Eg: asp arg val tyr phe leu
2. Secondary structure
- It refers to the regular patterns/
arrangement of sections of a
polypeptide chain such as - helix and
-pleated sheet stabilized by hydrogen
bonds between N-H and C=O groups
of the peptide bonds.
3. Tertiary structure
- It refers to the three-dimensional structure formed by folding of the polypeptide
chain into a specific shape held together by R group interactions such as disulfide
bonds between cysteine residues, ionic bonds
between charged groups, hydrogen bonds
between polar groups with N-H, O-H and C=O
bonds and Van der Waals forces between nonpolar groups.
4. Quaternary structure
- It refers to the three-dimensional structure
formed by 2 or more
polypeptide chains assembled together to give rise to a precise
structure held together by alkyl group interactions such as ionic bonds,
hydrogen bonds, disulfide bonds and Van der Waals forces
(instantaneous dipole-induced dipole attractions)

Table: Relating Protein Types to Protein Structures

Protein types Fibrous proteins
Globular proteins
Functions

These proteins have thin and threadlike arrangement. They serve as

structural molecules, providing
mechanical support to structures in living
organisms.

Protein
structures

Primary
Primary
+ Secondary + Secondary
+ Quaternary

Examples

-keratin
in hair
-keratin
in nails

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Collagen
present in flesh
and connective
tissues; made up
of 3 -helix
polypeptide chains

26

These proteins have conjugated,

compact and rounded
arrangement. They serve as
functional molecules to facilitate
metabolism in living organisms.

Primary
+ Secondary
+ Tertiary

Primary
+ Secondary
+ Tertiary
+ Quaternary
Myoglobin Haemoglobin
binds to
binds to oxygen
oxygen in
in blood
muscle
tissues

H2 A-level Chemistry

Organic Nitrogen Compounds

Question 7
Three orders of structure of the protein insulin are described as follows.
The molecule consists of two polypeptide chains joined and folded around one
another.
The sequence and number of amino acids in each polypeptide chain is known.
The amino acids in each chain are coiled into a helix and held in position by
hydrogen bonds.
Which set correctly gives the order described by each statement?

A
B
C
D

Statement 1
primary
primary
tertiary
quaternary

Statement 2
secondary
tertiary
secondary
primary

Statement 3
tertiary
secondary
primary
secondary

Question 8
Which statement describes a globular protein?
A
It is a protein with only primary and secondary structure.
B
It is insoluble in water.
C
It is a water-soluble protein with a tertiary structure.
D
It is a protein with only tertiary structure.
Question 9
What does a haemoglobin molecule contain?
A
Four iron(II) ions attached to each haem group
B
Four oxygen molecules attached to each haem group
C
Four polypeptide chains each with four attached haem groups
D
Four polypeptide chains each with one attached haem group

Question 10
Which statement best describes a quaternary protein?
A
It is a water-soluble protein.
B
It is a globular protein containing 2 or more polypeptide chains.
C
It is a globular protein containing polypeptide chains assembled together to give
a precise three-dimensional structure.
D
It is a water-soluble globular protein containing 2 or more polypeptide chains
assembled together to give a precise three-dimensional structure which is
stablised by interactions between the R groups.
Question 11
Which statement best describes hydrophobic interactions?
A
It refers to interactions between non-polar groups.
B
It refers to interactions of polar groups with water molecules.
C
It refers to aggregation of non-polar groups away from the aqueous surroundings
to achieve maximum stability.
D
It refers to aggregation of non-polar groups towards the aqueous surroundings to
achieve maximum stability.

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Organic Nitrogen Compounds

5. DESTRUCTION OF PROTEIN STRUCTURES

(DENATURATION of PROTEINS)

What is Denaturation?
Denaturation refers to disruption of the shape of protein without affecting the
primary structure but resulting in loss of biological activity as well as changes
in chemical and physical properties.

It causes solubility of proteins to decrease leading to coagulation and

precipitation (as a result of greater hydrophobic forces) and enzymes
(globular proteins) to lose their catalytic function (as a result of loss of 3dimensional protein structure).
Hydrophobic interactions refer to the aggregation of non-polar groups away
from the aqueous surroundings to achieve maximum stability. In globular
proteins, the non-polar R groups will aggregate internally, hence away from
the aqueous medium.

The peptide bonds in the polypeptide chain are not broken during
denaturation hence the primary structure is still intact.
Note: Peptide bonds can only be broken through hydrolysis.

When a globular protein is denatured, the structure unfolds from a welldefined globular shape to a randomly looped chain. Solubility decreases as
protein becomes more fibrous and the non-polar R groups are exposed to the
aqueous surroundings, leading to coagulation and precipitation as a result of
hydrophobic interactions.

Heat

Extreme conditions usually result in irreversible denaturation of most

proteins.

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Organic Nitrogen Compounds

6. FACTORS AFFECTING DENATURATION OF PROTEINS

i) Heat
Gentle heating can disrupt weak interactions such as
instantaneous dipole-induced dipole attractions
and hydrogen bonds between R groups.
Very strong heating can disrupt stronger R group
interactions such as disulfide bond or ionic bond.
This will break down protein structures (secondary,
tertiary & quaternary) causing the polypeptide chains to
unfold.
As a result, proteins will coagulate and lose their
functions (e.g. enzymes will lose their catalytic
abilities).
Globular proteins are denatured when heated above 60oC to 70oC.
Eg: Egg white coagulates on heating.

ii) pH
H+ and OH- react with acidic and basic R groups in
amino acids leading to disruption of ionic bonds.
This will break down protein structures (tertiary &
quaternary) causing the polypeptide chains to unfold.
As a result, proteins will coagulate and lose their
functions (e.g. enzymes will lose their catalytic
abilities).
Destruction of ionic bonds will be extensive at extreme
pH conditions.
-COO-NH3+

+
+

H+
OH-

-COOH
-NH2
+

H2O

iii) Mechanical agitation

Same effect as heating.
Eg: Foam produced by beating egg whites.

iv) Detergents

Detergents contain substances with both polar and non-polar groups.

The non-polar groups can disrupt instantaneous dipole-induced dipole
attractions between non-polar R groups.
This will break down protein structures (tertiary & quaternary) causing the
polypeptide chains to unfold.
As a result, proteins will coagulate and lose their functions (e.g. enzymes will
lose their catalytic abilities).

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H2 A-level Chemistry

Organic Nitrogen Compounds

v) Organic compounds

Organic solvents which provide a non-polar environment can disrupt

instantaneous dipole-induced dipole attractions between non-polar R
groups.
Polar solvents such as ethanol and propanone can interfere with hydrogen
bonds between R groups and those between peptide linkages.
This will break down protein structures (such as tertiary & quaternary) causing
the polypeptide chains to unfold.
As a result, proteins will coagulate and lose their functions (e.g. enzymes will
lose their catalytic abilities).
Eg: Disinfectant action of ethanol results from its ability to denature bacterial proteins
by disrupting the hydrogen bonds causing the protein structure to break down.

vi) Inorganic salts

Ions interfere with ionic bonds between charged R groups resulting in

denaturation. Metal cations such as Na+. Ag+, Hg2+ and Cu2+ can combine with
COO- groups while anions such as Cl- and CN- can combine with NH3+
groups.
This will break down protein structures (tertiary & quaternary) causing the
polypeptide chains to unfold.
As a result, proteins will coagulate and lose their functions (e.g. enzymes will
lose their catalytic abilities).
Heavy metal ions such as Ag+, Hg2+ and Cu2+ can also destroy protein
structures by disrupting S-S bonds between cysteine residues in the
polypeptide chain
Eg: Making of salted eggs by
introducing Na+ and Cl- ions.

SUMMARY on Protein Denaturation

FACTORS

Instantaneous
dipole induced
dipole attractions

Hydrogen
bonds

Heating

pH
Mechanical
agitation
Detergents
Organic
compounds
Inorganic salts
such as NaCl
Heavy
metal
ions such as
Ag+ or Cu2+
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Disulfide
bonds

Ionic
bonds

Protein structures
destroyed

H2 A-level Chemistry

Organic Nitrogen Compounds

Question 12
The graph shows how the structure of a protein (which consists entirely of repeating
residues of one amino acid) varies with pH.
Increasing symmetry

A
B
C
D

-helix

What conclusion can be drawn from the graph?

At high acidity the protein loses its secondary structure
At high acidity the protein loses its tertiary structure
At low acidity the protein loses its primary structure
At low acidity the protein loses its secondary structure

random coil

12 pH

Question 13
Which of the following R group interactions are disrupted when a protein is heated?
A
van der waals forces (id-id attractions)
B
ionic bonds
C
hydrogen bonds
D
All of the above

Question 14
Which of the following levels of protein structure can be destroyed when a protein is
treated with acids?
A
primary, secondary, tertiary and quaternary
B
primary, secondary, tertiary
C
secondary, tertiary and quaternary
D
tertiary and quaternary
Question 15
Which of the following can lead to denaturation of protein?
A
soaking the protein in concentrated NaCl solution
B
adding ethanol to the protein
C
adding hydrochloric acid to the protein
D
All of the above
Question 16
Which property enables proteins to act as pH buffers?
A
Globular proteins are soluble in water
B
Proteins contain carboxyl and amino groups
C
Proteins have a high molecular mass
D
Proteins contain both secondary and tertiary structures
Question 17
Which of the following cannot be present when a protein is hydrolysed?
A
H2NCH2CH2CO2H
B
H2NCH(CH2CO2H)CO2H
C
H2NCH(CH3)CO2H
D

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MCQ Answers
1

C
AAGG GGAA
AGAG GAGA
AGGA GAAG
Peptide linkages are
formed between
CO2H & -NH2 on -C
only

B
Amide linkage can be formed
between
COOH & -NH2 on -C as well
as those from R groups.

10

11 C

12

13

14

D
Addition of acids disrupt only
ionic bonds not present in sec
structure.

15 D

16

D The graph shows

that at high pH (low
acidity) the -helix
(sec structure) unfolds
to give random coil.
B Buffers contain
both acidic & basic
groups to react with
added H+ or OH- to
resist pH changes.

17

A
Proteins contain only
alpha amino acids

Self-test Answer
Amount of NaOH
added
pH of resulting
solution

1 mol

2 mol

3 mol

10

12

Towards cathode(-)

No movement

Towards
anode(+)

Structure of species

Direction of migration
during electrophoresis

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