NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

Nitrogen Compounds (Part II): Proteins Tutorial

Section A: Review Questions
TJC/2011/P1/Q28
1 Aspartic acid was first discovered in 1827 by Plisson. It is found in animal sources such as
luncheon meats and sausages as well as vegetable sources such as sprouting seeds, oat
flakes, avocado and asparagus.
O
O
OH
OH

NH2

Aspartic acid

There are three pKa values associated with aspartic acid: 2.10, 3.86, 9.82.
Using the pKa values, what is the major species present in solutions of aspartic acid at
pH 7?
O

O
OH
OH

NH3+

OOH

NH3+

O
O-

O-

NH3+

OO-

NH2

IJC/2011/P1/Q40
2 Which of the following is/are true about alanine (2-aminopropanoic acid) extracted from
silkworm silk?
1

Alanine is able to rotate plane polarised light.

Alanine has a higher solubility in water than in ether.

Alanine can react with ethanoic acid to give an amide.

NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

SAJC/2011/P1/Q37
3 The following is the molecular structure of a -amino acid. It is usually found in an aqueous
state at room temperature.

Which of the following statements of the -amino acid are true?

1

It forms a giant ionic structure.

It will react with 2 moles of sodium hydroxide.

It cannot rotate the plane of polarised light.

YJC/2011/P1/Q30
4 The amino acids, lysine and glutamine, can react with each other to form peptide linkages.
H
H2N

COOH

H2N

CH2CH2CH2CH2NH2

COOH

CH2CH2CONH2

lysine

glutamine

What is the maximum number of different compounds, each containing one peptide linkage that
can be formed from one molecule of lysine and one molecule of glutamine?
A

NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

NYJC/2011/P1/30
5 Partial hydrolysis of a decapeptide (containing 10 amino acid residues) using an
enzyme yielded the following tripeptide fragments:
HisTyrArg,

GlnThrAsp,

ArgHisTyr,

TyrArgThr,

AspArgHis,

ThrArgGln

Which of the following is the amino sequence of the decapeptide?

A

HisTyrArgThrAspArgGlnGlnThrArg

ThrArgGlnThrArgHisTyrThrAspArg

ThrAspArgGlnThrArgThr ArgHisTyr

ThrArgGlnThrAspArgHisTyrArgThr

A-Level/2014/P1/Q39
6 In which aspects of protein structure can hydrogen bonding occur?
1

the primary structure

the secondary structure

the tertiary structure

NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

When a nonapeptide (containing nine amino acid residues) isolated from rat brains was
hydrolysed, it gave the following smaller peptides as identifiable products:
GlyAlaPhe, AlaLeuVal, GlyAlaLeu, PheGluHis, HisGlyAla
Construct the amino acid sequence in the nonapeptide. Show your working clearly. [2]
GlyAlaPheGluHisGlyAlaLeuVal

In a laboratory setting, hydrolysis of a small portion of spider silk comprising of a

pentapeptide protion with three amino acids produced the following smaller tripeptide
fragments.

(a)

Suggest suitable reagents and conditions for the hydrolysis reaction. [2]
Reagents: HCl(aq) or H2SO4(aq) or NaOH(aq),
Conditions: Heat under reflux for several hours

(b)

Suggest a possible amino acid sequence for the pentapeptide portion of the spider silk.
Show your working clearly.
Present your answer using the threeletter abbreviations of the amino acids from the
Lecture Notes. [2]
The pentapeptide sequence is GlnSerGlySerGln

NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

Amino acids are the basic structural building units of proteins. Beyond the amino acids
that are found in all forms of life, many nonnatural amino acids play vital roles in
technology and industry.
Three amino acids with their Rgroups and isoelectric points are given in the table below.
Amino acid

Rgroup

Histidine

Isoelectric point
7.6

CH2
N
HN

(a)

Glutamic acid

-CH2CH2CO2H

3.2

Glycine

-H

6.0

Draw the structural formula of a tripeptide with the sequence hisglyglu, showing the
form in which it would exist at pH 2. [2]

NYJC H2 Chemistry

(b)

Nitrogen Compounds Proteins

JC2 2015

Amino acids can act as buffer in solutions. By means of equations, show how glycine can
act as a buffer when

dilute hydrochloric acid and

dilute NaOH

is added to separately into its solution. [4]

When a small amount of acid (H+) is added,

H+ + +NH3CH2COO-

H+ added is removed by a large reservoir of

+

NH3CH2COOH
+

NH3CH2COO- to form

NH3CH2COOH

pH of buffer solution remains fairly constant.

When a small amount of base (OH) is added,

OH + +NH3CH2COO-

OH added is removed by a large reservoir of

NH2CH2COO- + H2O
+

NH3CH2COO- to form

NH2CH2COO- and H2O

(c)

pH of buffer solution remains fairly constant.

Suggest with reasons a suitable pH which can be used to separate a mixture of histidine,
glutamic acid and glycine using electrophoresis. [2]
pH = 6.0
Glycine will have no net charge as the pH is at its isoelectric pH. Hence, it will remain
stationary.
Histidine will have a net positive charge and it will move towards the cathode
(negative electrode).
Glutamic acid will have a net negative charge and it will move towards the anode
(positive electrode).

(d)

Crystals of the simplest amino acid, glycine, NH2CH2COOH, melt between 230C and
235 C. Suggest why the melting point of glycine is higher than that of
2hydroxyethanamide, HOCH2CONH2 (m.p. 102104C). [2]
Glycine exists as zwitterions whereas 2hydroxyethanamide exists as simple molecules.
A larger amount of energy is required to overcome the stronger electrostatic forces of
attraction between the zwitterions in 2aminoethanoic acid than the hydrogen bonding
between 2hydroxyethanamide.

NYJC H2 Chemistry

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Nitrogen Compounds Proteins

JC2 2015

The formulae of four amino acids are given:

O
H2N

CH

OH

O
O

H2N

CH

CH3

Alanine (Ala)

CH2

O
OH

OH
H2N

HN

CH

CH3

OH

CH3

NH

Histidine (His)

CH

Proline (Pro)

Valine (Val)

(a)

Draw the structure of the tripeptide AlaProHis. Indicate clearly on your structure,
the Nterminus and the Cterminus. [2]

(b)

State the interactions that give rise to the different levels of protein structures found in
haemoglobin. [4]
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure

(c)

peptide linkage between amino acids

hydrogen bonds between C=O & NH groups of peptide
linkages
Rgroup interactions (e.g. ionic bonds, disulfide linkages,
hydrogen bonding or van der Waals interactions)
van der Waals forces (& ionic) between Rgroups of different
polypeptide chains

In sickle cell anaemia, which is a hereditary disease that restricts the flow of blood to vital
organs in the human body, a valine molecule replaces a glutamic acid molecule on two
polypeptide chains in haemoglobin. Suggest the type of intermolecular forces that arise
due to this substitution. [1]
van der Waals forces

NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

Section B: Discussion Questions

MJC/2011/P1/Q38
11 Part of the chain of the gelatin molecule is shown below.

O
O

H
N

C
O
H
N

H
C
CH3

H
N

C
H

H
C

H
H
N

C
H

(CH 2 )3
C

H
N

(CH 2 )2

NH
O
C

H
C

OH

NH

NH2

Based on the above structure, which of the following statement(s) is/are correct?
1

When gelatin is heated in 6 moldm-3 HCl for a prolonged period, NH2CH(CH3)(COOH) is

one of the products obtained.
NH
COOH

The amino acid

is rarely found in the -helix regions of proteins
due to its rigid structure and restricted geometry of the bulky five-membered ring.

The following amino acids are likely to be the amino acids on the outside of the gelatin
molecule:
H

H
H 2N

C
(CH2 )2
COOH

COOH

H 2N

COOH

(CH2 )3
NH
C

NH

NH 2

NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

HCI/2011/P1/Q40
12 Which groups within an amino acid are able to form a cross-chain link to stabilize the tertiary
structure of a protein?
1

CH2CONH2

CH2CH2CH2NHC

NH2
NH

CH2

N
H

NYJC H2 Chemistry

13

(a)

A polypeptide X
[RCH(NH2)CO2H].

Nitrogen Compounds Proteins

was

analysed

and

contained

JC2 2015

the

following

Amino acid

Abbreviation

Formula of Rgroup

aspartic acid

asp

CH2CO2H

glycine

gly

serine

ser

CH2OH

phenylalanine

phe

CH2

valine

val

CH(CH3)2

cysteine

cys

CH2SH

amino

acids,

Enzyme A digests proteins or polypeptides at the carboxylic acid end of the amino acid
valine, val.
The following peptides were identified after digestion of the polypeptide X with enzyme A,
and subsequent separation.
asp ser gly val,

ser phe cys,

phe val

Another enzyme B digests at the carboxylic acid end of serine, ser. The following
peptides were identified after digestion of the same polypeptide X with enzyme B, and
subsequent separation.
gly val ser,

phe cys,

phe val asp ser

Use the information to determine the primary structure of polypeptide X. Justify your
answer. [3]
From the partial hydrolysis by enzyme A, serphecys is the last fragment of the
polypeptide since it cleaved at the carboxyl end of the val.
From the partial hydrolysis by enzyme B, phecys is the last fragment of the polypeptide
since it cleaved at the carboxyl end of the ser. Hence cys is the C-terminus.
From the fragments obtained with A and B, there is overlapping amino acid sequence.
Hence the sequence is phevalaspserglyvalserphecys

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NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

(b)

Draw a displayed formula for the phecys dipeptide. [2]

(c)

State what Rgroup interactions are possible for the five amino acids in A at pH 7. [5]

Amino acid

Formula of Rgroup

Rgroup interactions

aspartic acid

CH2CO2H

ionic bonding

serine

CH2OH

hydrogen bonding

phenylalanine

CH2

van der Waals

valine

CH(CH3)2

van der Waals

cysteine

CH2SH

disulfide bond

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NYJC H2 Chemistry

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Nitrogen Compounds Proteins

JC2 2015

Myoglobin, like haemoglobin, is the oxygen-carrying proteins in vertebrates.

Myoglobin facilitates the transport of oxygen in muscle and serves as a reserve store of
oxygen in that tissue. Haemoglobin, which is packaged in erythrocytes (red blood cells),
is the oxygen carrier in blood.
Myglobin is a compact protein with a single polypeptide chain of 153 amino acid
residues, including the following residues: leucine, threonine, tyrosine and tryptophan.
The Rgroups of the amino acids are given below:
Leucine (leu)

Threonine (thr)

Tyrosine (tyr)

CH2
CH2
H3C

CH
CH3

(a)

Tryptophan (trp)

CH2

HO CH
CH3

N
OH

In an aqueous external environment, which of the above four amino acid residues are
orientated inward and outward of the compact structure? State your reasoning. [3]
Threonine will orientate outwards and leucine, tyrosine and tyrptophan orientate inwards.
Threonine contains a polar hydroxyl group and it has a relatively small nonpolar alkyl
group, therefore it can form hydrogen bonds with the water solvent.
Tyrosine and tryptophan, although have polar hydroxyl and amine group, they have
relatively large nonpolar group, similar to leucine, that form van der Waals attraction
forces with non-polar Rgroups of other amino acid residue.

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NYJC H2 Chemistry

(b)

Nitrogen Compounds Proteins

JC2 2015

Draw the structures of the predominant species of tyrosine and tryptophan when they are
placed in solutions of pH 2 and pH 12. [4]
Tyrosine
pH =2

pH =12

Tryptophan
pH =2

(c)

pH =12

Draw the displayed formula of leuthr, which is part of the polypeptide chain in
myoglobin. [2]

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NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

(d)

Write a general equation to show how a peptide bond in the primary structure is
hydrolysed by aqueous sodium hydroxide. [1]

(e)

Tyrosine exists as a white crystalline solid while phenol exists as a liquid at room
temperature. Account for this observation in terms of bonding and structure. [3]
Melting point of tyrosine is higher than phenol.
Tyrosine has giant ionic structure with strong ionic bonds between the zwitterions.
Phenol has simple molecular structure with weaker intermolecular hydrogen bonds
between the phenol molecules. Hence, more energy is required to overcome the stronger
ionic bonds, hence higher melting point.

(f)

Myoglobin consists of only 1 polypeptide chain arranged in a tertiary structure.

Describe the tertiary structure of myoglobin. [2]
The tertiary structure refers to the threedimensional shape of a protein molecule that
results from further folding, crosslinkings and coiling of the amino acid chains caused by
interactions between the Rgroups of the amino acids.
The four types of such interactions which stabilise the threedimensional shape of a
protein molecule are hydrophobic interactions, hydrogen bonding, Ionic bonding and
covalent bonding (disulfide linkages).

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NYJC H2 Chemistry

(g)

Nitrogen Compounds Proteins

JC2 2015

Explain, in term of bonding and structure, why myoglobin tends to coagulate and
precipitate when [6]
I

heated,
Heating disrupts the weak van der Waals forces and hydrogen bonding (to a
lesser extent) holding the quaternary, tertiary and secondary structures, resulting
in a more disordered arrangement which is irreversible at high temperatures.

II

subjected to changes in pH, and

pH changes disrupt the ionic bond holding the tertiary and quaternary structures in
place as pH change protonates or deprotonates the charged Rgroups.
At low pH, ionic Rgroups will be protonated while at high pH, ionic Rgroups will
be deprotonated which is irreversible at extreme pH changes.

III

Hg+ is added.
Addition of Hg+ ions disrupts the original ionic bonds between the charged
Rgroups of the amino acids by forming new ionic bonds with these charged
Rgroups of amino acids.
Disrupt the formation of disulfide bonds by forming bonds with SH group of
cysteine residue.

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NYJC H2 Chemistry

15

Nitrogen Compounds Proteins

JC2 2015

YJC/2011/P2/Q5
Natural polypeptides and proteins are made up of 20 different -amino acids, differing in
the nature of the Rgroup.
(a)

The structure of threonine, an -amino acid, is given below.

H
H 2N

COOH

CH2
H

OH

CH3

(i)

Explain what is meant by an -amino acid. Give the general structure of an

-amino acid. [2]
It is a compound which has both the carboxylic acid group and the amine group
attached to the same carbon atom. General structure is H2NCH(R)COOH.

(ii)

Threonine exhibits stereoisomerism. State the type of stereoisomerism and

draw two structures to illustrate this isomerism. [2]

(iii) Give the structural formulae of the organic products formed when threonine is
reacted with sodium carbonate, and heated with bromoethane in ethanol
respectively. [2]
with sodium carbonate

with bromoethane in ethanol

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NYJC H2 Chemistry

(b)

Nitrogen Compounds Proteins

JC2 2015

Insulin is a hormone central to regulating carbohydrate and fat metabolism in the

body. Insulin causes cells in the liver, muscle, and fat tissue to take up glucose from
the blood, storing it as glycogen in the liver and muscle.
The sequence of human insulin, shown below, is made up of two chains joined by
three covalent -S-S- bonds.

(i)

Human insulin is denatured when heavy metal ions are present in the body.
Explain the term denaturation and explain how denaturation of insulin occurs
due to the action of heavy metal ions.
Denaturation is an irreversible process whereby the protein loses its biological
activity. During denaturation, the Rgroup interactions are destroyed, only the
secondary, tertiary and quaternary structures are disrupted. The sequence of
amino acids (primary structure) is still intact as no covalent bonds of the
polypeptide are broken. This results in protein disintegrating to form random
coils of polypeptide chains.
Heavy metal ions react with the disulfide bonds and disrupt the disulfide
bridges causing the two chains to separate.

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NYJC H2 Chemistry

(ii)

Nitrogen Compounds Proteins

JC2 2015

The secondary structure of insulin consists of segments of -helices. With the

aid of a diagram, illustrate how the polypeptide chain is held in the structure of
an -helix. [4]

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NYJC H2 Chemistry

(c)

Nitrogen Compounds Proteins

JC2 2015

The R groups of some naturally occurring amino acids are shown in the table below:
Amino acid

Abbreviation

Formula of Rgroup

alanine

Ala

CH3

cysteine

Cys

CH2 SH

glutamic acid

Glu

O
CH2 CH2

OH

leucine

Leu

CH2 C

CH3

CH3

lysine

Lys

( CH2)4

phenylalanine

Phe

CH2

serine

Ser

tyrosine

Tyr

NH2

CH2 OH

CH2

OH

The folding of polypeptide chains is stabilised by the interactions between the

R groups of the amino acid residues. By selecting appropriate R groups from the
table above, draw diagrams to illustrate the following R-group interactions: [2]
(i)

van der Waals forces

(ii) ionic interactions

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NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

NitrogenCompoundsPartIIProteins
No Learning Outcomes
1 describe the formation of peptide (amide)
2
3

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
5 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
6 describe the secondary structure of
proteins: -helix and -pleated sheet and
the stabilisation of these structures by
hydrogen bonding
7 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)
8 describe
(i)
the quaternary structure of proteins
(ii)
the protein components of
haemoglobin
9 explain denaturation of proteins by heavy
metal ions, extremes of temperature and
pH changes
10 apply the knowledge of the loss and
formation of secondary and tertiary
structures to interpret common everyday
phenomena

Q1

Q2

Q3

Q4

Q5

Q6

Q7

Q8

Q9

Q10 Q11 Q12 Q13 Q14 Q15 Q16

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NYJC H2 Chemistry

Nitrogen Compounds Proteins

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Section C: Assignment Questions

Name: ____________________________

15

CT: ____________

16 Eggs are a good source of proteins.

(a)

Egg yolks are used in the making of mayonnaise.

The following amino acids are found in large quantities in egg yolk.

(i)

Amino acid

Formula of side chain

(R in RCH(NH2)CO2H)

pKb of R group

lysine

(CH2)4NH2

3.47

arginine

(CH2)3NHC(NH2)=NH

1.52

Given that the R group in arginine ionises in water as shown in the equation
below,

+ H2O

+ OH

explain why the R group in arginine has a smaller pKb than the R group in lysine.
[1]

(ii)

Suggest a reason why the R group in arginine will not undergo a second
ionisation in water. [1]

21

The structure of arginine is shown on the right.

When arginine is completely protonated, it has three
ionisable hydrogen atoms.

N
2
H

Three pKa values are associated with arginine: 2.17,

9.04 and 12.48.

JC2 2015

H
2
O 3
H
C 2H N
H
C N C

(iii)

Nitrogen Compounds Proteins

N
H C H2

NYJC H2 Chemistry

Make use of these pKa values to suggest the structures of the two species present
in an aqueous solution of arginine at pH 3. [2]

(iv)

Write an equation to show how arginine maintains the pH when a small amount of
H+ is added to an aqueous solution of arginine at pH 3. [1]

(v)

Similar to all naturally occurring amino acids, the solubility of arginine is lowest at
its isoelectric point. Explain why that is so. [2]

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NYJC H2 Chemistry

Nitrogen Compounds Proteins

JC2 2015

(b) Mayonnaise is an oil-in-water emulsion in which droplets of oil are dispersed in water
through the addition of emulsifiers.

Emulsifiers are compounds that contain both a polar, hydrophilic group, which is
attracted to water, and a hydrophobic group, which is attracted to non-polar solvents
such as oil. Lecithin is an important emulsifier found in egg yolk.
In the structure of lecithin given below, two groups, A and B, are enclosed separately in
rounded rectangles.

__________________

O
O

O
O
O
P
O

O
O

B
_______________

Use the information given above to complete the following table. [2]
Solvent

Group which
interacts with
solvent

Type of interactions between

group and solvent

Oil

Water

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NYJC H2 Chemistry

(c)

Nitrogen Compounds Proteins

JC2 2015

A meringue, which is a dessert, is made by whipping egg whites and sugar to form egg
foam that is stiff and firm.
The following amino acids are found in large quantities in egg white.
Amino acid

Formula of side chain (R in RCH(NH2)CO2H)

aspartic acid

CH2CO2H

glutamic acid

CH2CH2CO2H

lysine

(CH2)4NH2

arginine

(CH2)3NHC(NH2)=NH

histidine

(i)

The mechanical force from whipping introduces pockets of air into egg white.
Explain how this mechanical force results in the stiff consistency of egg foam
needed for making meringues. [2]

The common problem with egg foam is the inability to hold its shape due to the
reforming of R group interactions.
(ii)

Lemon juice is often added to egg white to enhance the stiff consistency needed
for making meringues.
By considering its interaction with the R groups present in egg white, suggest how
lemon juice stabilises the egg foam. [4]

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NYJC H2 Chemistry

(d)

Nitrogen Compounds Proteins

JC2 2015

Poached eggs are made when the pH of ovalbumin in egg is decreased by the addition
of vinegar in boiling water.
Explain why this process will result in the coagulation of egg white only, but is unable to
break ovalbumin into its constituent amino acids. [2]

25