TL

THE THREAD OF LIFE

Concept map
This concept map shows how the major chemical ideas in this teaching module develop throughout the course.
Concept
Relative atomic mass and relative formula mass

First introduced in
module
EL

Developed in
module(s)

Assumed in
module(s)
all

Amount of substance
Chemical formulae and inorganic nomenclature
Balanced chemical equations
Atomic structure
Covalent bonding
Shapes of molecules
Relationship between properties, and bonding and
structure
Catalysis
Isomerism
Homologous series
Nomenclature of organic compounds

EL
EL
EL
EL
EL
EL
EL

DF
ES
DF

DF, ES, PR
DF
MR, TL, AI, CD, O

all
all
all
all
all
all
DF, ES, PR, SS

DF
DF
DF
DF

several
MD
several
MD

Structural formulae (full, shortened and skeletal)

DF

A, TL, SS, AI
PR, TL
PR
ES, PR, WM, MR,
TL, CD
ES, PR

Organic functional groups

DF

Properties of alkanes
Structure of benzene
Ionic equations
Ionic substances
Electronegativity and bond polarity
Intermolecular bonds
Redox
Industrial applications

DF
DF
ES
ES
ES
ES
ES
ES

Atom economy
Rates of reactions
Bond ssion
Elimination reactions
Carboxylic acids
Polymers and polymerisation
Chromatography
Acids and bases
Condensation reactions
Delocalisation of electrons
Amines
Amides
Green chemistry
Amino acids
Proteins and enzymes
DNA and protein synthesis
Molecular recognition
Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.
This document may have been altered from the original.

ES
A
A
PR
PR
PR
WM
WM
WM
WM
MR
MR
MR
TL
TL
TL
TL

ES, PR, WM, MR,

TL, CD

CD
SS
O
PR, O
PR, MR, TL, O
SS, AI
WM, MR, TL, SS,
AI
WM
TL, AI
PR

WM, MR
MR, TL
TL, CD
O
MR, TL
CD
TL
TL
TL, AI

MD

all organic
modules
MD
several
WM, MR, TL, MD
several
several
several
AI, CD, MD
several
MD
TL, AI, MD

several
several
TL, AI, CD, MD
MD
AI, MD
TL, SS, MD
MD
several
CD, MD
CD, MD
CD, MD
MD
MD

241

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Advance warning

Advance warning
The following items needed for activities in this module may not be in your school currently, and might take a little time to
obtain.
Activity

Item(s)

Essential/optional

Typical quantity per activity

TL2.1

glycine
ethanoyl chloride

Essential
Essential

2g
2 cm3

TL2.3

aspartame (e.g. Canderel) tablets

aspartic acid
phenylalanine

Essential
Essential
Essential

13 tablets
Small amounts for chromatography
Small amounts for chromatography

TL2.4

mirror

Essential

access to 1

TL3

small sweets e.g. Micro Mix or Jelly Bears

strawberry sweet laces
cocktail sticks

Essential
Essential
Essential

10
1
6

TL4.1

glucose test strips (such as Clinistix or Diastix)*

Essential

510

TL4.2

potassium peroxodisulfate(VI) (K2S2O8)

Essential

0.0400 mol dm3 (10 cm3)

TL4.5

set of graphs and description boxes

Essential

1 set per group

TL5

plastic-coated wire (e.g. Radio Spares 30 0.25 mm

strand: code RS360239 to RS360295 depending on
colour)*
Minit molecular model peg type a: Ref 7a293
(white) to 7a300 (green) depending on colour*
21 cm plastic tubes: Ref 72289 (red)*
RASMOL or other electronic molecular structure les

Essential

1m

Essential

30

Essential
Optional

8
1

* Current suppliers are listed on the Salters Advanced Chemistry website.

Storyline: answers to assignments

Amino acids with non-polar side chains are:
Gly Ala Val Leu Ile Phe Pro (Trp Met)
ii Amino acids with polar side chains are:
Ser Thr Cys Asp Glu Asn Gln Tyr His Lys Arg
iii Amino acids with ionisable groups on their side
chains are:
Asp Glu His Lys Arg Tyr
b The side chains in Leu and Ile make them structural
isomers.
c i Ser
ii Thr
iii Tyr
iv Either Asp or Glu
2 a H2N CH CO
NH
CH
COOH
1 a i

CH3

242

H

O
H

O
H

Mg2+ already hydrated so unable to bond to phosphate

groups.
+

&22+
&

H

O Mg2

H

&

O

H

b i Ser
ii Ala
3 a Butenedioic acid.
b +22&
&22+
&

d HOOCCH2CH2CH2COOH
It might if the relevant parts can t on to the active
site. This is unlikely, however, so it probably would not
react and might be an inhibitor. If a product were
formed it would be pentenedioic acid.
4 a Franklin was close. The DNA structure is helical, with
phosphate groups on the outside. She did not
postulate a double helix, though.
b
H

H

&

+22&

OH
HO

OH

No, since butanedioic acid will bind to the active site in

only one way, so only one E/Z isomer will be formed.

All the OH groups.

Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.

TL

Activities: notes and answers to questions

5 a Both condensation.
b H
O
H
C

O
C

H
O

H
H

C
C
H

The individual him/herself.

Their doctors, for diagnosing genetic diseases but
see below.
The police, for solving crimes this is of benet to
the whole community, although many might
disagree.
ii Anyone else not mentioned above this is
condential personal information.
b Should parents have the right to have their children
tested?
Yes could help them to make decisions about how
their children could be treated for genetic diseases.
No children may object to it later on.
Should testing be performed for genetic diseases for
which there is no cure?
Yes know areas where care is needed; cure may be
discovered soon.
No just makes an individual anxious and they may
not suffer as a result of the condition.
Should an individual be given his/her personal genetic
information?
Yes its his/her right, the information relates to
themselves.
No it may make the individual anxious (possibly
without cause).
Should insurance companies make use of the data to
x premiums?
Yes its only an extension to different premiums on
grounds of age and gender, for example; those with
healthy genes will benet.
No they should distribute the risk equally for all.
a i

H
H

6 a Only two bases are important in coding for:

Ser Leu Pro Arg Thr Val Ala Gly
b Three bases are important for:
Phe Tyr Cys Trp His Glu Ile Met Asn Lys Asp Gln
7 a i Lys
Lys
ii Arg
Ala
Arg
Ala
iii Tyr
Leu
Thr
b i ACC
ii CUA or CUG
8 a GUCA
b GTCA
9 There are a few correct answers here. The object of the
assignment is to start the students thinking about these
matters. A few suggested answers are given to the right to
open discussion.

Activities: notes and answers to questions

TL2.1 Investigating an amino acid
Safety note Information about hazardous chemicals is given on
the activity sheet.
1 Glycine is soluble in water. It is largely present as
zwitterions, which are solvated by water resulting in
iondipole interactions.
2 Glycine solution is close to neutral (slightly acid). The pH
should remain fairly constant throughout the additions of
acid and alkali. The theory is covered in the Chemical
Ideas section on amino acids.
3 Only butylamine reacts with ethanoyl chloride. Both
dissolve in water. Butylamine is basic but glycine is neutral.
The zwitterion form of glycine is responsible for its
different behaviour. There is no NH2 group with its lone
pair of electrons to react with the acid chloride. The
zwitterion can be either a proton donor or a proton
acceptor in solution, which is why the amino acid is
neutral. Butylamine dissolves in water as a result
of hydrogen bonding, glycine dissolves as a result of
iondipole bonds.
4 Only relatively weak intermolecular bonds (dipoledipole
bonds, dipoleinduced dipole bonds and hydrogen
bonds) between molecules of butylamine. Glycine exists as
zwitterions with strong ionic bonds between the particles.

1 The structural formulae of the three amino acids are:

CH3
H2N

H
C

H2N

CH3
C

COOH
JO\FLQH

C
H

COOH
DODQLQH

CH
CH3

COOH
YDOLQH

5 One possible dipeptide is:

CH3

H
H
H 2N

C
H

COOH

H
O

Gly Ala

The six dipeptides are:

Gly Ala, Gly Val, Ala Gly, Ala Val, Ala Val, Val Ala
6 One possible tripeptide is:
H3C
H
H2N

TL2.2 The structures of peptides

This activity provides an opportunity for students to practise
using molecular models and molecular drawing software to
reinforce their ideas about molecular structures.

H 2N

CH3

CH3
CH

COOH

Gly Ala Val

The six tripeptides are:

Gly Ala Val,
Gly Val Ala,
Ala Val Gly,
Val Gly Ala,

Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.

Ala Gly Val,

Val Ala Gly

243

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Activities: notes and answers to questions

c

TL2.3 Whats in aspartame?

Safety note Information about hazardous chemicals is given on
the activity sheet.
Check that the articial sweetener you use contains
aspartame and not saccharin. Also, avoid aspartame tablets
such as Hermesetas, which also contain leucine.
Peptide hydrolysis normally requires reux for several hours
with moderately concentrated acid. However it is possible to get
adequate results after 30 minutes reux with 4 mol dm3 HCl.
1

All angles 109

109
O

H
H2N

H
NH2

H
C

(H3C)2HC

OCH3

N
H

HO

109 H 120 O

5 a

H2N

+ 1

CH(CH3)2

HOOC

COOH

1+

+
&

7 Molecules that are non-superimposable on their mirror

images are chiral. A carbon atom that is surrounded by
four different groups is called a chiral centre.

Acid
hydrolysis
O

TL3 Modelling protein structures

H2N
OH

+ CH3OH
OH

HO
H2N
O

O
aspartic acid

phenylalanine

methanol

2 It is important that the hydrolysed aspartame is checked

against both amino acids. Aspartame itself, being only a
dipeptide, will travel up the paper, and could be confused
with an amino acid. Also, some tablets contain
phenylalanine along with the aspartame. Both
phenylalanine and aspartic acid must be detected to be
sure hydrolysis has occurred.

TL2.4 The shapes of A-amino acids

The model building in step 3 can be shared round members
of a group to save time. If you have molecular modelling
software this can be used to good effect alongside the model
kits, and students can be given print-outs of, say, D-alanine
and L-alanine at the end of the session.
1
109 H 120
H

244

This activity aims to reinforce students ideas about the

structures of proteins in a more unusual way.
If students are allowed to eat the sweets they have used
after completing the activity, it is recommended that this
activity does not take place in a laboratory unless careful
measures have been taken to ensure that the sweets cannot
become contaminated with chemicals.
1 The small sweets represent amino acids.
2 Peptide links join the amino acids together (the lace).
3 Condensation reactions are involved in creating peptide
links.
4 The sequence of amino acids is the primary structure of
the protein.
5 The helix or pleated sheet is the secondary structure of
the protein.
6 The structure created when sections of the helix or
pleated sheet is folded upon itself is the tertiary structure
of the protein.
7 The cocktail sticks could represent instantaneous dipole
induced dipole, permanent dipolepermanent dipole,
hydrogen, ionic and sulfursulfur covalent bonds.
8 Phenylalanine and leucine are likely to form instantaneous
dipoleinduced dipole bonds.
9 Serine and asparagine are likely to form hydrogen bonds.

CH2

H
C

H
H

109
O

H
H

2 a

&+&22+

+22&

&22+

aspartame

109

&

+22&+&

OH
H

All angles 109

H2C

H
N
H

C
O

10 Aspartic acid and lysine are likely to form ionic bonds.

H2C

O
H

All angles 109

H2C

H2C
O

H3N

CH2

CH2

Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.

TL

Activities: notes and answers to questions

TL4.1 Testing for glucose

Safety note Information about hazardous chemicals is given on
the activity sheet.
In a simple experiment, the test strips could be placed in
dilute acid or alkali, or in boiling water, before being used to
prove that these conditions deactivate the enzyme. More
careful investigation might make use of solutions of different
pH or water at different temperatures, and students might try
to time how long a particular depth of colour takes to develop.
The pH of urine is 4.87.5.
The enzyme has no effect on other sugars.
The use of test strips makes this activity quicker and more
convenient than some other methods of studying enzyme
catalysis. They can, however, be expensive for large groups. It
helps to cut the test strips into thinner pieces.

TL4.2 Using the iodine clock method to nd

the order of a reaction
Safety note Information about hazardous chemicals is given in
the activity sheet.
2 Iodide concentrations vary from 0.5 mol dm3 to
0.1 mol dm3. The corresponding times should be between
about 80 s and 400 s.
3 I is always in excess.
4 8 s 105 mol I2 can be produced in each case.
5 a 2 s 105 mol S2O32
b 1 s 105 mol I2
c 12.5% of the total reaction is studied.
7 The reaction is rst order with respect to iodide.
8 a Rate = k[I] [S2O82]
b Second order
Rate units of k are dm3 mol1 s1
c k = _________
[I][S2O82]
Rate can be found from the gradient of the graph.
____
[I]
d The value of k depends on the temperature.

Two methods are described for following the course of this

reaction; by titration and by using a colorimeter. Teachers may
arrange for groups of students to use different methods, so that
they can compare the methods and the results they obtain.
The graph of concentration of iodine against time is a
straight line. This indicates that the rate of reaction is the same
at different iodine concentrations. The results show that the
reaction is zero order with respect to the iodine and the
students should conclude that iodine is not involved in the
rate-determining step.

TL4.4 Enzyme kinetics

1 At high substrate concentration the process is almost zero
order with respect to the substrate.
2 If the rst step in the mechanism were the ratedetermining step, the rate of the reaction would depend
on [S]. (It would be rst order with respect to the
substrate.)
3 At saturation, [ES] will be constant, and so the rate of
conversion of bound substrate to unbound product
(ESmP + E) remains constant. It is independent of [S],
i.e. the reaction is zero order with respect to substrate.
4 At lower substrate concentrations, the rate at which
the substrate binds to the enzyme decreases as the [S]
falls. Enzyme active sites will no longer be full. The stage
E + SmES eventually becomes rate-determining and
the reaction becomes rst order with respect to substrate.
5 The reaction is always rst order with respect to enzyme.
6 The enzyme concentration is always low compared with
the substrate concentration. The concentration of ES
formed depends on [E]. So the rate always depends on the
enzyme concentration, no matter which step is ratedetermining.

TL4.5 Kinetics graphs

TL4.3 Methods of following reactions
Safety note Information about hazardous chemicals is given in
the activity sheet.

In this activity students choose from a set of eight graphs the

one which best matches what they expect from a number of
different situations related to rates of reaction (see below).

Description

Graph

Reason

[reactant] v time for a zero-order reaction (with respect to

this reactant)

rate of change of concentration with time is constant

[reactant] v time for a rst-order reaction (with respect to

this reactant)

graph illustrates a change of concentration with a constant

half-life

[reaction product] v time

concentration increases from zero and reaches a constant

value as the reaction is completed

rate of reaction v [reactant] for a zero-order reaction (with

respect to this reactant))

the rate is constant

rate of reaction v [reactant] for a rst-order reaction (with

respect to this reactant)

straight line, because rate is directly proportional to

[reactant]

rate of reaction v [reactant] for a second-order reaction

(with respect to this reactant)

an exponentially increasing line

rate of reaction v [reactant]2 for a second-order reaction

(with respect to this reactant)

a straight line, because rate is directly proportional to

[reactant]2

rate of reaction v [substrate] for an enzyme-catalysed

decomposition reaction

the reaction is rst order at low substrate concentrations and

changes to zero order at higher substrate concentrations

number of collisions with Kinetic Energy E v Kinetic Energy

(E) at temperature T K

same prole as graph H, but is more narrow and has a

higher peak

number of collisions with Kinetic Energy E v Kinetic Energy

(E) at temperature (T + 10) K

same prole as graph G, but is wider and has a lower peak

Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.

245

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Activities: notes and answers to questions

TL5 Modelling DNA

CH3

Students gain a much better understanding of the structure of

DNA if they draw and build models of the bases and the
double helix. By doing this activity they should also realise that
hydrogen bonding and instantaneous dipoleinduced dipole
bonding are important for holding the structure together.
OH

H
N
H
O

N
H
O

OH

H
N

N
N

base pair cytosine and guanine

H

OH

O

sugarphosphate backbone
O
H
N
O

OH

O
H

O
O

sugarphosphate backbone with base thymine

CH3
O
H
N

TL7 Check your knowledge and

understanding

O

CH3

1 The centre of the double helix is full; there is no empty

space. This contrasts with the traditional ladder
representation of DNA, which gives the mistaken
impression that there are large gaps between the bases.
2 The helix could not be twisted more tightly because the
bases are already at their closest.
3 Instantaneous dipoleinduced dipole bonding.
4 Less twisting would take the bases further apart and the
structure would lose the instantaneous dipoleinduced
dipole bonding. This bonding may be weak between any
pair of bases, but it is signicant over the whole polymer.

OH

This activity ensures that students are aware of the learning

outcomes (specication statements) that their assessment will
be based on, and provides an opportunity for them to reect
on how well they understand the ideas that they have covered
in this module. Crucially, it enables teachers to identify areas
where individual students are less condent, and to provide
appropriate additional support to improve their
understanding.
This activity could be used as part of the preparation for an
end of module test.

H
N

H
O

N
N

base pair thymine and adenine

246

Salters Advanced Chemistry, Pearson Education Ltd 2009. University of York.

This document may have been altered from the original.