A Level Science Applications Support Booklet: Chemistry

Contents
INTRODUCTION 1
1 THE CHEMISTRY OF
LIFE :.............................................................................................................3
1.1
Introduction.............................................................................................................................3
Water Lifes matrix..........................................................................................................3
Importance of hydrogen bonding to life .............................................................................5
Condensation polymerisation ............................................................................................5
Shaping up ........................................................................................................................6
1.2 Protein
chemistry....................................................................................................................6
a) Proteins - the workhorses of life ........................................................................................6
b) Amino acids - the building blocks of proteins ....................................................................8
Common features of amino acids...............................................................................8
The ionisation of amino acids ...................................................................................10
c) Structure - the key to protein function .............................................................................11
Condensation polymerisation of amino acids ...........................................................11
Levels of protein structure ........................................................................................12
The primary structure of proteins..............................................................................12
The secondary structure of proteins .........................................................................13
Protein tertiary structure ...........................................................................................15
Haemoglobin the molecular breathing machine...................................................17
summary and required knowledge .........................................................................................18
d) Enzymes Natures catalysts .........................................................................................19
Catalytic efficiency....................................................................................................19
Shapely molecules ...................................................................................................20
The lock and key model ..........................................................................................20
Competitive inhibition of enzyme activity..................................................................22
Non-competitive inhibition of enzymes.....................................................................23
Factors affecting enzyme activity .............................................................................25
The effect of temperature .........................................................................................25
The effect of pH changes .........................................................................................26
Chemical denaturation..............................................................................................27
Prosthetic groups and coenzymes little helpers...................................................28
Ion channels in biological membranes .....................................................................29
summary and required knowledge .........................................................................................30
1.3 Genetic
information ..............................................................................................................31
a) DNA the source of
hereditheredity ..........................................................................................31
b) The structure of DNA.......................................................................................................33
The DNA double helix...............................................................................................34
c) The structure of RNA.......................................................................................................35
d) Gene expression .............................................................................................................37
The role of DNA chains of information...................................................................37
Replication the biological assembly of new DNA ..................................................38
Semi-conservative replication...................................................................................39
Expressing the message the role of RNA..............................................................41

Delivering the message transcription ....................................................................41

Protein synthesis translating the message............................................................42
The genetic code......................................................................................................42
Translating the message ..........................................................................................43
e) Mutations.........................................................................................................................43
Sickle cell anaemia...................................................................................................44
Cystic Fibrosis ..........................................................................................................44

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A Level Science Applications Support Booklet: Chemistry
University of Cambridge International Examinations 2010

Improving nature re-designing enzymes ...............................................................46

summary and required knowledge .........................................................................................47
1.4 ATP, Lifes energy
currency ................................................................................................49
summary and required knowledge .........................................................................................51
1.5 Metals in biological
systems.................................................................................................52
a) Iron and the haem proteins .............................................................................................52
b) Zinc as an enzyme cofactor ............................................................................................53
c) Sodium and potassium ion transfer across cell membranes...........................................53
d) Toxic trace metals in the environment.............................................................................54
summary and required knowledge .........................................................................................55
Conclusion.....................................................................................................................................5
6
1.6 Revision self-assessment
questions ....................................................................................56
1.7 Key
definitions ......................................................................................................................59
1.8
Resources ............................................................................................................................62
2 APPLICATIONS OF ANALYTICAL
CHEMISTRY ........................................................................63
2.1
Introduction...........................................................................................................................63
a) Astrobiology.....................................................................................................................63
Life on Mars?............................................................................................................63
2.2 Determining
structures .........................................................................................................64
a) Mass spectrometry ..........................................................................................................64
12C:13C ratio ..............................................................................................................65
(M), (M+2) and (M+4) peaks.....................................................................................66
Molecular formulae from accurate masses...............................................................66
The use of fragmentation patterns............................................................................67
b) Nuclear Magnetic Resonance (NMR) spespectroscopy........................................................70
Magnetic properties of the nucleus...........................................................................70
The NMR spectrometer ............................................................................................71
The 1H NMR spectra of organic compounds ............................................................72
The 1H NMR spectrum of ethanol.............................................................................73
Some examples of 1H NMR spectra.........................................................................76
Analysis of the data
Magnetic Resonance Imaging (MRI) ........................................................................78

c) X-ray crystallography.......................................................................................................78
Case study: The structure of myoglobin ...................................................................81
summary and required knowledge .........................................................................................85
2.3 Separating and identifying
substances.................................................................................86
a) The partition of a solute between two immiscible solvents..............................................86
Successive extractions .............................................................................................88
b) Chromatography..............................................................................................................90
The basic principles and techniques ........................................................................90
Paper chromatography.............................................................................................91
Thin layer chromatography ......................................................................................92
Gas/liquid chromatography (GLC)............................................................................93
High performance liquid chromatography (HPLC)....................................................95
Applications of Chromatography in Analysis ............................................................96
A Level Science Applications Support Booklet: Chemistry
University of Cambridge International Examinations 2010

c) Electrophoresis................................................................................................................97
Factors affecting mobility........................................................................................100
Some medical applications of gel electrophoresis..................................................100
Other types of electrophoresis................................................................................100
d) Genetic fingerprinting ....................................................................................................101
The principle and method.......................................................................................101
The uses of genetic fingerprinting ..........................................................................104
summary and required knowledge .......................................................................................106
2.4 Examples of applications of analytical
chemistry ...............................................................107
a) Three methods of dating using mass spectrometry.......................................................107
Carbon dating.........................................................................................................107
Potassium-argon dating..........................................................................................107
Oxygen isotope ratios in the dating of ice cores.....................................................107
b) The use of combined GLC-MS in environmental monitoring.........................................108
Biomarkers in the petrochemical industry...............................................................108
Detecting PCBs and dioxins...................................................................................108
The Mars Viking lander...........................................................................................109
c) Two stories of detection by mass spectrometry ............................................................109
The solving of a historical mystery .........................................................................109
An ecological detective story ..................................................................................109
summary and required knowledge .......................................................................................110
2.5 Key
definitions ....................................................................................................................111
2.6 Resource
list.......................................................................................................................114
3 MATERIALS AND
DESIGN.........................................................................................................115
3.1
Introduction.........................................................................................................................115
Designing new drugs to cure diseases..........................................................................115
Can chemists make artificial silk?..................................................................................115
Nanotechnology ............................................................................................................116
Green chemistry and sustainability................................................................................116
And finally......................................................................................................................117

3.2 Medicinal chemistry and drug

delivery ...............................................................................118
a) Designing drugs ............................................................................................................118
b) Delivering drugs ............................................................................................................120
summary and required knowledge .......................................................................................122
3.3 Properties of
polymers .......................................................................................................123
a) Addition polymerisation .................................................................................................123
b) Condensation polymerisation ........................................................................................123
c) Spider Silk .....................................................................................................................124
d) Plastics that conduct electricity or emit light ..................................................................125
The traffic lights are changing ................................................................................127
summary and required knowledge .......................................................................................129
3.4
Nanotechnology. ................................................................................................................130
a) What is nanotechnology? ..............................................................................................130
Getting down to nanometres ..................................................................................130
b) Buckyballs - a new allotrope of carbon..........................................................................131
Carbon nanotubes..................................................................................................132
c) Supramolecular chemistry making super-molecules ..................................................134
d) Quantum dots................................................................................................................135
A Level Science Applications Support Booklet: Chemistry
University