A Level Science Applications Support Booklet: Chemistry

A Level Science

Contents INTRODUCTION 1

Applications

A Level Science Applications Support

Support Booklet: Chemistry

Bookwlwetw:.

1 ? THE CHEMISTRY OF LIFE .............................................................................................................3

1.1 ? Introduction.............................................................................................................................3 Water ? Life's 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 ? Nature's 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 heredity ..........................................................................................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

? University of Cambridge International Examinations 2010

A Level Science Applications Support Booklet: Chemistry

Improving nature ? re-designing enzymes ...............................................................46 summary and required knowledge .........................................................................................47

1.4 ? ATP, Life's 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..................................................................................................................................... 56

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) spectroscopy........................................................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

? University of Cambridge International Examinations 2010

A Level Science Applications Support Booklet: Chemistry

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

? University of Cambridge International Examinations 2010

A Level Science Applications Support Booklet: Chemistry e) Promise and possible problems of nanotechnology ......................................................136 summary and required knowledge .......................................................................................136 3.5 ? Environment and energy ...........................................................................................................137 a) Chemistry to overcome environmental problems ..........................................................137

Oil slicks .................................................................................................................137 Remediation of contaminated soils.........................................................................137 Soil remediation using physical properties .............................................................137 Soil remediation using chemical properties ............................................................138 Remediation of contaminated ground water ? plants to the rescue .......................138 b) Trouble in the stratosphere - replacing CFCs................................................................139 c) Green chemistry and sustainability................................................................................139 Use of supercritical CO2 as a solvent .....................................................................140 Ionic liquids.............................................................................................................141 Rock-munching bacteria.........................................................................................142 d) Chemistry for energy .....................................................................................................143 Biofuels: diesel and ethanol fuels ...........................................................................143 Batteries and fuel cells ...........................................................................................143 Overcoming the hydrogen storage problem ...........................................................144 Sourcing hydrogen .................................................................................................144 The future of nuclear power, potentially the greenest of fuels?..............................144 summary and required knowledge .......................................................................................145 3.6 ? Key definitions ....................................................................................................................146 3.7 ? Resources ..........................................................................................................................147 Nanotechnology worksheet .........................................................................................................148 4 ? SPECIMEN EXAMINATION QUESTIONS ..................................................................................152

? University of Cambridge International Examinations 2010

A Level Science Applications Support Booklet: Chemistry

Acknowledgements

Thanks are due to Richard Harwood, Peter Cann and Brian Ratcliff for writing this booklet, to David Bevan for editing it and to the Royal Society of Chemistry for generous provision of source material.

Figure 1.1 NASA Images

Figures 1.2, 1.3, 1.7, 1.10, 1.11, 1.12, 1.13, 1.16, 1.18, 1.21, 1.23, 1.26, , 1.32, 1.33, 1.34, 1.35, 1.36, 1.38, 1.39, 1.40, 1.41, 1.42, 1.43 and 1.44 ? Richard Harwood (2002) Biochemistry in the Cambridge Advanced Sciences series, Cambridge University Press, ISBN: 0521797519

Figure 1.30 reproduced with permission from Joseph W. Lauher, SUNY Stony Brook

Figures 1.31 and 2.20 ? Science Photo Library, image G110/636

Figures 2.1, 2.9, 2.31, 2.33, 2.34 and 2.36 ? Ben Faust (1997) Modern Chemical Techniques, Royal Society of Chemistry, ISBN 1870343190

Figures 2.2 and 2.3 National Institute of Advanced Industrial Science and Technology Spectral Database for Organic Compounds, SDBS. A free website organized by the National Institute of Advanced Industrial Science and Technology (AIST), Japan, aist.go.jp/RIODB/SDBS/cgibin/cre_index.cgi

Figure 2.4 Spectroscopy for Schools and Colleges CD-ROM, Royal Society of Chemistry

Figures 2.19, 2.40 and 2.41 ? Ralph Levinson (2001) More Modern Chemical Techniques, Royal Society of Chemistry, ISBN 0854049290

Figure 2.24 Myoglobin,

Figure 2.27 ? Philip Matthews (2002) Gases, Liquids and Solids in the Cambridge Advanced Sciences series, Cambridge University Press, ISBN: 0521797500

Figures 2.29, 2.30, 2.35 and 2.44 ? Anne McCarthy (2001) Methods of Analysis and Detection in the Cambridge Advanced Sciences series, Cambridge University Press ISBN 0521787246

Figure 2.43 ? Thomas D Gelehrter, Francis Collins, David Ginsburg (Editor) (1998) Principles of Medical Genetics, Lippincott Williams and Wilkins, ISBN: 0683034456

Figure 2.45 ? Stephen M Carr,

Figure 3.2 reproduced with permission from Dr Corinne Baumgartner, ETH Z?rich

Figure 3.5 reproduced with permission from the University of Bristol,

Figure 3.6 reproduced with permission from Brian Ratcliff

Figure 3.7 reproduced with permission from Jessops

Figure 3.8 Wikipedia, Fullerene,

? University of Cambridge International Examinations 2010

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