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Contents Preface Acknowledgements Chapter 1 Basic Concepts 1.1 Introduction 1.1.1 The states of matter 1.1.2 Elements, Compounds and Mixtures 1.2 Measurement and units 1.2.1 Scales of units 1.2.2 A review of some commonly used measurements 1.2.3 Accuracy and precision 1.3 Atoms 1.3.1 Isotopes 1.3.2 Isotopes, radioactivity and the types of radiation 1.3.3 Electrons 1.3.4 Molecules 1.4 The concepts of stoichiometry: calculations of quantity in chemistry 1.4.1 Introduction 1.4.2 Avogadro |s number and the concept of the mole 1.4.3 Formulae and molecular mass 1.4.4 Mass percent composition 1.4.5 Empirical and molecular formulae 1.4.6 Writing and Balancing Chemical Equations 1.4.7 Balancing Equations: A systematic approach 1.4.8 Moles and masses 1.4.9 Concentration of solutions Questions Chapter 2. Atoms, Periodicity and Chemical Bonding 2.1 Electronic structure 2.2 Electromagnetic radiation 2.3 The Bohr Model of the Atom 2.4 An introduction to atomic orbitals 2.5 Electron configurations in atoms 2.6 The periodic table 2.6.1 Periodic properties 2.7 An introduction to bonding. How atoms become molecules. 2.7.1 Introduction 2.7.2 Ionic Bonding 2.7.3 Covalent Bonding 2.7.4 Formaloxidation states 2.7.5 Polarisation: covalent or ionic bonding? 2.7.6 Metallic Bonding 2.7.7 Shapes of molecules V the VSEPR approach 2.7.8 Resonance 2.8 Covalent bonding V atomic and molecular orbitals 2.9 Intermolecular Forces 2.9.1 Dipole-dipole interactions 2.9.2 Dispersion (London) Forces 2.9.3 Hydrogen Bonding 2.9.4 Biological implications of hydrogen bonding Questions Chapter 3. An Introduction to the Chemistry of Carbon 3.1 Introduction 3.2 Properties of carbon 3.3 Classification of organic molecules 3.3.1 Nomenclature (naming) of organic compounds 3.3.2 Systematic Nomenclature 3.3.3 Introduction to the Functional Groups concept 3.3.4 Naming of aliphatic compounds containing functional groups 3.4 The structure of organic molecules 3.4.1 Structural features of organic chemistry 3.4.2 Introduction to isomerism 3.4.3 Structural/constitutional isomerism 3.4.4 Introduction to stereoisomerism 3.4.5 Conformation 3.4.6 Introduction to configurational isomerism 3.4.7 Geometrical isomerism 3.4.8 Symmetry, chirality and optical isomerism 3.4.9 Why is shape important? V some examples. Questions Chapter 4 Energetics 4.1 Introduction 4.1.1 The idea of energy 4.1.2 Energy: heat, work and the first law of thermodynamics 4.2 Temperature and Heat 4.2.1 The nature of heat 4.2.2 Heat capacity, C and specific heat capacity, c 4.2.3 Endothermic and Exothermic Processes 4.3 The First Law of Thermodynamics V introducing the concept of work 4.3.1 The Nature of Work 4.3.2 Energy in the chemistry context 4.3.3 The Concept of Enthalpy 4.3.4 Examples of enthalpy changes in biological processes 4.3.5 The Determination of Enthalpies: Hess |s Law 4.4 Spontaneous processes, entropy and free energy 4.4.1 The 2nd Law of thermodynamics. 4.4.2 Free energy and ATP: Coupling of reactions 4.4.3 Biological example: Thermodynamic rationale of micelle behaviour Questions Chapter 5 Equilibria: How far does a reaction go? 5.1 Introduction 5.2 Developing the idea of equilibrium: the equilibrium constant 5.2.1 Calculation of equilibrium constants and concentrations 5.3 Equilibrium and energetics 5.3.1 Background 5.3.2 The reaction quotient 5.3.3 Calculating equilibrium constants in the gas phase, using partial pressures; Kp 5.4 The relationship between fGfa and K. 5.4.1 A more detailed look at reaction quotient Q and equilibrium constant, K. 5.5 Disturbing an equilibrium 5.5.1 Statement of Le Chatelier |s Principle 5.5.2 Le Chatelier |s principle and the effect of temperature on equilibria. 5.5.3 Examples involving Le Chatelier |s principle 5.6 Energetics and equilibria in the biological context. 5.6.1 Calculating fG o from experimentally determined compositions (via K values) 5.6.2 Calculating equilibrium compositions from fG o 5.6.3 Macromolecule-ligand interactions. 5.6.4 Haemoglobin - oxygen 5.7 Revisiting coupled reactions Questions Chapter 6 Aqueous Equilibria 6.1 Introduction 6.1.1 Why is this important in biology? 6.1.2 The importance of pH and pH control 6.2 Self ionisation of water 6.3 Acids and bases 6.3.1 What do the terms acid and base mean? 6.3.2 Properties of acids 6.3.3 Properties of bases6.3.4 Strong acids and strong bases 6.4 Acid Vbase equilibria 6.4.1 Behaviour of weak acids 6.4.2 Behaviour of weak bases 6.5 Dissociation of acids and bases - conjugate acids and bases 6.6 Acids and bases in aqueous solution V the concept of pH 6.6.1 Definition 6.6.2 What happens when acids are dissolved in water? 6.6.3 What happens when the water equilibrium is disturbed 6.6.4 Calculating pH values for acids 6.7 The control of pH - buffer solutions 6.7.1 Background 6.7.2 Theoretical aspects of buffers 6.7.3 General Strategy for making buffer solutions 6.8 Polyprotic acids 6.9 Salts 6.9.1 Titrations 6.10 Introducing solubility 6.10.1 Insoluble ionic compounds. The concept of solubility product. 6.10.2 The common ion effect Questions Chapter 7 Biomolecules and biopolymers 7.1 Introduction 7.2 Lipids 7.2.1 Fats, oils and fatty acids 7.2.2 Triglyceride fats 7.2.3 Uses of fats - micelles 7.2.4 Phospholipids 7.2.5 Waxes 7.2.6 Steroids 7.3 Carbohydrates 7.3.1 Monosaccharides 7.3.2 Carbohydrate stereochemistry 7.3.3 Cyclisation in sugars 7.3.4 Di- and polysaccharides 7.4 Amino acids, peptides and proteins 7.4.1 Introduction 7.4.2 Acid-base behaviour of amino acids: zwitterions 7.4.3 The isoelectric point 7.4.4 The stereochemistry of amino acids 7.4.5 Peptides and proteins 7.4.6 Primary, secondary, tertiary and quaternary structures 7.4.7 Denaturing of proteins 7.5 Nucleic acids 7.5.1 Introduction 7.5.2 Primary structure of nucleic acids 7.5.3 Secondary structure in nucleic acids 7.5.4 Structural features of RNA Questions Chapter 8 Reaction mechanisms 8.1 Introduction 8.2 Organic Reaction Types 8.2.1 Addition reactions 8.2.2 Elimination reactions 8.2.3 Substitution reactions 8.2.4 Isomerisation reactions 8.2.5 Oxidation and reduction 8.3 Reaction mechanisms 8.3.1 Catalysts 8.3.2 Homolysis: 8.3.3 Heterolysis: 8.3.4 Carbocations and carbanions; types and key points 8.4 Electronegativity and bond polarity 8.5 Addition Reactions 8.5.1 Electrophilic additions to alkenes and alkynes 8.5.2 Addition of HBr to unsymmetrical alkenes 8.5.3 Addition of other electrophiles to alkenes 8.5.4 Electrophilic addition in biology 8.5.5 Electrophilic addition without subsequent nucleophilic addition; loss of H+ 8.5.6 Addition of HBr to conjugated dienes 8.5.7 Additions to alkynes 8.6 Substitution and elimination reactions 8.6.1 Nucleophilic substitution at a saturated carbon atom 8.6.2 Bimolecular nucleophilic substitution SN2 8.6.3 Unimolecularnucleophilic substitution SN1 8.6.4 Determining which mechanism is followed 8.7 Elimination reactions 8.7.1 Bimolecular elimination, E2 8.7.2 Unimolecular elimination, E1 8.8 Biological example of an SN2 reaction 8.9 Reaction mechanisms of carbonyl compounds 8.9.1 Introduction 8.9.2 Structure of the carbonyl group, C=O 8.10 Reactions of aldehydes and ketones 8.10.1 Reaction of aldehydes and ketones with hydride 8.10.2 Hydration of aldehydes and ketones 8.10.3 Hemiacetal formation 8.10.4 Acetal (ketal) formation 8.10.5 Formation of Schiff |s bases and imines 8.10.6 Oxidation of aldehydes and ketones 8.11 Carboxylic acid derivatives 8.11.1 Esters 8.11.2 Acid catalysed hydrolysis of esters 8.11.3 Base (:OH-) induced hydrolysis of esters 8.11.4 Amides 8.12 Enolisation and enolisation reactions 8.12.1 Enols as carbon nucleophiles 8.12.2 Base-catalysedenolisation 8.13 Reactions resulting from enolisation 8.13.1 The Aldol reaction 8.13.2 Crossed aldol reactions / condensations 8.13.3 Claisen condensations 8.14 Reaction mechanisms in biological reactions: synthesis of steroids 8.15 Summary of mechanisms of carbonyl reactions under different conditions Questions Chapter 9. Chemical kinetics 9.1 Introduction 9.2 Rates, rate laws and rate constants 9.2.1 Rate of reaction 9.2.2 Rates and concentration 9.2.3 Units of the rate constant 9.2.4 Determination of rate laws and rate constants 9.3 Temperature dependence of reaction rates and rate constants 9.4 Reaction mechanisms 9.4.1 Deducing reaction mechanisms 9.4.2 A more comprehensive look at complex reaction mechanisms 9.5 Kinetics of enzyme catalysed reactions 9.5.1 Catalysts and catalysis 9.5.2 Enzymes as catalysts 9.5.3 Single-substrate enzyme reactions 9.5.4 Analysis of enzyme kinetic data 9.6 Enzyme inhibition 9.6.1 Mechanisms of inhibition Questions Chapter 10 Bioenergetics and Bioelectrochemistry 10.1 Introduction 10.2 Electrochemical cells 10.2.1 Cells and cell nomenclature 10.2.2 Types of half cell 10.2.3 Measurement of cell voltage 10.2.4 Free energy relationship 10.2.5 Determination of the reaction taking place in a cell 10.2.6 Effect of concentration 10.3 Sensors and reference electrodes 10.3.1 The silver electrode 10.3.2 The calomel electrode 10.3.3 Detecting pH 10.4 Biological Relevance 10.4.1 Biochemical/biological standard state 10.4.2. Biological membranes 10.4.3 The thermodynamics of membrane transport 10.4.4 Proton motive force 10.5 Summary Questions Chapter 11. The role of elements other than carbon 11.1 Introduction 11.2 Phosphorus and phosphate esters 11.2.1Phosphoric acid and phosphate esters 11.2.2Relevance to biology 11.3 Metals in the chemistry of biology 11.4 Transition metals and their role in biological systems 11.4.1 Introduction to ligands in biological systems. 11.4.2 Introduction to transition metals 11.4.3Crystal field theory 11.4.4Examples of transition metals in biological systems 11.5 The alkali and alkaline-earth metals 11.5.1 Introduction 11.5.2 Solid state structures 11.5.3 Coordination chemistry of group 1 and group 2 metals 11.5.4 Ions of alkali and alkaline-earth metal ions in biology Questions Chapter 12 Metabolism 12.1 Introduction 12.2Glycolysis 12.2.1 Introduction to glycolysis 12.2.2 The glycolysis pathway 12.3 Analysis of the mechanism of glycolysis 12.3.1 Glycolysis step 1 12.3.2 Glycolysis step 2 12.3.3 Glycolysis step 3 12.3.4 Glycolysis step 4 12.3.5 Glycolysis step 5 12.3.6 Glycolysis step 6 12.3.7 Glycolysis step 7 12.3.8 Glycolysis step 8 12.3.9 Glycolysis step 9 12.3.10 Glycolysis step 10 12.3.11 Summary 12.4 What now? Where does the pyruvate go? 12.4.1 Conversion of pyruvate into lactate 12.4.2 Conversion of pyruvate into ethanol 12.4.3 Conversion of pyruvate into acetyl-coenzyme-A 12.5 The TCA cycle 12.5.1 Introduction and overview 12.6 Analysis of the mechanism of the TCA cycle 12.6.1 TCA cycle, step 1 12.6.2 TCA cycle, step 2 12.6.3 TCA cycle, step 3 12.6.4 TCA cycle step 4 12.6.5 TCA cycle, step 5 12.6.6 TCA cycle, step 6 12.6.7 TCA cycle, step 7 12.6.8 TCA cycle, step 8 12.7 Summary of outcomes of the glycolysis and TCA cycles 12.8 Gluconeogenesis Questions Chapter 13 Structural Methods 13.1 Introduction 13.2 Mass Spectrometry 13.2.1 Background 13.2.2 Analysis of a mass spectrum 13.2.3 Isotopes: complicating factors or diagnostic tools? 13.2.4 Fragmentation pathways involving functional groups 13.2.5 Uses in biology 13.3 Introduction to electromagnetic radiation 13.3.1 Background principles 13.4 Ultraviolet and visible (UV-vis) spectroscopy 13.4.1 Introduction 13.4.2 Measurement of the spectrum 13.4.3 Using UV-vis Spectra for characterising compounds 13.4.4 Aromatic compounds 13.4.5 Using UV-visible spectra for measuring concentrations of biologically important compounds 13.5 Infrared (IR) Spectroscopy 13.5.1 Introduction 13.5.2 Measurement of the spectrum 13.5.3 Interpretation of IR Spectra 13.6 Nuclear Magnetic Resonance spectroscopy 13.6.1 Introduction and basic principles 13.6.2 Design of the NMR Spectrometer 13.6.3 The 1H NMR Spectrum 13.6.4 The Chemical Shift 13.6.5 Peak areas - integration 13.6.6 The solvent 13.6.7 Exchangeable hydrogens 13.6.8 Nuclear spin-spin coupling 13.6.9 Worked example 13.6.1013C nmr spectroscopy 13.7 X-ray Diffraction 13.7.1 Background 13.8 Summary of the techniques Questions Appendix 1 Basic Mathematical Tools for Biological Chemistry Appendix 2 Answers to end of chapter questions Appendix 3 - Periodic Table of the Elements

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