| |
| |
| Welcome to the book | |
| |
| |
| Acknowledgements | |
| |
| |
| Periodic table of the elements | |
| |
| |
| |
| Introduction: why bother with chemistry? | |
| |
| |
| |
| Science: revealing our world | |
| |
| |
| I'm a biologist: why bother with chemistry? | |
| |
| |
| |
| The essential concepts | |
| |
| |
| |
| The language of chemistry | |
| |
| |
| Units: making sense of numbers | |
| |
| |
| Symbols | |
| |
| |
| |
| Atoms: the foundations of life | |
| |
| |
| |
| The chemical elements | |
| |
| |
| |
| Atomic composition | |
| |
| |
| Protons, electrons, and electrical charge | |
| |
| |
| Identifying the composition of an atom: atomic number and mass number | |
| |
| |
| The formation of ions | |
| |
| |
| Isotopes: varying the number of neutrons | |
| |
| |
| Relative abundances and atomic mass | |
| |
| |
| Protons and chemical identity | |
| |
| |
| |
| Atomic structure | |
| |
| |
| Atomic orbitals | |
| |
| |
| |
| The energy of atoms | |
| |
| |
| Orbitals and energy levels | |
| |
| |
| Filling up orbitals - the building-up principle | |
| |
| |
| The energy of subshells | |
| |
| |
| Moving between orbitals: electron excitation | |
| |
| |
| Energy levels and quantization | |
| |
| |
| |
| Valence shells and valence electrons | |
| |
| |
| |
| The periodic table | |
| |
| |
| The variety of life: not so varied after all? | |
| |
| |
| |
| Compounds and chemical bonding: bringing atoms together | |
| |
| |
| |
| The formation of compounds | |
| |
| |
| The chemical bond: bridging the gap between atoms | |
| |
| |
| Which electron configuration is most stable? | |
| |
| |
| |
| Valence shells and Lewis dot symbols | |
| |
| |
| Lone pairs of electrons | |
| |
| |
| |
| Bond formation: redistributing valence electrons | |
| |
| |
| |
| The ionic bond: transferring electrons | |
| |
| |
| Ionic bonding and full shells: how many electrons are transferred? | |
| |
| |
| |
| The chemical formula | |
| |
| |
| |
| The covalent bond: sharing electrons | |
| |
| |
| Covalent compounds and electrical charge | |
| |
| |
| The molecular formula: identifying the components of a covalent compound | |
| |
| |
| Covalent bonding and the distribution of electrons | |
| |
| |
| Molecular orbitals | |
| |
| |
| Sigma and pi orbitals | |
| |
| |
| |
| The formation of multiple bonds | |
| |
| |
| Valency and number of bonds | |
| |
| |
| Sharing one pair of electrons: the single bond | |
| |
| |
| Sharing two pairs of electrons: the double bond | |
| |
| |
| Sharing three pairs of electrons: the triple bond | |
| |
| |
| |
| Dative bonding: covalent bonding with a twist | |
| |
| |
| |
| Aromatic compounds and conjugated bonds | |
| |
| |
| |
| Polyatomic compounds | |
| |
| |
| |
| Ionic versus covalent bonding | |
| |
| |
| Electronegativity: how easily can electrons be transferred? | |
| |
| |
| Ionic and covalent bonding in nature: which is most prevalent? | |
| |
| |
| |
| Molecular forces: holding it all together | |
| |
| |
| |
| Chemical bonding versus non-covalent forces | |
| |
| |
| Intramolecular versus intermolecular forces | |
| |
| |
| The significance of non-covalent forces | |
| |
| |
| |
| The key characteristics of non-covalent forces | |
| |
| |
| |
| Polarity and polarization | |
| |
| |
| How strongly is a bond polarized? | |
| |
| |
| Non-polar covalent bonds | |
| |
| |
| Polar bonds in non-polar molecules | |
| |
| |
| |
| The key non-covalent forces | |
| |
| |
| Dispersion forces | |
| |
| |
| Hydrophobic forces, and dispersion forces in biological systems | |
| |
| |
| Permanent dipolar interactions | |
| |
| |
| Hydrogen bonds | |
| |
| |
| Ionic forces | |
| |
| |
| |
| Non-covalent forces: strength in numbers | |
| |
| |
| |
| Breaking intermolecular forces: the three states | |
| |
| |
| Changing states | |
| |
| |
| The transition between states | |
| |
| |
| The impact of non-covalent interactions on melting and boiling points | |
| |
| |
| |
| Organic compounds 1: the framework of life | |
| |
| |
| |
| Organic chemistry | |
| |
| |
| Carbon: its defining features | |
| |
| |
| The nature of organic compounds | |
| |
| |
| |
| The framework of organic compounds | |
| |
| |
| Representing chemical structures: the structural formula | |
| |
| |
| The alkanes: the backbone of organic chemistry | |
| |
| |
| The shape of organic compounds | |
| |
| |
| Physical properties of the alkanes | |
| |
| |
| Chemical properties of the alkanes | |
| |
| |
| |
| Functional groups and the carbon framework | |
| |
| |
| The double bond | |
| |
| |
| Physical properties of alkenes | |
| |
| |
| |
| Adding functional groups to the carbon framework | |
| |
| |
| Alkyl groups | |
| |
| |
| The aryl group: a special hydrocarbon group | |
| |
| |
| Functional groups and the properties of organic compounds | |
| |
| |
| |
| Organic compounds 2: adding function to the framework of life | |
| |
| |
| |
| Organic compounds with oxygen-based functional groups | |
| |
| |
| The alcohols: the hydroxyl group | |
| |
| |
| The ethers: the alkoxy group | |
| |
| |
| The aldehydes and ketones: the carbonyl group | |
| |
| |
| The carboxylic acids: combining the hydroxyl and carbonyl groups | |
| |
| |
| The esters: a modified carboxyl group | |
| |
| |
| |
| Organic compounds and nitrogen-based functional groups | |
| |
| |
| The amines: the amino group | |
| |
| |
| The amides: the amide group | |
| |
| |
| |
| Other functional groups | |
| |
| |
| The thiols and the sulfur-based functional group | |
| |
| |
| The haloalkanes and the halogen-based functional group | |
| |
| |
| |
| Biological macromolecules: providing life's Infrastructure | |
| |
| |
| |
| Amino acids and proteins | |
| |
| |
| The composition of amino acids | |
| |
| |
| Formation of polypeptides | |
| |
| |
| |
| Carbohydrates | |
| |
| |
| The composition of monosaccharides | |
| |
| |
| |
| Lipids | |
| |
| |
| Steroids | |
| |
| |
| Triacylglycerols | |
| |
| |
| Glycerophospholipids | |
| |
| |
| |
| Nucleic acids | |
| |
| |
| Nucleotides and their composition | |
| |
| |
| Formation of nucleic acids | |
| |
| |
| The shape of nucleic acids | |
| |
| |
| Nucleic acids: nature's energy stores | |
| |
| |
| |
| Molecular shape and structure 1: from atoms to small molecules | |
| |
| |
| |
| The link between structure and function | |
| |
| |
| Hierarchies of structure | |
| |
| |
| |
| The shape of small molecules | |
| |
| |
| Bond lengths | |
| |
| |
| |
| Bond angles | |
| |
| |
| Valence Shell Electron Pair Repulsion (VSEPR) | |
| |
| |
| VSEPR theory and the shape of molecules with multiple bonds | |
| |
| |
| |
| Hybridization and shape | |
| |
| |
| Hybridizing different numbers of orbitals | |
| |
| |
| |
| Bond rotation and conformation | |
| |
| |
| Conformation versus configuration | |
| |
| |
| |
| Molecular shape and structure 2: the shape of large molecules | |
| |
| |
| |
| Constructing larger molecules | |
| |
| |
| The geometry of joined atoms | |
| |
| |
| The sequence of monomers within a polymer | |
| |
| |
| Bonding between monomers | |
| |
| |
| |
| The shape of larger molecules | |
| |
| |
| Building up structural complexity: a structural hierarchy | |
| |
| |
| The hierarchy of biological structure: an overview | |
| |
| |
| |
| Maintaining shape, and allowing flexibility | |
| |
| |
| The importance of structural flexibility: muscle contraction | |
| |
| |
| The importance of structural flexibility: enzymes | |
| |
| |
| |
| Chemical analysis 1: how do we know what is there? | |
| |
| |
| |
| What is chemical analysis? | |
| |
| |
| |
| How do we separate out what is there? | |
| |
| |
| Filtration | |
| |
| |
| Chromatography | |
| |
| |
| Electrophoresis | |
| |
| |
| |
| How do we determine what is there? | |
| |
| |
| Measuring mass: mass spectrometry | |
| |
| |
| |
| Building up the picture: spectroscopic techniques | |
| |
| |
| Spectroscopy and electromagnetic radiation | |
| |
| |
| Characterizing the carbon framework: nuclear magnetic resonance spectroscopy | |
| |
| |
| Identifying functional groups: infrared spectroscopy | |
| |
| |
| Establishing 3-D structure: X-ray crystallography | |
| |
| |
| |
| Chemical analysis 2: how do we know how much is there? | |
| |
| |
| |
| The mole | |
| |
| |
| Connecting molar quantities to mass | |
| |
| |
| |
| Concentrations | |
| |
| |
| Calculating the number of moles of substance in a sample of solution | |
| |
| |
| Preparing a solution of known concentration | |
| |
| |
| Calculating the concentration of a solution | |
| |
| |
| Changing the concentration: solutions and dilutions | |
| |
| |
| |
| Measuring concentrations | |
| |
| |
| UV-visible spectrophotometry | |
| |
| |
| Titrations | |
| |
| |
| Electrochemical sensors | |
| |
| |
| |
| Isomerism: generating chemical variety | |
| |
| |
| |
| Isomers | |
| |
| |
| |
| Structural isomers | |
| |
| |
| Distinguishing structural isomers | |
| |
| |
| Structural isomerism and the shape of the carbon framework | |
| |
| |
| Structural isomerism and the positioning of functional groups | |
| |
| |
| Structural isomerism: unifying chemical families | |
| |
| |
| |
| Stereoisomers | |
| |
| |
| Geometric isomers | |
| |
| |
| Enantiomers | |
| |
| |
| |
| Chirality | |
| |
| |
| How do we distinguish one enantiomer from its mirror image? | |
| |
| |
| Chirality in biological systems | |
| |
| |
| |
| The chemistry of isomers | |
| |
| |
| The biological chemistry of enantiomers | |
| |
| |
| The impact of chirality on medicinal chemistry | |
| |
| |
| |
| Chemical reactions: bringing molecules to life | |
| |
| |
| |
| What is a chemical reaction? | |
| |
| |
| The stoichiometry of chemical reactions | |
| |
| |
| |
| The molecular basis of chemical reactions | |
| |
| |
| How do valence electrons move during chemical reactions? | |
| |
| |
| Depicting the movement of electrons | |
| |
| |
| |
| Heterolytic reactions | |
| |
| |
| Oxidation and reduction | |
| |
| |
| Heterolytic reactions and the polarization of bonds | |
| |
| |
| |
| Homolytic reactions | |
| |
| |
| Initiation | |
| |
| |
| Propagation | |
| |
| |
| Termination | |
| |
| |
| |
| Reaction mechanisms | |
| |
| |
| Transition states and intermediates | |
| |
| |
| Substitution | |
| |
| |
| Addition | |
| |
| |
| Elimination | |
| |
| |
| Condensation | |
| |
| |
| Biochemical reactions: from food to energy | |
| |
| |
| |
| Energy: what makes reactions go? | |
| |
| |
| |
| What is energy? | |
| |
| |
| Kinetic energy | |
| |
| |
| Potential energy | |
| |
| |
| Chemical energy | |
| |
| |
| |
| Energy transfer | |
| |
| |
| The transfer of energy as work | |
| |
| |
| The transfer of energy as heat | |
| |
| |
| Heat versus temperature | |
| |
| |
| The spontaneous transfer of heat | |
| |
| |
| |
| Energy transfer and chemical reactions | |
| |
| |
| How can we determine the enthalpy change for a reaction? | |
| |
| |
| Depicting enthalpy changes: the energy diagram | |
| |
| |
| Enthalpy changes and the stability of chemical compounds | |
| |
| |
| |
| Entropy: the spread of energy as the engine of change | |
| |
| |
| The link between entropy and energy | |
| |
| |
| The overall entropy change in a universe | |
| |
| |
| |
| Gibbs free energy: the driving force of chemical reactions | |
| |
| |
| The Gibbs free energy of spontaneous reactions | |
| |
| |
| Gibbs free energy and cell metabolism | |
| |
| |
| |
| Kinetics: what affects the speed of a reaction? | |
| |
| |
| |
| The rate of a reaction | |
| |
| |
| What is the rate of a reaction? | |
| |
| |
| |
| The collision theory of reaction rates | |
| |
| |
| Increasing the concentration | |
| |
| |
| Increasing the temperature | |
| |
| |
| |
| The activation energy: getting reactions started | |
| |
| |
| Breaking the energy barrier: the transition state | |
| |
| |
| |
| Catalysis: lowering the activation energy | |
| |
| |
| The role of catalysts in chemical reactions | |
| |
| |
| |
| Enzymes: important biological catalysts | |
| |
| |
| The specificity of enzymes | |
| |
| |
| What happens during enzyme catalysis? | |
| |
| |
| |
| Enzyme kinetics | |
| |
| |
| Increasing substrate concentration: the limitation of the enzyme's active site | |
| |
| |
| Increasing temperature: the limitation of being a protein | |
| |
| |
| |
| Equilibria: how far do reactions go? | |
| |
| |
| |
| Equilibrium reactions | |
| |
| |
| Equilibrium reactions and chemical change | |
| |
| |
| Does it matter which reaction is 'forward' and which is 'back'? | |
| |
| |
| |
| Forward and back reactions: where is the balance struck? | |
| |
| |
| The equilibrium constant | |
| |
| |
| The magnitude of equilibrium constants | |
| |
| |
| |
| The reaction quotient | |
| |
| |
| Predicting the direction of a reaction | |
| |
| |
| |
| Perturbing an equilibrium | |
| |
| |
| Changing the concentration of the system | |
| |
| |
| Changing the pressure or volume of the system | |
| |
| |
| Changing the temperature | |
| |
| |
| Using chemical equilibria to our advantage | |
| |
| |
| Catalysts and chemical equilibria | |
| |
| |
| |
| Free energy and chemical equilibria | |
| |
| |
| Gibbs free energy and the position of equilibrium | |
| |
| |
| |
| The aqueous environment: the medium of life | |
| |
| |
| |
| Acids and bases: making life happen | |
| |
| |
| Defining acids and bases | |
| |
| |
| Acids and bases in aqueous solution | |
| |
| |
| Pairing up acids and bases: the conjugate acid-base pair | |
| |
| |
| |
| The strength of acids and bases: to what extent does the dissociation reaction occur? | |
| |
| |
| Juggling protons: the tug-of-war between conjugate acid-base pairs | |
| |
| |
| The acid dissociation constant: to what extent does an acid dissociate? | |
| |
| |
| The base dissociation constant: to what extent does a base dissociate? | |
| |
| |
| |
| Keeping things balanced: the ion product of water | |
| |
| |
| Making use of the ion product of water | |
| |
| |
| Linking K[subscript w prime] K[subscript a] and K[subscript b] | |
| |
| |
| |
| Measuring concentrations: the pH scale | |
| |
| |
| The pH of strong and weak acids | |
| |
| |
| Changing pH: neutralization reactions | |
| |
| |
| pOH: the basic equivalent of pH | |
| |
| |
| |
| Buffer solutions: keeping pH the same | |
| |
| |
| How does a buffer solution work? | |
| |
| |
| The pH of buffer solutions | |
| |
| |
| Epilogue | |
| |
| |
| Bibliography | |
| |
| |
| Answers to self-check questions | |
| |
| |
| Index | |