Chemistry for Biologists

Chemistry for Biologists

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Chemistry for Biologists provides a focused yet chemically and mathematically rigorous introduction to those key aspects of chemistry that form the basis of biological processes. Written in a straightforward, accessible style, the book begins with an overview of basic chemical concepts. Building on these core principles, the reader is guided through subjects such as the structure and properties of organic molecules, equilibria, energetics, kinetics, biomolecules, reaction mechanisms, metabolism and structural methods. The relevance of each chemical concept to the study of biology is clearly explained at every stage, enabling students to develop a deep appreciation of the chemistry that underpins their chosen subject, and become confident in applying this knowledge to their own studies.show more

Product details

  • Paperback | 520 pages
  • 191 x 244 x 25.4mm | 968g
  • Pearson Education Limited
  • Harlow, United Kingdom
  • English
  • Student edition
  • Student edition
  • 1408280825
  • 9781408280829
  • 52,539

Table of contents

ContentsPrefaceAcknowledgementsChapter 1 Basic Concepts1.1 Introduction1.1.1 The states of matter1.1.2 Elements, Compounds and Mixtures1.2 Measurement and units1.2.1 Scales of units1.2.2 A review of some commonly used measurements1.2.3 Accuracy and precision1.3 Atoms 1.3.1 Isotopes1.3.2 Isotopes, radioactivity and the types of radiation1.3.3 Electrons1.3.4 Molecules1.4 The concepts of stoichiometry: calculations of quantity in chemistry1.4.1 Introduction1.4.2 AvogadroΥ|s number and the concept of the mole1.4.3 Formulae and molecular mass1.4.4 Mass percent composition1.4.5 Empirical and molecular formulae1.4.6 Writing and Balancing Chemical Equations1.4.7 Balancing Equations: A systematic approach1.4.8 Moles and masses1.4.9 Concentration of solutionsQuestions Chapter 2. Atoms, Periodicity and Chemical Bonding2.1 Electronic structure2.2 Electromagnetic radiation2.3 The Bohr Model of the Atom2.4 An introduction to atomic orbitals2.5 Electron configurations in atoms2.6 The periodic table2.6.1 Periodic properties2.7 An introduction to bonding. How atoms become molecules.2.7.1 Introduction2.7.2 Ionic Bonding2.7.3 Covalent Bonding2.7.4 Formaloxidation states2.7.5 Polarisation: covalent or ionic bonding?2.7.6 Metallic Bonding2.7.7 Shapes of molecules ΥV the VSEPR approach2.7.8 Resonance2.8 Covalent bonding ΥV atomic and molecular orbitals2.9 Intermolecular Forces2.9.1 Dipole-dipole interactions2.9.2 Dispersion (London) Forces2.9.3 Hydrogen Bonding2.9.4 Biological implications of hydrogen bondingQuestions Chapter 3. An Introduction to the Chemistry of Carbon3.1 Introduction3.2 Properties of carbon3.3 Classification of organic molecules3.3.1 Nomenclature (naming) of organic compounds3.3.2 Systematic Nomenclature 3.3.3 Introduction to the Functional Groups concept3.3.4 Naming of aliphatic compounds containing functional groups3.4 The structure of organic molecules3.4.1 Structural features of organic chemistry3.4.2 Introduction to isomerism3.4.3 Structural/constitutional isomerism 3.4.4 Introduction to stereoisomerism 3.4.5 Conformation3.4.6 Introduction to configurational isomerism3.4.7 Geometrical isomerism3.4.8 Symmetry, chirality and optical isomerism3.4.9 Why is shape important? ΥV some examples.Questions Chapter 4 Energetics 4.1 Introduction4.1.1 The idea of energy 4.1.2 Energy: heat, work and the first law of thermodynamics4.2 Temperature and Heat4.2.1 The nature of heat4.2.2 Heat capacity, C and specific heat capacity, c4.2.3 Endothermic and Exothermic Processes4.3 The First Law of Thermodynamics ΥV introducing the concept of work4.3.1 The Nature of Work4.3.2 Energy in the chemistry context4.3.3 The Concept of Enthalpy4.3.4 Examples of enthalpy changes in biological processes4.3.5 The Determination of Enthalpies: HessΥ|s Law4.4 Spontaneous processes, entropy and free energy4.4.1 The 2nd Law of thermodynamics. 4.4.2 Free energy and ATP: Coupling of reactions4.4.3 Biological example: Thermodynamic rationale of micelle behaviourQuestions Chapter 5 Equilibria: How far does a reaction go? 5.1 Introduction5.2 Developing the idea of equilibrium: the equilibrium constant5.2.1 Calculation of equilibrium constants and concentrations5.3 Equilibrium and energetics5.3.1 Background5.3.2 The reaction quotient5.3.3 Calculating equilibrium constants in the gas phase, using partial pressures; Kp5.4 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 equilibrium5.5.1 Statement of Le ChatelierΥ|s Principle5.5.2 Le ChatelierΥ|s principle and the effect of temperature on equilibria.5.5.3 Examples involving Le ChatelierΥ|s principle5.6 Energetics and equilibria in the biological context.5.6.1 Calculating fGΥo from experimentally determined compositions (via K values)5.6.2 Calculating equilibrium compositions from fGΥo5.6.3 Macromolecule-ligand interactions.5.6.4 Haemoglobin - oxygen5.7 Revisiting coupled reactionsQuestions Chapter 6 Aqueous Equilibria6.1 Introduction6.1.1 Why is this important in biology?6.1.2 The importance of pH and pH control6.2 Self ionisation of water6.3 Acids and bases6.3.1 What do the terms acid and base mean?6.3.2 Properties of acids6.3.3 Properties of bases6.3.4 Strong acids and strong bases6.4 AcidΥVbase equilibria6.4.1 Behaviour of weak acids6.4.2 Behaviour of weak bases6.5 Dissociation of acids and bases - conjugate acids and bases6.6 Acids and bases in aqueous solution ΥV the concept of pH6.6.1 Definition6.6.2 What happens when acids are dissolved in water?6.6.3 What happens when the water equilibrium is disturbed6.6.4 Calculating pH values for acids6.7 The control of pH - buffer solutions6.7.1 Background6.7.2 Theoretical aspects of buffers6.7.3 General Strategy for making buffer solutions6.8 Polyprotic acids6.9 Salts6.9.1 Titrations6.10 Introducing solubility6.10.1 Insoluble ionic compounds. The concept of solubility product.6.10.2 The common ion effectQuestions Chapter 7 Biomolecules and biopolymers7.1 Introduction7.2 Lipids7.2.1 Fats, oils and fatty acids7.2.2 Triglyceride fats7.2.3 Uses of fats - micelles7.2.4 Phospholipids7.2.5 Waxes 7.2.6 Steroids7.3 Carbohydrates7.3.1 Monosaccharides7.3.2 Carbohydrate stereochemistry7.3.3 Cyclisation in sugars7.3.4 Di- and polysaccharides7.4 Amino acids, peptides and proteins7.4.1 Introduction7.4.2 Acid-base behaviour of amino acids: zwitterions7.4.3 The isoelectric point7.4.4 The stereochemistry of amino acids7.4.5 Peptides and proteins7.4.6 Primary, secondary, tertiary and quaternary structures7.4.7 Denaturing of proteins7.5 Nucleic acids7.5.1 Introduction7.5.2 Primary structure of nucleic acids7.5.3 Secondary structure in nucleic acids7.5.4 Structural features of RNAQuestions Chapter 8 Reaction mechanisms8.1 Introduction8.2 Organic Reaction Types8.2.1 Addition reactions 8.2.2 Elimination reactions 8.2.3 Substitution reactions 8.2.4 Isomerisation reactions 8.2.5 Oxidation and reduction8.3 Reaction mechanisms8.3.1 Catalysts8.3.2 Homolysis:8.3.3 Heterolysis: 8.3.4 Carbocations and carbanions; types and key points8.4 Electronegativity and bond polarity8.5 Addition Reactions8.5.1 Electrophilic additions to alkenes and alkynes8.5.2 Addition of HBr to unsymmetrical alkenes8.5.3 Addition of other electrophiles to alkenes8.5.4 Electrophilic addition in biology8.5.5 Electrophilic addition without subsequent nucleophilic addition; loss of H+8.5.6 Addition of HBr to conjugated dienes8.5.7 Additions to alkynes8.6 Substitution and elimination reactions8.6.1 Nucleophilic substitution at a saturated carbon atom8.6.2 Bimolecular nucleophilic substitution SN28.6.3 Unimolecularnucleophilic substitution SN18.6.4 Determining which mechanism is followed8.7 Elimination reactions8.7.1 Bimolecular elimination, E28.7.2 Unimolecular elimination, E18.8 Biological example of an SN2 reaction8.9 Reaction mechanisms of carbonyl compounds8.9.1 Introduction8.9.2 Structure of the carbonyl group, C=O8.10 Reactions of aldehydes and ketones8.10.1 Reaction of aldehydes and ketones with ΥhydrideΥ8.10.2 Hydration of aldehydes and ketones8.10.3 Hemiacetal formation 8.10.4 Acetal (ketal) formation8.10.5 Formation of SchiffΥ|s bases and imines8.10.6 Oxidation of aldehydes and ketones8.11 Carboxylic acid derivatives8.11.1 Esters8.11.2 Acid catalysed hydrolysis of esters8.11.3 Base (:OH-) induced hydrolysis of esters8.11.4 Amides8.12 Enolisation and enolisation reactions8.12.1 Enols as carbon nucleophiles8.12.2 Base-catalysedenolisation8.13 Reactions resulting from enolisation8.13.1 The Aldol reaction8.13.2 Crossed aldol reactions / condensations8.13.3 Claisen condensations 8.14 Reaction mechanisms in biological reactions: synthesis of steroids8.15 Summary of mechanisms of carbonyl reactions under different conditionsQuestions Chapter 9. Chemical kinetics 9.1 Introduction9.2 Rates, rate laws and rate constants9.2.1 Rate of reaction9.2.2 Rates and concentration9.2.3 Units of the rate constant9.2.4 Determination of rate laws and rate constants9.3 Temperature dependence of reaction rates and rate constants9.4 Reaction mechanisms9.4.1 Deducing reaction mechanisms9.4.2 A more comprehensive look at complex reaction mechanisms9.5 Kinetics of enzyme catalysed reactions9.5.1 Catalysts and catalysis9.5.2 Enzymes as catalysts9.5.3 Single-substrate enzyme reactions9.5.4 Analysis of enzyme kinetic data 9.6 Enzyme inhibition9.6.1 Mechanisms of inhibitionQuestions Chapter 10 Bioenergetics and Bioelectrochemistry10.1 Introduction10.2 Electrochemical cells10.2.1 Cells and cell nomenclature10.2.2 Types of half cell10.2.3 Measurement of cell voltage10.2.4 Free energy relationship10.2.5 Determination of the reaction taking place in a cell10.2.6 Effect of concentration10.3 Sensors and reference electrodes10.3.1 The silver electrode10.3.2 The calomel electrode10.3.3 Detecting pH10.4 Biological Relevance10.4.1 Biochemical/biological standard state10.4.2. Biological membranes10.4.3 The thermodynamics of membrane transport10.4.4 Proton motive force10.5 SummaryQuestions Chapter 11. The role of elements other than carbon11.1 Introduction11.2 Phosphorus and phosphate esters11.2.1Phosphoric acid and phosphate esters11.2.2Relevance to biology11.3 Metals in the chemistry of biology11.4 Transition metals and their role in biological systems11.4.1 Introduction to ligands in biological systems.11.4.2 Introduction to transition metals11.4.3Crystal field theory11.4.4Examples of transition metals in biological systems 11.5 The alkali and alkaline-earth metals11.5.1 Introduction11.5.2 Solid state structures11.5.3 Coordination chemistry of group 1 and group 2 metals11.5.4 Ions of alkali and alkaline-earth metal ions in biologyQuestions Chapter 12 Metabolism12.1 Introduction12.2Glycolysis12.2.1 Introduction to glycolysis12.2.2 The glycolysis pathway12.3 Analysis of the mechanism of glycolysis12.3.1 Glycolysis step 112.3.2 Glycolysis step 212.3.3 Glycolysis step 312.3.4 Glycolysis step 412.3.5 Glycolysis step 512.3.6 Glycolysis step 612.3.7 Glycolysis step 712.3.8 Glycolysis step 812.3.9 Glycolysis step 912.3.10 Glycolysis step 1012.3.11 Summary12.4 What now? Where does the pyruvate go?12.4.1 Conversion of pyruvate into lactate12.4.2 Conversion of pyruvate into ethanol12.4.3 Conversion of pyruvate into acetyl-coenzyme-A12.5 The TCA cycle12.5.1 Introduction and overview12.6 Analysis of the mechanism of the TCA cycle12.6.1 TCA cycle, step 112.6.2 TCA cycle, step 2 12.6.3 TCA cycle, step 312.6.4 TCA cycle step 412.6.5 TCA cycle, step 512.6.6 TCA cycle, step 612.6.7 TCA cycle, step 712.6.8 TCA cycle, step 812.7 Summary of outcomes of the glycolysis and TCA cycles12.8 GluconeogenesisQuestions Chapter 13 Structural Methods13.1 Introduction13.2 Mass Spectrometry13.2.1 Background13.2.2 Analysis of a mass spectrum13.2.3 Isotopes: complicating factors or diagnostic tools?13.2.4 Fragmentation pathways involving functional groups13.2.5 Uses in biology13.3 Introduction to electromagnetic radiation13.3.1 Background principles13.4 Ultraviolet and visible (UV-vis) spectroscopy13.4.1 Introduction13.4.2 Measurement of the spectrum 13.4.3 Using UV-vis Spectra for characterising compounds 13.4.4 Aromatic compounds13.4.5 Using UV-visible spectra for measuring concentrations of biologically important compounds13.5 Infrared (IR) Spectroscopy13.5.1 Introduction13.5.2 Measurement of the spectrum 13.5.3 Interpretation of IR Spectra13.6 Nuclear Magnetic Resonance spectroscopy13.6.1 Introduction and basic principles13.6.2 Design of the NMR Spectrometer 13.6.3 The 1H NMR Spectrum13.6.4 The Chemical Shift13.6.5 Peak areas - integration 13.6.6 The solvent 13.6.7 Exchangeable hydrogens13.6.8 Nuclear spin-spin coupling13.6.9 Worked example13.6.1013C nmr spectroscopy13.7 X-ray Diffraction 13.7.1 Background13.8 Summary of the techniquesQuestions Appendix 1 Basic Mathematical Tools for Biological Chemistry Appendix 2 Answers to end of chapter questions Appendix 3 - Periodic Table of the Elementsshow more

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