Chemistry for Biologists

Book Title

By David Reed
October 2013
Pearson Education
Distributed by Trans-Atlantic Publications Inc.
ISBN: 9781408280829
496 Page, Illustrated
$72.50 Paper Original


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.




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 Avogadroզs 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


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 ΥV the VSEPR approach

2.7.8 Resonance

2.8 Covalent bonding ΥV 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


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? ΥV some examples.


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 ΥV 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: Hessզs 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


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 īGć 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 Chatelierզs Principle

5.5.2 Le Chatelierզs principle and the effect of temperature on equilibria.

5.5.3 Examples involving Le Chatelierզs principle

5.6 Energetics and equilibria in the biological context.

5.6.1 Calculating ƒ´GΥò from experimentally determined compositions (via K values)

5.6.2 Calculating equilibrium compositions from ƒ´GΥò

5.6.3 Macromolecule-ligand interactions.

5.6.4 Haemoglobin - oxygen

5.7 Revisiting coupled reactions


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 AcidΥVbase 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 ΥV 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


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


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 էhydrideը

8.10.2 Hydration of aldehydes and ketones

8.10.3 Hemiacetal formation

8.10.4 Acetal (ketal) formation

8.10.5 Formation of Schiffզs 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


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


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


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


Chapter 12 Metabolism

12.1 Introduction


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


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


Appendix 1 Basic Mathematical Tools for Biological Chemistry

Appendix 2 Answers to end of chapter questions

Appendix 3 - Periodic Table of the Elements