Proteins

, by David Whitford (Queen Mary & Westfield College, London, UK)

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ISBN: 9780471498933 | 0471498939
Cover: Hardcover
Copyright: 5/1/2005

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This text provides a superb introduction to the study of proteins, focusing on their structure and function. It covers the importance of proteins in biochemistry and introduces the concepts connected with protein folding in a user-friendly manner. Written specifically for undergraduates, it will provide them with the foundation they need in order to undertake more advanced study and analysis. The accompanying web site will include animated protein structures, problems and answers, and links to protein databases and other sites of interest.

Preface

An Introduction to protein structure and function

(12)

A brief and very selective historical perspective

(4)

The biological diversity of proteins

(4)

Proteins and the sequencing of the human and other genomes

(1)

Why study proteins?

(4)

Amino acids: the building blocks of proteins

(26)

The 20 amino acids found in proteins

(1)

The acid -- base properties of amino acids

(1)

Stereochemical representations of amino acids

(1)

Peptide bonds

(7)

The chemical and physical properties of amino acids

(9)

Detection, identification and quantification of amino acids and proteins

(2)

Stereoisomerism

(1)

Non-standard amino acids

(1)

Summary

(1)

Problems

(2)

The three-dimensional structure of proteins

(46)

Primary structure or sequence

(1)

Secondary structure

(11)

Tertiary structure

(12)

Quaternary structure

(4)

The globin family and the role of quaternary structure in modulating activity

(8)

Immunoglobulins

(7)

Cyclic proteins

(1)

Summary

(2)

Problems

(2)

The structure and function of fibrous proteins

(20)

The amino acid composition and organization of fibrous proteins

(1)

Keratins

(6)

Fibroin

(1)

Collagen

(10)

Summary

102

(1)

Problems

103

(2)

The structure and function of membrane proteins

105

(56)

The molecular organization of membranes

105

(5)

Membrane protein topology and function seen through organization of the erythrocyte membrane

110

(4)

Bacteriorhodopsin and the discovery of seven transmembrane helices

114

(9)

The structure of the bacterial reaction centre

123

(3)

Oxygenic photosynthesis

126

(1)

Photosystem I

126

(2)

Membrane proteins based on transmembrane β barrels

128

(4)

Respiratory complexes

132

(1)

Complex III, the ubiquinol-cytochrome c oxidoreductase

132

(6)

Complex IV or cytochrome oxidase

138

(6)

The structure of ATP synthetase

144

(8)

ATPase family

152

(4)

Summary

156

(3)

Problems

159

(2)

The diversity of proteins

161

(28)

Prebiotic synthesis and the origins of proteins

161

(2)

Evolutionary divergence of organisms and its relationship to protein structure and function

163

(2)

Protein sequence analysis

165

(15)

Protein databases

180

(1)

Gene fusion and duplication

181

(1)

Secondary structure prediction

181

(2)

Genomics and proteomics

183

(4)

Summary

187

(1)

Problems

187

(2)

Enzyme kinetics, structure, function, and catalysis

189

(58)

Enzyme nomenclature

191

(1)

Enzyme co-factors

192

(1)

Chemical kinetics

192

(3)

The transition state and the action of enzymes

195

(2)

The kinetics of enzyme action

197

(5)

Catalytic mechanisms

202

(7)

Enzyme structure

209

(1)

Lysozyme

209

(3)

The serine proteases

212

(3)

Triose phosphate isomerase

215

(3)

Tyrosyl tRNA synthetase

218

(3)

EcoRI restriction endonuclease

221

(3)

Enzyme inhibition and regulation

224

(3)

Irreversible inhibition of enzyme activity

227

(4)

Allosteric regulation

231

(6)

Covalent modification

237

(4)

Isoenzymes or isozymes

241

(1)

Summary

242

(2)

Problems

244

(3)

Protein synthesis, processing and turnover

247

(66)

Cell cycle

247

(3)

The structure of Cdk and its role in the cell cycle

250

(2)

Cdk-cyclin complex regulation

252

(1)

DNA replication

253

(1)

Transcription

254

(7)

Eukaryotic transcription factors: variation on a `basic' theme

261

(4)

The spliceosome and its role in transcription

265

(1)

Translation

266

(1)

Transfer RNA (tRNA)

267

(2)

The composition of prokaryotic and eukaryotic ribosomes

269

(3)

A structural basis for protein synthesis

272

(1)

An outline of protein synthesis

273

(5)

Antibiotics provide insight into protein synthesis

278

(1)

Affinity labelling and RNA `footprinting'

279

(1)

Structural studies of the ribosome

279

(8)

Post-translational modification of proteins

287

(6)

Protein sorting or targeting

293

(9)

The nuclear pore assembly

302

(1)

Protein turnover

303

(7)

Apoptosis

310

(1)

Summary

310

(2)

Problems

312

(1)

Protein expression, purification and characterization

313

(34)

The isolation and characterization of proteins

313

(1)

Recombinant DNA technology and protein expression

313

(5)

Purification of proteins

318

(2)

Centrifugation

320

(3)

Solubility and `salting out' and `salting in'

323

(3)

Chromatography

326

(7)

Dialysis and ultrafiltration

333

(1)

Polyacrylamide gel electrophoresis

333

(7)

Mass spectrometry

340

(2)

How to purify a protein?

342

(2)

Summary

344

(1)

Problems

345

(2)

Physical methods of determining the three-dimensional structure of proteins

347

(48)

Introduction

347

(1)

The use of electromagnetic radiation

348

(1)

X-ray crystallography

349

(11)

Nuclear magnetic resonance spectroscopy

360

(15)

Cryoelectron microscopy

375

(4)

Neutron diffraction

379

(1)

Optical spectroscopic techniques

379

(8)

Vibrational spectroscopy

387

(2)

Raman spectroscopy

389

(1)

ESR and ENDOR

390

(2)

Summary

392

(1)

Problems

393

(2)

Protein folding in vivo and in vitro

395

(44)

Introduction

395

(1)

Factors determining the protein fold

395

(8)

Factors governing protein stability

403

(1)

Folding problem and Levinthal's paradox

403

(5)

Models of protein folding

408

(3)

Amide exchange and measurement of protein folding

411

(1)

Kinetic barriers to refolding

412

(3)

In vivo protein folding

415

(7)

Membrane protein folding

422

(4)

Protein misfolding and the disease state

426

(9)

Summary

435

(2)

Problems

437

(2)

Protein structure and a molecular approach to medicine

439

(42)

Introduction

439

(2)

Sickle cell anaemia

441

(1)

Viruses and their impact on health as seen through structure and function

442

(1)

HIV and AIDS

443

(14)

The influenza virus

457

(13)

p53 and its role in cancer

470

(5)

Emphysema and α1-antitrypsin

475

(3)

Summary

478

(1)

Problems

479

(2)

Epilogue

481

(2)

Glossary

483

(8)

Appendices

491

(4)

Bibliography

495

(4)

References

499

(12)

Index

511

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Proteins

Summary

Table of Contents

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Summary

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