Lehninger Principles of Biochemistry (vuoden 2008 painos)

Biochemistry

Biochemistry

I used this book in my undergraduate biochemistry course. I would have to say this is probably the best book to buy if you are looking for a good introduction on the many topics in biochemistry. The book is very well written, and the question presented at the end of the chapter are useful for your comprehension of the material. ( )

Lehninger
Principles of Biochemistry

David L. Nelson
Michael M. Cox

W. H. Freeman, Hardback, 2008.
4to. xxix+1158 pp.+G-17+C-8+A-4+AS-35+I-41. Fifth edition.

Fifth edition first published in 2008.

Contents [somewhat in brief, necessarily]

About the authors
A Note on the Nature of Science
Preface

1. The Foundations of Biochemistry
1.1. Cellular Foundations
1.2. Chemical Foundations
1.3. Physical Foundations
1.4. Genetic Foundations
1.5. Evolutionary Foundations

I. STRUCTURE AND CATALYSIS

2. Water
2.1. Weak Interactions in Aqueous Solution
2.2. Ionization of Water, Weak Acids, and Weak Bases
2.3. Buffering against pH Changes in Biological systems
2.4. Water as a Reactant
2.5. The Fitness of the Aqueous Environment for Living Organisms

3. Amino Acids, Peptides and Proteins
3.1. Amino Acids
3.2. Peptides and Proteins
3.3. Working with Proteins
3.4. The Structure of Proteins: Primary Structure

4. The Three-Dimensional Structure of Proteins
4.1. Overview of Protein Structure
4.2. Protein Secondary Structure
4.3. Protein Tertiary and Quaternary Structures
4.4. Protein Denaturation and Folding

5. Protein Function
5.1. Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
5.2. Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins
5.3. Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors

6. Enzymes
6.1. An Introduction to Enzymes
6.2. How Enzymes Work
6.3. Enzyme Kinetics as an Approach to Understanding Mechanism
6.4. Examples of Enzymatic Reactions
6.5. Regulatory Enzymes

7. Carbohydrates and Glycobiology
7.1. Monosaccharides and Disaccharides
7.2. Polysaccharides
7.3. Glycoconjugates: Proteoglycans, Glycoproteins and Glycolipids
7.4. Carbohydrates as Informational Molecules: The Sugar Code
7.5. Working with Carbohydrates

8. Nucleotides and Nucleic Acids
8.1. Some Basics
8.2. Nucleic Acid Structure
8.3. Nucleic Acid Chemistry
8.4. Other Functions of Nucleotides

9. DNA-Based Information Technologies
9.1. DNA Clonning: The Basics
9.2. From Genes to Genomes
9.3. From Genomes to Proteomes
9.4. Genome Alterations and New Products of Biotechnology

10. Lipids
10.1. Storage Lipids
10.2. Structural Lipids in Membranes
10.3. Lipids as Signals, Cofactors, and Pigments
10.4. Working with Lipids

11. Biological Membranes and Transport
11.1. The Composition and Architecture of Membranes
11.2. Membrane Dynamics
11.3. Solute Transport across Membranes

12. Biosignaling
12.1. General Features of Signal Transduction
12.2. G Protein-Coupled Receptors and Second Messengers
12.3. Receptor Tyrosine Kinases
12.4. Receptor Guanylyl Cyclases, cGMP, and Protein Kinase G
12.5. Multivalent Adaptor Proteins and Membrane Raffts
12.6. Gated Ion Channels
12.7. Integrins: Bidirectional Cell Adhesion Receptors
12.8. Regulation of Transcription by Steroid Hormones
12.9. Signaling in Microorganisms and Plants
12.10. Sensory Transduction in Vision, Olfaction, and Gustation
12.11. Regulation of the Cell Cycle by Protein Kinases
12.12. Oncogenes, Tumor Supressor Genes, and Programmed Cell Death

II BIOENERGETICS AND METABOLISM

13. Bioenergetics and Biochemical Reaction Types
13.1. Bioenergetics and Thermodynamics
13.2. Chemical Logic and Common Biochemical Reactions
13.3. Phosphoryl Group Transfer and ATP
13.4. Biological Oxidation-Reduction Reactions

14. Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
14.1. Glycolysis
14.2. Feeder Pathways for Glycolysis
14.3. Fates of Pyruvate under Anaerobic Conditions: Fermentation
14.4. Glugoneogenesis
14.5. Pentose Phosphate Pathway of Glucose Oxidation

15. Principles of Metabolic Regulation
15.1. Regulation of Metabolic Pathways
15.2. Analysis of Metabolic Control
15.3. Coordinated Regulation of Glycolysis and Gluconeogenesis
15.4. The Metabolism of Glycogen in Animals
15.5. Coordinated Regulation of Glycogen Synthesis and Breakdown

16. The Citric Acid Cycle
16.1. Production of Acetyl-CoA (Activated Acetate)
16.2. Reactions of the Citric Acid Cycle
16.3. Regulation of the Citric Acid Cycle
16.4. The Glyoxylate Cycle

17. Fatty Acid Catabolism
17.1. Digestion, Mobilization, and Transport of Fats
17.2. Oxidation of Fatty Acids
17.3. Ketone Bodies

18. Amino Acid Oxidation and the Production of Urea
18.1. Metabolic Fates of Amino Groups
18.2. Nitrogen Excretion and the Urea Cycle
18.3. Pathways of Amino Acid Degradation

19. Oxidative Phosphorylation and Photophosphorylation

OXIDATIVE PHOSPHORYLATION
19.1. Electron-Transfer Reactions in Mitochondria
19.2. ATP Synthesis
19.3. Regulation of Oxidative Phosphorylation
19.4. Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis
19.5. Mitochondrial Genes: Their Origin and the Effects of Mutations

PHOTOSYNTHESIS: HARVESTING LIGHT ENERGY
19.6. General Features of Photophosphorylation
19.7. Light Absorption
19.8. The Central Photochemical Event: Light-Driven Electron Flow
19.9. ATP Synthesis by Photophosphorylation
19.10. The Evolution of Oxygenic Photosynthesis

20. Carbohydrate Biosynthesis in Plants and Bacteria
20.1. Photosynthetic Carbohydrate Synthesis
20.2. Photorespiration and the C4 and CAM Pathways
20.3. Biosynthesis of Starch and Sucrose
20.4. Synthesis of Cell Wall Polysaccharides: Plant Cellulose and Bacterial Peptidoglycan
20.5. Integration of Carbohydrate Metabolism in the Plant Cell

21. Lipid Biosynthesis
21.1. Biosynthesis of Fatty Acids and Eicosanoids
21.2. Biosynthesis of Triacylglycerols
21.3. Biosynthesis of Membrane Phospholipids
21.4. Biosynthesis of Cholesterol, Steroids, and Isoprenoids

22. Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
22.1. Overview of Nitrogen Metabolism
22.2. Biosynthesis of Amino Acids
22.3. Molecules Derived from Amino Acids
22.4. Biosynthesis and Degradation of Nucleotides

23. Hormonal Regulation and Integration of Mammalian Metabolism
23.1. Hormones: Diverse Structures for Diverse Functions
23.2. Tissue-Specific Metabolism: The Division of Labour
23.3. Hormonal Regulation of Fuel Metabolism
23.4. Obesity and the Regulation of Body Mass
23.5. Obesity, the Metabolic Syndrome, and Type 2 Diabetes

III INFORMATIVE PATHWAYS

24. Genes and Chromosomes
24.1. Chromosomal Elements
24.2. DNA Supercoiling
24.3. The Structure of Chromosomes

25. DNA Metabolism
25.1. DNA Replication
25.2. DNA Repair
25.3. DNA Recombination

26. RNA Metabolism
26.1. DNA-Dependent Synthesis of RNA
26.2. RNA Processing
26.3. RNA-Dependent Synthesis of RNA and DNA

27. Protein Metabolism
27.1. The Genetic Code
27.2. Protein Synthesis
27.3. Protein Targeting and Degradation

28. Regulation of Gene Expression
28.1. Principles of Gene Regulation
28.2. Regulation of Gene Expression in Bacteria
28.3. Regulation of Gene Expression in Eukaryotes

Appendix A. Common Abbreviations in the Biochemical Research Literature [A-4]
Appendix B. Abbreviated Solutions to Problems [AS-35]
Glossary [G-17]
Credits [C-8]
Index [I-41]

Boxes [given here in toto only for the sake of clarity; first number indicates the actual chapter]
Box 1-1 Molecular Weight, Molecular Mass, and Their Correct Units
Box 1-2 Louis Pasteur and Optical Activity: In Vino, Veritas
Box 1-3 Entropy: The Advantages of Being Disorganized
Box 2-1 Medicine: On Being One's Own Rabbit (Don't Try This at Home!)
Box 3-1 Methods: Absorption of Light by Molecules: The Lambert-Beer Law
Box 3-2 Methods: Investigating Proteins with Mass Spectrometry
Box 3-3 Consensus Sequences and Sequence Logos
Box 4-1 Methods: Knowing the Right Hand from the Left
Box 4-2 Permanent Waving is Biochemical Engineering
Box 4-3 Medicine: Why Sailors, Explorers, and College Students Should Eat Their Fresh Fruits and Vegetables
Box 4-4 The Protein Data Bank
Box 4-5 Methods: Methods for Determining the Three-Dimensional Structure of Proteins
Box 4-6 Medicine: Death by Misfolding: The Prion Diseases
Box 5-1 Medicine: Carbon Monoxide: A Stealthy Killer
Box 6-1 Transformations of Michaelis-Menten Equation: The Double-Reciprocal Plot
Box 6-2 Kinetic Tests for Determining Inhibition Mechanisms
Box 6-3 Evidence for Enzyme-Transition State Complementarity
Box 7-1 Medicine: Blood Glucose Measurements in the Diagnosis and Treatment of Diabetes
Box 9-1 A Potent Weapon in Forensic Medicine
Box 9-2 Medicine: The Human Genome and Human Gene Therapy
Box 10-1 Sperm Whales: Fatheads of the Deep
Box 10-2 Medicine: Abnormal Accumulation of Membrane Lipids: Some Inherited Human Diseases
Box 11-1 Methods: Atomic Force Microscopy to Visualize Membrane Proteins
Box 11-2 Medicine: Defective Glucose and Water Transport in Two Forms of Diabetes
Box 11-3 Medicine: A Defective Ion Channel in Cystic Fibrosis
Box 12-1 Methods: Scatchard Analysis Quantifies the Receptor-Ligand Interaction
Box 12-2 Medicine: G Proteins: Binary Switches in Health and Disease
Box 12-3 Methods: FRET: Biochemistry Visualized in a Living Cell
Box 12-4 Medicine: Color Blindness: John Dalton's Experiment from the Grave
Box 12-5 Medicine: Development of Protein Kinase Inhibitors for Cancer Treatment
Box 13-1 Firefly Flashes: Glowing Reports of ATP
Box 14-1 Medicine High Rate of Glycolysis in Tumors Suggests Targets for Chemotherapy and Facilitates Diagnosis
Box 14-2 Athletes, Alligators and Coelacanths: Glycolysis at Limiting Concentrations of Oxygen
Box 14-3 Ethanol Fermentations: Brewing Beer and Producing Biofuels
Box 14-4 Medicine: Why Pythagoras Wouldn't Eat Falafel: Glucose-6-Phosphate Dehydrogenase Deficiency
Box 15-1 Methods: Metabolic Control Analysis: Quantitative Aspects
Box 15-2 Isozymes: Different Proteins That Catalyze the Same Reaction
Box 15-3 Medicine: Genetic Mutations That Lead to Rare Forms of Diabetes
Box 15-4 Carl and Gerty Cori: Pioneers in Glycogen Metabolism and Disease
Box 16-1 Moonlightning Enzymes: Proteins with More Than One Job
Box 16-2 Synthases and Synthetases; Ligases and Lyases; Kinases, Phosphatases, and Phosphorylases: Yes, the Names Are Confusing!
Box 16-3 Citrate: A Symmetric Molecule That Reacts Asymmetrically
Box 16-4 Citrate Synthase, Soda Pop, and the World Food Supply
Box 17-1 Fat Bears Carry Out beta Oxidation in Their Sleep
Box 17-2 Coenzyme B12: A Radical Solution to a Perplexing Problem
Box 18-1 Medicine: Assays for Tissue Damage
Box 18-2 Medicine: Scientific Sleuths Solve a Murder Mystery
Box 19-1 Hot, Stinking Plants and Alternative Respiratory Pathways
Box 21-1 Mixed-Function Oxidases, Oxygenases, and Cytochrome P-450
Box 21-2 Medicine: ApoE Alleles Predict Incidence of Alzheimer's Diseases
Box 21-3 Medicine: The Lipid Hypothesis and the Development of Statins
Box 22-1 Unusual Lifestyles of the Obscure but Abundant
Box 22-2 Medicine: On Kings and Vampires
Box 22-3 Medicine: Curing African Sleeping Sickness with a Biochemical Trojan Horse
Box 23-1 Medicine: How Is a Hormone Discovered? The Arduous Path to Purified Insulin
Box 24-1 Medicine: Curing Diseases by Inhibiting Topoisomerases
Box 24-2 Medicine: Epigenetics, Nucleosome Structure, and Histone Variants
Box 25-1 Medicine DNA Repair and Cancer
Box 26-1 Methods: RNA Polymerase Leaves Its Footprint on a Promoter
Box 26-2 Medicine: Fighting AIDS with Inhibitors of HIV Reverse Transcriptase
Box 26-3 Methods: The SELEX Method for Generating RNA Polymers with New Functions
Box 26-4 An Expanding RNA Universe Filled with TUF RNAs
Box 27-1 Exceptions That Prove the Rule: Natural Variations in the Genetic Code
Box 27-2 From an RNA World to a Protein World
Box 27-3 Natural and Unnatural Expansion of the Genetic Code
Box 27-4 Induced Variation in the Genetic Code: Nonsense Suppression
Box 28-1 Of Fins, Wings, Beaks, and Things

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Now, how does one write a review of such a book!

To begin with, a quarto hardback of more than 1200 pages is no joke. (Hang it all, only the Index is 41 pages!). What is more, Lehninger has long since been established as a classic introduction to the infinitely complex and endlessly fascinating world of biochemistry. The publishing history is somewhat lost in the misty valleys of the past, but it seems that the first version of this stupendous book appeared as early as 1970 and was written by Albert Lehninger himself. After his death in 1986, or perhaps a little bit earlier, the authorship was taken over by David Nelson and Michael Cox, and so they have continued to update and constantly trying to improve the contents as well as the presentation all through the years until the present Fifth edition which I believe is currently the last one. My personal experience with Lehninger goes back only until the Third edition but I am quite convinced that Messrs Nelson and Cox are doing a fine job.

Though the primary reasons for the existence of Lehninger: Principles of Biochemistry have always been didactic, I hesitate to call this book a textbook, for this does imply some tediousness, and tedious is most certainly what Lehninger is not. Indeed, considering the scope and the complexity of the subject, it is hard for me to imagine a more accessible, lucidly written and lavishly illustrated general introduction to biochemistry for both the undergraduate student and the intelligent layman. The only real competition in this category seems to come from Stryer's biochemistry, another legendary book, not so impressive in terms of illustrations as Lehninger, but every bit as good in terms of clarity and comprehensiveness; Voet & Voet's and the more medically orientated Harper's biochemistries are fine in their own but neither is even remotely in the league of Stryer and Lehninger.

Reviewing Lehninger is a daunting and intimidating task. But since I dislike the false modesty of the type ''what can I say that hasn't been said a thousand times'', I'll give it a short try.

Nor am I one of those people who never give a book five stars because of some vain search for perfection that hardly exists. I have heard some accusations against Lehninger's biochemistry in general and its Fifth edition in particular from specialists whose outstanding intelligence, it seems to me, is at the expense of elementary common sense. Some of them have complained that there is this and that missing, others have moaned that here and there there are mistakes, and third have admonished the inclusion of material that, mind you, might have been better suited to a molecular genetics textbook. This is all moonshine.

Scientists in the field of biochemistry of all people must know that the subject is absolutely inexhaustible, no matter the size of the book or the number of volumes; of course there will be omissions. If such conceited lot indeed have some common sense they may use Lehninger, and similar introductions into another areas of the biological science, to keep in touch with what is not their primary interest. One of the greatest tragedies of modern science is the extremely high degree of specialisation. Scientists are often so absorbed in their own specific areas that they know nothing outside. It is not at all seldom that they completely lose the big picture and indeed what the whole thing is all about.

I surmise it is these obtuse fellows who never stop whining that Lehninger contains lots of stuff it shouldn't because it is not biochemistry. This is a strangely inane complain. It doesn't require much intelligence or imagination for one to realise that even basic divisions of science (chemistry, physics, biology) are purely artificial conventions and make some sense only for teaching purposes; I don't even want to mention the more modern ''molecular'' branches which are frankly ridiculous. There is no such thing as an isolated science, let alone biological science. Biochemistry, for example, is supposed - theoretically! - to bother itself only with chemical reactions on cellular level. But if you really want to have some idea of their meaning, you have to study in detail their origins, the cellular structures they take place in, their relation to another cells, tissues, organs and systems, their physiological and pathophysiological significance; in other words, you have to study also genetics, cytology, physiology and medicine. And once you have come down to molecular level, you might be surprised how much of biology is actually pure physics or pure chemistry, not to mention that you often need to be not so bad a mathematician.

One of Lehninger's greatest strengths is its eclectic character. It always puts the biochemical aspects of life in a much broader context. As for mistakes, if there are any, I am either not aware of them or have thought pointing them as the purest form of nit-picking there is.

The Fifth edition of Lehninger: Principles of Biochemistry starts with a short but wonderful A Note on the Nature of Science, discussing briefly the logical and philosophical foundations of science in general, and a fascinating preface by Dave Nelson and Mike Cox in which they summarise the main revisions and new features in this edition. They are numerous. The compelling ''boxes'', which not for nothing have I listed as an important part of the contents, are not new, some of them indeed were already there in the Third edition, but a number of them have been added especially for his addition. They often carry labels like ''Methods'' or ''Medicine'' and give invaluable insights into how biochemistry really is done and why is so important to study it, respectively. One really does see that what at first glance seems far removed from reality is in fact of great practical importance.

A special highlight in this edition is the addition of many new teaching tools. Perhaps the most useful are the so called the in-text ''Worked Examples'' in which the inquisitive reader may enjoy playing with formulas and equations, calculating enzyme kinetics or membrane potentials, thus improving his quantitative problem-solving skills. Some of these are simply charming, like ''Worked Example 6-1'' which describes a hypothetical conversion of the compound SAD into the compound HAPPY, and the enzyme that catalyzes the reaction is of course called happyase. Now that's really cute. And in ''Worked Example 6-3'' you may learn the hardly surprising fact that the compound STRESS is a potent inhibitor of happyase. Personally, I can't imagine a more delightful calculation of the Michaelis constant and the effect that some enzyme inhibitors have on it. Surely it is also worth noting these more than 100 new ''end-of-chapter problems'', for which an abbreviated solutions are given in Appendix B, but one certainly would do better to try to solve them by oneself; few things are a better exercise in thinking over and applying of what one has learned - if anything.

For all those who are perfect newcommers to the world of biochemistry, this Fifth edition of Lehninger have a special new feature called ''Key Conventions'' in which many important details that specialists take for granted are given separately from the text and carefully explained. In addition to the book, there is some multimedia stuff, both on the site of W.H . Freeman and to be bought separately, and I have even heard about some ''absolute, ultimate guide'' to the problems in the Fifth edition, but I very much doubt the latter is much necessary; as for the former, animations of enzyme mechanisms or actions are entertaining, certainly, but one has to be completely unimaginative not to be able to imagine them while looking at the gorgeous illustrations. For my part Lehninger has always been a remarkably self-sufficient book. From the single water molecule to the hormonal regulation of the fuel metabolism: it can take you anywhere you like.

All in all, there is no need of my usual prolixity here. Suffice it to say that better general introduction to biochemistry in one single volume you are not likely to encounter anywhere else; at best, it can be equaled by Stryer; I very much doubt it is possible at all to be surpassed. It is as comprehensive as it is possible to compress so vast a subject into so limited a space. The illustrations are magnificent, the writing style is an epitome of lucidity and succinctness, giving completely the lie to all who claim that biochemistry is uncommonly dull stuff and consists of nothing but debilitating chanting of chemical formulas. Nothing could be further from the truth. Not only is biochemistry very firmly rooted in everyday's life, as any science indeed, but it represents the eternal desire to discover the secret of that mysterious phenomenon called life.

The book has only one drawback and it is a purely technical one: the binding is very inferior indeed; you needn't be surprised if you soon find some pages quite detached from the spine. But it is irritating - and saddening too. It is perhaps a hallmark of our age that many worthy things should be compromised by commercialism. Today it is just the binding - annoying, certainly, yet of no great consequence - but tomorrow it might be the contents as well. Should we be a bit more careless, Lehninger's Tenth edition may end as a fifth-rate textbook. Well, I don't know about that. What I do know is that the Fifth edition most certainly is a first rate nonfiction book. ( )