The Organic Chemistry of Biological Pathways

Citation

McMurry, J. E., & Begley, T. P. (2016). The Organic Chemistry of Biological Pathways (2nd ed.). W. H. Freeman (Macmillan Learning).

Chapter Summary

The book has nine chapters and four appendixes. It starts with a review of the organic mechanisms that recur in biochemistry, introduces the main classes of biomolecules, then works through the metabolic pathways of those classes (lipids, carbohydrates, proteins, nucleotides and secondary metabolites), and finishes by summarising the reaction patterns seen along the way and the general principles of enzymatic catalysis. The authors keep attention on the reactivity of the substrate molecules and on the arrow-pushing detail of each step, rather than on enzyme structure.

Chapter 1: Organic Mechanisms in Biological Chemistry

A brief review chapter on the fundamental organic reaction mechanisms found in biochemical pathways. It prepares readers who have taken a two-semester organic course to read the pathway chapters in mechanistic terms.

Chapter 2: Biomolecules and Their Chirality

A general introduction to the main classes of biomolecules, including their chirality.

Chapters 3–6: Lipids and Their Metabolism; Chapter 4; Amino Acid Metabolism; Nucleotide Metabolism

These chapters are the core of the book: full chapters on the major metabolic pathways of the main classes of biomolecules. Chapter 3 covers lipids and their metabolism. Chapter 4 falls where the publisher's description places carbohydrates, between lipids and proteins. Chapter 5 covers amino acid metabolism and Chapter 6 nucleotide metabolism. In the course of these chapters the common coenzymes appear and examples of the common kinds of biological transformation accumulate.

Chapter 7: Biosynthesis of Some Natural Products

The chapter on secondary metabolites, the last class of biomolecules in the book's sequence, treating the biosynthesis of selected natural products.

Chapter 8: A Summary of Biological Transformations

Pulls together the reaction patterns and mechanisms that nature uses repeatedly, so that the pathway chapters can be read as variations on a limited set of themes.

Chapter 9: Chemical Principles of Enzymatic Catalysis

A brief closing chapter on the general themes of enzymatic catalysis.

Appendixes

The four appendixes cover visualising protein structures with PyMOL; using the KEGG and BRENDA databases; answers to end-of-chapter problems; and abbreviations used in the book.

Key Concepts

Chapters 1–2

• Recurring organic mechanisms: the small set of bond-making and bond-breaking steps that underlie biochemical reactions.
• Biomolecule classes and chirality: the types of molecule whose pathways the book follows, and their stereochemistry.

Chapters 3–7

• Metabolic pathways of lipids, carbohydrates, amino acids and nucleotides: the breakdown and synthesis of each class, described step by step.
• Coenzymes: the cofactors that carry out many of the pathway transformations.
• Secondary-metabolite biosynthesis: how selected natural products are built.

Chapters 8–9

• Patterns of biological transformation: a limited set of reaction types that explain many pathways.
• General principles of enzymatic catalysis: the chemical themes shared by enzyme-catalysed reactions.

Critical Analysis

Strengths

• Mechanism-first organisation. The publisher says the authors keep their focus on the reactivity patterns of the substrate molecules and on the arrow-pushing details of individual reactions, which makes the book a bridge from organic chemistry to metabolism.
• Clear sequence. A mechanism review, an introduction to biomolecules, the pathway chapters, then two summarising chapters moves from mechanisms to pathways to general patterns.
• Updated for the second edition. The publisher states that all mechanisms were updated in the second edition and that several hundred references to recent literature are given for readers who want more detail.
• Tools for study. The appendixes include guides to PyMOL and to the KEGG and BRENDA databases, and answers to end-of-chapter problems.

Limitations

• Organic chemistry is assumed. The authors expect a background equivalent to a typical two-semester college organic course, and Chapter 1 is only a brief review.
• Narrow on enzyme structure and regulation. By the publisher's own account the focus is on substrate reactivity and individual reaction steps, and the contents list has no chapters on protein structure, gene expression or the regulation of metabolism; readers who need those will want a general biochemistry text.
• Compact coverage of some classes. With nine chapters in total, each class of biomolecule gets one chapter, so pathways are chosen rather than exhaustive.

Where It Fits in the Course

In the biochemistry course this book is the organic-mechanism companion to the general texts. Berg's Biochemistry is the comprehensive molecular treatment of protein structure and function, metabolism, gene expression and regulation, and Biochemistry: A Short Course is a one-semester version of that approach. Biochemistry: Concepts and Connections is written from a chemical perspective, emphasising the physical and chemical principles behind biological processes. Lorch's Biochemistry: A Very Short Introduction and Goodsell's The Machinery of Life are short orientation books for readers who are new to the field.

McMurry and Begley are best read after a first biochemistry survey and a full organic chemistry course, alongside the metabolism chapters of a general text, to see why the pathway steps work as they do.

How to Use This Book

The book was written for advanced undergraduates and graduate students who want a deeper understanding of the chemical reactions in living organisms. Organic chemistry at the level of the usual two-semester course is the stated prerequisite; an introductory biochemistry course is helpful but is not named as one.

A practical plan:

• Start with Chapters 1 and 2 even if organic chemistry is fresh; the mechanism vocabulary of Chapter 1 is used everywhere afterwards.
• Read the pathway chapters (3–7) in any order that matches the course, drawing the mechanisms by hand and keeping track of the coenzymes that recur.
• Use Chapter 8 as a consolidation after several pathway chapters, and Chapter 9 as a short close.
• Use the appendixes: PyMOL and the KEGG and BRENDA databases for exploring structures and pathways, and the answers to check end-of-chapter problems.