Biochemistry: Concepts and Connections

Citation

Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2019). Biochemistry: Concepts and Connections (2nd ed.). Pearson.

Chapter Summary

The book has 26 chapters in three blocks, as the preface describes them: the first 10 chapters cover the structure and function of biological molecules, the next 10 intermediary metabolism, and the final 6 genetic biochemistry. The narrative carries "CONCEPT" and "CONNECTION" statements that flag fundamental ideas and real-world applications, and 17 short "Tools of Biochemistry" sections are distributed through the book.

Chapters 1–4: Biochemistry and the Language of Chemistry; The Chemical Foundation of Life: Weak Interactions in an Aqueous Environment; The Energetics of Life; Nucleic Acids

Chapter 1 introduces the discipline, the elements and molecules of living systems and the cell. Chapter 2 treats noncovalent interactions, water, acid–base equilibria and buffers, and the behaviour of macroions in solution, with electrophoresis as its tool section. Chapter 3 develops free energy, its link to equilibrium and concentrations, phosphoryl-group transfer and oxidation–reduction potentials. Chapter 4 introduces nucleic acid structure, from the double helix and alternative DNA forms to a preview of replication, transcription and translation, with tool sections on manipulating DNA and X-ray diffraction.

Chapters 5–8: Introduction to Proteins: The Primary Level of Protein Structure; The Three-Dimensional Structure of Proteins; Protein Function and Evolution; Enzymes: Biological Catalysts

Amino acids, the peptide bond, sequence homology and protein purification and sequencing come first (Chapter 5). Chapter 6 covers secondary structure, fibrous and globular proteins, folding and misfolding, structure prediction and quaternary structure. Chapter 7 treats binding, the adaptive immune response and antibodies, myoglobin and hemoglobin, and the actin–myosin system of muscle. Chapter 8 develops enzymes: catalysis, coenzymes and vitamins, kinetics, inhibition, regulation and covalent modification.

Chapters 9–10: Carbohydrates: Sugars, Saccharides, Glycans; Lipids, Membranes, and Cellular Transport

Monosaccharides, oligosaccharides, polysaccharides and glycoproteins, then lipids, membrane structure, transport across membranes, ion pumps and excitable membranes.

Chapters 11–15: Chemical Logic of Metabolism; Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway; The Citric Acid Cycle; Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism; Photosynthesis

Chapter 11 sets out the reaction types, bioenergetics and control mechanisms common to pathways. Chapter 12 combines glycolysis, gluconeogenesis, glycogen metabolism and the pentose phosphate pathway in one chapter; Chapters 13–15 follow with the citric acid cycle, the mitochondrial respiratory chain and photosynthesis.

Chapters 16–20: Lipid Metabolism; Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates; Amino Acid and Nitrogen Metabolism; Nucleotide Metabolism; Mechanisms of Signal Transduction

Fatty acid oxidation and synthesis, phospholipid, sphingolipid and steroid metabolism; hormonal regulation of fuel metabolism and responses to metabolic stress; nitrogen utilisation and amino acid degradation and biosynthesis; purine and pyrimidine metabolism; and hormone and signalling systems including receptor tyrosine kinases and neurotransmission.

Chapters 21–26: Genes, Genomes, and Chromosomes; DNA Replication; DNA Repair, Recombination, and Rearrangement; Transcription and Posttranscriptional Processing; Information Decoding: Translation and Posttranslational Protein Processing; Regulation of Gene Expression

Genomes and sequence analysis (with the polymerase chain reaction as a tool section), replication, repair and recombination, transcription and RNA processing, the genetic code and the mechanism of translation, and finally regulation, from the lactose operon through chromatin, epigenetics, RNA interference, riboswitches and RNA editing.

Key Concepts

Chapters 1–4: Water, Energy and Nucleic Acids

• Noncovalent interactions: charge, dipole, van der Waals and hydrogen-bond interactions that hold biomolecules together.
• Henderson–Hasselbalch equation and buffers: the quantitative treatment of weak acids in Chapter 2.
• Free energy: ΔG and its relation to enthalpy, entropy and the equilibrium state.
• Phosphoryl group transfer potential: why organic phosphates serve as energy transducers.

Chapters 5–10: Proteins, Enzymes, Carbohydrates, Lipids and Membranes

• Peptide bond and primary structure: how sequence and homology connect gene to protein function.
• Protein folding: secondary, tertiary and quaternary structure, chaperones and misfolding.
• Enzyme kinetics and inhibition: Michaelis–Menten behaviour and regulation of activity.
• Membrane transport: ion pumps, cotransport and action potentials.

Chapters 11–20: Metabolism and Signalling

• Metabolic control: regulation points shared by many pathways.
• Glycolysis, citric acid cycle and oxidative phosphorylation: the central energy-yielding sequence.
• Hormonal regulation of fuel metabolism: interorgan coordination of energy supply.
• Signal transduction: receptors, tyrosine kinases and the link to growth control.

Chapters 21–26: Genetic Biochemistry

• DNA polymerases, fidelity and repair.
• Genetic code and translation mechanism.
• Operons and eukaryotic transcriptional control: from the lac operon to chromatin remodelling.
• RNA interference and riboswitches: regulation at the RNA level.

Critical Analysis

Strengths

• A stated design for a mixed-majors course. The preface lists the needs the authors aimed at: understanding molecular structure and function before metabolism, seeing the experimental basis of concepts, meeting real-world applications and grasping the quantitative basis of ideas such as the Henderson–Hasselbalch and Michaelis–Menten equations. The title expresses emphasis on fundamental concepts over lengthy descriptive detail.
• Experimental methods are part of the narrative. The 17 Tools of Biochemistry sections (for example electrophoresis, X-ray diffraction, protein expression and purification, metabolomics, PCR) and about 12 references per chapter, chosen for this audience and including links to Nobel Prize lectures, present biochemistry as an experimental science.
• Visual summaries. The second edition has 10 Foundation Figures that integrate chemistry and biology around a theme, such as protein structure, regulation of enzyme activity, cell signalling and information flow.
• Problem sets with partial answers. The preface gives 15 to 25 problems per chapter, with about half answered briefly at the end of the book.
• Compact metabolism section. Carbohydrate, lipid and amino acid metabolism each receive one chapter (Chapters 12, 16 and 18), which keeps the middle block to ten chapters.

Limitations

• Answers are partial. Only about half of the problems have brief answers in the book; complete solutions are in a separate manual that the publisher lists as an instructor resource.
• Some supports are outside the print text. The threshold-concept tutorials and interactive case studies the publisher advertises are assigned through Mastering Chemistry, not part of the book.
• Signalling comes late. The preface acknowledges that Chapter 20 is placed unconventionally, after hormonal control of carbohydrate and lipid metabolism, so courses that teach signalling earlier will need to reorder.
• Molecular biology is split between early and late chapters. Chapter 4 gives only a brief introduction to nucleic acid and protein synthesis, which the preface says is covered in much more detail at the end of the book, so a course that wants early molecular biology must jump ahead.

Where It Fits in the Course

Within the biochemistry list, Appling, Anthony-Cahill and Mathews is an undergraduate text written for mixed-majors courses. Mark Lorch's Biochemistry: A Very Short Introduction and David Goodsell's illustrated The Machinery of Life are brief introductions to read before or beside it. The Berg et al. Biochemistry in this list is a comprehensive textbook, and Voet, Voet and Pratt's Fundamentals of Biochemistry and Nelson et al.'s Lehninger Principles of Biochemistry are full textbooks from the biology side of the list. Pratt and Cornely's Essential Biochemistry and McKee and McKee's Biochemistry: The Molecular Basis of Life are, by their descriptions, shorter or more introductory. McMurry and Begley's The Organic Chemistry of Biological Pathways explains metabolism through reaction mechanisms and is a good partner for the metabolism chapters here, and Kuriyan, Konforti and Wemmer's The Molecules of Life approaches the subject through physical chemistry.

How to Use This Book

The preface describes the audience as students in mixed-majors courses. It does not list prerequisites, but Chapters 2 and 3 develop water, acid–base equilibria and thermodynamics from the start, and the publisher's online tutorials are meant to refresh earlier course material.

For a two-semester sequence, take Chapters 1–10 in order, since proteins, enzymes and membranes underpin everything after them. Chapter 11 is the key step into metabolism and should be read with Chapters 12–14; Chapters 15–19 can be selected according to the course. The authors place signalling (Chapter 20) just before genetic biochemistry; a course that prefers it earlier can read it after Chapter 17. Tools of Biochemistry sections suit lab-oriented readers and can be read with the chapter in which they appear. Work the end-of-chapter problems chapter by chapter, using the answers at the end for the first check; try the Concept and Connection statements as a quick self-review.