3. Proteins

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

1. The roots of biochemistry

This chapter traces the history of biochemistry, which is linked to the understanding of arguably the oldest uses of biotechnology—fermentation and the production of alcoholic beverages and cheese. In the 19th century, at the same time as the fermentation debates and enzymology flourished, the nature of proteins was under scrutiny. The chapter then considers the contribution that X-ray crystallography has made to structural biology. By the mid-20th century, the structures of the two massive molecular players, protein and nucleic acids (DNA along with ribonucleic acid), and their myriad roles were in place. It was becoming apparent that these were the fundamental molecular machines that marshal the chemistry within cells.

8. Biotechnology and synthetic biology

This chapter explores the fields of biotechnology and synthetic biology. The micro-scale of synthetic biology clearly indicates the use of knowledge drawn from biochemistry. But its philosophy is more closely aligned to the principles of engineering than those of pure science. The chapter then looks at some examples of synthetic biochemistry, and reflects on what this new field might herald. It studies the creation of synthetic organisms and genomes. The chapter also considers gene editing and the emergence of a powerful gene editing technique, known as CRISPR (from clustered, regularly interspaced, short palindromic repeats). Finally, it addresses ethical issues and the darker applications of these technologies.

2. Water, lipids, and carbohydrates

This chapter discusses some simpler but no less important molecules: water, lipids, carbohydrates, and nucleotides. These molecules form the physical structures that bound cells and the medium in which the very chemistry of life takes place. Water’s structure and composition allows it to participate makes it a polar molecule and an astonishingly good solvent. Meanwhile, lipids play three main roles in biochemistry: energy storage, signalling, and structure formation. Finally, carbohydrates provide the fuel that powers cells; they form the scaffolding around which so many structures are built; and they frequently embellish proteins, modifying their behaviours or adding functionality.

7. Following biochemistry within the cell

This chapter presents key advances in the study of individual molecules within cells. When one applies this individualistic methodology to biochemicals, one enters the realms of single-molecule biophysics. There are of course formidable technical challenges associated with single-molecule studies, not least of which is the signal-to-noise problem. The chapter discusses patch clamping, nanoscopes, and optical tweezers. Patch clamping provided insights into the protein machinery that controls the flow of ions in and out of cells. The chapter also examines cytokinesis, cytoskeletons, and motor proteins, and the use of Green Fluorescent Protein (GFP).

6. Manufacturing and maintaining DNA

This chapter assesses DNA replication. The double-helix of DNA could easily be separated into two individual strands, each of which acts as a template for the manufacturing of a new complementary strand. This became known as semi-conservative replication, to indicate that each daughter DNA double-helix contained one new strand and one old strand, conserved from the parent molecule. Discovering the ways by which cells replicate their DNA led to the question: can we harness these amazing natural machines to shed light on DNA itself? The chapter then examines two key biotechnological advances: DNA sequencing and the polymerase chain reaction (PCR).

4. Nucleic acids

This chapter focuses on nucleic acids. It begins by describing the central dogma of molecular biology. Fundamentally, the central dogma consists of DNA replication—the straightforward copying of information; transcription—the process of creating RNA from a DNA template; and translation—the creation of a protein sequence from an RNA template. The chapter then looks at the nucleic acid molecule’s secondary structures, their form and function, and how these underpin the three trunk data flows of the central dogma. The chapter also explores the idea of a primordial world without DNA or proteins, where RNA played the role of both cellular machinery and storage medium for genetic information.

5. Powering a cell

This chapter looks at some examples of how the groups of major macro- and micromolecules that play a role in biochemistry work in unison, creating interconnected pathways of chemical reactions. The biochemical process that collects the Sun’s rays and uses their energy to convert carbon dioxide and water into carbohydrate is photosynthesis. The most common light harvesting pigments are chlorophylls. Living organisms, including humans, then utilize the stored chemical energy in the carbohydrates, releasing carbon dioxide back into the atmosphere. The chapter then highlights the process of glycolysis, a ten-step metabolic pathway, with each step catalysed by specific proteins.