Chapter 13: Introduction to Metabolism: Bioenergetics, ATP, and Oxidation-Reduction Reactions

Section 13.1 introduces sequence databases such as GenBank and UniProt, and explains the importance of sequence alignment using tools like BLAST to identify homology and evolutionary relationships. It describes pairwise and multiple sequence alignment strategies, scoring matrices like PAM and BLOSUM, and their applications in functional annotation. Section 13.2 discusses genome sequencing technologies, including Sanger sequencing, next-generation sequencing (NGS), and third-generation approaches. It details the workflow of genome assembly, annotation, and interpretation, explaining open reading frames (ORFs), regulatory sequences, and noncoding RNAs. Section 13.3 covers functional genomics, which aims to define gene function on a global scale. Techniques such as DNA microarrays and RNA-Seq are introduced for measuring gene expression levels. This section also introduces proteomics—the large-scale study of proteins—and metabolomics, which investigates cellular metabolic profiles. Section 13.4 explores systems biology, emphasizing the integration of diverse data types to build predictive models of biological systems. It also covers interactomics (the study of protein-protein interactions), pathway databases, and network analysis. Section 13.5 discusses CRISPR-Cas9 and other genome-editing technologies that enable functional interrogation of specific genes. The chapter concludes by highlighting the impact of bioinformatics on personalized medicine, biotechnology, and evolutionary biology. By connecting DNA sequence information to gene expression, protein function, and metabolic output, this chapter illustrates how modern biochemistry is increasingly data-driven and computationally sophisticated.