Nutrient metabolism is a basic biochemical paradigm to which cells draw energy and produce biosynthetic precursors, as well as maintain homeostasis. At the molecular scale, the integrative processing of carbohydrates, lipids, and proteins are regulated by highly regulated enzymatic systems that dynamically react to cellular energy requirements, nutrient levels and physiological conditions. This review presents the existing knowledge of the molecular biochemistry in nutrient metabolism, with the focus being on the integrated character of metabolic pathways, as opposed to the reactions occurring in isolation. The process of carbohydrate metabolism is a fast and flexible energy source by glycolysis, gluconeogenesis, and pentose phosphate pathway which connects the production of ATP and the maintenance of redox homeostasis with anabolic needs. The long-term energy storage and structural components in lipid metabolism are based on fatty acid production, 2-oxidation as well as complex lipid remodeling and they are the centre of focus in the membrane dynamics as well as signaling processes. Protein metabolism provides functional macromolecules as well as metabolic intermediates, which the catabolism of amino acids connects to the relationships of central carbon metabolism and nitrogen homeostasis. In addition to the classics of pathway descriptions, this review identifies the regulatory processes that provide the flexibility of their metabolic reactions, such as allosteric enzyme regulation, post-translational changes, and intracellular compartmentalization. The interaction between carbohydrate, lipid and protein metabolism allows the cells to quickly adjust to changes in nutrient levels without compromising the metabolic effectiveness. These molecular processes are critical in explaining the biochemical basis of growth and development and disease because metabolic dysregulation causes many pathological conditions. The article offers a conceptual framework of future studies aimed at optimizing metabolism, therapeutic intervention, and system-level metabolic engineering by offering a single and sequential description of how nutrient metabolism works on the molecular level.