Understanding the role of individual components in a biological system is an important step to elucidate or predict its behavior. However, a major theme in systems biology is investigating these systems with an integrated approach. In fact, studying the interactions between different components also gives insights into the functioning and behavior of the components taken independently
Metabolites are the intermediates and end products (eg, amino acids, organic acid and bases, fatty acids, bile acids, lipids, and carbohydrates) of cellular regulatory processes, and it is the changes in their levels that are the ultimate response of biological systems to genetic differences or disease or environmental . Metabolites are organic compounds that are starting materials/intermediates in metabolism pathways. Metabolites are small simple structures absorbed in a diet. They include vitamins and essential amino acids. They can be used to construct more complex molecules, or they can be broken down into simpler ones.
Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).
Metabolites and small molecules are organized in biochemical pathways and in a wider metabolic network, which is itself dependent on various genetic and signaling networks for its regulation. Numerous biochemical methods to measure the concentrations of specific metabolites in human body fluids or tissue samples are available and partially used in diagnoses. Metabolomics is the emerging field of measuring ideally all small molecules in a biological sample in one single experiment. All small molecules present in a sample are termed metabolomes. Metabolomics reveals global insights into intermediate phenotypes not depicted by other diagnostic approaches. The metabolites are being considered not only as biological end points but as a driving force in the pathophysiology of human disease.
The metabolome comprises the complete set of metabolites, the non-genetically encoded substrates, intermediates, and products of metabolic pathways, associated to a cell. By representing integrative information across multiple functional levels and by linking DNA encoded processes with the environment, the metabolome offers a window to map core attributes responsible for different phenotypes.
Metabolite identification is necessary for untargeted metabolite analysis, since the metabolites of interest are unknown when the biological problem is defined. The list of possible metabolites can be generated using free databases and libraries, using either measured molecular mass (m/z) of the unknown metabolites and their retention time (for LC- or GC–MS data), or from chemical shifts and coupling constants (for NMR data). Common databases and libraries used in metabolomics include the Human Metabolome Database (HMDB), Spectral Database for Organic Compounds (SDBS), Comprehensive Species-Metabolite Relationship Database (KNApSAcK), Metlin, Golm Metabolome Database , MassBank, MassTRIX, PubChem, Chenomx, Chemical Entities of Biological Interest (ChEBI), BioMagResBank, and Kyoto Encyclopedia of Genes and Genomes (KEGG).
Primary metabolites are involved in growth, development, and reproduction of the organism. The primary metabolite is typically a key component in maintaining normal physiological processes; thus, it is often known as a central metabolite.
Secondary metabolites are typically organic compounds produced through the modification of primary metabolite synthases. Secondary metabolites do not play a role in growth, development, and reproduction like primary metabolites do, and are typically formed during the end or near the stationary phase of growth. Many of the identified secondary metabolites have a role in ecological function, including defense mechanism(s), by serving as antibiotics and by producing pigments.
Exquisite mechanisms have evolved that control the flux of metabolites through metabolic pathways to insure that the output of the pathways meets biological demand and that energy in the form of ATP is not wasted by having opposing pathways run concomitantly in the same cell.
